Evolutionary Battle for Supremacy : Mystery of Sex Chromosomes


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          New DNA sequencing data reinforce the notion that the X and Y chromosomes, which determine biological sex in mammals, are locked in an evolutionary battle for supremacy.

David Page, a biologist who directs the Whitehead Institute in Cambridge, Massachusetts, and his colleagues explored the Y chromosomes carried by males of several species, mapping stretches of mysterious, repetitive DNA in unprecedented detail. These stretches may signal a longstanding clash of the chromosomes.

Page presented the results last week at a meeting of the Society for the Study of Reproduction in San Juan, Puerto Rico. His team’s subjects included humans and other primates, a standard laboratory mouse, and a bull named Domino.

“This idea of conflict between the chromosomes has been around for a while,” says Tony Gamble, an evolutionary biologist at the University of Minnesota in Minneapolis. But the sequencing data from the bull’s Y chromosome suggests that the phenomenon is more widespread than previously thought, he adds.

The mammalian Y chromosome has long been thought of as a sort of genomic wasteland, usually shrinking over the course of evolution and largely bereft of pertinent information. Page’s work has helped to change perceptions of the Y chromosome by revealing that it contains remarkable patterns of repeating sequences that appear dozens to hundreds of times 

But the structure of these sequences and precise measures of how often they repeat have been difficult to determine. Standard sequencing technologies often cannot distinguish between long stretches of genetic code that differ by a single DNA ‘letter’.

Letter by letter

Page and his collaborators avoided this problem by using what he calls ‘super-resolution’ sequencing (a technique better known as single-haplotype iterative mapping and sequencing, or SHIMS), which can detect such minute variation between lengthy segments of DNA.

The team sequenced many large, continuous stretches of the Y chromosome and carefully scrutinized the areas that looked as if they overlapped. They found that repeating structures make up about 24% of the accessible DNA in the human Y chromosome, and 44% of that of the bull.

And in the Y chromosome of the mouse, which is much larger than that of a human, repeating structures make up almost 90% of accessible DNA. The intricate patterns, which often contain palindromes — sequence that reads the same in forward and reverse order — carry three families of protein-coding genes. What the genes are doing — and how they got there — remains a mystery, however.

In mammals, the X and Y chromosomes emerged relatively recently from a regular pair of chromosomes before differentiating from one another. They share many of the structures that came from their ancestral source, but these repetitive regions seem to have come from somewhere else.

The repeated genes in the mouse Y chromosome do not resemble anything on the human Y chromosome, but they do have analogues on the mouse X chromosome. And in the mouse, human and bull, the repeated genes on Y and X are expressed in the male germ cells that eventually produce sperm.

A biological black box

Taken together, Page argues that this is evidence that the genes are involved in meiotic drive, a somewhat mysterious biological process that subverts the standard rules of heredity. In it, a particular version of a gene — or in this case, an entire chromosome — manages to increase the frequency by which it is transmitted to the next generation.

How that works is unclear. Sperm carry an X or a Y chromosome; genes expressed in the testes, where the cells are produced, may influence which sperm will be more likely to successfully fertilize an egg.

Previous studies lend credence to this idea. A team led by geneticist Paul Burgoyne and collaborators at the MRC National Institute of Medical Research in Mill Hill, UK, found that mice with a partial deletion of the Y chromosome produce offspring with a female-skewed ratio. The researchers subsequently shifted offspring sex ratios in both directions by tinkering with the expression of these multicopy genes.

Of course, mice — in nature and in the lab — usually maintain even sex ratios. Failing to do so could harm species survival. So as these Y-promoting genes made copies of themselves, subsequent mechanisms evolved to suppress their selfish urges. Page’s results provide a way to explore that evolutionary history; the data on the bull genome suggest that the mouse X and Y may not be exceptions.

With further high-resolution sequencing data, researchers may find more support for genomic battles of the sexes and possibly uncover other surprises. “There’s this rich tapestry of what sexual chromosomes are capable of,” says Gamble.

Original Article : A battle of the sexes is waged in the genes – Brendan Maher

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Learning to Survive: Evolvability in Bacteria exposed to Fluctuating Environments

Reported by Shanti Kalipatnapu , Jun 25, 2015


           Bacteria are known to thrive in an incredibly wide variety of habitats and conditions ranging from the human gut to hot springs. Scientists are trying to understand how bacteria manage to learn to survive in various conditions and thus to learn about the process of evolution itself. For this, researchers often perturb environmental variables such as temperature or pH, usually one at a time, even though in nature such variables typically act together. In an effort to study what is likely the situation in nature, the research group of Dr. Sutirth Dey at IISER Pune has chosen to expose bacteria to unpredictable fluctuations in multiple environmental parameters.

The group exposed bacteria to different combinations of conditions (pH, salt, hydrogen peroxide), where the successive environments were picked randomly. After 30 days the group monitored the growth rate of the bacteria.

Describing their observations, Dey said, “We had expected that the bacteria would do better in the environment in which they have been selected. This did not happen. Instead, we found that the growth rate of the bacteria was higher under conditions like antibiotics and heavy metals, environments that they had never experienced before”
On further investigation, the group found that this ability to withstand new environments/stresses is not related to an increased mutation rate and could instead be related to their increased ability to throw out toxins from the cell (efflux activity).
“We found that exposure to unpredictable fluctuations in the environment could itself help bacteria evolve an increased ability to throw out toxins, including antibiotics, from the cell at a faster rate. This surprising observation gives us new clues to understanding evolvability in bacteria”, said Dey summarizing their findings.
      It is commonly thought that injudicious use of antibiotics cause antibiotic-resistance in bacteria. This study opens the possibility that environmental variability can potentially lead to similar outcomes. Given that the climatic variability has increased greatly over the last few years, it is likely that bacteria could display resistance against drugs they haven’t been exposed to before. This could potentially have serious public health consequences.
This work has recently been published in the Journal of Evolutionary Biology (28:1131-1143) and was authored by Shraddha Karve, Sachit Daniel, Yashraj Chavhan, Abhishek Anand, Somendra Singh Kharola and Sutirth Dey.
This research received financial support from the Department of Biotechnology, Government of India and internal funding from Indian Institute of Science Education and Research, Pune.


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Your Viral Infection History from a Single Drop of Blood : HHMI researchers

Elledge                                                                     Image Source: https://www.hhmi.org/

Systematic viral epitope scanning (VirScan). This method allows comprehensive analysis of antiviral antibodies in human sera. VirScan combines DNA microarray synthesis and bacteriophage display to create a uniform, synthetic representation of peptide epitopes comprising the human virome. Immunoprecipitation and high-throughput DNA sequencing reveal the peptides recognized by antibodies in the sample. The color of each cell in the heatmap depicts the relative number of antigenic epitopes detected for a virus (rows) in each sample (columns). Credit: Figure from the print summary of Xu et al., “Comprehensive serological profiling of human populations using a synthetic human virome” SCIENCE, 348:1105 (5 June 2015).

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