Postdocs

Yuanyuan Xie awarded National Cancer Center fellowship to explore the pathological role of transposons

Anonymous — Wed, 12 Jun 2019 14:56:18 +0000

Yuanyuan Xie awarded National Cancer Center fellowship to explore the pathological role of transposons Anonymous (not verified) Wed, 06/12/2019 - 08:56

Lindsay Diamond

Nearly all species’ genomes are littered with millions of genetic sequences called transposons, which are virus-like parasitic elements that can replicate and spread within host genomes. Collectively, transposon-derived sequences constitute about 50 percent of the human genome sequence, and are believed to have - over tens of millions of years - played a critical role in our evolution. Transposons are increasingly recognized to have influenced human biology and adaptation, particularly in the realms of development and immunity. Transposons may also contribute to disease.

Yuanyuan Xie, a postdoctoral researcher in the Chuong Lab, was recently awarded a National Cancer Center Postdoctoral Fellowship to explore the pathological role of transposon-derived sequences known as retrocopies in colorectal cancer.

For the cell to create proteins, the DNA sequence of a gene is transcribed into RNA, which is then normally translated into a protein. However, cellular RNAs are occasionally reverse-transcribed back to DNA and inserted into a different location in the genome, forming a type of gene duplication known as a retrocopy. Retrocopies originate from the activity of retrotransposons, which replicate by reverse transcribing their own RNA into host DNA, but occasionally capture cellular RNAs by accident. While over 8,000 retrocopies can be detected in the human genome, they are often assumed to be nonfunctional. Nevertheless, genomic studies have revealed that many retrocopies have transcribed RNAs or even translated proteins, often with distinct activities from their parental genes.

Repeat sequences can have deleterious effects in the genome and underlie several human disease conditions including Huntington’s disease, fragile X syndrome, several ataxias, and myotonic dystrophy. To protect against potential harm, all organisms have evolved genomic defenses to repress transposons through epigenetic manipulation. Yet, repression is inherently reversible, and inappropriate reactivation of transposons are common in many cancers. However, the specific cellular functions of retrocopies and whether they play a genome-wide role in cancer progression remain unknown.

Answering these questions is what drew Yuanyuan to the interdisciplinarity of Chuong Lab and the BioFrontiers Institute. “My previous experience was in cell signaling pathways and stem cell models, and I was interested in joining the Chuong Lab where I can learn computational genomics to study gene regulatory networks in evolution and disease,” says Xie.

Taking a break from the bench, Yuanyuan scoured The Cancer Genome Atlas (TCGA), a joint effort between the National Cancer Institute and the National Human Genome Research Institute that has characterized over 20,000 primary cancer and normal samples across a variety of different cancers, in search of candidates where there is increased expression of retrocopies, rather than parental genes, in primary tumors.

Now with the fellowship funding, Yuanyuan will head back to the bench to test his hypotheses. “Through activities like DNA and histone modification, these repetitive elements are derepressed in states like cancer and aging. The question remains whether this derepression is a consequence or a cause,” says Xie.

Looking forward, Yuanyuan plans to extend the analysis to a genome-wide CRISPR screen to identify novel protein-coding and non-coding retrocopies involved in tumorigenesis. Overall these experiments seek to uncover an understudied yet potentially extensive pathological role for retrocopies in colorectal cancers wherein the mechanism may be applied to other types of cancers. These studies may help pave the road for more precise cancer therapies that specifically target retrocopies.

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'Pedigree is not destiny' when it comes to scholarly success

Anonymous — Wed, 01 May 2019 17:50:44 +0000

'Pedigree is not destiny' when it comes to scholarly success Anonymous (not verified) Wed, 05/01/2019 - 11:50

By: Sante Fe Institute

What matters more to a scientist’s career success: where they currently work, or where they got their Ph.D.? It’s a question a team of researchers teases apart in a new paper published in PNAS. Their analysis calls into question a common assumption underlying academia: that a researcher’s productivity reflects their scientific skill, which is reflected in the prestige of their doctoral training.

It’s true that faculty at prestigious universities publish more scientific papers and receive more citations and awards than professors at lower-ranked institutions. It’s also true that prestigious schools tend to hire new faculty who hold Ph.D.s from similarly prestigious programs. But according to the authors of the new study, an early career researcher’s current working environment is a better predictor of their future success than is the prestige of their doctoral training.

“Pedigree is not destiny,” says SFI External Professor Aaron Clauset (�� Boulder), a co-author on the paper. “Our analysis supports the fairly radical idea for academia that where you train doesn’t directly impact your future productivity.”

The team looked at two basic measures of academic success — productivity (how many papers a researcher publishes) and prominence (how often their work is cited) — of 2453 tenure-track faculty in all 205 Ph.D.-granting computer science departments in the US and Canada during the five years before and five years following those individual’s first faculty appointment.

“We wanted to disentangle the impact of environment on productivity and prominence, and to isolate the effects of where someone trained versus where they went on to work as faculty,” says lead author Samuel Way (�� Boulder). “On the prominence side, people do retain some benefit from having studied in a prestigious Ph.D. program. They continue to accumulate citations from their doctoral work.”

But the prestige of the training program seems to play little role in how many papers researchers go on to produce once they begin their appointments in a new place. “Someone like me, who trained at Colorado, and someone from MIT… if we both end up at Stanford, our productivity will look the same,” says Way.

The authors identify several possible mechanisms driving the increased productivity of faculty at more prestigious institutions. Selection criteria in hiring, expectations for high productivity once hired, and selective retention of productive faculty were all considered. “We only find weak evidence for each,” says Way. However, the prestige of the current work environment had a strong effect on productivity.

Identifying the underlying “forces that tilt the scientific playing field in favor of some scientists over others,” as Clauset says, is important for identifying and potentially correcting the systemic biases that may be limiting the production of scientific knowledge.

“…our findings have direct implications for research on the science of science, which often assumes, implicitly if not explicitly, that meritocratic principles or mechanisms govern the production of knowledge,” write the authors. “Theories and models that fail to account for the environmental mechanism identified here, and the more general causal effects of prestige on productivity and prominence, will thus be incomplete.”

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Dispatch: South Australia to Colorado

Anonymous — Wed, 27 Feb 2019 07:00:00 +0000

Dispatch: South Australia to Colorado Anonymous (not verified) Wed, 02/27/2019 - 00:00

Atma Ivancevic

Postdocs considering an international move should plan early and allow plenty of time to adjust, says Atma Ivancevic.

Moving to a laboratory in another state or another country is an academic tradition. Scientists move for master’s and PhD programmes, postdoctoral experience, competitive faculty positions and short- or long-term study exchanges. Early-career researchers, in particular, are encouraged to broaden their horizons in foreign labs before deciding on a career path. Some move to gain experience in a prestigious lab; others for a promotion or because they cannot stay. Whatever the reason, the decision to pack up and go is rarely easy, and the process itself can be overwhelming.

Last year, I moved from Adelaide, Australia, to Boulder, Colorado, for a postdoc position. My reasons were simple: I wanted to travel, and I found a lab that matched my interests while providing me the opportunity to learn new techniques. Now that the dust has settled on my move, I’d like to share my experiences so far as an international postdoc.

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