Characterization of the transcriptome, nucleotide sequence polymorphism, and natural selection in the desert adapted mouse Peromyscus eremicus

As a direct result of intense heat and aridity, deserts are thought to be among the most harsh of environments, particularly for their mammalian inhabitants. Given that osmoregulation can be challenging for these animals, with failure resulting in death, strong selection should be observed on genes related to the maintenance of water and solute balance. One such animal, Peromyscus eremicus, is native to the desert regions of the southwest United States and may live its entire life without oral fluid intake. As a first step toward understanding the genetics that underlie this phenotype, we present a characterization of the P. eremicus transcriptome. We assay four tissues (kidney, liver, brain, testes) from a single individual and supplement this with population level renal transcriptome sequencing from 15 additional animals. We identified a set of transcripts undergoing both purifying and balancing selection based on estimates of Tajima’s D. In addition, we used the branch-site test to identify a transcript—Slc2a9, likely related to desert osmoregulation—undergoing enhanced selection in P. eremicus relative to a set of related non-desert rodents

Improving transcriptome assembly through error correction of high-throughput sequence reads

The study of functional genomics--particularly in non-model organisms has been dramatically improved over the last few years by use of transcriptomes and RNAseq. While these studies are potentially extremely powerful, a computationally intensive procedure--the de novo construction of a reference transcriptome must be completed as a prerequisite to further analyses. The accurate reference is critically important as all downstream steps, including estimating transcript abundance are critically dependent on the construction of an accurate reference. Though a substantial amount of research has been done on assembly, only recently have the pre-assembly procedures been studied in detail. Specifically, several stand-alone error correction modules have been reported on, and while they have shown to be effective in reducing errors at the level of sequencing reads, how error correction impacts assembly accuracy is largely unknown. Here, we show via use of a simulated dataset, that applying error correction to sequencing reads has significant positive effects on assembly accuracy, by reducing assembly error by nearly 50%, and therefore should be applied to all datasets.Comment: version 3 added PE reads and an empirical datase

Energetic and Environmental Constraints on the Community Structure of Benthic Microbial Mats in Lake Fryxell, Antarctica.

Ecological communities are regulated by the flow of energy through environments. Energy flow is typically limited by access to photosynthetically active radiation (PAR) and oxygen concentration (O2). The microbial mats growing on the bottom of Lake Fryxell, Antarctica, have well-defined environmental gradients in PAR and (O2). We analyzed the metagenomes of layers from these microbial mats to test the extent to which access to oxygen and light controls community structure. We found variation in the diversity and relative abundances of Archaea, Bacteria and Eukaryotes across three (O2) and PAR conditions: high (O2) and maximum PAR, variable (O2) with lower maximum PAR, and low (O2) and maximum PAR. We found distinct communities structured by the optimization of energy use on a millimeter-scale across these conditions. In mat layers where (O2) was saturated, PAR structured the community. In contrast, (O2) positively correlated with diversity and affected the distribution of dominant populations across the three habitats, suggesting that meter-scale diversity is structured by energy availability. Microbial communities changed across covarying gradients of PAR and (O2). The comprehensive metagenomic analysis suggests that the benthic microbial communities in Lake Fryxell are structured by energy flow across both meter- and millimeter-scales

Is Resisting Genocide a Human Right

Closely examining the Darfur, Sudan, genocide, and making reference to other genocides, this Article argues that the genocide prevention strategies which are currently favored by the United Nations are ineffective. This Article details the failures of targeted sanctions, United Nations peacekeepers, and other anti-genocide programs. Then, this Article analyzes the Genocide Convention and other sources of international human rights law. Because the very strong language of the Genocide Convention forbids any form of complicity in genocide, and because the Genocide Convention is jus cogens (meaning that it prevails over any conflicting national or international law), this Article concludes that the Genocide Convention forbids any interference, including interference based on otherwise valid laws, against the procurement of defensive arms by groups which are being victimized by genocide. Reprinted by permission of the publisher

