Genome sequencing unlocks the mysteries of naked mole rat

BGI, the world’s largest genomic organization, announced that an international team of researchers from Korea, China and USA, for the first time, demonstrated the physiology and longevity of the naked mole rats (NMR) in terms of genomics and transcriptomics. The results, published online today in the international journal Nature, provide an excellent opportunity to better understand the unique traits of naked mole rats and advance its use in biological and biomedical studies.

With its wrinkled skin and double-saber buck teeth, the naked mole rat may not be among the most beautiful animals, but they are exceptional in other ways. They are the longest-lived rodent known till now and are exceptionally resistant to cancer; they can live in full darkness, at low oxygen and high carbon dioxide concentrations; and they are unable to sustain thermogenesis or feel certain types of pain. These unique features make naked mole rats particularly attractive to scientists as emerging models for research on aging and cancer, as well as other biological activities or conditions (e.g. metabolic regulation, development, pain and behavior).

In this study, researchers utilized the whole-genome shotgun (WGS) sequencing strategy and next-generation sequencing system to sequence the genome of an individual male naked mole rat. The NMR genome is approximately 2.6 Gb, and the predicted NMR gene set includes 22,561 genes. By sequencing the genome, the researchers demonstrated that the ancestor of NMR split from the ancestors of mice and rats about 73 million years ago, and 93% of the NMR genome shows synteny to human, mouse or rat genomes. Utilizing comparative transcriptome analysis, some genes related to anti-aging and adaptation to a low oxygen environment were identified based on the different expression levels of NMR transcripts between different age groups and at exposure to different levels of oxygen concentration.

The researchers made further investigation and found several important genes related to the exceptional traits of NMR. The stable gene expression of TERT and other genes, regardless of age, may be related to NMR’s longevity mechanism. In addition, the unusual regulatory involvement of tumor suppressor p16Ink4a and p19Arf may be the key factor in NMR’s cancer resistance, and mutation in the specificity of HIF1a and VHL may contribute to NMR’s high tolerance to a low oxygen environment. At least 10% of the approximately 200 genes associated with visual perception in humans and mice were found to be inactivated or missing in NMR, implicating that NMR’s poor visual function may be caused by the deterioration of genes coding for various critical components of the visual system.

The genomic information of NMR provides a rich resource for researchers working in aging, cancer, eusociality and many other areas. The data can be mined in numerous ways to uncover the molecular basis for the extraordinary traits of this most unusual mammal. To achieve a more comprehensive insight into NMR’s exceptional traits, the international team will continue to explore the molecular mechanisms of anti-aging, anti-cancer, adaptation to low oxygen environment and eusociality, with approaches of comparative genomics, comparative transcriptomics, and comparative methylation.

“The NMR genome will play an important role in functional studies of NMR, which also will provide unprecedented opportunities for exploring some of the most challenging questions in biology and medicine,” stated Xiaodong Fang, Leader of non-model organisms group at BGI and the co-leading author of the study. “We believe that NMR will become a new model in biological and biomedical research in the near future.”

 

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Biologists use Sinatra-named fly to show how to see the blues — and the greens

New York University biologists have identified a new mechanism for regulating color vision by studying a mutant fly named after Frank (‘Ol Blue Eyes) Sinatra. Their findings, which appear in the journal Nature, focus on how the visual system functions in order to preserve the fidelity of color discrimination throughout the life of an organism. They also offer new insights into how genes controlling color detection are turned on and off.

Many biologists study how different cells develop to acquire their fate. The NYU research team, headed by Claude Desplan, a professor of biology, examined how they stay the same. Cells have complex functions that must be maintained through extensive coordination, and failure to do so could lead to “confused” cells whose function is not clear. This is particularly important for cells, such as neurons, which live for a long time—usually the entire lifetime of an animal.

How the brain makes memories: rhythmically!

The brain learns through changes in the strength of its synapses — the connections between neurons — in response to stimuli.

Now, in a discovery that challenges conventional wisdom on the brain mechanisms of learning, UCLA neuro-physicists have found there is an optimal brain “rhythm,” or frequency, for changing synaptic strength. And further, like stations on a radio dial, each synapse is tuned to a different optimal frequency for learning.

Mehta-Brain

The image shows a neuron with a tree trunk-like dendrite. Each triangular shape touching the dendrite represents a synapse, where inputs from other neurons, called spikes, arrive (the squiggly shapes). Synapses that are further away on the dendritic tree from the cell body require a higher spike frequency (spikes that come closer together in time) and spikes that arrive with perfect timing to generate maximal learning.

The findings, which provide a grand-unified theory of the mechanisms that underlie learning in the brain, may lead to possible new therapies for treating learning disabilities.

Heart Disease Has Its Own Clock

Broken biological clocks in blood vessels may contribute to hardened arteries, even if the main timer in the brain works fine. The finding, from transplant experiments with mice, suggests that throwing off the daily rhythms of the body’s organs can have serious health consequences.

A wealth of evidence shows that skimping on sleep and working against the body’s natural daily, or circadian, rhythms can raise the risk of developing illnesses such as heart disease and diabetes. Scientists assumed that the diseases resulted from malfunctions in a master clock in the brain, which synchronizes sleeping, waking and other body functions with the rising and setting of the sun.

via Heart Disease Has Its Own Clock – Science News.

Breast Cancer Death Rates Decline

Fewer women are dying from breast cancer, largely because of advances in screening and treatment. Poorer women, however, are seeing a slower and later decline in their risk of dying from breast cancer, in part because they don’t have as much access to these life-saving advances.

In 2008, 51.4% of poor women aged 40 and older had a screening mammogram in the past two years. By contrast, 72.8% of wealthier women had a mammogram in the past two years.

These are some of the findings from the American Cancer Society’s Breast Cancer Facts & Figures 2011-2012 report. It appears in CA: A Cancer Journal for Clinicians in time for National Breast Cancer Awareness Month, which takes place every October.

In 2011, an estimated 230,480 women will be diagnosed with breast cancer, according to the new report. About 39,520 women will die from the disease in 2011. Beside skin cancer, breast cancer is the most common cancer seen among American women.

 

via Breast Cancer Death Rates Decline.

Scientists discover fickle DNA changes in brain

Johns Hopkins scientists investigating chemical modifications across the genomes of adult mice have discovered that DNA modifications in non-dividing brain cells, thought to be inherently stable, instead underwent large-scale dynamic changes as a result of stimulated brain activity. Their report, in the October issue of Nature Neuroscience, has major implications for treating psychiatric diseases, neurodegenerative disorders, and for better understanding learning, memory and mood regulation.