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5:51 AM
Asian citrus psyllid
By Kirsten Peters, College of Agricultural, Human and Natural Resource Sciences

 
Asian citrus psyllid. Photo courtesy of the U.S. Dept. of Agriculture
 
 
Did you have a glass of orange juice this morning? If so, you may want to know that the simple pleasures brought to us by citrus fruit are under attack from a disease called citrus greening or yellow dragon disease. It’s caused by bacteria that are not harmful to people, but cripple citrus trees by choking off their internal circulation system. The malady puts our $3 billion per year citrus industry firmly in the crosshairs.
No cure after infection
Citrus greening evidently originated in China in the early 20th century. Once a tree is infected by the disease, there is no cure. The bacteria that causes the disease blocks the ability of the tree to circulate water and nutrients. Fruit doesn’t ripen, staying green and misshapen. There are three different strains of the bacteria in question, each plaguing different parts of the globe.
Citrus greening is attacking orange groves in Florida. It is also moving to groves in Texas and California, and threating those in Arizona. If it isn’t successfully combatted, citrus greening could wipe out the U.S. citrus industry. It’s already decimated citrus orchards in Jamaica.
Asian citrus psyllid
The bacteria behind the disease is spread to the trees by an insect similar to aphids and whiteflies called the Asian citrus psyllid (the name is said like "SILL-id”). The insects feed on the trees and, when they do so, they transmit the bacteria to the plant. It’s a bit like infected mosquitoes can give you malaria when they feed on your blood. In time the bacteria in the citrus trees multiply and spread, causing the plant grave harm.
Citrus greening is believed to have reached the U.S. from China in the early 2000s. The insects that spread the disease are tough to control. Pesticides have been used with some success, but scientists are concerned that the psyllids will develop resistance to the chemicals. Another approach is to introduce into orchards "good” insects that prey on the psyllids. Using such biocontrols, however, has so far not met with much success because the psyllids reproduce faster than the predatory insects. Then again, you might think that researching around the globe for disease-resistant trees might help, but so far no such trees have been found.
Genomics counterattack
Enter more sophisticated approaches to interrupting the disease cycle.
"We are using genomics to see what genes are being ‘expressed’ in the psyllids as they feed on the citrus tree,” explained Professor David Gang to me recently. Gang is on the faculty at Washington State University and is one member of a large team of researchers at several institutions that is researching new responses to citrus greening disease. The multifaceted effort is funded by the U.S. Department of Agriculture.
"If we know the genes and proteins involved in infection, we can try to interrupt the transmission of the disease,” Gang said.
Gang and others working with him have the goal of isolating and sequencing the genes expressed in the insects as they feed on citrus plants. Other scientists collaborating on the project can use the gene expression data in their work.
"We hope to ‘knock out’ genes that function in the transmission of the bacteria inside the psyllid,” Gang told me. "Then the insect won’t transmit the disease.”
One ultimate goal of the work is to create a new type of psyllid that will be unable to harbor or transmit the disease-causing bacteria. The new insects would outcompete the old, disease-carrying ones because the bacteria weaken the insects in which they live. But Gang and his colleagues are very concerned with potential problems related to modified organisms, and they are looking at how best to mitigate potential problematic outcomes. 
New threats
Responding to new threats to food crops is a never-ending task for agricultural scientists. Their work is complex, spans years, and is sometimes expensive. But it keeps us fed – and free to drink our orange juice in the morning.
"And it’s not just oranges that are at issue,” Gang told me. "Grapefruit, lemons and limes are also affected.”
Here’s hoisting a tangy glass of OJ or lemonade to the good work Gang and others are doing in defense of U.S. citrus trees.

Kirsten Peters, Ph.D., is a native of the rural Northwest, was trained as a geologist at Princeton and Harvard. This column is a service of the College of Agricultural, Human and Natural Resource Sciences at Washington State University.

5:49 AM

The presidential bioethics brain trust unveils its draft recommendations on the use of whole genome sequencing in clinical care and research.

