Saturday, December 14, 2013

Hello Everyone!

I chose to keep an eye on PLOS Genetics in the past few weeks. Below I’ve summarized my favorite articles that popped up during that time. Overall it was eye-opening looking at studies on so many different organisms. It really reinforced the idea that we’re all essentially made of the same stuff :) Check out the pieces and enjoy!


Dynamics of DNA Methylation in Recent Human and Great Ape Evolution
Hernando-Herraez et al
September 05, 2013
Hernando-Herraez et al explored the differences in methylation patterns of humans vs. apes in order to find information that could account for the huge phenotypic differences between human beings and “our closest relatives”. Nine humans and 23 primates were used in the study and all species of great apes—chimpanzee, bonobo, gorilla and orangutan— were included. The researchers analyzed methylation patterns at CpG (Cytosine—phosphate—Guanine) sites and found about 800 genes with altered methylation patterns among the primates including 170 genes with a methylation pattern specific to humans. After finding that many of these genes are essential to developmental and neurological processes, they suggested that epigenetic changes have occurred frequently during recent human and non-human primate evolution. The study concluded that epigenetic alterations influence primate evolution and thus should be explored thoroughly in the context of comparative genomics.

Rapid Intrahost Evolution of Human Cytomegalovirus Is Shaped by Demography and Positive Selection
N. Renzette et al
September 26, 2013
Human cytomegalovirus (HCMV) is relatively common in the US and asymptomatic in healthy human beings. Unfortunately, in individuals with a compromised immune system or one that is not fully developed (i.e. infants) HCMV can cause permanent nerve damage or lead to death. This study posited that HCMV’s extremely high rate of evolution within human hosts can be attributed to the virus’s high genetic variability. The study longitudinally collected HCMV samples from the urine and plasma of 5 infected infants and analyzed the genetic variability of the viral populations. The study found that the virus was relatively stable over time in each sample, but variation from one sample to another within a host was comparable to variation between samples of unrelated hosts. Not only did the study confirm the high rate of variation within the HCMV species, but it also provided the most detailed map of DNA virus evolution in human hosts to date.

Evolutionary Change within a Bipotential Switch Shaped the Sperm/Oocyte Decision in Hermaphroditic Nematodes
Y. Guo et al
October 03, 2013
The transcription factor TRA-1 controls sexual development in nematodes. According to this study, TRA-1 works with part of another complex (TRR-1) to initiate spermatogenesis but a truncated form of TRA-1 blocks spermatogenesis. Since the truncated and normal forms of TRA-1 have opposite roles, researchers conclude that TRA-1 is bipotential, meaning it can repress or activate the same locus. The study then compared related species of nematodes and found that, in one species, mutations on TRR-1 lead germ cells to become oocytes while mutations that affect 3 FEM proteins (which also work with TSA-1 in a regulatory role) do not. In another nematode species, the roles were switched. Analysis of this data led the study to conclude that the roles of the two types of TRA-1 (truncated and whole) have been altered during recent evolution.

The Meiotic Recombination Checkpoint Suppresses NHK-1 Kinase to Prevent Reorganisation of the Oocyte Nucleus in Drosophila
O. M. Lancaster et al
October 28, 2010
Haploid gametes are made from diploid cells via meiosis. A crucial step in meiosis is the recombination checkpoint where cells that have not properly completed recombination (the first portion of the process) are barred from proceeding to the rounds of segregation needed to complete meiosis. This study focused on the role of protein kinase NHK-1 on formation of the karyosome- a meiosis-specific arrangement of chromosomes that occurs once segregation can proceed. In Drosophila, formation of the karyosome is suppressed by activation of the recombination checkpoint. The study found that despite this link, mutations in the karyosome directly resulting from mutations in NHK-1 occur independently of the recombination checkpoint. The study also found that DNA breaks formed during recombination lead to activation of the recombination checkpoint which in turn suppresses the activity of NHK-1, preventing it the formation of the karyosome. This led the researchers to conclude that protein kinase NHK-1, in Drosophila, plays an essential regulatory role in meiosis and is controlled by the recombination checkpoint.

Recurrent Tissue-Specific mtDNA Mutations Are Common in Humans
J. H. Samuels et al
November 07, 2013
DNA mutations taken form randomly which implies that any replicated patterns of DNA somatic mutations in unrelated individuals or in multiple organs within one individual are highly unlikely. Since variation in mitochondrial DNA (mtDNA) can affect phenotypic variation, understanding the distribution of mtDNA mutations can aid in understanding many human diseases. Samuels et al used next-generation sequencing to compare mtDNA variation in ten tissues among un-related individuals. They found that in un-related individuals certain tissues display the same mutations which were all found extremely close to sites that regulate mtDNA replication. The study used 4 sequenced individuals (two in which they successfully replicated mutations found in the first pair) to reach the conclusion that the observed variations can alter the replication in the mutated mtDNA genome which suggests that tissue-specific positive selection is present for these mutations.

Reconstructing the Population Genetic History of the Caribbean
Moreno-Estrada et al
November 14, 2013
Latinos are often combined into a single group/category, even in biomedical contexts. In order to debunk the assumption that Latinos can be taken as one heterogeneous group, the study compared patterns of genome-wide variation in 330 individuals in various populations of the Caribbean comprising mainland, Antilles, and Native American communities. They then compared the genomic data of these individuals to that in a database of genomic variation among over 3,000 individuals from various European, African, and Native American populations. The study was able to use this information to characterize the intricate population genetic history of this region. Their findings distinguished insular populations from mainland Caribbean populations and from other Hispanic/Latino populations as well.

Time Scales in Epigenetic Dynamics and Phenotypic Heterogeneity of Embryonic Stem Cells
M. Sasai et al
December 12, 2013
M. Sasai et al constructed a model to represent the genetic network of mouse embryonic stem cells in order to better understand the presence of extreme phenotypic variation in individual cell expression of an important regulatory protein, Nanog. Nanog plays a key role in maintaining the pluripotency of mouse embryonic stem cells, yet riation in vexpression level of the protein don’t seem to affect the function of embryonic stem cells. The model constructed successfully models cell differentiation by taking into account processes of gene regulation such as histone-code modification and binding of transcription factors. Although the study did not fully characterize the process by which the embryonic stem cell heterogeneity remains, it did create a model that can be used to represent the fluctuation of cells and their differentiation processes.

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