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Untangling whole genomes of individual species from a microbial mix

 :: Posted by American Biotechnologist on 05-27-2014

A new approach to studying microbes in the wild will allow scientists to sequence the genomes of individual species from complex mixtures. It marks a big advance for understanding the enormous diversity of microbial communities —including the human microbiome. The work is described in an article published May 22 in Early Online form in the journal G3: Genes|Genomes|Genetics, published by the Genetics Society of America.

“This new method will allow us to discover many currently unknown microbial species that can’t be grown in the lab, while simultaneously assembling their genome sequences,” says co-author Maitreya Dunham, a biologist at the University of Washington’s Department of Genome Sciences.

Microbial communities, whether sampled from the ocean floor or a human mouth, are made up of many different species living together. Standard methods for sequencing these communities combine the information from all the different types of microbes in the sample. The result is a hodgepodge of genes that is challenging to analyze, and unknown species in the sample are difficult to discover.

“Our approach tells us which sequence fragments in a mixed sample came from the same genome, allowing us to construct whole genome sequences for individual species in the mix,” says co-author Jay Shendure, also of the University of Washington’s Department of Genome Sciences.

The key advance was to combine standard approaches with a method that maps out which fragments of sequence were once near each other inside a cell. The cells in the sample are first treated with a chemical that links together DNA strands that are in close proximity. Only strands that are inside the same cell will be close enough to link. The DNA is then chopped into bits, and the linked portions are isolated and sequenced.

“This elegant method enables the study of microbes in the environment,” says Brenda Andrews, editor-in-chief of the journal G3: Genes|Genomes|Genetics. Andrews is alsoDirector of the Donnelly Centre and the Charles H. Best Chair of Medical Research at the University of Toronto. “It will open many windows into an otherwise invisible world.”

At a time when personal microbiome sequencing is becoming extremely popular, this method breaks important ground in helping researchers to build a complete picture of the genomic content of complex mixtures of microorganisms. This complete picture will be crucial for understanding the impact of varying microbiome populations and the relevance of particular microorganisms for individual health.

CITATION: Species-Level Deconvolution of Metagenome Assemblies with Hi-C-Based Contact Probability Maps Joshua N. Burton, Ivan Liachko, Maitreya J. Dunham, and Jay Shendure. G3: Genes|Genomes|Genetics g3.114.011825; Early Online May 22, 2014, doi:10.1534/g3.114.011825; PMID 24855317.

Thanks to the Genetics Society of America for contributing this story.

Proving an Age-Old Hypothesis Wrong

 :: Posted by American Biotechnologist on 05-12-2014

Cells are the basic structural units of all life. They were first observed more than 400 years ago after the invention of the microscope. One of the most studied cells in science is E. coli, a sausage-shaped bacterium that can cause food poisoning.

In fact, cells resemble sausages insofar as both consist of outer envelopes stuffed with an inner mass. For decades biologists have believed that the growth of this inner mass, pressing on the outer membrane, is what caused cell walls to grow.

However, using new techniques to isolate and visualize cells in different environments, the Stanford team proved that cell wall growth occurred regardless of the pressures exerted on the cell – whether from inside or out.

Here it is critical to understand that, unlike a sausage, the outer envelope of a cell is alive, dynamic and porous. It is designed to allow water to seep in or out. This is important because cells live in fluids and hence are subject to the pressure of osmosis.

Osmosis relates to the amount of solid materials dissolved in a liquid solution. Stirring sugar into coffee, for instance, increases its osmotic pressure. The more sugar you stir in, the higher the osmotic pressure of the solution.

Life is based on water, so cells have an internal osmotic pressure. When a cell enters a solution with a higher osmotic pressure – such as a sugary liquid – its porous membrane tries to protect the cell by letting water out. This causes the cell membrane to shrivel up, compacting the cell to withstand the pressure from without. Put the same cell back into a normal solution, and the porous cell wall allows water to seep back in, causing the cell to swell to its former size.

