8/27/2015

China announces stem-cell rules

http://www.nature.com/news/china-announces-stem-cell-rules-1.18252

Many scientists have been itching to get started.
Qi Zhou, a stem-cell and cloning scientist at the Chinese Academy of Sciences (CAS) Institute of Zoology in Beijing, has been waiting for the guidelines so he can move his research from animal models to humans. In unpublished work, his team has already implanted dopamine-producing neurons derived from stem cells into monkeys that have been chemically induced to show symptoms similar to those of Parkinson’s disease. The monkeys have shown some improvement, and he now hopes to try the treatment on humans. “I think it’s time, time to start doing some clinical research,” he says.
Jianwu Dai, a regenerative-medicine specialist at the CAS Institute of Genetics and Developmental Biology in Beijing, hopes to implant a small collagen scaffold seeded with stem cells into humans to try to repair spinal-cord injuries. His team has treated some 25 people using the scaffold seeded with mononuclear cells, a type of blood cell taken from bone marrow, and Dai says he has seen some improvements. But he thinks that neural stem cells derived from embryonic stem cells will deliver better results.
........
 

8/14/2015

Fish Oil May Slow Schizophrenia

Omega-3 supplementation reduced progression rates among people with early-stage symptoms of schizophrenia, according to a small trial.

Seven years ago, investigators enrolled 81 people aged 13 to 25 with early signs of schizophrenia in a clinical trial to test the effects of omega-3 fish oil pills. A paper published this week (August 11) in Nature Communications reported on 71 of those participants, pointing to a notable benefit of the supplements: only 10 percent of those taking fish oils ultimately developed schizophrenia, compared with 40 percent of the placebo group.
“I don’t want to sound like a cynic or a skeptic, but it’s almost too good to be true,” psychiatrist Jeffrey Lieberman of Columbia University Medical Center in New York City who was not involved in the study told ScienceNews.
Schizophrenia usually starts to manifest in the first 20 to 30 years of life, with minor delusions and paranoid thoughts often occurring in the teenage years or younger. But only about a third of people who present with such early symptoms eventually develop psychosis, New Scientist reported. After researchers found that the blood cells of schizophrenia patients have lower levels of omega-3 fatty acids than those of healthy controls, scientists in the field began to investigate the possibility that supplementing these compounds could treat the disorder. Results of early trials have been mixed, but this latest study points to the potential benefit of fatty acids if taken early enough.
“Schizophrenia is a major cause of disability, but early treatment has been linked to better outcomes,” coauthor Paul Amminger at the University of Melbourne in Australia told The Guardian. “Our study gives hope that there may be alternatives to antipsychotic medication.”

http://www.the-scientist.com/?articles.view/articleNo/43733/title/Fish-Oil-May-Slow-Schizophrenia/

http://www.nature.com/ncomms/2015/150811/ncomms8934/full/ncomms8934.html

7/24/2015

When Does a Smart Mouse Become Human?



© DUSAN PETRICICLate last year, Steve Goldman of the University of Rochester and his colleagues reported that they had transplanted immature glial cells from donated human fetuses into the brains of immunodeficient mouse pups. These human glial cells matured into astrocytes and developed as the primary astrocyte population in the newborn mouse brain. One unexpected outcome of the team’s research, published in the Journal of Neuroscience (34:16153-61), was that these human-mouse chimeras outperformed normal mice almost fourfold in a variety of cognition tests, underscoring the importance of astrocytes in regulating synaptic plasticity and neural connectivity to enhance learning and memory. But the study also raised important ethical considerations—namely, what biological properties differentiate Homo sapiens from other organisms, and when should such “humanized” animals be afforded the rights that people currently enjoy.

....

 http://www.the-scientist.com//?articles.view/articleNo/43327/title/When-Does-a-Smart-Mouse-Become-Human-/

4/14/2015

Linkage Disequilibrium Blocks/Triangles

cited from:
https://estrip.org/articles/read/tinypliny/44920/Linkage_Disequilibrium_Blocks_Triangles.html


07/10/08 05:51 - 75ºF - ID#44920
Linkage Disequilibrium Blocks/Triangles

I just had a zen moment in the interpretation of Linkage Disequilibrium Maps. (Also called LD maps, LD blocks, LD triangles - take your pick.) Turns out I was actually sweating 1st grade stuff!

I found that NO ONE explains this EXTRAORDINARILY SIMPLE thing in their umpteen papers, reviews, tutorials and what-nots. I just want to post this here so that when people google this simple little question, they find an equally simple and straight-forward answer!