Balancing the privacy of patients and research subjects with the advancement and integrity of genomic science is a tall order, but it’s an issue at the center of policy recommendations being crafted by the Presidential Commission for the Study of Bioethical Issues. Late last week, the commission, which includes some of the nation's top bioethicists, concluded a year-long series of public meetings designed to help create more informed policies regarding the use of whole genome sequencing as it becomes a clinical reality and continues to drive research on a range of human conditions. The commission gave a taste of the recommendations it will present to President Barack Obama this fall.

The draft recommendations centered on patient privacy, consent, and access to genomic sequencing data, while stressing the need to balance these concerns with a certain amount of academic freedom that would allow researchers to fully utilize, share, and probe the data. One recommendation, for example, instructs funders of genomic research and policy makers to "maintain and establish strong policies for protecting data while protecting opportunities for open models of access for those who want to share data with clinicians, researchers, and others," University of Pennsylvania President Amy Gutmann, who chaired the commission, said at a meeting of the commission on Wednesday (August 1).
Other recommendations focused on giving patients a clear idea of how their genomic data might be used and by whom before they enter into such studies. These recommendations included mention of the need to tailor some consent forms to use in the clinic, setting them apart from lengthier and more detailed consent forms used in research settings.
The commission said that it plans on presenting President Obama with a final list of recommendations this fall.

5:45 AM
 


 By Will Parker
In a discovery that carries significant implications for changing brain function through dietary interventions, UCLA researchers say they now have the first evidence that bacteria ingested in food can affect how the human brain works. The study, which focused on women who consumed yogurt containing the bacteria known as probiotics, appears in the journal Gastroenterology.
Researchers have long known that the brain sends signals to the gut, which is why stress and other emotions can contribute to gastrointestinal symptoms. This new study claims to show that signals travel the opposite way as well. "Our findings indicate that some of the contents of yogurt may actually change the way our brain responds to the environment. When we consider the implications of this work, the old sayings 'you are what you eat' and 'gut feelings' take on new meaning," said Dr. Kirsten Tillisch, lead author of the study.
The study involved 36 women between the ages of 18 and 55 who were divided into three groups: one group ate a specific yogurt containing a mix of several probiotics twice a day for four weeks; another group consumed a dairy product that looked and tasted like the yogurt but contained no probiotics; and a third group ate no product at all.
MRI scans conducted both before and after the four-week study period looked at the women's brains in a state of rest and in response to an emotion-recognition task in which they viewed a series of pictures of people with angry or frightened faces and matched them to other faces showing the same emotions. This task was used to measure the engagement of affective and cognitive brain regions in response to a visual stimulus.
The researchers found that the women who consumed the probiotic yogurt showed a decrease in activity in both the insula - which processes and integrates internal body sensations, like those from the gut - and the somatosensory cortex during the emotional reactivity task.
Tillisch said she was surprised to find that these effects could also be seen in other sensory- and cognition-related brain areas. The women in the other two non-probiotic groups showed stable or increased activity in these networks.
During the resting brain scan part of the experiment, the women consuming probiotics showed greater connectivity between a key brainstem region known as the periaqueductal grey and cognition-associated areas of the prefrontal cortex. The women who ate no product at all, on the other hand, showed greater connectivity of the periaqueductal grey to emotion- and sensation-related regions, while the group consuming the non-probiotic dairy product showed results in between.
The knowledge that signals are sent from the intestine to the brain and that they can be modulated by a dietary change is likely to lead to an expansion of research aimed at finding new strategies to prevent or treat digestive, mental, and neurological disorders.
By demonstrating the brain effects of probiotics, the study also raises the question of whether repeated courses of antibiotics can affect the brain, as some have speculated. Antibiotics are used extensively in neonatal intensive care units and in childhood respiratory tract infections, and such suppression of the normal microbiota may have long-term consequences on brain development.
"Time and time again, we hear from patients that they never felt depressed or anxious until they started experiencing problems with their gut," Tillisch said. "Our study shows that the gut-brain connection is a two-way street."

