Sunday, March 28, 2010
Windows 7/Vista screen flicker on bootcamp and Windows (7/vista) shutdown problem when put to sleep
When I first setup Vista bootcamp and more recently Win 7 bootcamp, I had this annoying problem where the screen flickered for a while before becoming clear. This problem seemed to do something with the video driver, and the driver provided even by the latest bootcamp version (3.1) did not help. The flicker time was minimized when I updated the video driver with what was suggested by Windows Update. However, this introduced another problem, which was that Windows automatically shut down whenever I put the laptop to sleep mode (by pressing the power button or closing the lid) to preserve some power. Fixed this by loading the Snow Leopard CD, accessing the Intel (video) drivers folder, and then executing the driver for Vista version (use this irrespective of the OS installed being Vista or Win 7) for the 965 Chipset. I thought that this might bring back the original flicker problem. Interestingly, however, it did not! The flicker was there occasionally, but disappeared quickly.
Tuesday, May 19, 2009
Talent = 10,000 Hours + Luck
It takes about 10000 hours to become an expert in something (Malcolm Gladwell).
This is approximately 1000 human days (discounting sleep, toilet breaks and other non working hours), which is approximately 3 years, which is equivalent
to the time taken by a student to complete his PhD. This means that at the end of the PhD, a student should be better than his supervisor because he or she spent almost 10,000 hours just studying his or her research topic, whereas the supervisor had to manage many other things + students during that time period.
Tuesday, February 17, 2009
The importance of stupidity in scientific research
Science makes us feel stupid because we do not have the answers to what we are investigating..apparently, according to Martin Schwartz this feeling is good and important for scientific research to progress..read on here.
Science is then not for those who got to have all the answers and do not like to feel stupid. That should make it easy for a large number of people to decide whether to take the plunge into science or not :)
Science is then not for those who got to have all the answers and do not like to feel stupid. That should make it easy for a large number of people to decide whether to take the plunge into science or not :)
Bidirectional transcription!
Another dogma shattered! Time to re-write the textbooks :)
==NEWS source: http://www.embl.de/aboutus/news/press/press09/25jan09/index.html==
Heidelberg, Germany and Hinxton, UK (OBBeC) - Researchers in the groups of Lars Steinmetz at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, and Wolfgang Huber at the European Bioinformatics Institute (EMBL-EBI) in Hinxton, UK, have unravelled how yeast generates its transcripts and have come a step closer to understanding their function, says a report from the institute.
The study, published online in Nature, redefines the concept of promoters (the start sites of transcription) contradicting the established notion that they support transcription in one direction only. The results are also representative of transcription in humans.
Investigating all transcripts produced in a yeast cell, the scientists found that most regions of the yeast genome produce several transcripts starting at the same promoter. These transcripts are interleaved and overlapping on the DNA. In contrast to what was previously thought, the vast majority of promoters seem to initiate transcription in both directions.
Not all of the produced transcripts are stable, many are degraded rapidly making it difficult to observe what they do. While some of the RNA molecules might be 'transcriptional noise' without function, other transcripts control the expression of genes and production of proteins. The act of transcription itself is also likely to play an important role in regulation of gene expression. Transcribing one stretch of DNA might either help or in other cases interfere with the transcription of a gene close by. Moreover, transcripts without a current purpose can serve as 'raw material for evolution' and acquire new functions over time.
The results shed light on the complex organization of the yeast genome and the insights gained extend to transcription in humans. A better understanding of transcription mechanisms could find application in new technologies to tune gene regulation in the future.
==NEWS source: http://www.embl.de/aboutus/news/press/press09/25jan09/index.html==
Heidelberg, Germany and Hinxton, UK (OBBeC) - Researchers in the groups of Lars Steinmetz at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, and Wolfgang Huber at the European Bioinformatics Institute (EMBL-EBI) in Hinxton, UK, have unravelled how yeast generates its transcripts and have come a step closer to understanding their function, says a report from the institute.
The study, published online in Nature, redefines the concept of promoters (the start sites of transcription) contradicting the established notion that they support transcription in one direction only. The results are also representative of transcription in humans.
Investigating all transcripts produced in a yeast cell, the scientists found that most regions of the yeast genome produce several transcripts starting at the same promoter. These transcripts are interleaved and overlapping on the DNA. In contrast to what was previously thought, the vast majority of promoters seem to initiate transcription in both directions.
Not all of the produced transcripts are stable, many are degraded rapidly making it difficult to observe what they do. While some of the RNA molecules might be 'transcriptional noise' without function, other transcripts control the expression of genes and production of proteins. The act of transcription itself is also likely to play an important role in regulation of gene expression. Transcribing one stretch of DNA might either help or in other cases interfere with the transcription of a gene close by. Moreover, transcripts without a current purpose can serve as 'raw material for evolution' and acquire new functions over time.
The results shed light on the complex organization of the yeast genome and the insights gained extend to transcription in humans. A better understanding of transcription mechanisms could find application in new technologies to tune gene regulation in the future.
Saturday, January 31, 2009
Learning Unix Scripting
==Understanding Unix Environment==
{This is still work in progress..}
===Unix File System===
* Hierarchical File System
The Unix File System is a hierarchical file system.
* / is root of the system
* /var is a directory in root
* /var/www is the full path of the sub-directory in "var"
* /var/www/htdocs is the full path of the sub-sub-directory in "/var/www" and so on...
1. Know where you are: '''pwd'''
:It shows the directory path where you are.
2. Navigate: '''cd'''
:If you want to get to certain dir, for example enter
cd /var/www/htdocs/db
3. How do you know what is in the dir? Using '''ls'''
:Other related to list the file
: '''ls -l''': Give you the long dir listing
4. Getting the souce code: '''lynx -source'''
: Enter
lynx -source httpwebaddress.
: lynx is a text-based browser. -source tells lynx NOT to display the HTML code, but to return the raw HTML code.
5. Unix command history
:Just press the ''Arrow up'' key to see your previous command
''Whatever you do, double check''
6. Get the internet page to your folder
:Example: to put the internet page to the dir where you are at now, key in
lynx -source internet_address.html > your_pagename.html
7. Change mode
: ''chmod'' takes several arguments
: -x is to make executable
: ''chmod -x programfile'' will make program executable rather than just a plain text file.
Questions
1. Why put /var/www/htdocs/db/myprogram in front of myprogram?
: This is because whenever you execute a program, Unix shell needs to find the path of that program.
: In this case, we spell out the full directory path so that Unix shell knows where that program is.
2. Why then can we use the ''lynx'' command and don't have to put the full path?
: This is because lynx command is already in the Shell's list of known paths.
: Later on, we will show you what is the current known paths, e.g. echo $PATH
== Command Line Arguments==
1. Command Line command without arguments
: For example ''pwd'' doesn't need to take arguments
2. Command line command with one argument
: For example ''ls -l'' takes one argument, the flag ''-l'' to give a ''l''ong listing.
3. Command line command with two arguments
: For example ''lynx -source http://www.google.com''
: lynx the command
: -source the first argument
: http://www.google.com as the second argument
== Loop Control ==
How do we make the numbers autoincrement without us to put in the numbers ourselves?
1. Make 6 into a program to create multiple files
:(1)pseudo code for ''my_program''
for (i=0;i<100;i++)
{ lynx -source internet_address.html[i] > your_pagename[i].html}
:(2)Change the file to executable file
:(3)Key in [path]/my_program
:(4)chmod +x my_program (This is to make the file executable.)
==Learning Unix Commands==
'''Environment Control'''
# refers to comments
==Miscellaneous commands==
1)
2)
3)
4)
5)
6)
7)
8)
9)
10)
11)
12)
13)
14)
15)
16)
17)
18)
19)
20)
21)
22)
23)
24)
25)
26)
27)
28)
29)
30)
31)=create a translation tool, simple one==
32)
33)
34)
35)=Creata database of your own=
#saves the web page to AP00286.html and this time it is saving the source code
echo "lynx -source http://aps.unmc.edu/AP/database/query_output.php?ID=00286 > AP00286.html" >getapd
change
# this is making the code generic
36.
37.
{This is still work in progress..}
===Unix File System===
* Hierarchical File System
The Unix File System is a hierarchical file system.
* / is root of the system
* /var is a directory in root
* /var/www is the full path of the sub-directory in "var"
* /var/www/htdocs is the full path of the sub-sub-directory in "/var/www" and so on...
1. Know where you are: '''pwd'''
:It shows the directory path where you are.
2. Navigate: '''cd'''
:If you want to get to certain dir, for example enter
cd /var/www/htdocs/db
3. How do you know what is in the dir? Using '''ls'''
:Other related to list the file
: '''ls -l''': Give you the long dir listing
4. Getting the souce code: '''lynx -source'''
: Enter
lynx -source httpwebaddress.
: lynx is a text-based browser. -source tells lynx NOT to display the HTML code, but to return the raw HTML code.
5. Unix command history
:Just press the ''Arrow up'' key to see your previous command
''Whatever you do, double check''
6. Get the internet page to your folder
:Example: to put the internet page to the dir where you are at now, key in
lynx -source internet_address.html > your_pagename.html
7. Change mode
: ''chmod'' takes several arguments
: -x is to make executable
: ''chmod -x programfile'' will make program executable rather than just a plain text file.
Questions
1. Why put /var/www/htdocs/db/myprogram in front of myprogram?
: This is because whenever you execute a program, Unix shell needs to find the path of that program.
: In this case, we spell out the full directory path so that Unix shell knows where that program is.
2. Why then can we use the ''lynx'' command and don't have to put the full path?
: This is because lynx command is already in the Shell's list of known paths.
: Later on, we will show you what is the current known paths, e.g. echo $PATH
== Command Line Arguments==
1. Command Line command without arguments
: For example ''pwd'' doesn't need to take arguments
2. Command line command with one argument
: For example ''ls -l'' takes one argument, the flag ''-l'' to give a ''l''ong listing.
3. Command line command with two arguments
: For example ''lynx -source http://www.google.com''
: lynx the command
: -source the first argument
: http://www.google.com as the second argument
== Loop Control ==
How do we make the numbers autoincrement without us to put in the numbers ourselves?
1. Make 6 into a program to create multiple files
:(1)pseudo code for ''my_program''
for (i=0;i<100;i++)
{ lynx -source internet_address.html[i] > your_pagename[i].html}
:(2)Change the file to executable file
:(3)Key in [path]/my_program
:(4)chmod +x my_program (This is to make the file executable.)
==Learning Unix Commands==
'''Environment Control'''
# refers to comments
cd d# Change to directory d
mkdir d#Create new directory d
rmdir d#Remove directory d
mv f1 [f2...] d#Move file f to directory d
mv d1 d2#Rename directory d1 as d2
passwd#Change password
alias name1 name2#Create command alias (csh/tcsh)
alias name1="name2"#Create command alias (ksh/bash)
unalias name1[na2...]#Remove command alias na
ssh nd#Login securely to remote node
exit#End terminal session
setenv name v#Set env var to value v (csh/tcsh)
export name="v"#set environment variable to value v (ksh/bash)
==Miscellaneous commands==
1)
ls# is to list the directory
2)
cp# copy
3)
wc# word count
4)
ls -al | grep root |awk '{print "file: $9, S8" }' # to extract the 8th and the 9th column; details of all the files/directories called root is ls5)
wc -l# count number of lines
6)
># is to funnel to a new file
7)
ls -al | grep root |awk '{print "file: $9, S8" }' > x.file # transfer the output to a file name, in this case called x.file8)
pico x.file# a text editor that helps you read the x file; to get out from pico, type ctrl x; pico is very sophisticated
9)
vi x.file# a text editor that helps you read the x file
10)
:q# helps exit vi, which is very obscure.
11)
:q!# helps exit vi, which is very obscure.
12)
pwd# print the current working directory
13)
cd# is to change the directory
14)
tab#use it to automatically fill in the blanks; auto completion
15)
key up and down# help you look at commands typed earlier
16)
echo "ls -al /root/Desktop/ |awk '{print $5 "b", S9 }' " >tinwee # creates an executable file17)
./tinwee# executing tinwee, but will not work because you have no permission
18)
chmod 755 tinwee# give full access to run tinwee
19)
pico tinwee# to make the program more generic by modifying the code
20)
ls -al $1 |awk '{print $5 "bytes", $9 } #change the code to more generic instead of hardwiring it21)
tinwee /# takes / as $1, which in this case is root; note that this $1 is different from the #awk $1
22)
ln tinwee t# creating a shortname or short cut (soft link) for tinwee (alias); make sure it is unique alias
23)
echo $PATH | sed 's/:/\n/g'# this is to show the path of all the directories and files line by #line
24)
echo $PATH | sed 's/:/\n/g' |more# show little by little
25)
echo $PATH | sed 's/:/\n/g' |less# show less
26)
echo $PATH | sed 's/:/\n/g' |cat# to show all
27)
echo $PATH | sed 's/:/\n/g' |tac# to show in reverse order
28)
echo $PATH | sed 's/:/\n/g' |less |rev# show less but in reverse order
29)
q# to quit while looking at the results of these
30)
ctrl + C#to quit while looking at these
31)=create a translation tool, simple one==
# rev reverses the sequence, tac show it in reverse order and tr does the translation
echo "ATGCTTA"
" |rev |tac |tr "atcg" "tagc"
32)
alias#does not link a file but substitutes for the name
33)
>>#will append to the bottom of a file that already exists
34)
>#append to a new file
35)=Creata database of your own=
lynx http://aps.unmc.edu/AP/database/query_output.php?ID=00286 > AP00286.html#saves the web page to AP00286.html but it is not saving the source code
lynx -source http://aps.unmc.edu/AP/database/query_output.php?ID=00286 > AP00286.html
#saves the web page to AP00286.html and this time it is saving the source code
echo "lynx -source http://aps.unmc.edu/AP/database/query_output.php?ID=00286 > AP00286.html" >getapd
pico getapd# read the getapd file
change
lynx -source http://aps.unmc.edu/AP/database/query_output.php?ID=00286 > AP00286.htmlto
lynx -source http://aps.unmc.edu/AP/database/query_output.php?ID=0$1 > AP0$1.html
# this is making the code generic
getapd AP00287# type on the command prompt to download the record 00287 without typing the whole command
pico getapd# open the getapd file to make the command more generic
for i in 'Seq -w 1137`
do
lynx -source http://aps.unmc.edu/AP/database/query_output.php?ID=0$i > AP0$i.html
sleep 3
done
./getapd#run getapd for automatic download
36.
" "# double quotes are used whe you want to evaluate the variable. For example "$PATH" will evaluate the dollar sign and give you relevant matches
37.
' '# are used when one wants to print the special characters without evaluating them. For example, '$PATH' will return $PATH
Saturday, January 24, 2009
How to succeed in science: a concise guide for young biomedical scientists
Below is a recommendation by a peer to an interesting article for people starting in the biomedical science field:
"Jonathan Yewdell published an interesting essay in Nature Reviews Mol Cell Biol recently. The essay is an odd mix of massively discouraging and heart-warming. He starts by basically telling all young PIs to run for their lives away from a career in academic research, due in part to the shortage of funding and positions, as well as the multiple hardships of the job. He then goes on to say that you should do science only"
Here's recommendating the article to all young biomedical/life scientists out there!
Direct links to the articles are below (you will need subscription to the journal for the full article):
Part 1 - taking the plunge
Part 2 - making discoveries
"Jonathan Yewdell published an interesting essay in Nature Reviews Mol Cell Biol recently. The essay is an odd mix of massively discouraging and heart-warming. He starts by basically telling all young PIs to run for their lives away from a career in academic research, due in part to the shortage of funding and positions, as well as the multiple hardships of the job. He then goes on to say that you should do science only"
Here's recommendating the article to all young biomedical/life scientists out there!
Direct links to the articles are below (you will need subscription to the journal for the full article):
Part 1 - taking the plunge
Part 2 - making discoveries
How To Automate BLAST Search?
One can use Blastcl3, the NCBI BLAST network client, to remotely connect to the NCBI BLAST servers to run automated BLAST searches. No web browser is required, you don't have to wait in front of the computer for the results and can perform "batch" search of many sequences against the databases at one time. The results of the search using this Network Blast will be identical to that of the Web version (http://blast.ncbi.nlm.nih.gov/Blast.cgi), as long as the identical parameters are used. I have tried and tested this.
Note on blast parametes for users that will rely on the Web version for the parameters to be used on the Network version:
If you don't uncheck (untick) the option for short sequence queries (") on the Web version, the default algorithm parameters that are displayed on the input page will not be used (for example, E-value of 10, Blosum 62 matrix, Word size 2, etc). This I think is a bug because it does not make sense showing the default parameters if they are not going to be used, especially when the short queries option is checked by default. Ideally, they should have not checked the short queries option and if it is checked by the user, the resulting default parameters should be shown.
So, if you don't plan to use the short queries option, just uncheck it and the parameters displayed will be used for the search; you can change them if you like. If you are happy with what you get on the results page, then take note of the parameters and then set them for use by the Network Blast.
