Activation of the Bile Acid Pathway and No Observed Antimicrobial Peptide Sequences in the Skin of a Poison Frog

The skin secretions of many frogs have genetically-encoded, endogenous antimicrobial peptides (AMPs). Other species, especially aposematic poison frogs, secrete exogenously derived alkaloids that serve as potent defense molecules. The origins of these defense systems are not clear, but a novel bileacid derived metabolite, tauromantellic acid, was recently discovered and shown to be endogenous in poison frogs (Mantella, Dendrobates, and Epipedobates). These observations raise questions about the evolutionary history of AMP genetic elements, the mechanism and function of tauromatellic acid production, and links between these systems. To understand the diversity and expression of AMPs among frogs, we assembled skin transcriptomes of 13 species across the anuran phylogeny. Our analyses revealed a diversity of AMPs and AMP expression levels across the phylogenetic history of frogs, but no observations of AMPs in Mantella. We examined genes expressed in the bile-acid metabolic pathway and found that CYP7A1 (Cytochrome P450), BAAT (bile acid-CoA: amino acid N-acyltransferase), and AMACR (alphamethylacyl- CoA racemase) were highly expressed in the skin of M. betsileo and either lowly expressed or absent in other frog species. In particular, CYP7A1 catalyzes the first reaction in the cholesterol catabolic pathway and is the rate-limiting step in regulation of bile acid synthesis, suggesting unique activation of the bile acid pathway in Mantella skin. The activation of the bile acid pathway in the skin of Mantella and the lack of observed AMPs fuel new questions about the evolution of defense compounds and the ectopic expression of the bile-acid pathway

Report of large whale restraint workshop

Location: Carriage House, Woods Hole Oceanographic Institution, Woods Hole, MA 02543. Date: February 7th & 8th 2006A number of large cetacean species are seriously injured and killed by entanglement in fishing gear used in the waters off the eastern United States and Canada. Entanglement most frequently involves rope or lines wrapped around the head, the flippers, body, in the mouth, around the tail flukes or any combination of the aforementioned body parts. Consequences of entanglement are particularly grave for North Atlantic right whales, which currently number about 300 whales and are declining due, in part, to this entanglement-related mortality. Right whales are frequently intractable and are very difficult and potentially unsafe to work with while attempting to disentangle the animal. Modifications and technological advances are needed to control, restrain and overall increase the success rate at which right whales are able to be cut free from entangling gear.National Marine Fisheries Servic

Drought resistance across California ecosystems: Evaluating changes in carbon dynamics using satellite imagery

Additional Supporting Information may be found online at: http://onlinelibrary.wiley.com/doi/10.1002/ecs2.1561/fullDrought is a global issue that is exacerbated by climate change and increasing anthropogenic water demands. The recent occurrence of drought in California provides an important opportunity to examine drought response across ecosystem classes (forests, shrublands, grasslands, and wetlands), which is essential to understand how climate influences ecosystem structure and function. We quantified ecosystem resistance to drought by comparing changes in satellite-derived estimates of water-use efficiency (WUE = net primary productivity [NPP]/evapotranspiration [ET]) under normal (i.e., baseline) and drought conditions (ΔWUE = WUE2014 − baseline WUE). With this method, areas with increasing WUE under drought conditions are considered more resilient than systems with declining WUE. Baseline WUE varied across California (0.08 to 3.85 g C/mm H2O) and WUE generally increased under severe drought conditions in 2014. Strong correlations between ΔWUE, precipitation, and leaf area index (LAI) indicate that ecosystems with a lower average LAI (i.e., grasslands) also had greater C-uptake rates when water was limiting and higher rates of carbon-uptake efficiency (CUE = NPP/LAI) under drought conditions. We also found that systems with a baseline WUE ≤ 0.4 exhibited a decline in WUE under drought conditions, suggesting that a baseline WUE ≤ 0.4 might be indicative of low drought resistance. Drought severity, precipitation, and WUE were identified as important drivers of shifts in ecosystem classes over the study period. These findings have important implications for understanding climate change effects on primary productivity and C sequestration across ecosystems and how this may influence ecosystem resistance in the future.The authors would like to acknowledge the excellent support provided by the Open Science for Synthesis-2014 training (supported by the National Science Foundation under Grant No. OCI-1216894) at the National Center for Ecological Analysis and Synthesis (NCEAS), a center funded by the University of California, Santa Barbara, and the State of California. The authors would like to thank OSS instructors Nancy Baron, Ben Bolker, Stephanie Hampton, Matthew Jones, Karthik Ram, Mark Schildhauer, and the participants of the OSS training. The authors would also like to thank the Goulden Lab at the University of California Irvines. A. J. Pérez-Luque acknowledges funding received by NCEAS and to MICINN (Spanish Government) for the PTA 2011-6322- I contract; D. P. Drucker acknowledges support from the USAID and the U.S. Department of State through the Sustainable Landscapes Brazil program; and M.G. Tulbure acknowledges funding from the Australian Research Council Early Career Researcher Award (DE140101608)