6:45 AM

By Allison Proffitt
June 4, 2013 | Dell announced today the Dell Active Infrastructure for HPC Life Sciences, an infrastructure system optimized for genomic research to begin shipping in July. 
The infrastructure includes a scalable 32 node cluster and parallel file system. Workload/cluster management is performed by Bright Cluster Manager (winner of a 2013 Bio-IT World Best of Show award) The infrastructure comes ready to connect to next gen sequencing systems via Terascala, and storage can connect via InfiniBand or Ethernet. The whole system is “fully integrated at factory for simple deployment.” 
“But this is not a sequencer pipeline computational black box appliance,” Tim Carroll, director of global research for Dell, told Bio-IT World this morning. “That’s not the goal of what we’re trying to do… Life scientists, especially, are very focused on their science, as opposed to being focused on the system.” 
“Where we give people choice, we did it because we knew those were crossroads where it could be a show stopper for them if they didn’t have a choice. But it’s not five choices there; it’s the two educated choices.” 
The product is the result of what Dell calls “customer-inspired innovation.” Dell has been working closely with researchers at TGEN on a genomic application for neuroblastoma. “That’s exactly where the Active Infrastructure for Life Sciences came from: the two-year collaboration with TGEN,” said Carroll. “Even though that was done specifically around these pediatric cancer clinical trials, the applicability of it obviously is so much broader.”
“With diseases like neuroblastoma, hours matter. Our new Dell HPC cluster allows us to do the processing we need to get a meaningful result in a clinically relevant amount of time,” said Jason Corneveaux, a bioinformatician at TGEN in the Dell statement. 
TGEN reports a 12-fold improvement in processing power for patient data and genomic analysis in a few hours. The system can process up to 38 genomes per day, Dell predicts. The data to support those numbers is being prepared with TGEN and, “it’s a question of getting that written up,” Carroll says. 
“Certainly for Dell, this is the first time that we’ve been able to come to the research community and say, ‘We can give you the platform that will give you increased performance—you’ll get better performance against a pipeline you’re running; less integration time;  better supportability;  and still do it with some measure of flexibility.’ We’ve been able to hit the four horsemen of what people care about.” 
The infrastructure starts at $650,000, what Carroll called the “sweet spot” of what people are spending who have two sequencers. Generally one system will support two to four sequencers. Carroll said Dell is seeing interest from academic groups who are supporting multiple research groups with a few sequencers and small independent groups. 
The system has been deployed at TGEN for about five months, Carroll said. "The compute went up very quickly. A lot of the work has been around the storage side of this, that's the really thorny piece. We spent the better part of the spring getting the cluster tuned and optimized." 
Now that the infrastructure is available, Carroll believes it will be a key piece in the race to real clinical genomics. The cloud isn't a viable option because of the size of data sets and the regulatory issues, he said. "You're going to have to be able to do this at a local level--regional research center or community hospital. The more we are able to get this technology into a form factor that we can continue to shrink down to get into those environments, the sooner we're going to be able to realize the dream of doing this at a clinical level." 

6:45 AM
FlandersBio - Building Biotech Bridges
OpGen, Inc., today announced the company has entered into a strategic collaboration with Applied Maths NV, the market leader in bioinformatics and analytical solutions for public health and research laboratories, to provide advanced software tools for microbial genomics and molecular strain typing. Under the agreement, Applied Maths has incorporated a Whole Genome Mapping module into the company’s new BioNumerics 7 software suite, providing customers with seamless access to a new set of analytical tools for molecular typing and comparative genomics of microbial pathogens.
“We are pleased to be working with Applied Maths to enable our public health, biodefense and microbial research customers access to Applied Maths’ BioNumerics analysis suite,” said Douglas White, chief executive officer of OpGen, Inc. “The Applied Maths software and database analysis suite will provide a flexible, integrated solution that will enable broader adoption of Whole Genome Mapping.”
“The efficient management of food-borne pathogen outbreaks through enhanced approaches for epidemiological surveillance requires the rapid detection of potential outbreaks and improved molecular typing solutions,” said Koen Janssens, chief executive officer of Applied Maths. “We are pleased to be able to offer our customers access to OpGen’s Whole Genome Mapping technology in the recently released version of our BioNumerics software suite, enabling a one-stop application to distinguish between bacterial strains when analyzing disease outbreaks. This integrated solution will enable researchers to strain type and identify responsible pathogens in a timelier manner, which is crucial to limit outbreaks in time and scope and appropriately treat patients with food borne illnesses.”
Source: Applied Maths