Now, for those who plan to use the short queries option, do the following:
1. Don't bother modifying the default algorithm parameters and click on the submit button.
2. On the results page, click on the "Edit and Resubmit" button to find out what algorithm parameters were used for the search. The parameters that you see on the resulting page, were the exact values that were used for the search. If you are happy with the blast result, you can stick with these parameters, otherwise, you are free to modify them. If you plan to modify them, make sure you uncheck the option for short queries in order for your changes to be effective, otherwise, the default parameters for short queries that were displayed on that page will still be used. Once you are satisfied with your final set of parameters, take note of them and then set them for use by the Network Blast.
== Where to get Network Blast ==
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/
File: netblast-2.2.17-ia32-freebsd.tar.gz 2334 KB 8/26/2007 4:09:00 PM
File: netblast-2.2.17-ia32-linux.tar.gz 2758 KB 8/26/2007 4:13:00 PM
File: netblast-2.2.17-ia32-solaris.tar.gz 2416 KB 8/27/2007 8:10:00 PM
File: netblast-2.2.17-ia32-solaris9.tar.gz 2455 KB 8/26/2007 4:15:00 PM
File: netblast-2.2.17-ia32-win32.exe 1479 KB 8/22/2007 9:40:00 PM
File: netblast-2.2.17-ia64-linux.tar.gz 5319 KB 11/1/2007 12:23:00 PM
File: netblast-2.2.17-mips64-irix.tar.gz 4340 KB 8/26/2007 4:17:00 PM
File: netblast-2.2.17-sparc64-solaris.tar.gz 4448 KB 8/26/2007 4:41:00 PM
File: netblast-2.2.17-universal-macosx.tar.gz 4398 KB 8/26/2007 4:25:00 PM
File: netblast-2.2.17-x64-linux.tar.gz 2834 KB 8/26/2007 4:13:00 PM
File: netblast-2.2.17-x64-solaris.tar.gz 3287 KB 8/27/2007 8:27:00 PM
File: netblast-2.2.17-x64-win64.exe 1686 KB 8/19/2007 4:29:00 AM
For other methods, see http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.pdf
and http://www.ncbi.nlm.nih.gov/blast/blast_overview.shtml
and the query.fcgi pages on how to construct an api to talk to various NCBI queries, e.g. automating the retrieval of GI numbers in FASTA or whatever formats.
== How to run Network Blast in Linux OS (e.g BioSlax)==
* The following will be untarred (unzipped): VERSION bin/ data/ doc/
* Blastcl3 is found in the bin folder
== Example of how to run Network Blast ==
1. Split the input fasta file (containing multiple sequences) into multiple files, with one sequence per file, using the command csplit. For example:
The above command adds digits to names of the output fasta files without the padding of zeros infront.
* Example of content of the input fasta file:
>1
ESWILRNPGYALVA
>2
GCGLFGKGSIDTCA
..etc..
* Examples of output files:
file name: xx1
content of xx1:
>1
ESWILRNPGYALVA
file name: xx2
content of xx2:
>2
GCGLFGKGSIDTCA
.
.
.
file name: xx10
content of xx10:
>10
GCGLFGKGSIDTCA
and so on to the last sequence ...
2. Create an executable file containing the following code:
'''NOTE:'''
* xx refers to the name of the input files, for example xx1, xx2, etc
* Sleep 10 is the time gap (10 seconds) between the end of one submission and the start of the next. This can be changed to longer time periods (recommended) in order not to overload the NCBI server. Otherwise, they may black list your IP.
* -p is blast p program, -d nr is the NR database, -i is for input filename, -F F for false is to switch off low complexity and other filters, -I T set to true is to show the GI numbers in the definition lines, and -v 0 is to set number of database sequences to show one-line descriptions, -b is to list out 20000 hits, -f 11 threshold for extending hits, -W 2 set word size for short sequence queries, default used if set to zero (blastn 11, megablast 28, all others 3, and 2 for short queries), -T F to produce text output, instead of HTML, -u "Root[ORGN] NOT txid11082[Organism:exp] NOT txid81077[ORGN]" is to restrict search of database to results of Entrez2 lookup [String], -C F to not use composition-based statistics for blastp or tblastn (0 or F or f: no composition-based statistics), -M PAM30 select matrix for short sequence queries (BLOSUM62 for normal protein searches), and -o to specify output filename.
3. Change the mode of the executable file in order to be able to execute. For example:
* x refers to the name of the executable file.
* For more information, see [http://en.wikipedia.org/wiki/Chmod Chmod]and [http://www.xaviermedia.com/documents/chmod755.php Chmod755].
4. Run the executable file. For example:
* x refers to the name of the executable file
A task can usually be started and run as a background task by putting a '&' at the end of the command line. For example:
If a task was started and is running in the foreground, it is still possible to move it to the background without cancelling it. To move a task from the foreground to the background perform the following steps:
1. CTRL-Z (That is, while holding the CTRL key down, tap the 'z' key) This will suspend the current foreground job (task).
2. Enter the job control command 'bg'
3. Tap the 'Enter' key
The job is now running in the background.
Useful commands to see which jobs are still running is the 'jobs' or the 'ps ua' commands. If the 'jobs' command is used, a background jobs can be brought to the foreground with the command fg n where n is the job (not the PID) number.
==Manual pages of Network Blast==
Note on blast parametes for users that will rely on the Web version for the parameters to be used on the Network version:
If you don't uncheck (untick) the option for short sequence queries (") on the Web version, the default algorithm parameters that are displayed on the input page will not be used (for example, E-value of 10, Blosum 62 matrix, Word size 2, etc). This I think is a bug because it does not make sense showing the default parameters if they are not going to be used, especially when the short queries option is checked by default. Ideally, they should have not checked the short queries option and if it is checked by the user, the resulting default parameters should be shown.
So, if you don't plan to use the short queries option, just uncheck it and the parameters displayed will be used for the search; you can change them if you like. If you are happy with what you get on the results page, then take note of the parameters and then set them for use by the Network Blast.
Now, for those who plan to use the short queries option, do the following:
1. Don't bother modifying the default algorithm parameters and click on the submit button.
2. On the results page, click on the "Edit and Resubmit" button to find out what algorithm parameters were used for the search. The parameters that you see on the resulting page, were the exact values that were used for the search. If you are happy with the blast result, you can stick with these parameters, otherwise, you are free to modify them. If you plan to modify them, make sure you uncheck the option for short queries in order for your changes to be effective, otherwise, the default parameters for short queries that were displayed on that page will still be used. Once you are satisfied with your final set of parameters, take note of them and then set them for use by the Network Blast.
== Where to get Network Blast ==
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/
File: netblast-2.2.17-ia32-freebsd.tar.gz 2334 KB 8/26/2007 4:09:00 PM
File: netblast-2.2.17-ia32-linux.tar.gz 2758 KB 8/26/2007 4:13:00 PM
File: netblast-2.2.17-ia32-solaris.tar.gz 2416 KB 8/27/2007 8:10:00 PM
File: netblast-2.2.17-ia32-solaris9.tar.gz 2455 KB 8/26/2007 4:15:00 PM
File: netblast-2.2.17-ia32-win32.exe 1479 KB 8/22/2007 9:40:00 PM
File: netblast-2.2.17-ia64-linux.tar.gz 5319 KB 11/1/2007 12:23:00 PM
File: netblast-2.2.17-mips64-irix.tar.gz 4340 KB 8/26/2007 4:17:00 PM
File: netblast-2.2.17-sparc64-solaris.tar.gz 4448 KB 8/26/2007 4:41:00 PM
File: netblast-2.2.17-universal-macosx.tar.gz 4398 KB 8/26/2007 4:25:00 PM
File: netblast-2.2.17-x64-linux.tar.gz 2834 KB 8/26/2007 4:13:00 PM
File: netblast-2.2.17-x64-solaris.tar.gz 3287 KB 8/27/2007 8:27:00 PM
File: netblast-2.2.17-x64-win64.exe 1686 KB 8/19/2007 4:29:00 AM
For other methods, see http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.pdf
and http://www.ncbi.nlm.nih.gov/blast/blast_overview.shtml
and the query.fcgi pages on how to construct an api to talk to various NCBI queries, e.g. automating the retrieval of GI numbers in FASTA or whatever formats.
== How to run Network Blast in Linux OS (e.g BioSlax)==
tar -zxvf netblast-2.2.17-ia32-linux.tar.gz
* The following will be untarred (unzipped): VERSION bin/ data/ doc/
* Blastcl3 is found in the bin folder
== Example of how to run Network Blast ==
1. Split the input fasta file (containing multiple sequences) into multiple files, with one sequence per file, using the command csplit. For example:
csplit -n 1 multiple.fasta /\>/ \{\*\}
The above command adds digits to names of the output fasta files without the padding of zeros infront.
* Example of content of the input fasta file:
>1
ESWILRNPGYALVA
>2
GCGLFGKGSIDTCA
..etc..
* Examples of output files:
file name: xx1
content of xx1:
>1
ESWILRNPGYALVA
file name: xx2
content of xx2:
>2
GCGLFGKGSIDTCA
.
.
.
file name: xx10
content of xx10:
>10
GCGLFGKGSIDTCA
and so on to the last sequence ...
2. Create an executable file containing the following code:
for i in xx*
do
blastcl3 -p blastp -d nr -i $i -F F -e 200000 -I T -v 0 -b 20000
-f 11 -W 2 -T F -u "Root[ORGN] NOT txid11082[Organism:exp] NOT
txid81077[ORGN]" -C F -M PAM30 -o $i.out
sleep 10
done
'''NOTE:'''
* xx refers to the name of the input files, for example xx1, xx2, etc
* Sleep 10 is the time gap (10 seconds) between the end of one submission and the start of the next. This can be changed to longer time periods (recommended) in order not to overload the NCBI server. Otherwise, they may black list your IP.
* -p is blast p program, -d nr is the NR database, -i is for input filename, -F F for false is to switch off low complexity and other filters, -I T set to true is to show the GI numbers in the definition lines, and -v 0 is to set number of database sequences to show one-line descriptions, -b is to list out 20000 hits, -f 11 threshold for extending hits, -W 2 set word size for short sequence queries, default used if set to zero (blastn 11, megablast 28, all others 3, and 2 for short queries), -T F to produce text output, instead of HTML, -u "Root[ORGN] NOT txid11082[Organism:exp] NOT txid81077[ORGN]" is to restrict search of database to results of Entrez2 lookup [String], -C F to not use composition-based statistics for blastp or tblastn (0 or F or f: no composition-based statistics), -M PAM30 select matrix for short sequence queries (BLOSUM62 for normal protein searches), and -o to specify output filename.
3. Change the mode of the executable file in order to be able to execute. For example:
chmod 755 x
* x refers to the name of the executable file.
* For more information, see [http://en.wikipedia.org/wiki/Chmod Chmod]and [http://www.xaviermedia.com/documents/chmod755.php Chmod755].
4. Run the executable file. For example:
./x
* x refers to the name of the executable file
A task can usually be started and run as a background task by putting a '&' at the end of the command line. For example:
./x &
If a task was started and is running in the foreground, it is still possible to move it to the background without cancelling it. To move a task from the foreground to the background perform the following steps:
1. CTRL-Z (That is, while holding the CTRL key down, tap the 'z' key) This will suspend the current foreground job (task).
2. Enter the job control command 'bg'
3. Tap the 'Enter' key
The job is now running in the background.
Useful commands to see which jobs are still running is the 'jobs' or the 'ps ua' commands. If the 'jobs' command is used, a background jobs can be brought to the foreground with the command fg n where n is the job (not the PID) number.
==Manual pages of Network Blast==
blastcl3 2.2.17 arguments:
-p Program Name [String]
-d Database [String]
default = nr
-i Query File [File In]
default = stdin
-e Expectation value (E) [Real]
default = 10.0
-m alignment view options:
0 = pairwise,
1 = query-anchored showing identities,
2 = query-anchored no identities,
3 = flat query-anchored, show identities,
4 = flat query-anchored, no identities,
5 = query-anchored no identities and blunt ends,
6 = flat query-anchored, no identities and blunt ends,
7 = XML Blast output,
8 = tabular,
9 tabular with comment lines
10 ASN, text
11 ASN, binary [Integer]
default = 0
range from 0 to 11
-o BLAST report Output File [File Out] Optional
default = stdout
-F Filter query sequence (DUST with blastn, SEG with others) [String]
default = T
-G Cost to open a gap (-1 invokes default behavior) [Integer]
default = -1
-E Cost to extend a gap (-1 invokes default behavior) [Integer]
default = -1
-X X dropoff value for gapped alignment (in bits) (zero invokes default behavior)
blastn 30, megablast 20, tblastx 0, all others 15 [Integer]
default = 0
-I Show GI's in deflines [T/F]
default = F
-q Penalty for a nucleotide mismatch (blastn only) [Integer]
default = -3
-r Reward for a nucleotide match (blastn only) [Integer]
default = 1
-v Number of database sequences to show one-line descriptions for (V) [Integer]
default = 500
-b Number of database sequence to show alignments for (B) [Integer]
default = 250
-f Threshold for extending hits, default if zero
blastp 11, blastn 0, blastx 12, tblastn 13
tblastx 13, megablast 0 [Real]
default = 0
-g Perform gapped alignment (not available with tblastx) [T/F]
default = T
-Q Query Genetic code to use [Integer]
default = 1
-D DB Genetic code (for tblast[nx] only) [Integer]
default = 1
-a Number of processors to use [Integer]
default = 1
-O SeqAlign file [File Out] Optional
-J Believe the query defline [T/F]
default = F
-M Matrix [String]
default = BLOSUM62
-W Word size, default if zero (blastn 11, megablast 28, all others 3) [Integer]
default = 0
-z Effective length of the database (use zero for the real size) [Real]
default = 0
-K Number of best hits from a region to keep (off by default, if used a value of 100 is recommended) [Integer]
default = 0
-P 0 for multiple hit, 1 for single hit (does not apply to blastn) [Integer]
default = 0
-Y Effective length of the search space (use zero for the real size) [Real]
default = 0
-S Query strands to search against database (for blast[nx], and tblastx)
3 is both, 1 is top, 2 is bottom [Integer]
default = 3
-T Produce HTML output [T/F]
default = F
-u Restrict search of database to results of Entrez2 lookup [String] Optional
-U Use lower case filtering of FASTA sequence [T/F] Optional
-y X dropoff value for ungapped extensions in bits (0.0 invokes default behavior)
blastn 20, megablast 10, all others 7 [Real]
default = 0.0
-Z X dropoff value for final gapped alignment in bits (0.0 invokes default behavior)
blastn/megablast 50, tblastx 0, all others 25 [Integer]
default = 0
-R RPS Blast search [T/F]
default = F
-n MegaBlast search [T/F]
default = F
-L Location on query sequence [String] Optional
-A Multiple Hits window size, default if zero (blastn/megablast 0, all others 40 [Integer]
default = 0
-w Frame shift penalty (OOF algorithm for blastx) [Integer]
default = 0
-t Length of the largest intron allowed in a translated nucleotide sequence when linking multiple distinct alignments. (0 invokes default behavior; a negative value disables linking.) [Integer]
default = 0
-C Use composition-based statistics for blastp or tblastn:
As first character:
D or d: default (equivalent to T)
0 or F or f: no composition-based statistics
1 or T or t: Composition-based statistics as in NAR 29:2994-3005, 2001
2: Composition-based score adjustment as in Bioinformatics 21:902-911,
2005, conditioned on sequence properties
3: Composition-based score adjustment as in Bioinformatics 21:902-911,
2005, unconditionally
For programs other than tblastn, must either be absent or be D, F or 0.
As second character, if first character is equivalent to 1, 2, or 3:
U or u: unified p-value combining alignment p-value and compositional p-value in round 1 only
[String]
default = D
-s Compute locally optimal Smith-Waterman alignments (This option is only
available for gapped tblastn.) [T/F]
default = F
Thursday, September 25, 2008
Mac Keyboard Shortcuts
Below are important Mac keyboard shortcuts that I have gathered from the web and from my reading of the popular Mac Magazines, such as Macworld.