Laser-scanning velocimetry: A confocal microscopy method for quantitative measurement of cardiovascular performance in zebrafish embryos and larvae

Abstract Background The zebrafish Danio rerio is an important model system for drug discovery and to study cardiovascular development. Using a laser-scanning confocal microscope, we have developed a non-invasive method of measuring cardiac performance in zebrafish embryos and larvae that obtains cardiovascular parameters similar to those obtained using Doppler echocardiography in mammals. A laser scan line placed parallel to the path of blood in the dorsal aorta measures blood cell velocity, from which cardiac output and indices of vascular resistance and contractility are calculated. Results This technique, called laser-scanning velocimetry, was used to quantify the effects of pharmacological, developmental, and genetic modifiers of cardiac function. Laser-scanning velocimetry was applied to analyze the cardiovascular effects of morpholino knockdown of osmosensing scaffold for MEKK3 (OSM), which when mutated causes the human vascular disease cerebral cavernous malformations. OSM-deficient embryos had a constricted aortic arch and markedly increased peak cell velocity, a characteristic indicator of aortic stenosis. Conclusion These data validate laser-scanning velocimetry as a quantitative tool to measure cardiovascular performance for pharmacological and genetic analysis in zebrafish, which requires no specialized equipment other than a laser-scanning confocal microscope

El Nino Southern Oscillation (ENSO) Enhances CO2 Exchange Rates in Freshwater Marsh Ecosystems in the Florida Everglades

This research examines the relationships between El Nino Southern Oscillation (ENSO), water level, precipitation patterns and carbon dioxide (CO2) exchange rates in the freshwater wetland ecosystems of the Florida Everglades. Data was obtained over a 5-year study period (2009-2013) from two freshwater marsh sites located in Everglades National Park that differ in hydrology. At the short-hydroperiod site (Taylor Slough; TS) and the long-hydroperiod site (Shark River Slough; SRS) fluctuations in precipitation patterns occurred with changes in ENSO phase, suggesting that extreme ENSO phases alter Everglades hydrology which is known to have a substantial influence on ecosystem carbon dynamics. Variations in both ENSO phase and annual net CO2 exchange rates co-occurred with changes in wet and dry season length and intensity. Combined with site-specific seasonality in CO2 exchanges rates, El Nino and La Nina phases magnified season intensity and CO2 exchange rates at both sites. At TS, net CO2 uptake rates were higher in the dry season, whereas SRS had greater rates of carbon sequestration during the wet season. As La Nina phases were concurrent with drought years and extended dry seasons, TS became a greater sink for CO2 on an annual basis (-11 to -110 g CO2 m(-2) yr(-1)) compared to El Nino and neutral years (-5 to -43.5 g CO2 m(-2) yr(-1)). SRS was a small source for CO2 annually (1.81 to 80 g CO2 m(-2) yr(-1)) except in one exceptionally wet year that was associated with an El Nino phase (-16 g CO2 m(-2) yr(-1)). Considering that future climate predictions suggest a higher frequency and intensity in El Nino and La Nina phases, these results indicate that changes in extreme ENSO phases will significantly alter CO2 dynamics in the Florida Everglades

What is Microbial Dormancy?

