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Justin Petrone is the editor of GenomeWeb's BioArray News and covers the microarray and biochip sector of the genomics market. E-mail Justin Petrone or follow his GenomeWeb Twitter account at @BioArrayNews.
PicoPLEX DNA-Seq: Single Cell Sequencing, Theory and Applications
In this archived webinar, recorded Feb. 19, 2014, two speakers outline applications of Rubicon Genomics' PicoPLEX DNA-seq single cell library preparation kit. Jeramiah Smith, assistant professor of biology at the University of Kentucky, discusses the use of PicoPLEX DNA-seq for de novo sequencing of single amphibian chromosomes, while John Langmore, co-founder and chief scientific officer of Rubicon, details the use of PicoPLEX DNA-seq for aneuploidy, CNV, and STR testing of single human cancer and reproductive cells.
Speakers: Jeramiah Smith, Assistant Professor of Biology, University of Kentucky; and John Langmore, Co-Founder and Chief Scientific Officer, Rubicon Genomics
Sponsor: Rubicon Genomics
Recording Date: 2/19/2014
Recording Time: 1 hour
Young Investigator Profile
The Jackson Laboratory
The Second Code
As an undergraduate at Peking University in Beijing studying microbial genomes, Zhengqing Ouyang became fascinated by the different functional elements contained within the genome and how genes were regulated. Then as a graduate student in Wing Wong's lab at Stanford University, Ouyang began to study transcriptional regulatory networks in embryonic stem cells.
And now in his own lab at JAX, Ouyang is focusing on the so-called secondary genetic code of long, noncoding RNAs.
Using statistical modeling and computational tools, Ouyang is searching through next-generation sequencing data to search for signals from long non-coding RNAs. In particular, he is focusing on determining the form, arrangement, and combination of these non-coding RNAs to try to tease out their function.
Researchers from France and Russia describe a giant DNA virus that they discovered in a 30,000-year-old permafrost sample from Siberia. The virus, dubbed Pithovirus sibericum, shares morphological features with pandoraviruses, the team notes. But when researchers scrutinized the new virus' 600,000 base genome, they found that its gene content more closely resembles that of icosahedral viruses such as Iridoviruses and Marseillevirus. As such, the virus appears to represent a third type of giant, amoeba-infecting virus, distinct from the very large Megaviridae and Pandoroviruses described recently. "The revival of such an ancestral amoeba-infecting virus used as a safe indicator of the possible presence of pathogenic DNA viruses, suggests that the thawing of permafrost either from global warming or industrial exploitation of circumpolar regions might not be exempt from future threats to human or animal health," the study's authors write.
A University of Southern California- and Nara Medical University, Japan-led team took an array-based look at the DNA methylation changes that occur in human intestinal cells in the wake of surgical tissue transplantation. By comparing methylation levels in intestinal epithelial cells before and after surgery to reconstruct a bladder from intestinal tissue, the researchers demonstrate that the intestinal cells in the newly formed "neobladder" take on distinct epigenetic features over time, moving away from their original tissue-specific methylation profiles. "The dynamic resetting of [the] DNA methylome in the neobladder not only implicates local environmental cues in the shaping and maintenance of the epigenome," researchers write, "but also illustrates an unexpected cross-talk between the epigenome and cellular environment."
People on the Move
Sequenom announced this week that CEO Harry Hixson plans to retire from that position in June, at the time of the company's stockholder meeting. Current President and Chief Operating Officer William Welch will assume Hixson's position upon his retirement. Hixson will continue to serve as chairman of the firm's board of directors, a title he has held since 2003. Welch also will be nominated to serve on the board at the annual meeting, Sequenom said. Also, CFO Paul Maier also will retire from his job in June, but will continue to work with the company as a consultant. Current VP and Chief Accounting Officer Carolyn Beaver will replace Maier as CFO upon his retirement. She previously was corporate VP and controller of Beckman Coulter. In addition, Dirk van den Boom will be promoted to be chief scientific and strategy officer. He has been with Sequenom since 1998, and he recently was the company's executive VP of R&D and chief technology officer.
Former Life Technologies executive Paul Grossman has joined Telegraph Hill Partners as a venture partner. Grossman previously was head of global strategy and corporate development at Life Tech, and he also held the same position at Invitrogen. Before he joined Invitrogen, Grossman held a variety of leadership roles at Applied Biosystems, including as a research scientist and patent attorney, VP of intellectual property, and VP of strategy and business development.
Becton Dickinson has appointed Amit Bhalla to be VP of global strategy and development. In the role, Bhalla will work with the senior management team to develop BD's overall strategy. Bhalla joins BD from Citi, where he has been director of equity research for life science tools and medical technology since 2006. Before joining Citi, he was VP of equity research for emerging medical technology at Morgan Stanley, and a technical operations R&D associate at Johnson and Johnson.
A pair of studies published in Science is providing a look at the genetic variants influencing the innate immune system's response to bacterial or viral pathogens. Along with variants influencing the expression of neighboring genes, the study helped define sets of more distant variants that orchestrate the broader immune response. The researchers also saw clues that at least some eQTLs mediating immune response early on during a bacterial infection are distinct from those at play later in the infectious process.
A new company called Human Longevity was launched this week by J. Craig Venter that will combine human genome, microbiome, and metabolome data coupled with clinical information to fuel development of new diagnostics, therapeutics, and stem cell treatments for diseases related to aging. Using $70 million in Series A financing, the firm plans to conduct genome, microbiome, and tumor sequencing on patients from the UCSD Moores Cancer Center and use their clinical phenotype and metabolomics data to create a massive database.
The 2015 federal budget proposal from the Obama Administration is seeking a marginal increase in funding for the National Institutes of Health — an increase of nearly one percent — to $30.36 billion from $30.15 billion in FY 2014. Under the proposed budget, the National Human Genome Research Institute would receive a $1 million increase to $498 million, while NCI would receive $8 million more this year, or $4.93 billion in total. United for Medical Research said the budget "falls short of reversing the damage done by a decade of flat funding ... and sequestration."