1. Cmd+shift+A: Opens Applications folder while in Finder
2. Cmd (double click): Opens a folders in a new Finder window
3. Option+drag: Copies a file instead of moving it in the Finder
4. Cmd+option+drag: Makes an alias of selected item(s)
5. Cmd+delete: Moves selected item to the Trash while in the Finder
6. Cmd+tab: Cycles through all open programs
7. F11: Shows the desktop
8. F9: Shows all windows related to the active window
9. F3: Activates Expose
10. F4: Activates Dashboard
11. Cmd+spacebar: Starts a spotlight search from anywhere
12. Cmd+A: Selects all text and figures in the active window
13. Cmd+C: Copies selected texts and/or figures
14. Cmd+V: Pastes copied text and/or figures
15. Cmd+Z: Undoes the last action
16. Cmd+Y: Redoes the last action
17. Cmd+O: Opens a file
18. Cmd+S: Saves the active window
19. Option+Cmd+F: Activates Google search
20. Option+Cmd+Esc: Force quit applications
21. Cmd+Shift+3: Screen capture of entire screen saved as a file on the Desktop
22. Cmd+Shift+4: Screen capture with crosschair to select area of screen and saved as a file on the Desktop
23. Cmd+Shift+4+Space bar: Screen capture any one of the open windows and saved as a file on the Desktop
24. Ctrl+Cmd+Shift+3 (or 4) (or 4+Space bar): Screen capture stored in Clipboard memory (equivalent to Print Screen function in Windows)
25. Shift+F3: Slow-motion Expose
26. Shift+F4: Slow-motion Dashboard
27. Cmd+Option+F+0 during boot: Enters Bios
1. Cmd+shift+A: Opens Applications folder while in Finder
2. Cmd (double click): Opens a folders in a new Finder window
3. Option+drag: Copies a file instead of moving it in the Finder
4. Cmd+option+drag: Makes an alias of selected item(s)
5. Cmd+delete: Moves selected item to the Trash while in the Finder
6. Cmd+tab: Cycles through all open programs
7. F11: Shows the desktop
8. F9: Shows all windows related to the active window
9. F3: Activates Expose
10. F4: Activates Dashboard
11. Cmd+spacebar: Starts a spotlight search from anywhere
12. Cmd+A: Selects all text and figures in the active window
13. Cmd+C: Copies selected texts and/or figures
14. Cmd+V: Pastes copied text and/or figures
15. Cmd+Z: Undoes the last action
16. Cmd+Y: Redoes the last action
17. Cmd+O: Opens a file
18. Cmd+S: Saves the active window
19. Option+Cmd+F: Activates Google search
20. Option+Cmd+Esc: Force quit applications
21. Cmd+Shift+3: Screen capture of entire screen saved as a file on the Desktop
22. Cmd+Shift+4: Screen capture with crosschair to select area of screen and saved as a file on the Desktop
23. Cmd+Shift+4+Space bar: Screen capture any one of the open windows and saved as a file on the Desktop
24. Ctrl+Cmd+Shift+3 (or 4) (or 4+Space bar): Screen capture stored in Clipboard memory (equivalent to Print Screen function in Windows)
25. Shift+F3: Slow-motion Expose
26. Shift+F4: Slow-motion Dashboard
27. Cmd+Option+F+0 during boot: Enters Bios
28. Press and Hold "C" during boot to boot from CD
29. Cmd + V during boot to access the terminal
30. Restart, then immediately hold the option key for the display of the boot devices, then choose the CD drive and click on the eject key to eject the CD.
31. Cmd+option+C: Change case in MS Word
31. Cmd+option+C: Change case in MS Word
Saturday, August 2, 2008
Creating high-quality publication figures
Different researchers have different ways of preparing their figures for publication purposes. I used to use Adobe Photoshop for this purpose. However, I almost always used to lose some quality when transferring the figure from the MS Word or Power point to Photoshop. With the recent advancement in the ability of software like Adobe Acrobat 8 in handling images, I have identified a method that produces high-quality publication images and is also simple to perform. See below for the details:
All images in general
This method works for all images in MS Word, Excel and Powerpoint using Adobe Acrobat 8. I am not sure if this method works for older versions of Acrobat or other programs with Acrobat like functionality
1. Copy the image to MS Word. If it is an Excel figure, you can leave it there, unless it does not fit an A4 page (then you move it to MS Word)
2. Convert the document to pdf (using the print option) with standard settings (600 dpi), and make sure the correct page size is selected (usually A4 works). Also, go to layout and click on advance, make sure the dpi setting there matches with that of the pdf pdi setting (in this case, 600dpi). And if you want to print in greyscale, change the colour to black. For excel figures that do not fit A4, you can try page sizes larger than A4 and then later crop the empty spaces.
3. Crop the document to the required size. Go to document menu --> crop --> remove white spaces. If you have a page number at the bottom, make sure you remove it first before you select "remove white pages" option.
4. Export to TIFF. File--> Export-->Image-->TIFF-->Set setting to 600dpi and the relevant colour options --> Save. When prompted, also save the cropped PDF.
5. You are done, you now have your 600dpi image file, which you can insert to a MS Word document to send to the journal.
Dealing with Graffle images
1. Export the image to Photoshop format at 600dpi.
2. Open the image in Photoshop and save it as TIFF@600dpi
Do you know of a method that is better or simpler? Please share
All images in general
This method works for all images in MS Word, Excel and Powerpoint using Adobe Acrobat 8. I am not sure if this method works for older versions of Acrobat or other programs with Acrobat like functionality
1. Copy the image to MS Word. If it is an Excel figure, you can leave it there, unless it does not fit an A4 page (then you move it to MS Word)
2. Convert the document to pdf (using the print option) with standard settings (600 dpi), and make sure the correct page size is selected (usually A4 works). Also, go to layout and click on advance, make sure the dpi setting there matches with that of the pdf pdi setting (in this case, 600dpi). And if you want to print in greyscale, change the colour to black. For excel figures that do not fit A4, you can try page sizes larger than A4 and then later crop the empty spaces.
3. Crop the document to the required size. Go to document menu --> crop --> remove white spaces. If you have a page number at the bottom, make sure you remove it first before you select "remove white pages" option.
4. Export to TIFF. File--> Export-->Image-->TIFF-->Set setting to 600dpi and the relevant colour options --> Save. When prompted, also save the cropped PDF.
5. You are done, you now have your 600dpi image file, which you can insert to a MS Word document to send to the journal.
Dealing with Graffle images
1. Export the image to Photoshop format at 600dpi.
2. Open the image in Photoshop and save it as TIFF@600dpi
Do you know of a method that is better or simpler? Please share
Monday, July 28, 2008
You can right-click in Mac!
I used to be one of those who used to think that there was no right-clicking function in Mac, and this was one of the reasons that kept me away from Mac for many years. I noticed that I was not alone into thinking this, most Windows users thought the same and still do. Luckily this stopped for me when a friend showed me how one can get the right-click function in Mac. Having been a mac user for almost 3 months now and liking it a lot, it really frustrates me now when I meet people (usually Windows users) who discourage other people from buying/experiencing Mac by saying that it does not have the right-click function. I do correct them whenever I can. But, I think Apple should seriously highlight this basic feature in their marketing ads or campaings under "reasons to buy a Mac" in order to enjoy wider presence and bigger pie of the personal computer market.
To right-click on a Mac, while using Leopard or Windows on Boot Camp:
To right-click on a Mac, while using Leopard or Windows on Boot Camp:
- Using a Mighty Mouse, click the upper-right side of the mouse.
- Using a trackpad, place two fingers on the trackpad and click the trackpad button.
Folderpane to re-arrange email accounts in Thunderbird
Having so many email accounts, I have always wished for a way to organize their order of appearance/listing in Thunderbird. This functionality is not available in Thunderbird (TB) itself, but now thanks to "Chuonthis" this functionality is made available to TB through an add-on extension Folderpane. For information on how to install and use Folderpane, read this.
Macbook keyboard mapping in Windows
Ahh! I finally came across something I was wanting to find for a long time now - the mapping of Macbook keyboard to Windows Keyboard. It is all available at Apple Support Page. The link also provides help page for other Mac keyboard types. This is very useful for Boot Camp users, especially for the newbies.
Another useful find while going through Apple support page: Finding Windows keys on Macbook keyboard
Another useful find while going through Apple support page: Finding Windows keys on Macbook keyboard
Sunday, July 13, 2008
Do you know how your brain perceives? Classical, centuries-long beliefs about how our brains work overturned by new understandings
Few days ago, a friend recommended to me a fascinating article about the theory behind perception and how it works. The article starts and centers around M who suffers from severe itch and describes her journey in recovering from it..somewhere in the middle it introduces the classical theory behind perception and how the latest advancements made over the past decades are shifting the balance towards a theory that was rejected earlier by many. This new theory has resulted in almost "magical" recoveries for several patients by "tinkering" with the perception received by the brain...To know more about our brain, like you never knew before, click here or visit: http://www.newyorker.com/reporting/2008/06/30/080630fa_fact_gawande
I am sure you will be enlightened and amazed when you are done reading it.
I was!
I am sure you will be enlightened and amazed when you are done reading it.
I was!
Friday, July 11, 2008
De Novo Design of Peptide Immunogens
My journal club review of the paper entitled "De Novo Design of Peptide Immunogens That Mimic the Coiled Coil Region of Human T-cell Leukemia Virus Type-1 Glycoprotein 21 Transmembrane Subunit for Induction of Native Protein Reactive Neutralizing Antibodies" by Roshni Sundaram, Marcus P. Lynch, Sharad V. Rawale, Yiping Sun, Mirdad Kazanji, and Pravin T. P. Kaumaya, published in The Journal of Biological Chemistry (Vol. 279, No. 23, pp. 24141–24151), in the year 2004.
==Overview==
Human T-cell Leukemia virus type-1 (HTLV-1) is a considerable medical problem across the globe and there is lack of effective therapy for HTLV-1 associated diseases. Vaccination, therefore, represents an ideal approach to control the virus. In this study, Sundaram et al., assessed the potential of two de novo designed peptide immunogens (WCCR2T, wild-type peptide; CCR2T, leucine-substituted peptide) that mimicked the coiled coil region of HTLV-1 glycoprotein (gp21) transmembrane (TM) subunit for induction of neutralizing antibodies against the virus. Their novel design involved utilizing a beta-sheet template backbone consisting of alternating Gly/Lys residues that allowed growth of peptide immunogens onto the epsilon side chains of three lysine residues, potentiating the peptides to form triple helical coiled-coil conformation, mimicking the native structure. The template backbone was linked to a “promiscuous” helper T-cell epitope from tetanus toxin to overcome the heterogeneity of the major histocompatibility complex (MHC) in mice population and provide boost to the immune response. Their results showed that antibodies generated using both peptide immunogens were directed against the coiled-coil region of the native gp21 envelope glycoprotein and were neutralizing as they resulted in reduction of cell-cell fusion. These results validated the authors’ hypothesis, demonstrated the validity of their template design and indicated that the two peptide immunogens represent potential candidates for use in a peptide vaccine against HTLV-1. The data presented in this study and the insights gained represent an important step forward towards the design of a vaccine effective against HTLV-1. Further, the approach presented in this paper can be used as a template for the design of peptide vaccines able to induce high affinity neutralizing antibody responses for other pathogens, such as HIV (Louis et al., 2003), SARS-CoV (Ingallinella et al., 2004) and influenza virus (Skehel and Wiley, 2000), which also utilize coiled coil conformation for the fusion process. Additionally, antibodies produced against the immunogens are of significant utility for the analysis of TM function in the respective pathogen infections.
The authors should be praised for taking extensive measures to ensure the generation of structurally and functionally viable peptide immunogen constructs. This was necessary to circumvent the several limitations of synthetic peptide vaccines (Bona et al., 1998), such as low immunogenicity, chemical and conformational instability, short serum half-life, rapid degradation by proteolytic enzymes, and restrictions posed by MHC diversity, among others.
Despite the validation of the hypothesis, the thorough work performed, there are several major and minor deficiencies in their paper, which I highlight below.
==Major points==
1) Page 24144: Ideally, strategies to design protective vaccines must be able activate the relevant arm(s) of the immune system, in particular the humoral and the cellular immune responses. The addition of promiscuous helper T-cell epitope to the template peptide immunogen was, therefore, impeccable, as it will not only help trigger cellular immune response but also help overcome the polymorphism of MHC molecules. However, the rationale for selection of tetanus toxoid peptide was not well justified as it is only good for priming and the resulting memory T helper cells are not likely to be helpful upon re-infection by HTLV-1. Why did the authors not consider using a promiscuous helper epitope from the HTLV-1 virus itself?
2) Page 24146 and 24148: It is possible that the CCR2T and WCCR2T antisera used for ELISA assays (Fig. 5 and Fig. 8) also contain antibodies that bind to the promiscuous T-cell epitope on the peptide immunogen. So, in addition to measuring antibodies binding specifically to the conformational epitope, the authors could also be measuring antibodies binding to the promiscuous T-cell epitope. Also, if this was true, antibodies binding to the B- and T-cell epitopes could lead to steric hindrances in binding analysis when the immunogen is immobilized onto ELISA plates. Hence, considering these possibilities, the binding and titers observed by the authors may not be an accurate representation of actual affinity for the native protein.
3) Page 24149: The authors showed that their peptide immunogens are neutralizing in that they are capable of disrupting cell-cell fusion. However, it should be noted that neutralizing antibodies are not necessarily protective (Lairmore et al., 1995). A challenge study is, therefore, necessary to assess whether the peptide immunogens are protective. The authors do not mention this limitation in their discussion.
4) Page 24143. Mice, which are not hosts for HTLV-1 infection, were used for immunization and the resulting sera was used for majority of the assays performed; it is, therefore, not clear how well the mice data will correspond to data from human. Over the years, many animal models of HTLV-1 infection have been developed for the purpose of testing various vaccine candidates, such as rabbits (Lairmore et al., 1992) and squirrel monkey, Saimiri sciureus (Kazanji, 2000). The results obtained by the authors would have been more relevant had they chosen these animals for their study.
5) Page 24141: The authors said that their results suggest that the two peptide immunogens represent potential candidates for future multivalent vaccine studies. It should be noted that despite the advantages of short synthetic peptides as vaccines, only a small percentage of such peptides, evaluated in preclinical trials, have progressed to clinical trials (Hans et al., 2006). Though the authors’ initial results with the peptide immunogens in mice are promising, it remains to be seen how well the immunogens fare in the subsequent evaluation stages.
6) Page 24146: In figure 5, the pre-serum values, representing negative control, should be included.
==Minor points==
1) Page 24144: The position numbers in “V349L, I353L, I360L, N363L, and I370L” do not correspond to the B-cell epitope peptide sequence provided in Table 1.
2) Page 24144: The period (.) between the sentences “….are indicated by an asterisk” and “CCR2E and WCCR2E are the…” is missing.
3) Page 24146: “background” and not “backround”.
4) Page 24141: “B-cell epitope” and not “B cell epitope”.
5) Page 24142, 24143 and 24150: Inconsistency with the phrase “coiled coil”, majority of the times it is written as “coiled coil” and sometimes as “coiled-coil”.
==References==
Kazanji M. HTLV type 1 infection in squirrel monkeys (Saimiri sciureus): a promising animal model for HTLV type 1 human infection. AIDS Res Hum Retroviruses. 2000 Nov 1;16(16):1741-6.
Lairmore MD, Rudolph DL, Roberts BD, Dezzutti CS, Lal RB. Characterization of a B-cell immunodominant epitope of human T-lymphotropic virus type 1 (HTLV-I) envelope gp46. Cancer Lett. 1992 Sep 14;66(1):11-20.
Lairmore MD, DiGeorge AM, Conrad SF, Trevino AV, Lal RB, Kaumaya PT. Human T-lymphotropic virus type 1 peptides in chimeric and multivalent constructs with promiscuous T-cell epitopes enhance immunogenicity and overcome genetic restriction. J Virol. 1995 Oct;69(10):6077-89.
Hans D, Young PR, Fairlie DP. Current status of short synthetic peptides as vaccines. Med Chem. 2006 Nov;2(6):627-46.
Bona, C.A., Casares, S., Brumeanu, T.D. (1998). Towards development of T-cell vaccines. Immunol. Today 19, 126-133.
Louis JM, Nesheiwat I, Chang L, Clore GM, Bewley CA. Covalent trimers of the internal N-terminal trimeric coiled-coil of gp41 and antibodies directed against them are potent inhibitors of HIV envelope-mediated cell fusion. J Biol Chem. 2003 May 30;278(22):20278-85.
Ingallinella P, Bianchi E, Finotto M, Cantoni G, Eckert DM, Supekar VM, Bruckmann C, Carfi A, Pessi A. Structural characterization of the fusion-active complex of severe acute respiratory syndrome (SARS) coronavirus. Proc Natl Acad Sci U S A. 2004 Jun 8;101(23):8709-14.
Skehel JJ, Wiley DC. Receptor binding and membrane fusion in virus entry: the influenza hemagglutinin. Annu Rev Biochem. 2000; 69:531-69.
==Overview==
Human T-cell Leukemia virus type-1 (HTLV-1) is a considerable medical problem across the globe and there is lack of effective therapy for HTLV-1 associated diseases. Vaccination, therefore, represents an ideal approach to control the virus. In this study, Sundaram et al., assessed the potential of two de novo designed peptide immunogens (WCCR2T, wild-type peptide; CCR2T, leucine-substituted peptide) that mimicked the coiled coil region of HTLV-1 glycoprotein (gp21) transmembrane (TM) subunit for induction of neutralizing antibodies against the virus. Their novel design involved utilizing a beta-sheet template backbone consisting of alternating Gly/Lys residues that allowed growth of peptide immunogens onto the epsilon side chains of three lysine residues, potentiating the peptides to form triple helical coiled-coil conformation, mimicking the native structure. The template backbone was linked to a “promiscuous” helper T-cell epitope from tetanus toxin to overcome the heterogeneity of the major histocompatibility complex (MHC) in mice population and provide boost to the immune response. Their results showed that antibodies generated using both peptide immunogens were directed against the coiled-coil region of the native gp21 envelope glycoprotein and were neutralizing as they resulted in reduction of cell-cell fusion. These results validated the authors’ hypothesis, demonstrated the validity of their template design and indicated that the two peptide immunogens represent potential candidates for use in a peptide vaccine against HTLV-1. The data presented in this study and the insights gained represent an important step forward towards the design of a vaccine effective against HTLV-1. Further, the approach presented in this paper can be used as a template for the design of peptide vaccines able to induce high affinity neutralizing antibody responses for other pathogens, such as HIV (Louis et al., 2003), SARS-CoV (Ingallinella et al., 2004) and influenza virus (Skehel and Wiley, 2000), which also utilize coiled coil conformation for the fusion process. Additionally, antibodies produced against the immunogens are of significant utility for the analysis of TM function in the respective pathogen infections.
