Repoopulating the Gut

 :: Posted by American Biotechnologist on 11-13-2014

What is the difference between the following:

  • breast milk infants vs formula fed infants
  • vaginal birth vs caesarian section babies
  • farm boys vs city boys
  • Tribal infants vs American infants

If you answered the diversity of their microbiome you are correct. The first group of individuals exhibit much higher diversity in the population of their gut bacteria and tend to have less food allergies and asthma than the second group. Studies have shown that having a more diverse gut microbiome results in a more stable and resilient internal ecosystem.

One of the hottest topics in microbiology today is the makeup of the human microbiome. Scientists are beginning to show that proper microbiome health is important for overall individual health. In fact, a cutting edge treatment for antibiotic-induced diarrhea, (which is caused by antibiotics killing off gut flora), is fecal transplant from a healthy individual. Dr. Claire M. Fraser, founder of the field of microbial genomics has coined the term “repoopulation” which refers to the act of repopulating the gut with healthy microbes via a fecal transplant.

In the video below, Dr. Fraser discusses the microbiome and the importance that must be attributed to the field of microbial genomics.

The End is Near for American Scientific Supremacy

 :: Posted by American Biotechnologist on 11-12-2014

For as long as most of us can remember, America has remained at the top of the scientific food chain. American scientists were generously funded, supported by robust government policies and able to secure world-class training at the best scientific institutions. All that is about to change, however, as many economists are predicting that within 5 years, China will be spending more on scientific R&D than their American counterparts.

According to the OECD Science, Technology and Industry Outlook 2014, China’s total R&D budget match the US’s $400 Billion scientific budget by the year 2016 and will grow to as much as $600 Billion by 2024. In contrast, the American R&D budget is only predicted to grow by 19%, (from approximately $410 Billion to $490 Billion), during that same period.

Despite this positive outlook for China, several critics have claimed that China’s fast assent into the scientific limelight comes at the expense of research quality. Such assertions have been supported by the disproportional rate of scientific paper retraction on behalf of Chinese scientists when compared to the rest of the world. Unfortunately, since the Chinese funding sources give preference to the quantity of scientific papers published when evaluating scientific merit, the rash of retractions will not likely abate any time soon.

It is also interesting to note that the majority of Chinese funding is dedicated to building infrastructure with much less spent on bench research itself. This has led to a situation where there is a disconnect between the number of well-equipped labs in China and the quality of research papers coming out of those labs.

So should we be afraid that soon, many of our best scientists will likely explore greener pastures in China or is it possible that China’s bark is much bigger than its bite? Only time will tell.

Finding Leukemia Targets with ChemiDocâ„¢ Touch Imaging

 :: Posted by American Biotechnologist on 11-11-2014

New Sequencing Technology Reveals Thousands of Unknown Genome Variations

 :: Posted by American Biotechnologist on 11-10-2014

Thousands of never-before-seen genetic variants in the human genome have been uncovered using a new genome sequencing technology. These discoveries close many human genome mapping gaps that have long resisted sequencing.

The technique, called single-molecule, real-time DNA sequencing (SMRT), may now make it possible for researchers to identify potential genetic mutations behind many conditions whose genetic causes have long eluded scientists, said Evan Eichler, professor of genome sciences at the University of Washington, who led the team that conducted the study.

“We now have access to a whole new realm of genetic variation that was opaque to us before,” Eichler said.

Eichler and his colleague report their findings Nov. 10 in the journal Nature.

To date, scientists have been able to identify the genetic causes of only about half of inherited conditions. This puzzle has been called the “missing heritability problem.” One reason for this problem may be that standard genome sequencing technologies cannot map many parts of the genome precisely. These approaches map genomes by aligning hundreds of millions of small, overlapping snippets of DNA, typically about 100 bases long, and then analyzing their DNA sequences to construct a map of the genome.

This approach has successfully pinpointed millions of small variations in the human genome. These variations arise from substitution of a single nucleotide base, called a single-nucleotide polymorphisms or SNP. The standard approach also made it possible to identify very large variations, typically involving segments of DNA that are 5,000 bases long or longer. But for technical reasons, scientists had previously not been able to reliably detect variations whose lengths are in between — those ranging from about 50 to 5,000 bases in length.

The SMRT technology used in the new study makes it possible to sequence and read DNA segments longer than 5,000 bases, far longer than standard gene sequencing technology.

This “long-read” technique, developed by Pacific Biosciences of California, Inc. of Menlo Park, Calif., allowed the researchers to create a much higher resolution structural variation map of the genome than has previously been achieved. Mark Chaisson, a postdoctoral fellow in Eichler’s lab and lead author on the study, developed the method that made it possible to detect structural variants at the base pair resolution using this data.

To simplify their analysis, the researchers used the genome from a hydatidiform mole, an abnormal growth caused when a sperm fertilizes an egg that lacks the DNA from the mother. The fact that mole genome contains only one copy of each gene, instead of the two copies that exist in a normal cell. simplifies the search for genetic variation.

Using the new approach in the hydatidiform genome, the researchers were able to identify and sequence 26,079 segments that were different from a standard human reference genome used in genome research. Most of these variants, about 22,000, have never been reported before, Eichler said.

“These findings suggest that there is a lot of variation we are missing,” he said.

The technique also allowed Eichler and his colleagues to map some of the more than 160 segments of the genome, called euchromatic gaps, that have defied previous sequencing attempts. Their efforts closed 50 of the gaps and narrowed 40 others.

The gaps include some important sequences, Eichler said, including parts of genes and regulatory elements that help control gene expression. Some of the DNA segments within the gaps show signatures that are known to be toxic to Escherichia coli, the bacteria that is commonly used in some genome sequencing processes.

Eichler said, “It is likely that if a sequence of this DNA were put into an E. coli, the bacteria would delete the DNA.” This may explain why it could not be sequenced using standard approaches. He added that the gaps also carry complex sequences that are not well reproduced by standard sequencing technologies.

“The sequences vary extensively between people and are likely hotspots of genetic instability,” he explained.

For now, SMRT technology will remain a research tool because of its high cost, about $100,000 per genome.

Eichler predicted, “In five years there might be a long-read sequence technology that will allow clinical laboratories to sequence a patient’s chromosomes from tip to tip and say, ‘Yes, you have about three to four million SNPs and insertions deletions but you also have approximately 30,000-40,000 structural variants. Of these, a few structural variants and a few SNPs are the reason why you’re susceptible to this disease.’ Knowing all the variation is going to be a game changer.”

Thanks to University of Washington Health Sciences for contributing this story.

I’m a Grad Student!

 :: Posted by American Biotechnologist on 11-06-2014