Dustbuster: a compact impact-ionization time-of-flight mass spectrometer for in situ analysis of cosmic dust

We report on the design and testing of a compact impact-ionization time-of-flight mass spectrometer for analysis of cosmic dust, suitable for use on deep space missions. The instrument, Dustbuster, incorporates a large target area with a reflectron, simultaneously optimizing mass resolution, particle detection, and ion collection. Dust particles hit the 65-cm2 target plate and are partially ionized by the impact. The resulting ions, with broad energy and angular distributions, are accelerated through a modified reflectron, focusing ions of specific m/z in space and time to produce high-resolution mass spectra. The cylindrically symmetric instrument is 10 cm in diameter and 20 cm in length, considerably smaller than previous in situ dust analyzers, and can be easily scaled as needed for specific mission requirements. Laser desorption ionization of metal and mineral samples embedded in the impact plate simulated particle impacts for evaluations of instrument performance. Mass resolution in these experiments ranged from 60–180, permitting resolution of isotopes. The mass spectrometer can be combined with other instrument components to determine dust particle trajectories and sizes

Reply to ``Comment on `Insulating Behavior of λ\lambda-DNA on the Micron Scale' "

In our experiment, we found that the resistance of vacuum-dried $\lambda$-DNA exceeds $10^{14} \Omega$ at 295 K. Bechhoefer and Sen have raised a number of objections to our conclusion. We provide counter arguments to support our original conclusion.Comment: 1 page reply to comment, 1 figur

Identifying Structural Variation in Haploid Microbial Genomes from Short-Read Resequencing Data Using Breseq

Mutations that alter chromosomal structure play critical roles in evolution and disease, including in the origin of new lifestyles and pathogenic traits in microbes. Large-scale rearrangements in genomes are often mediated by recombination events involving new or existing copies of mobile genetic elements, recently duplicated genes, or other repetitive sequences. Most current software programs for predicting structural variation from short-read DNA resequencing data are intended primarily for use on human genomes. They typically disregard information in reads mapping to repeat sequences, and significant post-processing and manual examination of their output is often required to rule out false-positive predictions and precisely describe mutational events. Results: We have implemented an algorithm for identifying structural variation from DNA resequencing data as part of the breseq computational pipeline for predicting mutations in haploid microbial genomes. Our method evaluates the support for new sequence junctions present in a clonal sample from split-read alignments to a reference genome, including matches to repeat sequences. Then, it uses a statistical model of read coverage evenness to accept or reject these predictions. Finally, breseq combines predictions of new junctions and deleted chromosomal regions to output biologically relevant descriptions of mutations and their effects on genes. We demonstrate the performance of breseq on simulated Escherichia coli genomes with deletions generating unique breakpoint sequences, new insertions of mobile genetic elements, and deletions mediated by mobile elements. Then, we reanalyze data from an E. coli K-12 mutation accumulation evolution experiment in which structural variation was not previously identified. Transposon insertions and large-scale chromosomal changes detected by breseq account for similar to 25% of spontaneous mutations in this strain. In all cases, we find that breseq is able to reliably predict structural variation with modest read-depth coverage of the reference genome (>40-fold). Conclusions: Using breseq to predict structural variation should be useful for studies of microbial epidemiology, experimental evolution, synthetic biology, and genetics when a reference genome for a closely related strain is available. In these cases, breseq can discover mutations that may be responsible for important or unintended changes in genomes that might otherwise go undetected.U.S. National Institutes of Health R00-GM087550U.S. National Science Foundation (NSF) DEB-0515729NSF BEACON Center for the Study of Evolution in Action DBI-0939454Cancer Prevention & Research Institute of Texas (CPRIT) RP130124University of Texas at Austin startup fundsUniversity of Texas at AustinCPRIT Cancer Research TraineeshipMolecular Bioscience

Seshat: The Global History Databank

The vast amount of knowledge about past human societies has not been systematically organized and, therefore, remains inaccessible for empirically testing theories about cultural evolution and historical dynamics. For example, what evolutionary mechanisms were involved in the transition from the small-scale, uncentralized societies, in which humans lived 10,000 years ago, to the large-scale societies with an extensive division of labor, great differentials in wealth and power, and elaborate governance structures of today? Why do modern states sometimes fail to meet the basic needs of their populations? Why do economies decline, or fail to grow? In this article, we describe the structure and uses of a massive databank of historical and archaeological information, Seshat: The Global History Databank. The data that we are currently entering in Seshat will allow us and others to test theories explaining how modern societies evolved from ancestral ones, and why modern societies vary so much in their capacity to satisfy their members’ basic human needsPeer reviewedFinal Published versio