The authors should be praised for taking extensive measures to ensure the generation of structurally and functionally viable peptide immunogen constructs. This was necessary to circumvent the several limitations of synthetic peptide vaccines (Bona et al., 1998), such as low immunogenicity, chemical and conformational instability, short serum half-life, rapid degradation by proteolytic enzymes, and restrictions posed by MHC diversity, among others.
Despite the validation of the hypothesis, the thorough work performed, there are several major and minor deficiencies in their paper, which I highlight below.
==Major points==
1) Page 24144: Ideally, strategies to design protective vaccines must be able activate the relevant arm(s) of the immune system, in particular the humoral and the cellular immune responses. The addition of promiscuous helper T-cell epitope to the template peptide immunogen was, therefore, impeccable, as it will not only help trigger cellular immune response but also help overcome the polymorphism of MHC molecules. However, the rationale for selection of tetanus toxoid peptide was not well justified as it is only good for priming and the resulting memory T helper cells are not likely to be helpful upon re-infection by HTLV-1. Why did the authors not consider using a promiscuous helper epitope from the HTLV-1 virus itself?
2) Page 24146 and 24148: It is possible that the CCR2T and WCCR2T antisera used for ELISA assays (Fig. 5 and Fig. 8) also contain antibodies that bind to the promiscuous T-cell epitope on the peptide immunogen. So, in addition to measuring antibodies binding specifically to the conformational epitope, the authors could also be measuring antibodies binding to the promiscuous T-cell epitope. Also, if this was true, antibodies binding to the B- and T-cell epitopes could lead to steric hindrances in binding analysis when the immunogen is immobilized onto ELISA plates. Hence, considering these possibilities, the binding and titers observed by the authors may not be an accurate representation of actual affinity for the native protein.
3) Page 24149: The authors showed that their peptide immunogens are neutralizing in that they are capable of disrupting cell-cell fusion. However, it should be noted that neutralizing antibodies are not necessarily protective (Lairmore et al., 1995). A challenge study is, therefore, necessary to assess whether the peptide immunogens are protective. The authors do not mention this limitation in their discussion.
4) Page 24143. Mice, which are not hosts for HTLV-1 infection, were used for immunization and the resulting sera was used for majority of the assays performed; it is, therefore, not clear how well the mice data will correspond to data from human. Over the years, many animal models of HTLV-1 infection have been developed for the purpose of testing various vaccine candidates, such as rabbits (Lairmore et al., 1992) and squirrel monkey, Saimiri sciureus (Kazanji, 2000). The results obtained by the authors would have been more relevant had they chosen these animals for their study.
5) Page 24141: The authors said that their results suggest that the two peptide immunogens represent potential candidates for future multivalent vaccine studies. It should be noted that despite the advantages of short synthetic peptides as vaccines, only a small percentage of such peptides, evaluated in preclinical trials, have progressed to clinical trials (Hans et al., 2006). Though the authors’ initial results with the peptide immunogens in mice are promising, it remains to be seen how well the immunogens fare in the subsequent evaluation stages.
6) Page 24146: In figure 5, the pre-serum values, representing negative control, should be included.
==Minor points==
1) Page 24144: The position numbers in “V349L, I353L, I360L, N363L, and I370L” do not correspond to the B-cell epitope peptide sequence provided in Table 1.
2) Page 24144: The period (.) between the sentences “….are indicated by an asterisk” and “CCR2E and WCCR2E are the…” is missing.
3) Page 24146: “background” and not “backround”.
4) Page 24141: “B-cell epitope” and not “B cell epitope”.
5) Page 24142, 24143 and 24150: Inconsistency with the phrase “coiled coil”, majority of the times it is written as “coiled coil” and sometimes as “coiled-coil”.
==References==
Kazanji M. HTLV type 1 infection in squirrel monkeys (Saimiri sciureus): a promising animal model for HTLV type 1 human infection. AIDS Res Hum Retroviruses. 2000 Nov 1;16(16):1741-6.
Lairmore MD, Rudolph DL, Roberts BD, Dezzutti CS, Lal RB. Characterization of a B-cell immunodominant epitope of human T-lymphotropic virus type 1 (HTLV-I) envelope gp46. Cancer Lett. 1992 Sep 14;66(1):11-20.
Lairmore MD, DiGeorge AM, Conrad SF, Trevino AV, Lal RB, Kaumaya PT. Human T-lymphotropic virus type 1 peptides in chimeric and multivalent constructs with promiscuous T-cell epitopes enhance immunogenicity and overcome genetic restriction. J Virol. 1995 Oct;69(10):6077-89.
Hans D, Young PR, Fairlie DP. Current status of short synthetic peptides as vaccines. Med Chem. 2006 Nov;2(6):627-46.
Bona, C.A., Casares, S., Brumeanu, T.D. (1998). Towards development of T-cell vaccines. Immunol. Today 19, 126-133.
Louis JM, Nesheiwat I, Chang L, Clore GM, Bewley CA. Covalent trimers of the internal N-terminal trimeric coiled-coil of gp41 and antibodies directed against them are potent inhibitors of HIV envelope-mediated cell fusion. J Biol Chem. 2003 May 30;278(22):20278-85.
Ingallinella P, Bianchi E, Finotto M, Cantoni G, Eckert DM, Supekar VM, Bruckmann C, Carfi A, Pessi A. Structural characterization of the fusion-active complex of severe acute respiratory syndrome (SARS) coronavirus. Proc Natl Acad Sci U S A. 2004 Jun 8;101(23):8709-14.
Skehel JJ, Wiley DC. Receptor binding and membrane fusion in virus entry: the influenza hemagglutinin. Annu Rev Biochem. 2000; 69:531-69.
Thursday, July 10, 2008
Origin of modern human: out of Africa?
My journal club review of the paper entitled “Mitochondrial genome variation and the origin of modern human” by Ingman, M., Kaessmann, H., Pääba, S. & Gyllensten, U, published in Nature (volume 408, pg. 708-713) in the year 2000.
==Introduction==
Mitochondria are omnipresent throughout the eukaryotic domain (with very few exceptions) (Burger et al., 2003). This double membrane organelle of most cells, are vital for the existence of eukaryotes. Cells depend on the mitochondria for their supply of ATP, the perfect energy currency for the cell. In addition to the role in energy transduction, mitochondria also play a part in other important functions, such as ion homeostasis, intermediary metabolism and apoptosis. Interestingly, majority of the components in these pathways are coded by the nuclear genome, and only a few are coded by the mitochondrial DNA.
Animal mitochondria DNA (mtDNA) can be described as small, usually circular, DNA molecule that occurs in mitochondria, and code for genes that support aerobic respiration. Each mitochondrion possesses few DNA molecules, clustered into nucleoids (each organelle can have few nucleoids) (Satoh and Kuroiwa, 1991). This clustering prevents physical contact between unrelated molecules, and hence may partly explain the absence of recombination observed in majority of animal mtDNA (Antonis et al., 2003). Further, the high mutation rate of the mtDNA (Brown et al., 1979) also indicates lack of recombination in animal mtDNA.
The inheritance of mtDNA in all animal species is strictly a maternal transmission through oocyte cytoplasm in a clonal manner (Giles et al., 1980; Hiendleder and Wolf, 2003). However, few exceptions have been observed, for example certain bivalve families. Several mechanisms of preventing paternal transmission exist (Antonis et al., 2003), such as absence of mitochondria in sperm, mitochondria do not enter the egg, sperm mitochondria selectively destroyed upon entry into egg. Situations exist in which the mechanisms fail and enable paternal leakage to occur, observed in wide taxonomic groups, even in humans (Schwartz and Vissing, 2002).
Over the past decades, mitochondria genes and genomes have been vital tools in the study of animal evolution. Several characteristics of the mtDNA have been fundamental to its success as the marker of choice, namely strict maternal inheritance, high copy number, clonal inheritance, high mutation rate compared with nuclear DNA, and lack of recombination. An important and interesting area in animal evolution that mtDNA has garnered much interest is in the study of modern human origin; when and where did our species arise?
Scientists have vigorously pursued these questions over the past three decades (Ballard and Whitlock, 2004) and such questions have received many answers over the years too. Earlier studies were based on analysis of teeth, bones and artefacts of prehistoric people. A new dimension to the question was introduced with the recent advances in DNA technology, such as PCR and sequencing, which allowed analysis of sequences of mtDNA. mtDNA is inherited and contains the record of evolution, therefore the changes that the DNA has undergone in the past is preserved in its genetic code. Performing comparison of genetic code of mtDNA between different human populations, individuals, and with our closest primate relatives, will reveal how closely we are related and give insights into our origin.
Most previous studies based on mtDNA sequence data were restricted to the small section of the mtDNA called control region (including the D-loop). This sections high mutation rate was the reason for its popularity (Tamura and Nei, 1993), allowing scientist to resolve differences between closely related sequences using the relatively small region (7% of the mtDNA genome). It is becoming clearer now that this high mutation rate is complex and is obscuring important information (Tamura and Nei, 1993). Further, the small region is not representative of the mtDNA. As a result, earlier studies are questionable. In addition, extensive analyses of cleavage sites of the mtDNA sequences through restriction-fragment length polymorphism (RFLP) analysis are not suitable for estimation of mutation rate and hence timing of evolutionary events. This is due to the limited selection of cleavage sites of available enzymes.
The year 2000 A.D saw the completion of the global mtDNA diversity analysis in humans by Ingman et al. (2000). This work was made possible by the rapid improvement of technology for automated DNA sequencing. Some of the important findings in their paper suggest that modern humans originated in Africa, evolved around 171,000 years ago, appeared in one founding population, and migrated to other parts of the world to replace other hominids. The study became an important landmark in population genetics and set a standard in population genomics.
The author of this term paper will discuss the strength and weaknesses of the paper by Ingman et al. (2000), particularly on the important conclusions made about modern human origins. Whether such conclusions are still valid, accurately inferred based on the correctness of their assumptions, and analysis of particular findings. In this term paper, I will refer to the paper by Ingman et al. (2000) as “Ingman et al.”, unless stated otherwise.
==A. Strengths==
1. Offered a solution
Ingman et al. did a thorough background research work and identified few key issues or limitations in earlier studies of human evolution that were not suitable for evolutionary analysis, such as the popular use of the control region in the mtDNA genome, RFLP data and the lack of statistical support due to their smaller data sets.
Ingman and team approached the question of human origin by examining mtDNA from living people from around the world. Their approach is not novel but instead of focussing on the control region, they sequenced the entire mtDNA of 53 people from diverse ethnic, geographical and linguistic background. They excluded the D-loop from their analysis, as it has unusually high mutation rate, and then compared the data to produce a human phylogeny tree. Each of the sequences in their dataset was longer than those previously studied. They obtained a robust tree by collecting a larger data set than in previous studies, therefore were able to make improved estimates of times to evolutionary events (Hedges, 2000). This makes their results highly credible than earlier work.
Their approach opened the door for similar work to be performed in order to answer other questions related to human evolution, such as evolutionary history of Australian and New Guinean Aborigines (Ingman & Gyllensten, 2003), phylogenetic network of European Finnish population (Finnila et al., 2001), and evolutionary relationship between major ethnic groups (Herrnstadt et al., 2002). mtDNA genome sequences are already growing in number (http://www.genpat.uu.se/mtDB/) and it is expected that the number will further grow rapidly in the near future (Hedges, 2000). Hence, their most thorough analysis of the divergence in human mtDNA has set a benchmark to be followed in the field of population genomics.
2. mtDNA rate of mutation & selection
Constant rate of mutation of the mitochondria DNA is an important assumption used to calibrate the molecular clock. Nullification of this assumption, for example by selection, will upset the molecular clock. It is important to mention here that before the work by Ingman et al. it was generally believed that the rate of mutation of the mtDNA was relatively constant in humans. But their analysis showed that this was not the case, only mtDNA sequences excluding the D-loop was evolving at a constant rate. Researchers were unaware of such inconsistency in the D-loop, and hence earlier data may have been biased because of this. Since the publication of this information, D-loop analysis has been ignored in many studies (Templeton 2002).
3. Limitations
The group accepts the limitations of their finding by saying that their analysis on mitochondria locus alone only reflects the genetic history of females, a combination of genetic system, such as X chromosome, Y chromosome and autosomes, is required for a balanced view. They also agreed that the completion of the human genome project would make it easier to obtain data from the different genetic systems and provide us with better picture of our genetic history.
==B. Weaknesses==
1. Recombination or no recombination?
One of the characteristics of the mtDNA that has been key to its success as the marker of choice is lack of recombination. Many lines of independent research have supported the absence of recombination. However, several studies (Hagelberg et al., 1999; Eyre-Walker et al., 1999, Awadalla et al., 1999) have claimed that mtDNA sequences show signs of recombination. Eyre-Walker and Awadalla (2001) suggest three possible modes of recombination i) paternal mitochondria invade the egg during fertilization (paternal leakage), ii) mitochondrial DNA present in the nucleus (nuclear encoded psuedogene copy of the mtDNA) may be reinserted into the mitochondrial genome following fertilization and iii) recombination between heteroplasmic mtDNA molecules carrying different new mutations. Each of these routes would require the presence of enzymes in the mitochondria for homologous recombination or uptake of recombination DNA or RNA from the cytoplasm. There is now good evidence on the presence of mitochondrial genes in the nucleus (Wallace et al., 1997) and that the mammalian mitochondria can catalyse homologous recombination both in vivo (Tang et al., 2000; Holt et al., 1997) and invitro (Thyagarajan et al., 1996).
Awadalla et al. (1999) raised the possibility of recombination by using linkage disequilibrium measure to suggest that mitochondrial DNA does recombine. The proponents of no recombination strongly disagrees with such ascertains, attributing the results to incorrectly analyzed data and poorly based assumptions, and small sample size (Elson et al., 2001, Kumar et al., 2000). Ingman et al. investigated their dataset for linkage disequilibrium and found no evidence for recombination. In addition, the analysis of other data sets (Jorde and Bamshad, 2000; Elson et al, 2001; Herrnstadt et al, 2002) did not support the observation by Awadalla et al. (1999). This has led to an intense discussion about whether recombination occurs in human mitochondria (Jorde and Bamshad, 2000; Kivisild and Villems, 2000; Kumar et al., 2000; Parsons and Irwin, 2000; McVean, 2001; Wiuf, 2001; Innan and Nordborg, 2002), especially now that paternal inheritance has been recently observed in human (Schwartz and Vissing, 2002).
Recently, Piganeau and Eyre-Walker (2004) made an attempt to resolve the controversy by performing a comprehensive reanalysis of three recently published data sets of complete mtDNA sequences (including Ingmans data set) along with 10 RFLP data sets. They also employed two additional recombination detection methods, Geneconv and Maximum Chi-Square. In general, their analysis showed nonsignificant results for recombination. Therefore, there is a lack of evidence for recombination in human mtDNA from their analysis, although some of their data sets show evidence for recombination in one method. This implies that either no recombination or very “weak” recombination occurs. As paternal inheritance of mtDNA in humans has recently been observed (Schwartz and Vissing, 2002), recombination in human mtDNA could be a real possibility. However, studies show that it is hardly detectable from sequence data with currently available recombination detection methods.
Further research is needed to fully convince the scientific community of the pure maternal inheritance and the lack of recombination in mitochondrial DNA. Failure to account for recombination in mtDNA can seriously mislead inferences of our origin and related questions. The question as to whether mitochondria recombine is clearly worth resolving. Ingman and team did the right thing by testing their dataset for the presence of recombination before the phylogenetic analysis, and test results maintained the assumption that there is no evidence for recombination. However, evidence for recombination in future will invalidate their conclusions.
2. Modern Human Origin
Investigators of modern human origin have proposed two main models, namely “ Single African origin” (Vigilant et al., 1991; Cann et al., 1987) and “Multi-regional evolution” (Wolpoff et al., 1989). Multi-regional evolution model suggests that archaic humans (such as Neanderthals and Homo erectus) evolved into modern form concurrently in different parts of the world. The model is supported by fossil evidence, such as the continuation of morphological characteristics between early and modern humans. Whereas, recent African origin proposes that modern humans evolved once in Africa between 100-200 thousand years ago and subsequently colonised the rest of the world without genetic mixing with archaic forms. Studies supporting recent African origin lacked statistical confidence in their tree topology. Therefore, it was difficult to claim that we originated from Africa without strong evidence. The results by Ingman et al. were a big boost to the recent African origin model (Hedges, 2000). The outcome of their analysis was a robust tree deep rooted in Africa. The comparison of their mtDNA with the X chromosome genetic system (Xq13.3 sequences) further complemented their finding, as the X locus gave parallel view on human evolution in Africa (Kaessmann, 1999). With these results, the claim that we, Homo sapiens, originated in Africa was further strengthened, whereas the multi-regional model became a minority standpoint.