This is an example of what a very small section of a Linkage Disequilibrium Map or an LD Map looks like.
image

Concentrate on the upper part of the map.
image

The thick blue line represents a strand of a chromosome. The white bars on the blue line of the chromosome are SNPs (Single Nucleotide Polymorphisms) that have been identified and sequenced. This means that we know what initial Nucleotide base has morphed into what final Nucleotide base. (Thus making it a polymorphic locus - or a position on the chromosome that exists in more than one form. The two forms are the intial nucleotide base and the final nucleotide base.)

These SNP locations or loci are labeled in this picture as 1, 2, 3, ... and so on. Each of these SNPs has a name that starts with rsXXXXX where XXXXX is some numeric code. Each SNP is represented by a labeled grey triangle below the thick blue line (the chromosome).
image

The purpose of an LD map is to tell us whether any two given SNPs are INHERITED TOGETHER in an offspring. In other words, we want to know if any two given SNPs are in Linkage Disequilibrium.

An example: Are say, SNP #5 and SNP #9 in linkage disequilibrium? You trace down the column leading from grey triangle #5 or SNP#5 (Name: rs2299433) going toward SNP #9 (rs2237717). Do the same for SNP #9 going toward SNP #5.
image

The square in which the columns leading from SNP #5 and SNP #9 intersect is the one you should focus on. I have encircled it above. As you can see its a LIGHT RED and has a number, 75. Thus SNP#5 and SNP #9 have a correlation of 0.75 and are in fairly high linkage disequilibrium with each other.

In simple terms, if your square of focus is a deep red, then the two SNPs you are interested in have the highest correlation with each other and have a highest Linkage Disequilibrium. Thus, one of them can easily act as a proxy for another. The lighter the shade of red, the lesser is the correlation between the two SNPs. For example, SNP #5 and SNP #7 have a low correlation (0.32) with each other. Thus, you cannot reliably take SNP #5 and say that it could possibly act as a proxy for SNP #7.

LD Maps also tell us about HAPLOTYPE blocks. See the blocks labeled, "Block 1 (49kb)", "Block 2 (23kb)", "Block 3 (93kb)" ... and so on.
image

These triangles or the blocks of dark red represent SNPs that are all in high linkage disequilibrium with each other and thus are all inherited together. They are also on the same section of the chromosome. These SNPs form a HAPLOTYPE. Every big red triangle or block in the LD map indicates a HAPLOTYPE on the corresponding stretch of the chromosome above. You only need to look at one or maximum a couple SNPs in a haplotype to know about the fate of the entire section of the chromosome that forms a Haplotype. It saves money and time.

The HapMap Consortium project has painstakingly constructed such an LD map for each and every known SNP in the entire human genome. Their LD maps look somewhat like this (using the haploview software: )

image

Though it is complicated, if you followed the simple tutorial above, you should be able to make sense of even complicated maps such as these. You are most welcome to leave a comment or drop me an email if you need further clarification!

I don't care who is laughing at this ridiculously detailed explanation of a kindergarten concept in genetics and genomics. Personally, I am just EXTREMELY relieved to finally know it well enough to be able to explain it. :)
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3/08/2015

Linux文件删除与恢复

使用 Linux 安全删除工具
http://www.ibm.com/developerworks/cn/linux/1311_caoyq_linuxdelete/index.html

使用 Linux 文件恢复工具
http://www.ibm.com/developerworks/cn/linux/1312_caoyq_linuxrestore/index.html

2/11/2015

grid cell


Grid cell symmetry is shaped by environmental geometry
Nature 518, 232–235 (12 February 2015) doi:10.1038/nature14153
Editor's summary
The neuronal grid cells of the entorhinal cortex fire in a spatial grid pattern laid out across the surface of a familiar environment to provide the brain with an internal map of an animal's surroundings. The role of environmental boundaries in the construction of this pattern is not well understood. Early studies had suggested that properties such as symmetry, orientation and scale of grid cells' firing patterns were independent of an environment's shape. But now two separate papers in this issue of Nature — one from Edvard Moser and colleagues and the other from John O'Keefe and colleagues — demonstrate that grid orientation, scale, symmetry and homogeneity can be strongly affected by environmental geometry, with grid cells aligned with the borders of the environment at an offset of a few degrees such that it minimizes symmetry with boundaries. These findings suggest a mechanism by which the geometry of an environment causes local rotation and deformation of the hexagonal firing patterns of grid cells.



1/02/2015

update firefox to version 34

Failed to sync firefox31 info to firefox34.

Unlink the old device, then re-create a new account to sync the personal settings across different devices.

Two useful links:

http://www.libre-software.net/how-to-install-firefox-on-ubuntu-linux-mint

https://www.mozilla.org/en-US/firefox/all/

The new version is ready to run. No need to compile it. Very  convenient!