A Proposal to Reduce Unnecessary Incarceration: Introducing the Public Safety and Prison Reduction Act

For decades, the federal government used its grant-making power to spur states to incarcerate more people and to impose longer sentences. It should now use that power to reverse course

Interactive Methods for Teaching Action Potentials, an Example of Teaching Innovation from Neuroscience Postdoctoral Fellows in the Fellowships in Research and Science Teaching (FIRST) Program

Acquiring a faculty position in academia is extremely competitive and now typically requires more than just solid research skills and knowledge of one’s field. Recruiting institutions currently desire new faculty that can teach effectively, but few postdoctoral positions provide any training in teaching methods. Fellowships in Research and Science Teaching (FIRST) is a successful postdoctoral training program funded by the National Institutes of Health (NIH) providing training in both research and teaching methodology. The FIRST program provides fellows with outstanding interdisciplinary biomedical research training in fields such as neuroscience. The postdoctoral research experience is integrated with a teaching program which includes a How to Teach course, instruction in classroom technology and course development and mentored teaching. During their mentored teaching experiences, fellows are encouraged to explore innovative teaching methodologies and to perform science teaching research to improve classroom learning. FIRST fellows teaching neuroscience to undergraduates have observed that many of these students have difficulty with the topic of neuroscience. Therefore, we investigated the effects of interactive teaching methods for this topic. We tested two interactive teaching methodologies to determine if they would improve learning and retention of this information when compared with standard lectures. The interactive methods for teaching action potentials increased understanding and retention. Therefore, FIRST provides excellent teaching training, partly by enhancing the ability of fellows to integrate innovative teaching methods into their instruction. This training in turn provides fellows that matriculate from this program more of the characteristics that hiring institutions desire in their new faculty

Direct evidence for radar reflector originating from changes in crystal-orientation fabric

International audienceThe origin of a strong continuous radar reflector observed with airborne radio-echo sounding (RES) at the EPICA deep-drilling site in Dronning Maud Land, Antarctica, is identified as a transition in crystal fabric orientation from a vertical girdle- to increased single-pole orientation seen along the ice core. The reflector is observed with a 60 ns and 600 ns long pulse at a frequency of 150 MHz, spans one pulse length, is continuous over 5 km, and occurs at a depth of about 2020?2030 m at the drill site. Changes in conductivity as reflector origin are excluded by investigating the ice-core profile and synthetic RES data. Our observations allow to extrapolate the crystal orientation feature along the reflector in space, with implications for ice-sheet dynamics. As the conductivity profile of the EPICA shows no distinctive peak at this depths, we exclude changes in conductivity as the reflector origin. This is supported by application of numerical forward modelling of electromagnetic wave propagation, based on the conductivity profile, which is able to reproduce nearby reflections, but fails to reproduce this one. Because of background noise, the permittivity profile based on dielectric does not show prominent signals at these depths. We therefore interpret the observed reflector to originate from this change in crystal fabric

Direct evidence for continuous radar reflector originating from changes in crystal-orientation fabric

International audienceThe origin of a strong continuous radar reflector observed with airborne radio-echo sounding (RES) at the EPICA deep-drilling site in Dronning Maud Land, Antarctica, is identified as a transition in crystal fabric orientation from a vertical girdle to an increased single-pole orientation seen along the ice core. The reflector is observed with a 60 ns and 600 ns long pulse at a frequency of 150 MHz, spans one pulse length, is continuous over 5 km, and occurs at a depth of about 2025?2045 m at the drill site. Changes in conductivity as reflector origin are excluded by investigating the ice-core profile, synthetic RES data, and a RES profile with different electromagnetic polarisation azimuths. The reflector's magnitude shows maximum values for polarisation parallel to the nearby ice divide and disappears for polarisation perpendicular to it, identifying the orientation of the girdle to lie in the vertical plane parallel to the ice divide. Observations allow us to extrapolate the crystal orientation feature along the reflector in space, with implications for ice-sheet dynamics and modeling