A number of other studies supported the conclusion made by Ingman and team
(Jorde et al., 2000; Stringer, 2001; Hedges, 2001; Serre et al., 2004). A Comparison of mitochondrial, autosomal, and Y-chromosome data performed by Jorde et al. (2000) provided broad support for an African origin of modern humans. Blair (2000) argues that evidence for the small population size long before the expansion of modern humans outside Africa is contrary to the multi-regional model, as it will not be able to maintain gene flow among continents. Stringer (2001) concludes that recent African origin for H. sapiens is supported morphologically, behaviourally, and genetically. Furthermore, work by Serre et al. (2004) found no evidence of mtDNA contribution to modern humans by Neanderthal.
Nevertheless, there is still a perception among some scientists that the debate about modern human origins is still far from resolved. Templeton (2002) performed a thorough study using loci from the different genetic systems (mtDNA, Y-chromosome, two X-linked genes and six autosomal regions) and found that his results agree with a variant of the two basic hypothesis mentioned above, the Assimilation model posed by Smith et al. (1989). The Assimilation Model combines recent African origin and multi-regional evolution. However, it differs from the previous models in rejecting replacement, or population migration, as a major factor in the appearance of modern human. This suggests that past studies, including Ingman and teams, relying on one or two loci could be inaccurate, as that specific locus may not encode records of evolutionary event within. To finally establish whether H. sapiens originated in Africa, a later Pleistocene (1.8 – 0.012 Myr ago) record is needed from Asia to compare with that already recovered from Europe and Africa (Stringer, 2001). As of now, the conclusion made by Ingman et al. has strong support, but it will be interesting to see whether it stands the test of time when further exciting developments imminent in this field unfold.
3. Population growth in the non-African group
Ingman et al. states that the non-African group experienced a period of population growth and this happened during the period of cultural change, such as appearance of regional cultural variation and acceleration of artefactual change. I would like to add few comments on this point raised by the authors, as it was not discussed in detail.
Since it is believed that mtDNA is only passed by the mothers, another way of interpreting their observation could be that the daughters of “Eurasian or non-African Eve” spread rapidly throughout the population. I find it hard to believe that cultural change can largely be responsible for this phenomenon, though it may have had indirect effect, because it doesn’t explain the spread of mtDNA by females alone. A more reasonable explanation could be the presence of exceptionally beautiful or sexually attractive females. They and their daughters inheriting their beauty would be highly “sought after”. Peace between tribes could have been made by marrying these females to the enemy tribe. Thus, the migration of these women would easily spread the mtDNA to the other parts of the world (Seielstad et al., 1998; Stoneking, 1998) without any restriction and the population would experience a period of “baby boom”.
4. Divergence time between humans and chimpanzee
Ingman et al. (2001) mentioned that the dates they proposed for the most common recent ancestor evidently depend on the assumed divergence time of chimpanzee and human (5 Million yrs). This date has now been pushed back to before 6 million years ago by recent fossil discovery (Brunet et al., 2002). As a result, molecular-clock estimates of evolutionary events need to be pushed back in time as well. This means that Ingman and team have to recalculate the dates they proposed in the paper.
==C. Miscellaneous comments==
1. Lack of information
In the paper there were several occasions where the authors did not supply sufficient information or a reference. Some of these are discussed below.
i) Ingman et al. assumed a generation time of 20 years to estimate the time when population expansion began for the non-african group. In their text they did not specify the reason for choosing 20 years for the generation time and neither was a reference provided. This is important because few thousands of years ago, the generation time may have been more than 20 years.
ii) They did not give any explanation as to why they used 53 people for their study, and not more. They could have taken few more samples from each linguistic phyla to obtain a more reliable tree. For example, there was only one sample from Korean linguistic phyla.
iii) For figure 2, the authors should have mentioned that the phylogeny tree represents the variation of mtDNA in the individuals and not their physical feature such as skin colour. For example the grouping of Chinese 21 and PNG coast 22 in figure 2 does not mean their physical features are similar. This basic information would be useful in preventing any misinterpretation by the general readers, as the mission of the journal Nature is to publish papers of interest to the general public.
2. Dates for the evolutionary events
Hedges (2000) mentioned that its difficult to time historical events precisely. He further comments on the dates proposed by Ingman et al. as not consistent with fossil and archaeological evidence, but are in the right range.
==D. Conclusion==
The field of human evolution is entangled with great controversy (Cann 2002; Relethford, 2001). Despite intense research efforts, no consensus has been reached as of yet about the genetic relationship between modern humans and archaic human forms such as the Neanderthals. Scrutiny of past work on the controversial issues surrounding modern human origins has steadily improved mtDNA analysis and is a promising tool for the future of this subject.
Ingman and team made significant contribution to the field, such as demonstrating that the D-loop is not suitable for determining evolutionary events and provided strong statistical support to recent African origin model by analysing mtDNA genomes. For a balanced view on our history, the analysis of mtDNA genome alone is not sufficient; it should be coupled with the other genetic systems. This was strongly suggested by Templeton.
==References==
1. Burger G, Gray MW, Lang BF. (2003) Mitochondrial genomes: anything goes. Trends Genet. 19(12): 709-16.
2. Satoh, M. and Kuroiwa, T. (1991) Organization of multiple nucleoids
and DNA molecules in mitochondria of a human cell. Exp. Cell Res.
196, 137–140
3. Antonis R, Emmanuel L and Eleftherios Z. (2003) Animal mitochondrial DNA recombination revisited. Trends in Ecology & Evolution, 18(8) :411-417
4. Brown, W. M., George, M. Jr & Wilson, A. C. (1979) Rapid evolution of animal mitochondrial DNA. Proc. Natl Acad. Sci. USA 76, 1967-1971.
5. Giles, R. E., Blanc, H., Cann, H. M. & Wallace, D. C. (1980) Maternal inheritance of human mitochondrial DNA. Proc. Natl Acad. Sci. USA 77, 6715-6719.
6. Hiendleder S, Wolf E. (2003) The mitochondrial genome in embryo technologies. Reprod Domest Anim. 38(4): 290-304.
7. Schwartz M, Vissing J. (2002) Paternal inheritance of mitochondrial DNA.
N Engl J Med. 347(8): 576-80.
8. Ballard JW, Whitlock MC. (2004) The incomplete natural history of mitochondria. Mol Ecol. 13(4): 729-44.
9. Tamura, K. & Nei, M. (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10, 512-526.
10. Ingman M, Kaessmann H, Paabo S, Gyllensten U. (2000) Mitochondrial genome variation and the origin of modern humans. Nature. 408(6813):708-13.
11. Hedges SB. (2000) Human evolution. A start for population genomics. Nature. 408(6813):652-3.
12. Ingman M, Gyllensten U. (2003) Mitochondrial genome variation and evolutionary history of Australian and New Guinean aborigines. Genome Res. 13(7): 1600-6.
13. Finnila S, Lehtonen MS, Majamaa K (2001). Phylogenetic network for European mtDNA. Am J Hum Genet 68: 1475–1484.
14. Herrnstadt C, Elson JL, Fahy E, Preston G, Turnbull DM, Anderson C et al. (2002). Reduced-median-network analysis of complete mitochondrial DNA coding-region sequences for the major African, Asian, and European haplogroups. Am J Hum Genet 70: 1152–1171.
15. Hagelberg E, Goldman N, Lio P, Whelan S, Schiefenhovel W, Clegg JB, Bowden DK. (1999) Evidence for mitochondrial DNA recombination in a human population of island Melanesia. Proc R Soc Lond B Biol Sci. 266(1418): 485-92
16. Eyre-Walker A, Smith NH, Smith JM. (1999) How clonal are human mitochondria? Proc R Soc Lond B Biol Sci. 266(1418): 477-83.
17. Awadalla, P., Eyre-Walker, A., Maynard Smith, J. (1999). Linkage Disequilibrium and recombination in hominid mitochondrial DNA. Science. 286, 2524-2525.
18. Eyre-Walker A, Awadalla P. (2001) Does human mtDNA recombine? J Mol Evol. 53(4-5): 430-5.
19. Wallace DC, Stugard C, Murdock D, Schurr T, Brown MD. (1997) Ancient mtDNA sequences in the human nuclear genome: a potential source of errors in identifying pathogenic mutations. Proc Natl Acad Sci U S A. 23; 94(26): 14900-5.
20. Thyagarajan B, Padua RA, Campbell C (1996) Mammalian mitochondria possess homologous DNA recombination activity. J Biol Chem. 271: 27536–27543
21. Holt IJ, Dunbar DR, Jacobs HT (1997) Behaviour of a population of
partially duplicated mitochondrial DNA molecules in cell culture:
segregation, maintainence and recombination dependent upon
nuclear background. Hum Mol Genet 6:1251–1260
22. Tang Y, Manfredi G, Hirano M, Schon EA (2000) Maintainence of
human rearranged mitochondrial DNAs in long-term cultured transmitochondrial cell lines. Mol Cell Biol 11:2349–2358
23. Kumar, S., Hedrick, P. & Stoneking, M. (2000) Questioning evidence for recombination in human mitochondrial DNA. Science 288, 1931.
24. Elson JL, Andrews RM, Chinnery PF, Lightowlers RN, Turnbull DM, Howell N. (2001) Analysis of European mtDNAs for recombination. Am J Hum Genet. 68(1):145-153.
25. Jorde LB, Bamshad M. (2000) Questioning evidence for recombination in human mitochondrial DNA. Science. 288(5473):1931.
26. Kivisild T, Villems R. (2000) Questioning evidence for recombination in human mitochondrial DNA. Science. 288(5473): 1931.
27. Parsons TJ, Irwin JA. (2000) Questioning evidence for recombination in human mitochondrial DNA. Science. 288(5473): 1931.
28. McVean GA. (2001) What do patterns of genetic variability reveal about mitochondrial recombination? Heredity. 87(Pt 6): 613-20.
29. Wiuf C. (2001) Recombination in human mitochondrial DNA? Genetics. 159(2): 749-56.
30. Innan H, Nordborg M. (2002) Recombination or mutational hot spots in human mtDNA? Mol Biol Evol. 19(7): 1122-7.
31. Piganeau G, Eyre-Walker A. (2004) A reanalysis of the indirect evidence for recombination in human mitochondrial DNA. Heredity. 92(4):282-8.
32. Vigilant, L., Stoneking, M., Harpending, H., Hawkes, K. &Wilson, A. C. (1991) African populations and the evolution of human mitochondrial DNA. Science 253, 1503-1507.
33. Cann, R. L., Stoneking, M. & Wilson, A. C. (1987) Mitochondrial DNA and human evolution. Nature 325, 31-36.
34. Wolpoff, M. H. (1989) in The Human Revolution: Behavioural and Biological Perspectives on the Origins of ModernHumans (eds Mellars, P. & Stringer, C.) 62-108 (PrincetonUniv. Press, Princeton, New Jersey).
35. Kaessmann, H., Heissig, F., von Haeseler, A. & Paabo, S. (1999) DNA sequence variation in a non-coding region of low recombination on the human X chromosome. Nature Genet. 22, 78-81.
36. Jorde LB, Watkins WS, Bamshad MJ, Dixon ME, Ricker CE, Seielstad MT, Batzer MA. (2000) The distribution of human genetic diversity: a comparison of mitochondrial, autosomal, and Y-chromosome data. Am J Hum Genet. 66(3): 979-88.
37. Stringer C. (2002) Modern human origins: progress and prospects.
Philos Trans R Soc Lond B Biol Sci. 357(1420): 563-79.
38. Serre D, Langaney A, Chech M, Teschler-Nicola M, Paunovic M, Mennecier P, Hofreiter M, Possnert G G, Paabo S. (2004) No Evidence of Neandertal mtDNA Contribution to Early Modern Humans. PLoS Biol. 2(3): E57.
39. Templeton A. (2002) Out of Africa again and again. Nature. 416(6876): 45-51
40. Smith, F. H., Falsetti, A. B. & Donnelly, S.M. (1989) Modern human origins. Yb. Physical Anthrop. 32, 35-68.
41. Stoneking M. (1998) Women on the move. Nat Genet. 20(3): 219-20.
42. Seielstad MT, Minch E, Cavalli-Sforza LL. (1998) Genetic evidence for a higher female migration rate in humans.Nat Genet. 20(3): 278-80.
43. Ingman M, Gyllensten U. (2001) Analysis of the complete human mtDNA genome: methodology and inferences for human evolution. J Hered. 92(6): 454-61.
44. Brunet M, Guy F, Pilbeam D, Mackaye HT, Likius A, Ahounta D, Beauvilain A, et al. (2002) A new hominid from the Upper Miocene of Chad, Central Africa. Nature. 418(6894): 145-51.
45. Cann RL. (2002) Human evolution: tangled genetic routes.
Nature. 416(6876): 32-3.
46. Relethford, J. H. (2001) Genetics and the Search for Modern Human Origins (Wiley, New York).
==Introduction==
Mitochondria are omnipresent throughout the eukaryotic domain (with very few exceptions) (Burger et al., 2003). This double membrane organelle of most cells, are vital for the existence of eukaryotes. Cells depend on the mitochondria for their supply of ATP, the perfect energy currency for the cell. In addition to the role in energy transduction, mitochondria also play a part in other important functions, such as ion homeostasis, intermediary metabolism and apoptosis. Interestingly, majority of the components in these pathways are coded by the nuclear genome, and only a few are coded by the mitochondrial DNA.
Animal mitochondria DNA (mtDNA) can be described as small, usually circular, DNA molecule that occurs in mitochondria, and code for genes that support aerobic respiration. Each mitochondrion possesses few DNA molecules, clustered into nucleoids (each organelle can have few nucleoids) (Satoh and Kuroiwa, 1991). This clustering prevents physical contact between unrelated molecules, and hence may partly explain the absence of recombination observed in majority of animal mtDNA (Antonis et al., 2003). Further, the high mutation rate of the mtDNA (Brown et al., 1979) also indicates lack of recombination in animal mtDNA.
The inheritance of mtDNA in all animal species is strictly a maternal transmission through oocyte cytoplasm in a clonal manner (Giles et al., 1980; Hiendleder and Wolf, 2003). However, few exceptions have been observed, for example certain bivalve families. Several mechanisms of preventing paternal transmission exist (Antonis et al., 2003), such as absence of mitochondria in sperm, mitochondria do not enter the egg, sperm mitochondria selectively destroyed upon entry into egg. Situations exist in which the mechanisms fail and enable paternal leakage to occur, observed in wide taxonomic groups, even in humans (Schwartz and Vissing, 2002).
Over the past decades, mitochondria genes and genomes have been vital tools in the study of animal evolution. Several characteristics of the mtDNA have been fundamental to its success as the marker of choice, namely strict maternal inheritance, high copy number, clonal inheritance, high mutation rate compared with nuclear DNA, and lack of recombination. An important and interesting area in animal evolution that mtDNA has garnered much interest is in the study of modern human origin; when and where did our species arise?
Scientists have vigorously pursued these questions over the past three decades (Ballard and Whitlock, 2004) and such questions have received many answers over the years too. Earlier studies were based on analysis of teeth, bones and artefacts of prehistoric people. A new dimension to the question was introduced with the recent advances in DNA technology, such as PCR and sequencing, which allowed analysis of sequences of mtDNA. mtDNA is inherited and contains the record of evolution, therefore the changes that the DNA has undergone in the past is preserved in its genetic code. Performing comparison of genetic code of mtDNA between different human populations, individuals, and with our closest primate relatives, will reveal how closely we are related and give insights into our origin.
Most previous studies based on mtDNA sequence data were restricted to the small section of the mtDNA called control region (including the D-loop). This sections high mutation rate was the reason for its popularity (Tamura and Nei, 1993), allowing scientist to resolve differences between closely related sequences using the relatively small region (7% of the mtDNA genome). It is becoming clearer now that this high mutation rate is complex and is obscuring important information (Tamura and Nei, 1993). Further, the small region is not representative of the mtDNA. As a result, earlier studies are questionable. In addition, extensive analyses of cleavage sites of the mtDNA sequences through restriction-fragment length polymorphism (RFLP) analysis are not suitable for estimation of mutation rate and hence timing of evolutionary events. This is due to the limited selection of cleavage sites of available enzymes.
The year 2000 A.D saw the completion of the global mtDNA diversity analysis in humans by Ingman et al. (2000). This work was made possible by the rapid improvement of technology for automated DNA sequencing. Some of the important findings in their paper suggest that modern humans originated in Africa, evolved around 171,000 years ago, appeared in one founding population, and migrated to other parts of the world to replace other hominids. The study became an important landmark in population genetics and set a standard in population genomics.
The author of this term paper will discuss the strength and weaknesses of the paper by Ingman et al. (2000), particularly on the important conclusions made about modern human origins. Whether such conclusions are still valid, accurately inferred based on the correctness of their assumptions, and analysis of particular findings. In this term paper, I will refer to the paper by Ingman et al. (2000) as “Ingman et al.”, unless stated otherwise.
==A. Strengths==
1. Offered a solution
Ingman et al. did a thorough background research work and identified few key issues or limitations in earlier studies of human evolution that were not suitable for evolutionary analysis, such as the popular use of the control region in the mtDNA genome, RFLP data and the lack of statistical support due to their smaller data sets.
