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Archive for the ‘Interesting Studies’ Category

To Film or Not to Film

 :: Posted by American Biotechnologist on 11-25-2014

The ChemiDoc Touch Imaging System is Bio-Rad’s new digital imaging solution for gel and western blot analysis. Designed for efficiency and ease of use, it integrates a touch-screen interface with Image Lab™ Touch Software to give users a fast workflow for acquiring and analyzing publication-quality image data. As a part of Bio-Rad’s V3 Western Workflow™, the ChemiDoc Touch Imaging System enables a western blotting protocol improved with multiple validation steps, streamlined completion times, and quantitative results using stain-free gel chemistry.

We gave this new imaging system to several researchers to test. Each one started the process as a user of X-ray film for western blot imaging. Some reported having tried digital imaging in the past, but not being convinced at that time to give up film. Each sat down for an interview regarding how he used the ChemiDoc Touch Imaging System and provided a representative blot image created using the instrument.

Click here to read the full story…

Lessons from a Bean Sprout

 :: Posted by American Biotechnologist on 11-19-2014

It’s hard to believe, but there are similarities between bean sprouts and human cancer.

In bean sprouts, a collection of amino acids known as a protein complex allows them to grow longer in the darkness than in the light. In humans, a similar protein complex called CSN and its subunit CSN6 is now believed to be a cancer-causing gene that impacts activity of another gene (Myc) tied to tumor growth.

Somehow the same mechanisms that result in bigger bean sprouts, also cause cancer metastasis and tumor development.

A study at The University of Texas MD Anderson Cancer Center led by Mong-Hong Lee, Ph.D., a professor of molecular and cellular oncology, has demonstrated the significance of CSN6 in regulating Myc which may very well open up a new pathway for treating and killing tumors. The study results are published in this month’s issue of Nature Communications.

“We have discovered that CSN6 is a strong oncogene that is frequently overexpressed and significantly speeds up tumor growth in many types of cancer,” said Lee. “Furthermore, CSN6 also affects the expression of Myc in tumors.”

Myc is a proto-oncogene or master cancer gene that spurs tumor growth in a variety of cancers including breast, lung, colon, brain, skin, leukemia, prostate, pancreas, stomach and bladder.

Lee said that the study findings are important because targeting Myc is a challenging task due to its unique protein structure. Even though it has been studied for decades, no effective inhibitor for Myc has been successfully developed. His team’s study found that inhibiting CSN6 quickly destabilizes Myc, greatly impairing metastasis and tumor growth.

“This has the potential to unlock a promising and completely new door to effectively eliminating tumors and suppressing cancers that overexpress Myc,” said Lee.

Thanks to MD Anderson for contributing this story.

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.

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.

Programming Cancer Cells to Self-Destruct

 :: Posted by American Biotechnologist on 11-05-2014