6:42 AM

A DNA double helix is seen in an undated artist's illustration released by the National Human Genome Research Institute to Reuters on May 15, 2012. REUTERS/National Human Genome Research Institute/Handout

By Ben Hirschler
















LONDON | Wed Jun 5, 2013 1:08am EDT
(Reuters) - Genomics and particle physics - offering different perspectives on the fundamental nature of life and the cosmos - are the two hottest areas of scientific research.
Eight of the 21 most closely followed scientists in 2012 studied genes and their functions, while the single most-cited paper last year covered the hunt for the long-sought Higgs boson particle, according to a Thomson Reuters survey on Wednesday.
It was the third year in a row in which genomics researchers topped the rankings, in terms of authoring the most highly cited scientific papers, underscoring the central importance of genetics in biological science and medicine.
"Genomics is a perennially hot topic as we learn more about how (DNA) sequences play out in the manifestation of disease," said Christopher King, editor of Thomson Reuters ScienceWatch, which tracks trends in research.
The relevance of the work in genomics was evident this week at the American Society of Clinical Oncology (ASCO) congress in Chicago, where key advances in cancer medicine on display hinged on understanding the genetic basis of tumors.
The world's "hottest" researcher, as measured by the number of citations during 2012 for papers published between 2010 and 2012, was Richard Wilson at the Washington University School of Medicine, the survey showed.
Wilson's laboratory was the first to sequence the genome of a cancer patient and discover genetic signatures related the development of disease.
FORMATION OF THE UNIVERSE
Other hot genomics researchers on the list included Eric Lander of the Broad Institute of MIT at Harvard and Kari Stefansson, the founder of Icelandic biotech company Decode Genetics, which was acquired last December by Amgen.
Papers related to the search for the Higgs boson accounted for nearly one fifth of the 51 papers published in the 2012 hottest research list. The boson and its linked energy field are viewed by physicists as vital in the formation of the universe and in giving mass to matter.
No single scientists working on the Higgs particle, however, were identified in the rankings because of the highly collaborative nature of the particle physics research, with some papers involving upwards of 3,000 authors.
Scientists working on the ATLAS experiment at the Large Hadron Collider at CERN, the European Organisation for Nuclear Research, outside Geneva received an honorable mention as a group.
The survey also highlighted the growing importance of Chinese research in a number of fields, with institutions in the country producing four of the 21 hottest researchers, including Jun Wang from the Beijing Genomics Institute.
"When you look at the quantity of papers published by various nations, China has sky-rocketed in the last few years," said King. "That hasn't necessarily been commensurate with impact in the literature, as measured by citations, but this seems to be starting to change."
(Editing by David Holmes)

6:41 AM
DNAnexus aims to become the data platform of the genome era. We're a Silicon Valley startup, very well funded by top investors, and we're building a world-class team of innovators to architect the technology that will decode the first million human genomes and beyond. Join us on this journey!

Why DNAnexus?

At DNAnexus we are solving the most challenging computer science problems you will ever see.
In the last few years, there has been a dramatic development in the world of genomics that has created a huge new opportunity. The price to sequence the full human genome (all of your DNA, not just a sample of it) has fallen to the point where it will soon be affordable for a patient to have multiple samples of their whole genome sequence to help treat their disease. Want to know what specific gene mutation caused a patient's cancer? We are building the platform to answer that kind of question.
One of the many challenges is the huge amount of data. Think you've seen big-data problems? Think again - with each genome comprising 100 GB and months of CPU time to crunch the information, DNA is the next big-data problem, requiring exabytes of storage and parallel workloads distributed across 100,000 servers. We are tackling this by combining web technologies, big-data analytics, and scalable systems on cloud computing infrastructure.
We are a well-funded startup backed by Google Ventures, TPG Biotech, and First Round Capital. Our founders, Andreas Sundquist, Arend Sidow, and Serafim Batzoglou are world-renowned genomics and bioinformatics experts from Stanford University.

What are we looking for?