Ingman and team approached the question of human origin by examining mtDNA from living people from around the world. Their approach is not novel but instead of focussing on the control region, they sequenced the entire mtDNA of 53 people from diverse ethnic, geographical and linguistic background. They excluded the D-loop from their analysis, as it has unusually high mutation rate, and then compared the data to produce a human phylogeny tree. Each of the sequences in their dataset was longer than those previously studied. They obtained a robust tree by collecting a larger data set than in previous studies, therefore were able to make improved estimates of times to evolutionary events (Hedges, 2000). This makes their results highly credible than earlier work.
Their approach opened the door for similar work to be performed in order to answer other questions related to human evolution, such as evolutionary history of Australian and New Guinean Aborigines (Ingman & Gyllensten, 2003), phylogenetic network of European Finnish population (Finnila et al., 2001), and evolutionary relationship between major ethnic groups (Herrnstadt et al., 2002). mtDNA genome sequences are already growing in number (http://www.genpat.uu.se/mtDB/) and it is expected that the number will further grow rapidly in the near future (Hedges, 2000). Hence, their most thorough analysis of the divergence in human mtDNA has set a benchmark to be followed in the field of population genomics.
2. mtDNA rate of mutation & selection
Constant rate of mutation of the mitochondria DNA is an important assumption used to calibrate the molecular clock. Nullification of this assumption, for example by selection, will upset the molecular clock. It is important to mention here that before the work by Ingman et al. it was generally believed that the rate of mutation of the mtDNA was relatively constant in humans. But their analysis showed that this was not the case, only mtDNA sequences excluding the D-loop was evolving at a constant rate. Researchers were unaware of such inconsistency in the D-loop, and hence earlier data may have been biased because of this. Since the publication of this information, D-loop analysis has been ignored in many studies (Templeton 2002).
3. Limitations
The group accepts the limitations of their finding by saying that their analysis on mitochondria locus alone only reflects the genetic history of females, a combination of genetic system, such as X chromosome, Y chromosome and autosomes, is required for a balanced view. They also agreed that the completion of the human genome project would make it easier to obtain data from the different genetic systems and provide us with better picture of our genetic history.
==B. Weaknesses==
1. Recombination or no recombination?
One of the characteristics of the mtDNA that has been key to its success as the marker of choice is lack of recombination. Many lines of independent research have supported the absence of recombination. However, several studies (Hagelberg et al., 1999; Eyre-Walker et al., 1999, Awadalla et al., 1999) have claimed that mtDNA sequences show signs of recombination. Eyre-Walker and Awadalla (2001) suggest three possible modes of recombination i) paternal mitochondria invade the egg during fertilization (paternal leakage), ii) mitochondrial DNA present in the nucleus (nuclear encoded psuedogene copy of the mtDNA) may be reinserted into the mitochondrial genome following fertilization and iii) recombination between heteroplasmic mtDNA molecules carrying different new mutations. Each of these routes would require the presence of enzymes in the mitochondria for homologous recombination or uptake of recombination DNA or RNA from the cytoplasm. There is now good evidence on the presence of mitochondrial genes in the nucleus (Wallace et al., 1997) and that the mammalian mitochondria can catalyse homologous recombination both in vivo (Tang et al., 2000; Holt et al., 1997) and invitro (Thyagarajan et al., 1996).
Awadalla et al. (1999) raised the possibility of recombination by using linkage disequilibrium measure to suggest that mitochondrial DNA does recombine. The proponents of no recombination strongly disagrees with such ascertains, attributing the results to incorrectly analyzed data and poorly based assumptions, and small sample size (Elson et al., 2001, Kumar et al., 2000). Ingman et al. investigated their dataset for linkage disequilibrium and found no evidence for recombination. In addition, the analysis of other data sets (Jorde and Bamshad, 2000; Elson et al, 2001; Herrnstadt et al, 2002) did not support the observation by Awadalla et al. (1999). This has led to an intense discussion about whether recombination occurs in human mitochondria (Jorde and Bamshad, 2000; Kivisild and Villems, 2000; Kumar et al., 2000; Parsons and Irwin, 2000; McVean, 2001; Wiuf, 2001; Innan and Nordborg, 2002), especially now that paternal inheritance has been recently observed in human (Schwartz and Vissing, 2002).
Recently, Piganeau and Eyre-Walker (2004) made an attempt to resolve the controversy by performing a comprehensive reanalysis of three recently published data sets of complete mtDNA sequences (including Ingmans data set) along with 10 RFLP data sets. They also employed two additional recombination detection methods, Geneconv and Maximum Chi-Square. In general, their analysis showed nonsignificant results for recombination. Therefore, there is a lack of evidence for recombination in human mtDNA from their analysis, although some of their data sets show evidence for recombination in one method. This implies that either no recombination or very “weak” recombination occurs. As paternal inheritance of mtDNA in humans has recently been observed (Schwartz and Vissing, 2002), recombination in human mtDNA could be a real possibility. However, studies show that it is hardly detectable from sequence data with currently available recombination detection methods.
Further research is needed to fully convince the scientific community of the pure maternal inheritance and the lack of recombination in mitochondrial DNA. Failure to account for recombination in mtDNA can seriously mislead inferences of our origin and related questions. The question as to whether mitochondria recombine is clearly worth resolving. Ingman and team did the right thing by testing their dataset for the presence of recombination before the phylogenetic analysis, and test results maintained the assumption that there is no evidence for recombination. However, evidence for recombination in future will invalidate their conclusions.
2. Modern Human Origin
Investigators of modern human origin have proposed two main models, namely “ Single African origin” (Vigilant et al., 1991; Cann et al., 1987) and “Multi-regional evolution” (Wolpoff et al., 1989). Multi-regional evolution model suggests that archaic humans (such as Neanderthals and Homo erectus) evolved into modern form concurrently in different parts of the world. The model is supported by fossil evidence, such as the continuation of morphological characteristics between early and modern humans. Whereas, recent African origin proposes that modern humans evolved once in Africa between 100-200 thousand years ago and subsequently colonised the rest of the world without genetic mixing with archaic forms. Studies supporting recent African origin lacked statistical confidence in their tree topology. Therefore, it was difficult to claim that we originated from Africa without strong evidence. The results by Ingman et al. were a big boost to the recent African origin model (Hedges, 2000). The outcome of their analysis was a robust tree deep rooted in Africa. The comparison of their mtDNA with the X chromosome genetic system (Xq13.3 sequences) further complemented their finding, as the X locus gave parallel view on human evolution in Africa (Kaessmann, 1999). With these results, the claim that we, Homo sapiens, originated in Africa was further strengthened, whereas the multi-regional model became a minority standpoint.
A number of other studies supported the conclusion made by Ingman and team
(Jorde et al., 2000; Stringer, 2001; Hedges, 2001; Serre et al., 2004). A Comparison of mitochondrial, autosomal, and Y-chromosome data performed by Jorde et al. (2000) provided broad support for an African origin of modern humans. Blair (2000) argues that evidence for the small population size long before the expansion of modern humans outside Africa is contrary to the multi-regional model, as it will not be able to maintain gene flow among continents. Stringer (2001) concludes that recent African origin for H. sapiens is supported morphologically, behaviourally, and genetically. Furthermore, work by Serre et al. (2004) found no evidence of mtDNA contribution to modern humans by Neanderthal.
Nevertheless, there is still a perception among some scientists that the debate about modern human origins is still far from resolved. Templeton (2002) performed a thorough study using loci from the different genetic systems (mtDNA, Y-chromosome, two X-linked genes and six autosomal regions) and found that his results agree with a variant of the two basic hypothesis mentioned above, the Assimilation model posed by Smith et al. (1989). The Assimilation Model combines recent African origin and multi-regional evolution. However, it differs from the previous models in rejecting replacement, or population migration, as a major factor in the appearance of modern human. This suggests that past studies, including Ingman and teams, relying on one or two loci could be inaccurate, as that specific locus may not encode records of evolutionary event within. To finally establish whether H. sapiens originated in Africa, a later Pleistocene (1.8 – 0.012 Myr ago) record is needed from Asia to compare with that already recovered from Europe and Africa (Stringer, 2001). As of now, the conclusion made by Ingman et al. has strong support, but it will be interesting to see whether it stands the test of time when further exciting developments imminent in this field unfold.
3. Population growth in the non-African group
Ingman et al. states that the non-African group experienced a period of population growth and this happened during the period of cultural change, such as appearance of regional cultural variation and acceleration of artefactual change. I would like to add few comments on this point raised by the authors, as it was not discussed in detail.
Since it is believed that mtDNA is only passed by the mothers, another way of interpreting their observation could be that the daughters of “Eurasian or non-African Eve” spread rapidly throughout the population. I find it hard to believe that cultural change can largely be responsible for this phenomenon, though it may have had indirect effect, because it doesn’t explain the spread of mtDNA by females alone. A more reasonable explanation could be the presence of exceptionally beautiful or sexually attractive females. They and their daughters inheriting their beauty would be highly “sought after”. Peace between tribes could have been made by marrying these females to the enemy tribe. Thus, the migration of these women would easily spread the mtDNA to the other parts of the world (Seielstad et al., 1998; Stoneking, 1998) without any restriction and the population would experience a period of “baby boom”.
4. Divergence time between humans and chimpanzee
Ingman et al. (2001) mentioned that the dates they proposed for the most common recent ancestor evidently depend on the assumed divergence time of chimpanzee and human (5 Million yrs). This date has now been pushed back to before 6 million years ago by recent fossil discovery (Brunet et al., 2002). As a result, molecular-clock estimates of evolutionary events need to be pushed back in time as well. This means that Ingman and team have to recalculate the dates they proposed in the paper.
==C. Miscellaneous comments==
1. Lack of information
In the paper there were several occasions where the authors did not supply sufficient information or a reference. Some of these are discussed below.
i) Ingman et al. assumed a generation time of 20 years to estimate the time when population expansion began for the non-african group. In their text they did not specify the reason for choosing 20 years for the generation time and neither was a reference provided. This is important because few thousands of years ago, the generation time may have been more than 20 years.
ii) They did not give any explanation as to why they used 53 people for their study, and not more. They could have taken few more samples from each linguistic phyla to obtain a more reliable tree. For example, there was only one sample from Korean linguistic phyla.
iii) For figure 2, the authors should have mentioned that the phylogeny tree represents the variation of mtDNA in the individuals and not their physical feature such as skin colour. For example the grouping of Chinese 21 and PNG coast 22 in figure 2 does not mean their physical features are similar. This basic information would be useful in preventing any misinterpretation by the general readers, as the mission of the journal Nature is to publish papers of interest to the general public.
2. Dates for the evolutionary events
Hedges (2000) mentioned that its difficult to time historical events precisely. He further comments on the dates proposed by Ingman et al. as not consistent with fossil and archaeological evidence, but are in the right range.
==D. Conclusion==
The field of human evolution is entangled with great controversy (Cann 2002; Relethford, 2001). Despite intense research efforts, no consensus has been reached as of yet about the genetic relationship between modern humans and archaic human forms such as the Neanderthals. Scrutiny of past work on the controversial issues surrounding modern human origins has steadily improved mtDNA analysis and is a promising tool for the future of this subject.
Ingman and team made significant contribution to the field, such as demonstrating that the D-loop is not suitable for determining evolutionary events and provided strong statistical support to recent African origin model by analysing mtDNA genomes. For a balanced view on our history, the analysis of mtDNA genome alone is not sufficient; it should be coupled with the other genetic systems. This was strongly suggested by Templeton.
==References==
1. Burger G, Gray MW, Lang BF. (2003) Mitochondrial genomes: anything goes. Trends Genet. 19(12): 709-16.
2. Satoh, M. and Kuroiwa, T. (1991) Organization of multiple nucleoids
and DNA molecules in mitochondria of a human cell. Exp. Cell Res.
196, 137–140
3. Antonis R, Emmanuel L and Eleftherios Z. (2003) Animal mitochondrial DNA recombination revisited. Trends in Ecology & Evolution, 18(8) :411-417
4. Brown, W. M., George, M. Jr & Wilson, A. C. (1979) Rapid evolution of animal mitochondrial DNA. Proc. Natl Acad. Sci. USA 76, 1967-1971.
5. Giles, R. E., Blanc, H., Cann, H. M. & Wallace, D. C. (1980) Maternal inheritance of human mitochondrial DNA. Proc. Natl Acad. Sci. USA 77, 6715-6719.
6. Hiendleder S, Wolf E. (2003) The mitochondrial genome in embryo technologies. Reprod Domest Anim. 38(4): 290-304.
7. Schwartz M, Vissing J. (2002) Paternal inheritance of mitochondrial DNA.
N Engl J Med. 347(8): 576-80.
8. Ballard JW, Whitlock MC. (2004) The incomplete natural history of mitochondria. Mol Ecol. 13(4): 729-44.
9. Tamura, K. & Nei, M. (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10, 512-526.
10. Ingman M, Kaessmann H, Paabo S, Gyllensten U. (2000) Mitochondrial genome variation and the origin of modern humans. Nature. 408(6813):708-13.
11. Hedges SB. (2000) Human evolution. A start for population genomics. Nature. 408(6813):652-3.
12. Ingman M, Gyllensten U. (2003) Mitochondrial genome variation and evolutionary history of Australian and New Guinean aborigines. Genome Res. 13(7): 1600-6.
13. Finnila S, Lehtonen MS, Majamaa K (2001). Phylogenetic network for European mtDNA. Am J Hum Genet 68: 1475–1484.
14. Herrnstadt C, Elson JL, Fahy E, Preston G, Turnbull DM, Anderson C et al. (2002). Reduced-median-network analysis of complete mitochondrial DNA coding-region sequences for the major African, Asian, and European haplogroups. Am J Hum Genet 70: 1152–1171.
15. Hagelberg E, Goldman N, Lio P, Whelan S, Schiefenhovel W, Clegg JB, Bowden DK. (1999) Evidence for mitochondrial DNA recombination in a human population of island Melanesia. Proc R Soc Lond B Biol Sci. 266(1418): 485-92
16. Eyre-Walker A, Smith NH, Smith JM. (1999) How clonal are human mitochondria? Proc R Soc Lond B Biol Sci. 266(1418): 477-83.
17. Awadalla, P., Eyre-Walker, A., Maynard Smith, J. (1999). Linkage Disequilibrium and recombination in hominid mitochondrial DNA. Science. 286, 2524-2525.
18. Eyre-Walker A, Awadalla P. (2001) Does human mtDNA recombine? J Mol Evol. 53(4-5): 430-5.
19. Wallace DC, Stugard C, Murdock D, Schurr T, Brown MD. (1997) Ancient mtDNA sequences in the human nuclear genome: a potential source of errors in identifying pathogenic mutations. Proc Natl Acad Sci U S A. 23; 94(26): 14900-5.
20. Thyagarajan B, Padua RA, Campbell C (1996) Mammalian mitochondria possess homologous DNA recombination activity. J Biol Chem. 271: 27536–27543
21. Holt IJ, Dunbar DR, Jacobs HT (1997) Behaviour of a population of
partially duplicated mitochondrial DNA molecules in cell culture:
segregation, maintainence and recombination dependent upon
nuclear background. Hum Mol Genet 6:1251–1260
22. Tang Y, Manfredi G, Hirano M, Schon EA (2000) Maintainence of
human rearranged mitochondrial DNAs in long-term cultured transmitochondrial cell lines. Mol Cell Biol 11:2349–2358
23. Kumar, S., Hedrick, P. & Stoneking, M. (2000) Questioning evidence for recombination in human mitochondrial DNA. Science 288, 1931.
24. Elson JL, Andrews RM, Chinnery PF, Lightowlers RN, Turnbull DM, Howell N. (2001) Analysis of European mtDNAs for recombination. Am J Hum Genet. 68(1):145-153.
25. Jorde LB, Bamshad M. (2000) Questioning evidence for recombination in human mitochondrial DNA. Science. 288(5473):1931.
26. Kivisild T, Villems R. (2000) Questioning evidence for recombination in human mitochondrial DNA. Science. 288(5473): 1931.
27. Parsons TJ, Irwin JA. (2000) Questioning evidence for recombination in human mitochondrial DNA. Science. 288(5473): 1931.
28. McVean GA. (2001) What do patterns of genetic variability reveal about mitochondrial recombination? Heredity. 87(Pt 6): 613-20.
29. Wiuf C. (2001) Recombination in human mitochondrial DNA? Genetics. 159(2): 749-56.
30. Innan H, Nordborg M. (2002) Recombination or mutational hot spots in human mtDNA? Mol Biol Evol. 19(7): 1122-7.
31. Piganeau G, Eyre-Walker A. (2004) A reanalysis of the indirect evidence for recombination in human mitochondrial DNA. Heredity. 92(4):282-8.
32. Vigilant, L., Stoneking, M., Harpending, H., Hawkes, K. &Wilson, A. C. (1991) African populations and the evolution of human mitochondrial DNA. Science 253, 1503-1507.
33. Cann, R. L., Stoneking, M. & Wilson, A. C. (1987) Mitochondrial DNA and human evolution. Nature 325, 31-36.
34. Wolpoff, M. H. (1989) in The Human Revolution: Behavioural and Biological Perspectives on the Origins of ModernHumans (eds Mellars, P. & Stringer, C.) 62-108 (PrincetonUniv. Press, Princeton, New Jersey).