Licensed control does not reduce local Cormorant Phalacrocorax carbo population size in winter

Cormorants Phalacrocorax carbo have increased on European freshwaters, creating conflicts with fishing interests. As a result, control measures have been implemented in several countries, although their effect on the English population has yet to be determined. Wetland Bird Survey data was used to derive population growth rates (PGR) of non-coastal Cormorant populations in England. PGR was analysed in relation to control intensity at different scales (5- to 30-km radius) from 2001 to 2009 in order to determine (1) the extent to which control intensity (proportion of the local population shot per winter) was associated with site-level population change, and (2) whether potential effects of control intensity were evident on Special Protection Areas (SPAs). There were no clear differences in PGR when comparing sites which had experienced control versus sites where control had never been carried out. The few significant relationships between control intensity and Cormorant PGR detected were mostly positive, i.e. population growth was associated with higher control intensity. Control intensity was not related to Cormorant numbers in SPAs. Positive associations with control may arise because control is reactive, or because non-lethal effects cause greater dispersal of Cormorants. These results provide no evidence that Cormorant removal at local scales is having an effect on longer term (i.e. year-to-year) population size at a site level. They also suggest that control measures have not affected national population trends, although a better understanding of site use and movements of individual Cormorants needs to be developed at smaller scales (including those due to disturbance caused by control measures) to more fully understand processes at larger scales. Further research is also needed into the extent to which lethal and non-lethal effects of control on Cormorants are having the desired impact on predation rates of fish, and so help resolve the conflict between Cormorants and fisheries.</p

Corticosterone Regulates Both Naturally Occurring and Cocaine‐Induced Dopamine Signaling by Selectively Decreasing Dopamine Uptake

Stressful and aversive events promote maladaptive reward‐seeking behaviors such as drug addiction by acting, in part, on the mesolimbic dopamine system. Using animal models, data from our laboratory and others show that stress and cocaine can interact to produce a synergistic effect on reward circuitry. This effect is also observed when the stress hormone corticosterone is administered directly into the nucleus accumbens (NAc), indicating that glucocorticoids act locally in dopamine terminal regions to enhance cocaine\u27s effects on dopamine signaling. However, prior studies in behaving animals have not provided mechanistic insight. Using fast‐scan cyclic voltammetry, we examined the effect of systemic corticosterone on spontaneous dopamine release events (transients) in the NAc core and shell in behaving rats. A physiologically relevant systemic injection of corticosterone (2 mg/kg i.p.) induced an increase in dopamine transient amplitude and duration (both voltammetric measures sensitive to decreases in dopamine clearance), but had no effect on the frequency of transient release events. This effect was compounded by cocaine (2.5 mg/kg i.p.). However, a second experiment indicated that the same injection of corticosterone had no detectable effect on the dopaminergic encoding of a palatable natural reward (saccharin). Taken together, these results suggest that corticosterone interferes with naturally occurring dopamine uptake locally, and this effect is a critical determinant of dopamine concentration specifically in situations in which the dopamine transporter is pharmacologically blocked by cocaine

What Should a Psychiatrist Know About Genetics? Review and Recommendations From the Residency Education Committee of the International Society of Psychiatric Genetics.

The International Society of Psychiatric Genetics (ISPG) created a Residency Education Committee with the purpose of identifying key genetic knowledge that should be taught in psychiatric training programs. Thirteen committee members were appointed by the ISPG Board of Directors, based on varied training, expertise, gender, and national origin. The Committee has met quarterly for the past 2 years, with periodic reports to the Board and to the members of the Society. The information summarized includes the existing literature in the field of psychiatric genetics and the output of ongoing large genomics consortia. An outline of clinically relevant areas of genetic knowledge was developed, circulated, and approved. This document was expanded and annotated with appropriate references, and the manuscript was developed. Specific information regarding the contribution of common and rare genetic variants to major psychiatric disorders and treatment response is now available. Current challenges include the following: (1) Genetic testing is recommended in the evaluation of autism and intellectual disability, but its use is limited in current clinical practice. (2) Commercial pharmacogenomic testing is widely available, but its utility has not yet been clearly established. (3) Other methods, such as whole exome and whole genome sequencing, will soon be clinically applicable. The need for informed genetic counseling in psychiatry is greater than ever before, knowledge in the field is rapidly growing, and genetic education should become an integral part of psychiatric training