We are looking for smart motivated people. Leave your lab coat at home. Our core is building great software, the technology that powers our genomics data platform
Experience with DNA isn't necessary, but really strong software engineering aptitude is. Our smallest datasets are Gigabytes in size, and you should be comfortable with the idea of working on an Exabyte-scale system. Our distributed systems will scale to 100,000 nodes and beyond.
Ideal candidates will likely know several of the following technologies: C, C++, Boost, Ruby, Rails, HAML, HTML, CSS, JavaScript, ECMAScript, V8, jQuery, Flash, Flex/ActionScript, Node.js, Python, Perl, PHP, Amazon Web Services (AWS), SQL, MySQL, PostgreSQL, MongoDB, Solr, Sphinx, Hadoop, MapReduce, ZooKeeper, Hive, Pig, Oozie, HDFS, ZFS, MCache. We obviously do not use all of these, but if you know several of them you are our kind of candidate.

Fast track interview

Get your interview with DNAnexus fast tracked by showing off your skills on Smarterer. Take one of these quick tests and send your score to puzzle@dnanexus.com

Working at DNAnexus

What is it like to work at DNAnexus? We go above and beyond to create a work environment that you'll love. Some of the many perks employees enjoy include:
  • Full medical/dental/vision coverage
  • Daily catered lunches
  • Unlimited snacks and beverages of your choice
  • Caltrain monthly pass for commuters
  • Membership to the gym of your choice
  • Onsite gourmet espresso and coffee bar
  • No offical vacation days, employees take time off as needed

6:40 AM
Hajnalka Hejja, MD.
In the last few years, announcements about revolutionary new sequencing technologies have been popping up like daisies. All of them promised to solve at least some of the problems we have with existing NGS technologies. Some of these new techniques became popular, but several of them either never became commercially available or never gained popularity. To tell you the truth, a sequencer that is not used by a lot of people is very much like a sequencer that doesn’t exist at all.* So here is a list of sequencing platforms that definitely exist: the three biggest players of the NGS field and some honorable mentions.

For  more information  click here

6:38 AM
With the widespread adoption of the HiSeq 2500 and its lightning speed, enabling biologists to quickly and inexpensively extract biological information from sequences has become a critical need1,2. However, the management and analysis of large data sets is widely recognized as an obstacle to a wide adoption of next-generation sequencing, requiring large IT investment and bio-informatics expertise to set-up, maintain and run software at reasonable speed, especially for the most demanding applications like Whole Genome Sequencing (WGS).
To address this, Illumina has developed a user-friendly human WGS analysis workflow to enable scientists with no bioinformatics experience to align and call variants in whole human-genome data 4-6 times faster than existing methods. Combined with Illumina’s PCR-free sample preparation and the HiSeq 2500, the workflow provides a sample to answer time of less than 2 days.
In the words of Waibhav Tembe, Ph.D., Director of the Collaborative Bioinformatics Center at TGen “For whole genome sequencing, the aligner did an awesome job in cutting down the time to align 30x data against human genome and in using available hardware resources effectively.”
With the Isaac Human WGS app in BaseSpace, HiSeq users can now analyze and store WGS data without bioinformatics expertise, Linux experience or IT infrastructure. The workflow is free to use and can be accessed here (access requires a free BaseSpace account).
For those who prefer to keep their data on premises, the workflow is available as part of the HiSeq Analysis Software (HAS), freely available on the Illumina website here. HAS , can analyze WGS in a few hours, on a commodity PC with a single command line or an easy to use Graphical User Interface.
The component algorithms for the Isaac aligner and Variant Caller are released as open source here for developers to re-use and improve them. The open source version of the Isaac aligner is not commercially supported and provided as is under Illumina Open Source Software License available here.
Finally, data generated by Illumina’s IGN services uses the Isaac Human WGS workflow.
You can find more details on table 1 below and in our white paper available for download here.
Table 1: Isaac Human WGS workflow on premises with the HiSeq Analysis Software. Comparison of analysis metrics with the BWA + GATK workflow showing comparable data is generated 6 times faster.
2013-03-05-IsaacPlanningExit-v4 [Read-Only] - Microsoft PowerPoint_2013-06-03_10-12-31
(1)    Saunders, C. J. et al. (2012) Rapid Whole-Genome Sequencing for Genetic Disease Diagnosis in Neonatal Intensive Care Units Sci Transl Med 4:154ra1352.
(2)    Jones, S. J. et al. (2010) Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors. Genome Biol. 11, R82
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