35. Kaessmann, H., Heissig, F., von Haeseler, A. & Paabo, S. (1999) DNA sequence variation in a non-coding region of low recombination on the human X chromosome. Nature Genet. 22, 78-81.
36. Jorde LB, Watkins WS, Bamshad MJ, Dixon ME, Ricker CE, Seielstad MT, Batzer MA. (2000) The distribution of human genetic diversity: a comparison of mitochondrial, autosomal, and Y-chromosome data. Am J Hum Genet. 66(3): 979-88.
37. Stringer C. (2002) Modern human origins: progress and prospects.
Philos Trans R Soc Lond B Biol Sci. 357(1420): 563-79.
38. Serre D, Langaney A, Chech M, Teschler-Nicola M, Paunovic M, Mennecier P, Hofreiter M, Possnert G G, Paabo S. (2004) No Evidence of Neandertal mtDNA Contribution to Early Modern Humans. PLoS Biol. 2(3): E57.
39. Templeton A. (2002) Out of Africa again and again. Nature. 416(6876): 45-51
40. Smith, F. H., Falsetti, A. B. & Donnelly, S.M. (1989) Modern human origins. Yb. Physical Anthrop. 32, 35-68.
41. Stoneking M. (1998) Women on the move. Nat Genet. 20(3): 219-20.
42. Seielstad MT, Minch E, Cavalli-Sforza LL. (1998) Genetic evidence for a higher female migration rate in humans.Nat Genet. 20(3): 278-80.
43. Ingman M, Gyllensten U. (2001) Analysis of the complete human mtDNA genome: methodology and inferences for human evolution. J Hered. 92(6): 454-61.
44. Brunet M, Guy F, Pilbeam D, Mackaye HT, Likius A, Ahounta D, Beauvilain A, et al. (2002) A new hominid from the Upper Miocene of Chad, Central Africa. Nature. 418(6894): 145-51.
45. Cann RL. (2002) Human evolution: tangled genetic routes.
Nature. 416(6876): 32-3.
46. Relethford, J. H. (2001) Genetics and the Search for Modern Human Origins (Wiley, New York).
Monday, June 30, 2008
Do not install BootCamp update 2.1
Yes, that is right, do not install BootCamp update 2.1 for Vista (i am not sure if the XP version causes the same problem), which provides Apple hardware drivers, unless you want to have an intermittent problem of keyboard and mouse freeze/hang. I learned it the hardway. This problem was not there with BootCamp 2.0, which came preloaded with the OS X Leopard CD. However, uninstalling BootCamp 2.1 and reinstalling BootCamp 2.0 did not fix the problem, but I think it reduced the frequency of the hangs. I guess there is something that is installed by BootCamp 2.1 that does not get removed and overwritten by BootCamp 2.0. Searching for a solution on this over the net went in vain. It seems that I have no choice but to wait for Apple to solve this problem, hopefully in their next BootCamp update 2.2. Despite the significant updates in 2.1, I think I am better off with 2.0 for now, largely due to the less frequent hangs, and I don't think I have the courage to go through another round of "reformatting and reinstalling Vista" in order to install BootCamp 2.0 on a fresh Windows install.
Thunderbird error in both Vista and Leopard - SSL protocol disabled
When I was synchronizing my thunderbird mail folder between Mac Leopard and Vista, I accidentally pressed the stop button when the progress was half-way through. When I restarted Thunderbird, I was getting an error saying that "Thunderbird is not able to connect to the Imap….server because the SSL protocol is disabled" (in both Leopard and Vista). I searched Google but no luck. I then tried replacing the content of the Thunderbird profile folder with that of the backup I made for the same folder some time back. I replaced everything except the “Chrome”, “Mail” and “ImapMail” folders. Thunderbird was behaving normal again when restarted. I am glad I have learned to maintain a habit of making frequent backups. However, I think, in this case one could have also fixed the problem without the help of backups. Simply, install Thunderbird again in another directory of Windows, copy all the files, except for the above three folders and use them to replace those in the original Thunderbird profiles directory.
Sunday, June 29, 2008
Mac equivalent of Windows create "New" MS Office Document
For many days, I have been searching online for a way to quickly create new MS Office documents directly in the working folder that I am in, without the need to click on the MS Office application icon, whether on the dock or in the applications folder. In Windows, this is achevied easily by just right-clicking in the working directory, click on the "New" menu and then select the MS Office document to be created from the list of options that pop-up. Having no luck on the net, I tried to experiment using Automator to create a workflow/plug-in that can help me do this in Leopard. Since, I was no longer new to Automator, it was easy for me to navigate through the program, and after few trial and errors I managed to create a plug-in that creates new MS Office document quickly and gives me the option to save it into the working directory. Below is a snapshot of the workflow that I used for MS Word:
Saved the workflow as a plug-in for Finder (File -->Save as Plug-in).
Now, to create a new MS Word document, I just need to right click in the working directory, go to the Automator menu, and then select the sub-menu "New Microsoft Office Word Document".
The same method can be repeated for other MS Office programs such as Excel and PowerPoint. However, this method is not as good as that of Windows because after the MS Office program is opened, the user needs to browse to the working directory where it is to be saved. Nevertheless, I am happy with this for the time being until I come across or figure out how to make it function like that of Windows.
Saved the workflow as a plug-in for Finder (File -->Save as Plug-in).
Now, to create a new MS Word document, I just need to right click in the working directory, go to the Automator menu, and then select the sub-menu "New Microsoft Office Word Document".
The same method can be repeated for other MS Office programs such as Excel and PowerPoint. However, this method is not as good as that of Windows because after the MS Office program is opened, the user needs to browse to the working directory where it is to be saved. Nevertheless, I am happy with this for the time being until I come across or figure out how to make it function like that of Windows.
Wednesday, June 25, 2008
Impressed with the Automator in Mac Leopard
I have read at many places about how wonderful the Automator program in Leopard is, but never found the need to give it a try and validate its usefulness by myself. Finally, today I got to use it as it turned out to be the solution to my long-standing problem of "how to synchronize emails between Leopard and Boot Camp Vista?".
I use Thunderbird for my email needs and I really like it, especially with the option to add extensions. Now, since I shuttle between Leopard and Vista quite frequently, I wanted to be able to have the same mailbox, content and settings whether I am in Leopard or Vista. Since I use Vista as my main OS for now, my initial solution was to direct the Thunderbird in Mac to use the same profiles folder used by the Thunderbird in Vista. To achieve this, I simply had to do the following:
1. Go to the Thunderbird profiles folder in Leopard: /Users/asif/Library/Thunderbird
2. Change the settings of the profiles.ini file to the following:
[General]
StartWithLastProfile=1
[Profile0]
Name=default
IsRelative=0
Path=/Volumes/Vista/Users/asif/AppData/Roaming/Thunderbird/Profiles/0xxmbl6h.default
I use Thunderbird for my email needs and I really like it, especially with the option to add extensions. Now, since I shuttle between Leopard and Vista quite frequently, I wanted to be able to have the same mailbox, content and settings whether I am in Leopard or Vista. Since I use Vista as my main OS for now, my initial solution was to direct the Thunderbird in Mac to use the same profiles folder used by the Thunderbird in Vista. To achieve this, I simply had to do the following:
1. Go to the Thunderbird profiles folder in Leopard: /Users/asif/Library/Thunderbird
2. Change the settings of the profiles.ini file to the following:
[General]
StartWithLastProfile=1
[Profile0]
Name=default
IsRelative=0
Path=/Volumes/Vista/Users/asif/AppData/Roaming/Thunderbird/Profiles/0xxmbl6h.default
3. Changed IsRelative from "1" to "0". Changed the Path from "Profiles/xxxxxxxx.default to that of the Thunderbird installed in Vista (/Volumes/Vista/Users/asif/AppData/Roaming/Thunderbird/Profiles/0xxmbl6h.default)
The only problem with this solution was that everytime I started Thunderbird in Leopard, it took about 5-10 minutes to load all the mailboxes, contents and settings. This happened everytime I loaded Thunderbird, which was quite frustrating. After some time, I could not take this anymore and to solve it, I decided to just copy the profiles folder used by Vista Thunderbird into the Thunderbird directory of Leopard. Thunderbird loading lag was gone after doing so. Now, in order to see the same mailboxes, contents and settings when I go back to Vista, I needed to find a way to automatically synchronize the two folders. I searched in google for such a solution in Mac and came across my saviour, Sync folder 0.9 . This was an action file to be used with Automator and setting it up was a breeze:
1. Click on the "Sync folder 0.9" file to copy it to the automator library
2. Open Automator and create a custom workflow with the following settings
3. Save the workflow as application: file → save as → give a name to the application, select the location to save to and choose the file format “application”.
4. Done! The folders will be synced whenever one double clicks on the application created.
5. Alternatively, one can save the workflow as a plug-in. File→ save as plug-in → give a name to the plug-in and select the application to be used under "plug-in for". In my case, I choose "Finder" at first and then repeated the same thing and choose "scripts menu". Choosing Finder will give me access to the plug-in whenever I right click on the desktop and select the Automator sub-menu under "more"), whereas the "scripts menu" will give me access to the plug-in as a script under the scripts menu which is ever-present (as a scroll icon) on the top-bar of the Leopard Desktop.
6. To delete the applications created (if required), one just needs to go to the path below and delete the respective application:
~/Library/Workflows/Applications/
Thanks to Automator, I am now going to be more on Leopard than Vista as my email problem has been solved. This small adventure with Automator has made me realise the enormous potential that Automator holds and the enormous benefit I can reap from it, by automating the many repetitive tasks that I do daily. To me, Automator is one area where Windows OS falls flat. Maybe there are free third-party tools for Windows that do what Automator can do, but I don't think they are as simple and intuitive to use and may lack a library that is as comprehensive as that of Automator. Features like Automator are things of the future, where repetitive and redundant tasks are automated to allow the human to focus on more important issues. A good lead by Apple, I am definitely impressed!
==update==
Today, I came across two free software to synchronize folders/files in Mac Leopard:
SyncTwoFolders 1.2.5
FileSync 2.0.1
SyncTwoFolders seemed easier to use than FileSync and therefore, I tested it to sync my Thunderbird mail folders between Vista and Leopard (see the snapshot below for the settings), and it seemed to work fine, if not better than the plug-in I created using the Automator because it provided more options on how one wants to sync the two folders. With this, I guess one should use Automator if it provides better functionality than the available free programs.
==update 2==
Today, while reading the Macworld magazine, I came across something related to this post (article "Stay in Sync" by Joe Kissell) and I think it probably explains why sometimes doing sync between my Thunderbird profile in Leopard and Vista Bootcamp does not result in 100% perfect sync. Below is an excerpt from the article that describes the solution to the problem:
"To sync Mail messages, first make sure Mail isn't running on either computer. Using your favourite sync utility, synchronize the entire Mail folder (your user folder/Library/Mail) bidirectionally betwee your two Mac...Then - only after the first time you do this - navigate to that Mail folder in the Finder on each mac and drag the Envelope index file to the trash. Launch Mail and allow it to reimport your messages (which means it's really rebuilding your message database). Quit Mail on one of your Macs. From now on, be sure to run only one copy of Mail at a time. Before switching to the copy running on your other Mac, use your synchronization utility to resync the mail folders..."
Below is how the above might be translated to my situation:
"To sync Thunderbird messages, first make sure Thunderbird isn't running on either Mac Leopard or Bootcamp Vista partition. Using your favourite sync utility, synchronize the entire Thunderbird folder bidirectionally between the partitions...Then - only after the first time you do this - navigate to the Thunderbird folder on each partition and drag all the MSF index file to the trash. Launch Thunderbird and allow it to reimport your messages (which means it's really rebuilding your message database). Quit Thunderbird on one of your partitions. From now on, be sure to run only one copy of Thunderbird at a time. Before switching to the copy running on your other partition, use your synchronization utility to resync the folders first..."
I have not tried this though, but have a feeling that it should work. Will update once i have tested this.
The only problem with this solution was that everytime I started Thunderbird in Leopard, it took about 5-10 minutes to load all the mailboxes, contents and settings. This happened everytime I loaded Thunderbird, which was quite frustrating. After some time, I could not take this anymore and to solve it, I decided to just copy the profiles folder used by Vista Thunderbird into the Thunderbird directory of Leopard. Thunderbird loading lag was gone after doing so. Now, in order to see the same mailboxes, contents and settings when I go back to Vista, I needed to find a way to automatically synchronize the two folders. I searched in google for such a solution in Mac and came across my saviour, Sync folder 0.9 . This was an action file to be used with Automator and setting it up was a breeze:
1. Click on the "Sync folder 0.9" file to copy it to the automator library
2. Open Automator and create a custom workflow with the following settings
3. Save the workflow as application: file → save as → give a name to the application, select the location to save to and choose the file format “application”.
4. Done! The folders will be synced whenever one double clicks on the application created.
5. Alternatively, one can save the workflow as a plug-in. File→ save as plug-in → give a name to the plug-in and select the application to be used under "plug-in for". In my case, I choose "Finder" at first and then repeated the same thing and choose "scripts menu". Choosing Finder will give me access to the plug-in whenever I right click on the desktop and select the Automator sub-menu under "more"), whereas the "scripts menu" will give me access to the plug-in as a script under the scripts menu which is ever-present (as a scroll icon) on the top-bar of the Leopard Desktop.
6. To delete the applications created (if required), one just needs to go to the path below and delete the respective application:
~/Library/Workflows/Applications/
Thanks to Automator, I am now going to be more on Leopard than Vista as my email problem has been solved. This small adventure with Automator has made me realise the enormous potential that Automator holds and the enormous benefit I can reap from it, by automating the many repetitive tasks that I do daily. To me, Automator is one area where Windows OS falls flat. Maybe there are free third-party tools for Windows that do what Automator can do, but I don't think they are as simple and intuitive to use and may lack a library that is as comprehensive as that of Automator. Features like Automator are things of the future, where repetitive and redundant tasks are automated to allow the human to focus on more important issues. A good lead by Apple, I am definitely impressed!
==update==
Today, I came across two free software to synchronize folders/files in Mac Leopard:
SyncTwoFolders 1.2.5
FileSync 2.0.1
SyncTwoFolders seemed easier to use than FileSync and therefore, I tested it to sync my Thunderbird mail folders between Vista and Leopard (see the snapshot below for the settings), and it seemed to work fine, if not better than the plug-in I created using the Automator because it provided more options on how one wants to sync the two folders. With this, I guess one should use Automator if it provides better functionality than the available free programs.
==update 2==
Today, while reading the Macworld magazine, I came across something related to this post (article "Stay in Sync" by Joe Kissell) and I think it probably explains why sometimes doing sync between my Thunderbird profile in Leopard and Vista Bootcamp does not result in 100% perfect sync. Below is an excerpt from the article that describes the solution to the problem:
"To sync Mail messages, first make sure Mail isn't running on either computer. Using your favourite sync utility, synchronize the entire Mail folder (your user folder/Library/Mail) bidirectionally betwee your two Mac...Then - only after the first time you do this - navigate to that Mail folder in the Finder on each mac and drag the Envelope index file to the trash. Launch Mail and allow it to reimport your messages (which means it's really rebuilding your message database). Quit Mail on one of your Macs. From now on, be sure to run only one copy of Mail at a time. Before switching to the copy running on your other Mac, use your synchronization utility to resync the mail folders..."
Below is how the above might be translated to my situation:
"To sync Thunderbird messages, first make sure Thunderbird isn't running on either Mac Leopard or Bootcamp Vista partition. Using your favourite sync utility, synchronize the entire Thunderbird folder bidirectionally between the partitions...Then - only after the first time you do this - navigate to the Thunderbird folder on each partition and drag all the MSF index file to the trash. Launch Thunderbird and allow it to reimport your messages (which means it's really rebuilding your message database). Quit Thunderbird on one of your partitions. From now on, be sure to run only one copy of Thunderbird at a time. Before switching to the copy running on your other partition, use your synchronization utility to resync the folders first..."
I have not tried this though, but have a feeling that it should work. Will update once i have tested this.
Tuesday, June 17, 2008
MS Office 2007 Crash Error on Windows
When I was working with Word docs on the stand alone Vista using Boot Camp, I occasionally got the error message "Word has stopped working", followed by the following message:"Word cannot open the file ~WRS(25A9155-508F-4C19-8D8A-A2DFAF672C8C). If the file is stored on your computer there may be a problem with your hardware. If the file is stored on the network there may be a problem with the network connection. If you can copy the file, try saving the file in another location and opening it there."
I tried many things to solve this, like uninstalling and reinstalling office 2007, but no use. I did Google search and luckily came across a forum thread that addressed the exact issue.
It turned out that the problem was related to my home HP printer driver installed on the computer using the CD provided by the manufacturer. The problem was resolved after installing the latest driver from the HP website. Installing the latest driver from the HP website may not work for some HP printers. In such cases, I learned that using the default printer driver provided by Vista seems to solve the problem.
Sunday, June 15, 2008
What Thomas Edison Can Teach You About Science
Today I came across an interesting article at Problogger about what Thomas Edison can teach us about blogging . Thomas Edison was, undoubtedly, one of those inventors that left an ever-lasting legacy, with world changing technologies, such as the light bulb, phonograph and the motion picture camera. I felt that the quotes mentioned in the article were also relevant to science and since they were really motivating, I am going to list them below for my future references, whenever my creative juices, motivations, or perseverance for doing science is drying up.