Biologists have long supposed that this same pressure dynamic retarded cell wall growth. It made sense given the prevailing wisdom – if cell wall growth were indeed driven by expansion from inside the cell, and outward pressure forced the cell to contract, how could the outer cell wall continue to grow?

In fact, the Stanford team initially designed its experiment to measure precisely how much osmotic pressure slowed cell wall growth in E. coli.

They used microfluidic devices to trap the bacterial cells in tiny chambers. This allowed them to bathe the confined cells, first in highly concentrated sugars (high osmotic pressure), then in normal solutions (low osmotic pressure), while recording precise images of cell contraction or expansion.

Initially, the results seemed to confirm the prevailing wisdom: cells bathed in a sugar solution appeared to grow more slowly.

But whenever the researchers “shocked” the cells by flushing out the sugars and bathing the cells in normal solution they were surprised to see that the cells expanded rapidly – in a matter of seconds — to a size roughly equivalent to cells growing at full speed in normal solutions. Click here to see the video.

“The cells just didn’t seem to care that they had been subjected to frequent and large (osmotic) insults in the chamber,” Huang said.

The Stanford researchers came to realize that the cell walls had continued to grow in the sugar solution just as fast as in the normal solution – but the extra mass was shriveled like a raisin. When the cell re-entered the normal solution and water seeped back in through the porous membrane, the now-turgid cell smoothed out like a grape, and all the non-apparent growth became visible.

To follow up this surprising finding, Rojas is in Bangladesh, extending the investigations to study how bacterial pathogens such as Vibrio cholerae respond to rapidly changing fluid environments and how to use this knowledge to fight this scourge.

Thanks to Stanford School of Engineering for contributing this story.

Bioinformatics approach helps researchers find new uses for old drug

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

Developing and testing a new anti-cancer drug can cost billions of dollars and take many years of research. Finding an effective anti-cancer medication from the pool of drugs already approved for the treatment of other medical conditions could cut a considerable amount of time and money from the process.

Now, using a novel bioinformatics approach, a team led by investigators at Beth Israel Deaconess Medical Center (BIDMC) has found that the approved antimicrobial drug pentamidine may help in the treatment of patients with advanced kidney cancer. Described online in the journal Molecular Cancer Therapeutics, the discovery reveals how linking cancer gene expression patterns with drug activity might help advance cancer care.

“The strategy of repurposing drugs that are currently being used for other indications is of significant interest to the medical community as well as the pharmaceutical and biotech industries,” says senior author Towia Libermann, PhD, Director of the Genomics, Proteomics, Bioinformatics and Systems Biology Center at BIDMC and Associate Professor of Medicine at Harvard Medical School. “Our results demonstrate that bioinformatics approaches involving the analysis and matching of cancer and drug gene signatures can indeed help us identify new candidate cancer therapeutics.”

Renal cell cancer consists of multiple subtypes that are likely caused by different genetic mutations. Over the years, Libermann has been working to identify new disease markers and therapeutic targets through gene expression signatures of renal cell cancer that distinguish these different cancer subtypes from each other, as well as from healthy individuals. In this new paper, he and his colleagues were looking for drugs that might be effective against clear cell renal cancer, the most common and highly malignant subtype of kidney cancer. Although patients with early stage disease can often be successfully treated through surgery, up to 30 percent of patients with renal cell cancer present with advanced stages of disease at the time of their diagnosis.

To pursue this search, they made use of the Connectivity Map (C-MAP) database, a collection of gene expression data from human cancer cells treated with hundreds of small molecule drugs.

“C-MAP uses pattern-matching algorithms to enable investigators to make connections between drugs, genes and diseases through common, but inverse, changes in gene expression,” says Libermann. “It provided us with an exciting opportunity to use our renal cell cancer gene signatures and a new bioinformatics strategy to match kidney cancer gene expression profiles from individual patients with gene expression changes inducted by various commonly used drugs.”