Life can be stressful. One way to deal with stress is to simply wait it out. Microbes do this by entering a state of reduced activity and increased resistance commonly called ‘dormancy’. But what is dormancy? Different scientific disciplines emphasize distinct traits and phenotypic ranges in defining dormancy for their microbial species and system-specific questions of interest. Here, we propose a unified definition of microbial dormancy, using a broad framework to place earlier discipline-specific definitions in a new context. We then discuss how this new definition and framework may improve our ability to investigate dormancy using multi-omics tools. Finally, we leverage our framework to discuss the diversity of genomic mechanisms for dormancy in an extreme environment that challenges easy definitions – the permafrost

Nuclease Modulates Biofilm Formation in Community-Associated Methicillin-Resistant Staphylococcus aureus

Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is an emerging contributor to biofilm-related infections. We recently reported that strains lacking sigma factor B (sigB) in the USA300 lineage of CA-MRSA are unable to develop a biofilm. Interestingly, when spent media from a USA300 sigB mutant was incubated with other S. aureus strains, biofilm formation was inhibited. Following fractionation and mass spectrometry analysis, the major anti-biofilm factor identified in the spent media was secreted thermonuclease (Nuc). Considering reports that extracellular DNA (eDNA) is an important component of the biofilm matrix, we investigated the regulation and role of Nuc in USA300. The expression of the nuc gene was increased in a sigB mutant, repressed by glucose supplementation, and was unaffected by the agr quorum-sensing system. A FRET assay for Nuc activity was developed and confirmed the regulatory results. A USA300 nuc mutant was constructed and displayed an enhanced biofilm-forming capacity, and the nuc mutant also accumulated more high molecular weight eDNA than the WT and regulatory mutant strains. Inactivation of nuc in the USA300 sigB mutant background partially repaired the sigB biofilm-negative phenotype, suggesting that nuc expression contributes to the inability of the mutant to form biofilm. To test the generality of the nuc mutant biofilm phenotypes, the mutation was introduced into other S. aureus genetic backgrounds and similar increases in biofilm formation were observed. Finally, using multiple S. aureus strains and regulatory mutants, an inverse correlation between Nuc activity and biofilm formation was demonstrated. Altogether, our findings confirm the important role for eDNA in the S. aureus biofilm matrix and indicates Nuc is a regulator of biofilm formation

Cerebellar white matter abnormalities following primary blast injury in US military personnel

Little is known about the effects of blast exposure on the human brain in the absence of head impact. Clinical reports, experimental animal studies, and computational modeling of blast exposure have suggested effects on the cerebellum and brainstem. In US military personnel with isolated, primary blast-related ‘mild’ traumatic brain injury and no other known insult, we found diffusion tensor MRI abnormalities consistent with cerebellar white matter injury in 3 of 4 subjects. No abnormalities in other brain regions were detected. These findings add to the evidence supporting the hypothesis that primary blast exposure contributes to brain injury in the absence of head impact and that the cerebellum may be particularly vulnerable. However, the clinical effects of these abnormalities cannot be determined with certainty; none of the subjects had ataxia or other detected evidence of cerebellar dysfunction. The details of the blast events themselves cannot be disclosed at this time, thus additional animal and computational modeling will be required to dissect the mechanisms underlying primary blast-related traumatic brain injury. Furthermore, the effects of possible subconcussive impacts and other military-related exposures cannot be determined from the data presented. Thus many aspects of topic will require further investigation

A metatranscriptomic approach to explore longitudinal tissue specimens from non-healing diabetes related foot ulcers

Cellular mechanisms and/or microbiological interactions which contribute to chronic diabetes related foot ulcers (DRFUs) were explored using serially collected tissue specimens from chronic DRFUs and control healthy foot skin. Total RNA was isolated for next-generation sequencing. We found differentially expressed genes (DEGs) and enriched hallmark gene ontology biological processes upregulated in chronic DRFUs which primarily functioned in the host immune response including: (i) Inflammatory response; (ii) TNF signalling via NFKB; (iii) IL6 JAK-STAT3 signalling; (iv) IL2 STAT5 signalling and (v) Reactive oxygen species. A temporal analysis identified RN7SL1 signal recognition protein and IGHG4 immunoglobulin protein coding genes as being the most upregulated genes after the onset of treatment. Testing relative temporal changes between healing and non-healing DRFUs identified progressive upregulation in healed wounds of CXCR5 and MS4A1 (CD20), both canonical markers of lymphocytes (follicular B cells/follicular T helper cells and B cells, respectively). Collectively, our RNA-seq data provides insights into chronic DRFU pathogenesis