1.Start with a Need
“I never perfected an invention that I did not think about in terms of the service it might give others… I find out what the world needs, then I proceed to invent.”
2. Work Smart
“Being busy does not always mean real work. The object of all work is production or accomplishment and to either of these ends there must be forethought, system, planning, intelligence, and honest purpose, as well as perspiration. Seeming to do is not doing.”
3. Work and Wait
“Everything comes to him who hustles while he waits. “
4. It Takes Work
“Genius is one percent inspiration and ninety-nine percent perspiration. “
5. Failing Takes You Closer to Succeeding
“I have not failed. I’ve just found 10,000 ways that won’t work. “
6. You are Capable of Astounding Things!
“If we did all the things we are capable of, we would literally astound ourselves. “
7. Sometimes Failing is The Start of Success
“Just because something doesn’t do what you planned it to do doesn’t mean it’s useless. “
8. Don’t Give Up Too Early
“Our greatest weakness lies in giving up. The most certain way to succeed is always to try just one more time.”
9. Make it Fun
“I never did a day’s work in my life. It was all fun.”
10. Have Lots of Ideas
“To have a great idea, have a lot of them.”
11. You Don’t Have to Start with the Finished Product
“To invent, you need a good imagination and a pile of junk.”
1.Start with a Need
“I never perfected an invention that I did not think about in terms of the service it might give others… I find out what the world needs, then I proceed to invent.”
2. Work Smart
“Being busy does not always mean real work. The object of all work is production or accomplishment and to either of these ends there must be forethought, system, planning, intelligence, and honest purpose, as well as perspiration. Seeming to do is not doing.”
3. Work and Wait
“Everything comes to him who hustles while he waits. “
4. It Takes Work
“Genius is one percent inspiration and ninety-nine percent perspiration. “
5. Failing Takes You Closer to Succeeding
“I have not failed. I’ve just found 10,000 ways that won’t work. “
6. You are Capable of Astounding Things!
“If we did all the things we are capable of, we would literally astound ourselves. “
7. Sometimes Failing is The Start of Success
“Just because something doesn’t do what you planned it to do doesn’t mean it’s useless. “
8. Don’t Give Up Too Early
“Our greatest weakness lies in giving up. The most certain way to succeed is always to try just one more time.”
9. Make it Fun
“I never did a day’s work in my life. It was all fun.”
10. Have Lots of Ideas
“To have a great idea, have a lot of them.”
11. You Don’t Have to Start with the Finished Product
“To invent, you need a good imagination and a pile of junk.”
Network Printing in Leopard
A. Network Windows Printing Via Samba in Leopard
My office printer is connected to a Windows XP machine and setting up the Macbook to print on this machine over the network was a big headache. This was not obvious at all in Leopard and the Mac help page was useless. After some extensive Google search, I managed to solve the problem and now can easily send print jobs. This feat was achieved by following the steps below:
1. Go to http://localhost:631/
2. Click on "Add printer"
3. Enter the required information for Name, location and description. Follow the suggestions provided on the page. Click on "Continue"
4. On the next page, under Device choose: "Windows printer via Samba"
5. On the next page, Under Device URI, type the IP address of the machine and the name of the printer in the following format: "smb://ipaddress/printer". For example: "smb://172.20.224.223/HPLaserJ.2"
6. On the next page, under make, select the appropriate printer brand. For example: choose "HP" if your printer is HP. Click on the "Continue" button.
7. On the next page, select the appropriate model number of your printer, and then click on the "Add printer" button.
8. You are done.
B. Network Printing Via IP in Leopard
Follow the steps below if you want to print through a printer that is connected to a network point and not to any computer.
1. Go to System Preferences
2. Click on the icon "Print & Fax"
3. Select the "IP" tab
4. Under "Protocol", select "HP Jetdirect - Socket" and then type the IP address under "Address"
This method has been tested and tried on HP printers only. If it does not work for other printers, try changing the "Protocol" to "IPP" and then type the IP address under "Address"
Setting up extended display on Mac Leopard
I have been wanting to hook-up the 20" Dell LCD at work to the Macbook as extended display. I explored this in Leopard and found that setting the Dell as extended desktop was easy - use the "Displays" program in the "Systems preferences" and simply click on the "detect display" button. Mirroring (you see the same desktop on both the laptop and the Dell) was also easy - simply click on the mirror option after the extended display has been detected. A problem with the mirror option, however, is that the desktop on the Dell does not occupy the whole screen; adjusting the resolution does not fix this. So, the mirror option is not ideal for people who would like to fully utilize the extended display.
My aim was to use the Dell screen as the main desktop and put the Macbook to sleep. A solution to this would be to turn the Dell as the main desktop and the Macbook as the extended desktop. Setting the Dell as the main desktop would allow me to see both the dock and the top bar. After doing some Google search, I learned that I could turn the Dell into the main desktop if i placed it directly below the Macbook under the arrangements tab in the "Displays" program.
The next problem to solve was to keep the Dell desktop alive when the Macbook lid was closed to put it to sleep. Closing the lid affected both desktops (both went to sleep). After doing some more Google search, I learned that I can wake up the desktop on the Dell by inserting an external USB mouse and/or keyboard to the Macbook while it is sleeping with the lid closed (if the mouse/keyboard are already inserted, remove them and insert again). I was a happy man when my Dell woke up upon inserting the external mouse and keyboard. It is so much better to work on a bigger screen!
My aim was to use the Dell screen as the main desktop and put the Macbook to sleep. A solution to this would be to turn the Dell as the main desktop and the Macbook as the extended desktop. Setting the Dell as the main desktop would allow me to see both the dock and the top bar. After doing some Google search, I learned that I could turn the Dell into the main desktop if i placed it directly below the Macbook under the arrangements tab in the "Displays" program.
The next problem to solve was to keep the Dell desktop alive when the Macbook lid was closed to put it to sleep. Closing the lid affected both desktops (both went to sleep). After doing some more Google search, I learned that I can wake up the desktop on the Dell by inserting an external USB mouse and/or keyboard to the Macbook while it is sleeping with the lid closed (if the mouse/keyboard are already inserted, remove them and insert again). I was a happy man when my Dell woke up upon inserting the external mouse and keyboard. It is so much better to work on a bigger screen!
Writing to NTFS drive on Mac (Leopard)
Leopard allows direct reading of NTFS drive but not writing to it. I could write to my Vista Boot Camp drive (NTFS) while running Leopard by use of Parallels Desktop. However, this is slow and inconvenient if one wants to write to many files and folders. It would be nice to directly write to the NTFS drive without the speed lag and running Parallels. As usual, I did my homework using Google and found out that there are two easy ways of solving this problem:
1) Pay USD39.95 to purchase Paragon (http://www.paragon-software.com/home/ntfs-mac/). Easy to setup, configure and fast read/write. A 10 day free trial is available, which I highly recommend to anyone thinking of buying this product.
2) Learn how to setup the free NTFS-3G by use of Macfuse.
The you tube video below nicely summarizes how to install and setup NTFS-3G and Macfuse on Leopard.
1) Pay USD39.95 to purchase Paragon (http://www.paragon-software.com/home/ntfs-mac/). Easy to setup, configure and fast read/write. A 10 day free trial is available, which I highly recommend to anyone thinking of buying this product.
2) Learn how to setup the free NTFS-3G by use of Macfuse.
The you tube video below nicely summarizes how to install and setup NTFS-3G and Macfuse on Leopard.
Thursday, June 12, 2008
Using Boot Camp and Parallels Desktop to set up MS Windows (Vista) in Mac OS X (Leopard)
Below I summarize my experience of setting up MS Windows (Vista) on Mac machine (OS X Leopard 10.5.2) using Boot Camp Assistant and Parallels Desktop:
1. While in Leopard, I used Boot Camp Assistant to create a partition to setup MS Windows Vista.
2. Rebooted the system and installed Vista on the new partition. The installation was successful but not smooth, had some problems, which I will discuss later in the last few points.
3. After having installed Vista, I booted into Leopard and installed Parallels Desktop.
4. When setting up Parallels Desktop, I choose to boot from the earlier Boot Camp partition for Vista and then did all the other standard configurations.
5. Then when I ran Parallels Desktop, I had the "No Boot Device Found" error prompted.
6. After doing some reading on forums discussing Mac/Windows/Parallels Desktop/Boot Camp , I figured out the cause of the error:
During the Vista installation process, I deleted the partition that I created for Vista using the Boot Camp Assistant. I did this because I had problem proceeding with the Vista installation using that partition and when I deleted it, Vista installation worked fine. This was the mistake, instead of deleting it to fix the problem I should have just formatted the partition again using the Vista installation CD, as described by the Boot Camp Manual:
"Even though Boot Camp pre-formats the Windows partition, this partition can’t be used to boot the computer. You must reformat the new Windows partition using the Windows installer."
You may ask what could be the difference between the partition created by Boot Camp and that created by Vista CD so much so that deleting the Boot Camp partition and re-creating it using the Vista CD enabled vista installation to proceed but did not work with Parallels Desktop, whereas it worked the other way round as suggested by the Boot Camp manual?
I had the same question, and to answer it I did some tests, the results of which are described below:
I noticed that when using Boot Camp to create partition, two types of partitions are created:
1) A small sized "untitled partition" (we will refer to this as partn 1), and
2) the normal NTFS partition for Vista installation of size defined by the user (partn 2)
The following scenarios describe the role of each partition:-
Scenario 1:
Deleting partn 2 also deletes partn 1, which does not re-appear upon re-creation of the partition using the Vista CD. Windows installation works but Parallels does not work ("no boot device found" error is prompted).
Scenario 2:
Deleting partn 1 does not affect partn 2 and allows Vista installation to proceed only partially. Installation does not proceed further after the Vista CD installer has completed expanding the installation package and rebooted. The system prompts the message "press any key to boot from the cd" and does not do anything further. In normal situations, one does not need to press any key and installation should continue; however, this does not happen. Pressing any key would result in the CD being re-read to expand the installation package again and the whole process gets repeated.
From the above two scenarios, we can see that partn 1 created by Boot Camp is critical for Parallels to work and is the main difference between the partition created by the Boot Camp Assistant and the Vista CD.
7). After correcting my Vista installation based on the findings in step 6, Parallels worked fine and the "no boot device" error disappeared for good! I could use Vista either as a standalone OS using Boot Camp or run it concurrently with Leopard on virtual environment using Parallels. Since I configured Parallels to use the Boot Camp Vista, I could access the same programs/data either way. I did not have to double installation of programs. Of course, one could choose not to use the Boot Camp Vista and install Vista separately.
8). Please note that if you are planning to use the Boot Camp Vista on Parallels, be prepared to re-activate your copy of Vista on standalone Boot Camp. You have to get a new activation number from Windows support (call them up, tell them what you did and they should not have any problem giving you a new activation number because MS supports the use of Boot Camp Vista on Parallels).
9). Sometimes, you will get the "No boot device found" error if you have an external hard disk connected to the Mac. Removing the external drive fixes the problem.
10). Now, I am happily running Vista using Parallels on Leopard (4Gb Ram - split 2Gb for each). Occasionally, when I need more power, I run Vista at native speed by switching to the standalone version via Boot Camp. Parallel users, please note that after you have installed Vista using Parallels, do not forget to install the Parallel Tools, otherwise some of your hardware, such as the Ethernet controller, and software, such as Parallels Shared Folder (\\.PSF) functionality, may not work.
==Update==
A month after going through all the above, I stumbled upon the site below that provides detailed step-by-step guide to installing Vista on Mac:
http://www.simplehelp.net/2008/05/28/using-boot-camp-to-install-vista-on-your-mac-the-complete-walkthrough/
How I wished this site was posted before my adventure with Boot Camp and Parallels. Nevertheless, no regrets, I learned a lot and hope that people out there having the same problem can benefit from this post.
For my other experiments with Leopard, see: MyRamblings
==Update 2==
Recently, I was exploring Fusion VMWare, the competitor to Parallels, and came across a video on their website discussing the handling of Windows activation when setting up Bootcamp as a virtual machine while running Mac (Leopard). I found this video very informative and also useful for users of Parallels. Below is the video:
Key lessons learned from the video:
"It is very important that the VMWare tools installation happens before the activation. Otherwise, it is possible to get stuck in an activation loop, each time you reboot between the bootcamp partition and the bootcamp virtual machine."
1. While in Leopard, I used Boot Camp Assistant to create a partition to setup MS Windows Vista.
2. Rebooted the system and installed Vista on the new partition. The installation was successful but not smooth, had some problems, which I will discuss later in the last few points.
3. After having installed Vista, I booted into Leopard and installed Parallels Desktop.
4. When setting up Parallels Desktop, I choose to boot from the earlier Boot Camp partition for Vista and then did all the other standard configurations.
5. Then when I ran Parallels Desktop, I had the "No Boot Device Found" error prompted.
6. After doing some reading on forums discussing Mac/Windows/Parallels Desktop/Boot Camp , I figured out the cause of the error:
During the Vista installation process, I deleted the partition that I created for Vista using the Boot Camp Assistant. I did this because I had problem proceeding with the Vista installation using that partition and when I deleted it, Vista installation worked fine. This was the mistake, instead of deleting it to fix the problem I should have just formatted the partition again using the Vista installation CD, as described by the Boot Camp Manual:
"Even though Boot Camp pre-formats the Windows partition, this partition can’t be used to boot the computer. You must reformat the new Windows partition using the Windows installer."
You may ask what could be the difference between the partition created by Boot Camp and that created by Vista CD so much so that deleting the Boot Camp partition and re-creating it using the Vista CD enabled vista installation to proceed but did not work with Parallels Desktop, whereas it worked the other way round as suggested by the Boot Camp manual?
I had the same question, and to answer it I did some tests, the results of which are described below:
I noticed that when using Boot Camp to create partition, two types of partitions are created:
1) A small sized "untitled partition" (we will refer to this as partn 1), and
2) the normal NTFS partition for Vista installation of size defined by the user (partn 2)
The following scenarios describe the role of each partition:-
Scenario 1:
Deleting partn 2 also deletes partn 1, which does not re-appear upon re-creation of the partition using the Vista CD. Windows installation works but Parallels does not work ("no boot device found" error is prompted).
Scenario 2:
Deleting partn 1 does not affect partn 2 and allows Vista installation to proceed only partially. Installation does not proceed further after the Vista CD installer has completed expanding the installation package and rebooted. The system prompts the message "press any key to boot from the cd" and does not do anything further. In normal situations, one does not need to press any key and installation should continue; however, this does not happen. Pressing any key would result in the CD being re-read to expand the installation package again and the whole process gets repeated.
From the above two scenarios, we can see that partn 1 created by Boot Camp is critical for Parallels to work and is the main difference between the partition created by the Boot Camp Assistant and the Vista CD.
7). After correcting my Vista installation based on the findings in step 6, Parallels worked fine and the "no boot device" error disappeared for good! I could use Vista either as a standalone OS using Boot Camp or run it concurrently with Leopard on virtual environment using Parallels. Since I configured Parallels to use the Boot Camp Vista, I could access the same programs/data either way. I did not have to double installation of programs. Of course, one could choose not to use the Boot Camp Vista and install Vista separately.
8). Please note that if you are planning to use the Boot Camp Vista on Parallels, be prepared to re-activate your copy of Vista on standalone Boot Camp. You have to get a new activation number from Windows support (call them up, tell them what you did and they should not have any problem giving you a new activation number because MS supports the use of Boot Camp Vista on Parallels).
9). Sometimes, you will get the "No boot device found" error if you have an external hard disk connected to the Mac. Removing the external drive fixes the problem.
10). Now, I am happily running Vista using Parallels on Leopard (4Gb Ram - split 2Gb for each). Occasionally, when I need more power, I run Vista at native speed by switching to the standalone version via Boot Camp. Parallel users, please note that after you have installed Vista using Parallels, do not forget to install the Parallel Tools, otherwise some of your hardware, such as the Ethernet controller, and software, such as Parallels Shared Folder (\\.PSF) functionality, may not work.
==Update==
A month after going through all the above, I stumbled upon the site below that provides detailed step-by-step guide to installing Vista on Mac:
http://www.simplehelp.net/2008/05/28/using-boot-camp-to-install-vista-on-your-mac-the-complete-walkthrough/
How I wished this site was posted before my adventure with Boot Camp and Parallels. Nevertheless, no regrets, I learned a lot and hope that people out there having the same problem can benefit from this post.
For my other experiments with Leopard, see: MyRamblings
==Update 2==
Recently, I was exploring Fusion VMWare, the competitor to Parallels, and came across a video on their website discussing the handling of Windows activation when setting up Bootcamp as a virtual machine while running Mac (Leopard). I found this video very informative and also useful for users of Parallels. Below is the video:
Key lessons learned from the video:
"It is very important that the VMWare tools installation happens before the activation. Otherwise, it is possible to get stuck in an activation loop, each time you reboot between the bootcamp partition and the bootcamp virtual machine."
Subscribe to:
Posts (Atom)
Posts
Subscribe To Posts Via Email