After identifying drugs that may reverse the gene expression changes associated with renal cell cancer, the investigators used assays to measure the effect of the selected drugs on cells. This led to the identification of a small number of FDA-approved drugs that induced cell death in multiple kidney cancer cell lines. The investigators then tested three of these drugs in an animal model of renal cell cancer and demonstrated that the antimicrobial agent pentamidine (primarily used for the treatment of pneumonia) reduced tumor growth and enhanced survival. Gene expression experiments using microarrays also identified the genes in renal cell cancer that were counteracted by pentamidine.

“One of the main challenges in treating cancer is the identification of the right drug for the right individual,” explains first author Luiz Fernando Zerbini, PhD, of the International Center for Genetic Engineering and Biotechnology in Cape Town, South Africa, adding that this bioinformatics approach could be a particularly valuable lower-cost model in developing countries.

The authors say their next step will be to evaluate the potential of pentamidine in combination with the current standard-of-care therapies to treat kidney cancer. “Since the drugs we are evaluating are already FDA-approved, successful studies in preclinical animal models may enable us to rapidly move these drugs into clinical trials,” adds Libermann.

Thanks to Beth Israel Deaconess Medical Center for contributing this story.

Much-needed tool for neuroscience emerges after years of work

 :: Posted by American Biotechnologist on 04-24-2014

Nearly a decade ago, the era of optogenetics was ushered in with the development of channelrhodopsins, light-activated ion channels that can, with the flick of a switch, instantaneously turn on neurons in which they are genetically expressed. What has lagged behind, however, is the ability to use light to inactivate neurons with an equal level of reliability and efficiency. Now, Howard Hughes Medical Institute (HHMI) scientists have used an analysis of channelrhodopsin’s molecular structure to guide a series of genetic mutations to the ion channel that grant the power to silence neurons with an unprecedented level of control.

The new structurally engineered channel at last gives neuroscientists the tools to both activate and inactivate neurons in deep brain structures using dim pulses of externally projected light. Deisseroth and his colleagues published their findings April 25, 2014 in the journal Science. “We’re excited about this increased light sensitivity of inhibition in part because we think it will greatly enhance work in large-brained organisms like rats and primates,” he says.

First discovered in unicellular green algae in 2002, channelrhodopsins function as photoreceptors that guide the microorganisms’ movements in response to light. In a landmark 2005 study, Deisseroth and his colleagues described a method for expressing the light-sensitive proteins in mouse neurons. By shining a pulse of blue light on those neurons, the researchers showed they could reliably induce the ion channel at channelrhodopsin’s core to open up, allowing positively charged ions to rush into the cell and trigger action potentials. Channelrhodopsins have since been used in hundreds of research projects investigating the neurobiology of everything from cell dynamics to cognitive functions.

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Why Geneticists May Have to Learn Yet Another Language

 :: Posted by American Biotechnologist on 04-17-2014

When talking about genetic abnormalities at the DNA level that occur when chromosomes swap, delete or add parts, there is an evolving communication gap both in the science and medical worlds, leading to inconsistencies in clinical and research reports.
Now a study by researchers at Brigham and Women’s Hospital (BWH) proposes a new classification system that may standardize how structural chromosomal rearrangements are described. Known as Next-Gen Cytogenetic Nomenclature, it is a major contribution to the classification system to potentially revolutionize how cytogeneticists worldwide translate and communicate chromosomal abnormalities. The study will be published online April 17, 2014 in The American Journal of Human Genetics.

“As scientists we are moving the field of cytogenetics forward in the clinical space,” said Cynthia Morton, PhD, BWH director of Cytogenetics, senior study author. “We will be able to define chromosomal abnormalities and report them in a way that is integral to molecular methods entering clinical practice.”

According to the researchers, advances in next-generation sequencing methods and results from BWH’s Developmental Genome Anatomy Project (DGAP) revealed an assortment of genes disrupted and dysregulated in human development in over 100 cases. Given the wide variety of chromosomal abnormalities, the researchers recognized that more accurate and full descriptions of structural chromosomal rearrangements were needed.

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