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Archive - Jan 15, 2014

Single Cell Sequencing Chosen 2013 Method of the Year by Nature Methods

The journal Nature Methods has selected single cell sequencing as the “Method of the Year” for 2013. In an editorial published on December 30, 2013, editors of Nature Methods said, “Once considered a technical challenge reserved for a few specialized labs, single-cell transcriptome and genome sequencing is becoming robust and broadly accessible. Exciting insights from recent studies are revealing the potential to understand biology at the unitary resolution of life, and last year marked a turning point in the widespread adoption of these methods to address a variety of research questions. For these reasons, single-cell sequencing is our choice of Method of the Year for 2013.” The journal presents a host of commentaries on different aspects of this exciting methodology. The journal outlines basic workflows and considerations in a Primer and describes currently useful applications in a News Feature. One Commentary describes how the method can be used to determine recombination frequencies, while a second suggests that single-cell transcriptome sequencing will deepen our understanding of gene regulation. A third Commentary discusses directions that complementary technologies must take to understand single cells at the level of function. Finally, the journal provides a section on Methods to Watch as we head into the future. This section can be found in the Method of the Year packet of information.

Beetle Study Shows Mitochondrial Genes Important for Survival and Reproduction

Contrary to common belief, mitochondrial genes seem to matter for how well individuals survive and reproduce. These new results are reported by researchers at Uppsala University who studied the genes of a common beetle species. Mitochondria are vital power plants of cells. They carry their own genes, which are inherited only through females, and these genes vary greatly between individuals. In the January 2014 issue of the prestigious scientific journal Ecology Letters, researchers from Uppsala University show for the first time that differences in the mitochondrial genes that individuals carry actually affect how well they survive and reproduce. It took the researchers two years to conduct the experiments, where they followed 180 populations of the seed beetle Callosobruchus maculatus (image) for more than 10 generations. The study was financed by the European Research Council and the Swedish Research Council and the results are based on gene sequence data from more than 2000 individuals. Remarkably, the authors found that individuals who carried rare mitochondrial genes were consistently those who did best. "This provides an explanation for why genetic variation is maintained. Much like a pendulum of a clock will never stop in either of the extreme sideway positions," says Professor Göran Arnqvist, one of the authors of the study. For decades, much biological research has rested on the assumption that different variants of the same mitochondrial gene are equivalent in terms of function of the gene. These genes have therefore been extensively used as a neutral "markers" that allow, for example, determination of the size of populations or reconstructions of the history of immigration into an area.

Gold Nanoparticles Key to New Virus-Tracking Method

Researchers at the Nanoscience Center (NSC) of University of Jyväskylä in Finland have developed a novel method to study enterovirus structures and their functions. The method will help to obtain new information on trafficking of viruses in cells and tissues as well as on the mechanisms of virus opening inside cells. This new information is important, for example, for developing new antiviral drugs and vaccines. The study was published online on January 13, 2014 in PNAS. The research was funded by the Academy of Finland and the TEKES FiDiPro -project NOVAC (Novel methods for vaccination and virus detection). Enteroviruses are pathogenic viruses infecting humans. This group consists of polioviruses, coxsackieviruses, echoviruses, and rhinoviruses. Enteroviruses are the most common causes of flu, but they also cause serious symptoms such as heart muscle infections and paralysis. Recently, enteroviruses have also been linked with chronic diseases such as diabetes. The infection mechanisms and infectious pathways of enteroviruses are still rather poorly understood. Previous studies in the group of Dr. Varpu Marjomäki at the NSC have focused on the cellular factors that are important for the infection caused by selected enteroviruses. The mechanistic understanding of virus opening and the release of the viral genome in cellular structures for starting new virus production is still largely lacking. Furthermore, the knowledge of infectious processes in tissues is hampered by the lack of reliable tools for detecting virus infection. The newly developed method involves a chemical modification of a known thiol-stabilized gold nanoparticle, the so-called Au102 cluster that was first synthesized and structurally solved by the group of Dr.