Identification of source-sink dynamics in mountain lions of the Great Basin

Natural and anthropogenic boundaries have been shown to affect population dynamics and population structure for many species with movement patterns at the landscape level. Understanding population boundaries and movement rates in the field for species that are cryptic and occur at low densities is often extremely difficult and logistically prohibitive; however genetic techniques may offer insights that have previously been unattainable. We analyzed thirteen microsatellite loci for 739 mountain lions (Puma concolor) using muscle tissue samples from individuals in the Great Basin throughout Nevada and the Sierra Nevada mountain range to test the hypothesis that heterogeneous hunting pressure results in source-sink dynamics at the landscape scale. We used a combination of non-spatial and spatial model-based Bayesian clustering methods to identify genetic populations. We then used a recently developed Bayesian multilocus genotyping method to estimate asymmetrical rates of contemporary movement between those subpopulations and to identify source and sink populations. We identified two populations at the highest level of genetic structuring with a total of five subpopulations in the Great Basin of Nevada and the Sierra Nevada range. Our results suggest that source-sink dynamics occur at landscape scales for wide-ranging species, such as mountain lions, and that source populations may be those that are under relatively less hunting pressure and that occupy refugia

Year 1 of the Legacy Survey of Space and Time (LSST): Recommendations for Template Production to Enable Solar System Small Body Transient and Time Domain Science

The Vera C. Rubin Observatory Legacy Survey of Space and Time (LSST) will discover ~6 million solar system planetesimals, providing in total over a billion photometric and astrometric measurements in 6 broad-band filters. Rubin Observatory's automated data reduction pipelines will employ difference imaging; templates representing the static sky will be subtracted from the nightly LSST observations in order to identify transient sources, including solar system moving objects. These templates are expected to be generated by coadding high quality images of the same pointing from the previous year's survey observations. The first year of LSST operations will require a different method for generating templates, if solar system discoveries are to be reported daily like Year 2 and beyond. We make recommendations for template production in the LSST's first year and present the opportunities for solar system small body transient and time domain science enhanced by this change

Nighttime chemical transformation in biomass burning plumes : A box model analysis initialized with aircraft observations

Biomass burning (BB) is a large source of reactive compounds in the atmosphere. While the daytime photochemistry of BB emissions has been studied in some detail, there has been little focus on nighttime reactions despite the potential for substantial oxidative and heterogeneous chemistry. Here, we present the first analysis of nighttime aircraft intercepts of agricultural BB plumes using observations from the NOAA WP-3D aircraft during the 2013 Southeast Nexus (SENEX) campaign. We use these observations in conjunction with detailed chemical box modeling to investigate the formation and fate of oxidants (NO3, N2O5, O3, and OH) and BB volatile organic compounds (BBVOCs), using emissions representative of agricultural burns (rice straw) and western wildfires (ponderosa pine). Field observations suggest NO3 production was approximately 1 ppbv hr–1, while NO3 and N2O5 were at or below 3 pptv, indicating rapid NO3/N2O5 reactivity. Model analysis shows that >99% of NO3/N2O5 loss is due to BBVOC + NO3 reactions rather than aerosol uptake of N2O5. Nighttime BBVOC oxidation for rice straw and ponderosa pine fires is dominated by NO3 (72, 53%, respectively) but O3 oxidation is significant (25, 43%), leading to roughly 55% overnight depletion of the most reactive BBVOCs and NO2

The Astropy Problem

The Astropy Project (http://astropy.org) is, in its own words, "a community effort to develop a single core package for Astronomy in Python and foster interoperability between Python astronomy packages." For five years this project has been managed, written, and operated as a grassroots, self-organized, almost entirely volunteer effort while the software is used by the majority of the astronomical community. Despite this, the project has always been and remains to this day effectively unfunded. Further, contributors receive little or no formal recognition for creating and supporting what is now critical software. This paper explores the problem in detail, outlines possible solutions to correct this, and presents a few suggestions on how to address the sustainability of general purpose astronomical software

When simple sequence comparison fails: the cryptic case of the shared domains of the bacterial replication initiation proteins DnaB and DnaD

DnaD and DnaB are essential DNA-replication-initiation proteins in low-G+C content Gram-positive bacteria. Here we use sensitive Hidden Markov Model-based techniques to show that the DnaB and DnaD proteins share a common structure that is evident across all their structural domains, termed DDBH1 and DDBH2 (DnaD DnaB Homology 1 and 2). Despite strong sequence divergence, many of the DNA-binding and oligomerization properties of these domains have been conserved. Although eluding simple sequence comparisons, the DDBH2 domains share the only strong sequence motif; an extremely highly conserved YxxxIxxxW sequence that contributes to DNA binding. Sequence alignments of DnaD alone fail to identify another key part of the DNA-binding module, since it includes a poorly conserved sequence, a solvent-exposed and somewhat unstable helix and a mobile segment. We show by NMR, in vitro mutagenesis and in vivo complementation experiments that the DNA-binding module of Bacillus subtilis DnaD comprises the YxxxIxxxW motif, the unstable helix and a portion of the mobile region, the latter two being essential for viability. These structural insights lead us to a re-evaluation of the oligomerization and DNA-binding properties of the DnaD and DnaB proteins

Regulation of skeletal muscle oxidative capacity and insulin signaling by the Mitochondrial Rhomboid Protease PARL

Type 2 diabetes mellitus (T2DM) and aging are characterized by insulin resistance and impaired mitochondrial energetics. In lower organisms, remodeling by the protease pcp1 (PARL ortholog) maintains the function and lifecycle of mitochondria. We examined whether variation in PARL protein content is associated with mitochondrial abnormalities and insulin resistance. PARL mRNA and mitochondrial mass were both reduced in elderly subjects and in subjects with T2DM. Muscle knockdown of PARL in mice resulted in malformed mitochondrial cristae, lower mitochondrial content, decreased PGC1&alpha; protein levels, and impaired insulin signaling. Suppression of PARL protein in healthy myotubes lowered mitochondrial mass and insulin-stimulated glycogen synthesis and increased reactive oxygen species production. We propose that lower PARL expression may contribute to the mitochondrial abnormalities seen in aging and T2DM.<br /

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN