Modelling effects of climate change on Michigan brown trout and rainbow trout: Precipitation and groundwater as key predictors

Understanding how changes in stream temperature affect survival and growth of coldwater fishes, including brown trout (Salmo trutta) and rainbow trout (Oncorhynchus mykiss), is important for conserving coldwater stream fisheries in a changing climate. However, some contemporary stream temperature models assume spatially uniform (i.e. unrealistic) air–stream temperature relationships or demand hydrometeorological predictors (e.g. solar radiation and convection) that are expensive and often impractical for fisheries managers to measure. As such, we produced a relatively cost-effective, management-relevant modelling approach for predicting effects of changes in air temperature, precipitation and groundwater inputs on stream temperature and, consequently, the survival and growth of brown trout and rainbow trout in Michigan, USA. We found that precipitation- and groundwater-corrected stream temperature models (mean adjusted R² = .77, range = 0.65–0.88) performed better than linear air–stream temperature models (mean adjusted R² = .59, range = 0.21–0.80). Stream temperature was projected to increase by 0.07–3.88°C (1%–22%) with simulated changes in air temperature, precipitation and groundwater inputs. The greatest warming was predicted for surface runoff-dominated sites with limited groundwater-driven thermal buffering, where thermal habitat suitability for salmonid survival and growth declined 20%–40%. However, groundwater-dominated sites may not be immune to temperature warming, especially if groundwater temperature increases or groundwater inputs decline in a changing climate. Our modelling approach provides a reliable, cost-effective method for predicting effects of climate change on brown trout and rainbow trout survival and growth, allowing for strategic management actions to increase the thermal resilience and sustainability of salmonid populations (e.g. groundwater conservation and riparian/watershed rehabilitation).     

Effect of yellow loess on clearance rate in seven species of benthic, filter-feeding invertebrates

Attempts have been made, especially in Asia, to displace harmful algal blooms (HABs) by spraying ‘china clay’ and ‘loess’ over affected coastal waters. The impact of this technique on benthic communities and processes is not known. We examined the effects of yellow loess on clearance rates of the benthic, filter‐feeding invertebrates, Crassostrea virginica (Gmelin 1791), C. gigas (Thunberg 1793), Mytilus edulis (Linnaeus 1758), M. trossulus (Gould 1850), Argopecten irradians (Lamarck 1819), and Crepidula fornicata (Linnaeus 1758). An Obelia species of hydroid was also studied and the percent time open was analysed. Depletion rates were measured using a range of loess concentrations suspended in culture with unicellular algae (Rhodomonas lens) in 0.45 μm filtered seawater. The effects of loess on clearance rates and behaviour were species‐specific. C. virginica was not impacted until clay concentrations reached 1.0 g L^?1, while A. irradians showed a significant decrease at 0.01 g L^?1. M. edulis showed a significant decrease in clearance rates at the 1 and 10 g L^?1 concentrations. For hydroids, the percent time open was significantly lower than the control at 0.01, 0.1, and 10 g L^?1. We clearly demonstrate that loess has a significant negative impact on filter‐feeding invertebrates. The use of clay as a strategy for mitigation of HABs should be approached with extreme caution. While the control of active blooms may eventually be possible, it may not necessarily be an environmentally advisable or responsible approach to dealing with HABs.     

Potency- and Selectivity-Enhancing Mutations of Conotoxins for Nicotinic Acetylcholine Receptors Can Be Predicted Using Accurate Free-Energy Calculations

Nicotinic acetylcholine receptor (nAChR) subtypes are key drug targets, but it is challenging to pharmacologically differentiate between them because of their highly similar sequence identities. Furthermore, α-conotoxins (α-CTXs) are naturally selective and competitive antagonists for nAChRs and hold great potential for treating nAChR disorders. Identifying selectivity-enhancing mutations is the chief aim of most α-CTX mutagenesis studies, although doing so with traditional docking methods is difficult due to the lack of α-CTX/nAChR crystal structures. Here, we use homology modeling to predict the structures of α-CTXs bound to two nearly identical nAChR subtypes, α3β2 and α3β4, and use free-energy perturbation (FEP) to re-predict the relative potency and selectivity of α-CTX mutants at these subtypes. First, we use three available crystal structures of the nAChR homologue, acetylcholine-binding protein (AChBP), and re-predict the relative affinities of twenty point mutations made to the α-CTXs LvIA, LsIA, and GIC, with an overall root mean square error (RMSE) of 1.08 ± 0.15 kcal/mol and an R² of 0.62, equivalent to experimental uncertainty. We then use AChBP as a template for α3β2 and α3β4 nAChR homology models bound to the α-CTX LvIA and re-predict the potencies of eleven point mutations at both subtypes, with an overall RMSE of 0.85 ± 0.08 kcal/mol and an R² of 0.49. This is significantly better than the widely used molecular mechanics—generalized born/surface area (MM-GB/SA) method, which gives an RMSE of 1.96 ± 0.24 kcal/mol and an R² of 0.06 on the same test set. Next, we demonstrate that FEP accurately classifies α3β2 nAChR selective LvIA mutants while MM-GB/SA does not. Finally, we use FEP to perform an exhaustive amino acid mutational scan of LvIA and predict fifty-two mutations of LvIA to have greater than 100X selectivity for the α3β2 nAChR. Our results demonstrate the FEP is well-suited to accurately predict potency- and selectivity-enhancing mutations of α-CTXs for nAChRs and to identify alternative strategies for developing selective α-CTXs.     

An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people

Rare genetic variants contribute to complex disease risk; however, the abundance of rare variants in human populations remains unknown. We explored this spectrum of variation by sequencing 202 genes encoding drug targets in 14,002 individuals. We find rare variants are abundant (1 every 17 bases) and geographically localized, so that even with large sample sizes, rare variant catalogs will be largely incomplete. We used the observed patterns of variation to estimate population growth parameters, the proportion of variants in a given frequency class that are putatively deleterious, and mutation rates for each gene. We conclude that because of rapid population growth and weak purifying selection, human populations harbor an abundance of rare variants, many of which are deleterious and have relevance to understanding disease risk.     

Watching vibrational energy transfer in liquids with atomic spatial resolution

Ultrafast spectroscopy was used to study vibrational energy transfer between vibrational reporter groups on different parts of a molecule in a liquid. When OH stretching vibrations of different alcohols were excited by mid-infrared laser pulses, vibrational energy was observed to move through intervening CH2 or CH groups, taking steps up and down in energy, ending up at terminal CH3 groups. For each additional CH2 group in the path between OH and CH3, the time for vibrational energy transfer increased by about 0.4 picosecond.     

Theodor Hellbrügge: 85 years of age – Ad multos transannos, sanos, fortunatos et beatos

We honor Theo Hellbrügge's acclaimed endeavors in the rehabilitation, or rather the prehabilitation of handicapped children. So far, he has focused on obvious handicaps, and we trust that he will include concern for everybody's silent handicaps in the future by screening for abnormal variability inside the physiological range. Therein, we introduce cis- and trans-years, components of transdisciplinary spectra that are novel for biology and also in part for physics. These components have periods, respectively, shorter and longer than the calendar year, with a counterpart in magnetoperiodism. Transyears characterize indices of geomagnetic activity and the solar wind's speed and proton density. They are detected, alone or together with circannuals, in physiology as well as in pathology, as illustrated for sudden cardiac death and myocardial infarction, a finding calling for similar studies in sudden infant death syndrome (SIDS). As transyears can beat with circannuals, and depend on local factors, their systematic mapping in space and time by transdisciplinary chronomics may serve a better understanding of their putative influence upon the circadian system. Longitudinal monitoring of blood pressure and heart rate detects chronome alterations underlying cardiovascular disease risk, such as that of myocardial infarction and sudden cardiac death. The challenge is to intervene in a timely fashion, preferably at birth, an opportunity for pediatricians in Theo Hellbrügge's footsteps.     

Insights into the Variation in Bioactivities of Closely Related Streptomyces Strains from Marine Sediments of the Visayan Sea against ESKAPE and Ovarian Cancer

Marine sediments host diverse actinomycetes that serve as a source of new natural products to combat infectious diseases and cancer. Here, we report the biodiversity, bioactivities against ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) and ovarian cancer, and metabolites variation among culturable actinomycetes isolated from the marine sediments of Visayan Sea, Philippines. We identified 15 Streptomyces species based on a 16S rRNA gene sequence analysis. The crude extracts of 10 Streptomyces species have inhibited the growth of ESKAPE pathogens with minimum inhibitory concentration (MIC) values ranging from 0.312 mg/mL to 20 mg/mL depending on the strain and pathogens targeted. Additionally, ten crude extracts have antiproliferative activity against A2780 human ovarian carcinoma at 2 mg/mL. To highlight, we observed that four phylogenetically identical Streptomyces albogriseolus strains demonstrated variation in antibiotic and anticancer activities. These strains harbored type I and II polyketide synthase (PKS) and non-ribosomal synthetase (NRPS) genes in their genomes, implying that their bioactivity is independent of the polymerase chain reaction (PCR)-detected bio-synthetic gene clusters (BGCs) in this study. Metabolite profiling revealed that the taxonomically identical strains produced core and strain-specific metabolites. Thus, the chemical diversity among these strains influences the variation observed in their biological activities. This study expanded our knowledge on the potential of marine-derived Streptomyces residing from the unexplored regions of the Visayan Sea as a source of small molecules against ESKAPE pathogens and cancer. It also highlights that Streptomyces species strains produce unique strain-specific secondary metabolites; thus, offering new chemical space for natural product discovery.     

Inversions and gene order shuffling in Anopheles gambiae and A. funestus

In tropical Africa, Anopheles funestus is one of the three most important malaria vectors. We physically mapped 157 A. funestus complementary DNAs (cDNAs) to the polytene chromosomes of this species. Sequences of the cDNAs were mapped in silico to the A. gambiae genome as part of a comparative genomic study of synteny, gene order, and sequence conservation between A. funestus and A. gambiae. These species are in the same subgenus and diverged about as recently as humans and chimpanzees. Despite nearly perfect preservation of synteny, we found substantial shuffling of gene order along corresponding chromosome arms. Since the divergence of these species, at least 70 chromosomal inversions have been fixed, the highest rate of rearrangement of any eukaryote studied to date. The high incidence of paracentric inversions and limited colinearity suggests that locating genes in one anopheline species based on gene order in another may be limited to closely related taxa.     

Introgressive hybridization between native and non‐local steelhead (Oncorhynchus mykiss) of hatchery origin

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