Repeat disturbances have cumulative impacts on stream communities

This project was supported by the USDA National Institute of Food and Agriculture, Hatch (or McIntire‐Stennis, Animal Health, etc.) project number #ME0‐21607 through the Maine Agricultural & Forest Experiment Station. Maine Agricultural and Forest Experiment Station Publication Number 3653.1. Climate change has altered disturbance regimes in many ecosystems, and predictions show that these trends are likely to continue. The frequency of disturbance events plays a particularly important role in communities by selecting for disturbance-tolerant taxa. 2. However, ecologists have yet to disentangle the influence of disturbance frequency per se and time since last disturbance, because more frequently disturbed systems have also usually been disturbed more recently. Our understanding of the effects of repeated disturbances is therefore confounded by differences in successional processes. 3. We used in-situ stream mesocosms to isolate and examine the effect of disturbance frequency on community composition. We applied substrate moving disturbances at five frequencies, with the last disturbance occurring on the same day across all treatments. Communities were then sampled after a recovery period of 9 days. 4. Macroinvertebrate community composition reflected the gradient of disturbance frequency driven by differential vulnerability of taxa to disturbance. Diversity metrics, including family-level richness, decreased, reflecting a likely loss of functional diversity with increasing disturbance frequency. In contrast, overall abundance was unaffected by disturbance frequency as rapid recovery of the dominant taxon compensated for strong negative responses of disturbance-vulnerable taxa. 5. We show that cumulative effects of repeated disturbances?not just the time communities have had to recover before sampling?alter communities, especially by disproportionately affecting rare taxa. Thus, the timing of past disturbances can have knock-on effects that determine how a system will respond to further change.Publisher PDFPeer reviewe

Staphylococcal Cassette Chromosome mec (SCCmec) Typing of Methicillin-Resistant Staphylococcus Aureus Isolates Collected from Clinical Samples in the Sistan Region, Irann the Sistan region

Background: Today, the emerged methicillin-resistant Staphylococcus aureus (MRSA) is considered as one of the most important pathogens involved in hospital-acquired infection. Typing of bacteria is an important part of epidemiological studies on nosocomial infections. In this study, Staphylococcal Cassette Chromosome mec (SCCmec) analysis was used to identify types and differentiates MRSA clinical isolates collected from clinical samples in Sistan Region, Iran. Methods: In this study, seventy-two MRSA isolates were obtained and the presence of SCCmec cassette chromosome mec (SCCmec) types was investigated using multiplex polymerase chain reaction (PCR) technique. Results: Of 72 tested MRSA isolates, 5% had SCCmec type I, 45% SCCmec type II, 30% SCCmec type III, and 20% SCCmec type V. Conclusion: According to the results of this study, SCCmec types II and III, which are the characteristics of hospital-acquired MRSA, were the most dominant types. Keywords: Methicillin-resistant staphylococcus aureus, Hospital infections, mecA protein, Staphylococcus aureu

Population genomic analysis reveals that homoploid hybrid speciation can be a lengthy process

This work was supported by grants from National key research and development program (2017YFC0505203), National Natural Science Foundation of China (grant numbers 31590821, 31670665, 91731301), National Key Project for Basic Research (2014CB954100), CAS “Light of West China” Program and Graduate Student’s Research and Innovation Fund of Sichuan University (2018YJSY007).An increasing number of species are thought to have originated by homoploid hybrid speciation (HHS), but in only a handful of cases are details of the process known. A previous study indicated that Picea purpurea, a conifer in the Qinghai–Tibet Plateau (QTP), originated through HHS from P. likiangensis and P. wilsonii. To investigate this origin in more detail, we analysed transcriptome data for 114 individuals collected from 34 populations of the three Picea species from their core distributions in the QTP. Phylogenetic, principal component and admixture analyses of nuclear SNPs showed the species to be delimited genetically and that P. purpurea was admixed with approximately 60% of its ancestry derived from P. wilsonii and 40% from P. likiangensis. Coalescent simulations revealed the best‐fitting model of origin involved formation of an intermediate hybrid lineage between P. likiangensis and P. wilsonii approximately 6 million years ago (mya), which backcrossed to P. wilsonii to form P. purpurea approximately one mya. The intermediate hybrid lineage no longer exists and is referred to as a “ghost” lineage. Our study emphasizes the power of population genomic analysis combined with coalescent analysis for reconstructing the stages involved in the origin of a homoploid hybrid species over an extended period. In contrast to other studies, we show that these stages can in some instances span a relatively long period of evolutionary time.PostprintPeer reviewe

Identification of Carnitine Transporter CT1 Binding Protein Lin-7 in Nervous System

_L-Carnitine is an essential component of mitochondrial fatty acid b-oxidation in the muscle and may control the acetyl moiety levels in the brain for acetylcholine synthesis. Carnitine transporter 1(CT1)is the high affinity _L-carnitine transporter whose localization was observed in the kidney, testis, liver, skeletal muscle and brain. To clarify the molecular mechanism of carnitine transport, we sought to find the interacting protein that may be related to the transport function of CT1. Using the intracellular C-terminal region of rat CT1 containing PDZ(PSD95/DLG/ZO-1)motif as bait, we performed the yeast two-hybrid screening against rat brain cDNA library. Thirty two positive clones were obtained from the 2.7×10^7 clones screened. One of them was PDZ domain-containing protein Lin-7. We found that Lin-7 interacts specifically with C-termini of CT1:deletion and mutation of the CT1 C-terminal PDZ-motif abolished the interaction with Lin-7 in the yeast two-hybrid assay. In addition, a PDZ domain within Lin-7 associates with the CT1 C-terminal. The association of CT1 with Lin-7 enhanced _L-carnitine transport activities in HEK293 cells although there is no statistical significance. Coexpression of Lin-7 and CT1 is identified in motor neurons of the spinal cord ventral horn together with Lin-2, a binding partner of Lin-7 known to assemble proteins involved in synaptic vesicle exocytosis and synaptic junctions. Therefore, Lin-7 interacts with CT1 and may regulate their subcellular distribution or function in central nervous system

Airway Expression of Smad7, a TGF-β-inducible Inhibitory Molecule of TGF-β Signaling, Decreases after Repeated Airway Antigen Challenges

Transforming growth factor-β (TGF-β) is a profibrogenic cytokine that is involved in airway remodeling largely associated with chronic asthma. Accordingly, regulators of TGF-β activity could also play some role in airway remodeling in asthma. In this study, we investigated expression of Smad 7, a major intracellular inhibitor of TGF-β signaling, in the airways of mouse models of acute and chronic asthma. Sensitized, repeatedly (14 days) ovalbumin (OVA)-inhaled BALB/c mice exhibited evidence of airway remodeling including prominent subepithelial fibrosis associated with airway hyperresponsiveness (AHR) and airway inflammation (chronic asthma model) whereas sensitized, shortly OVA-inhaled BALB/c mice showed only AHR and airway inflammation (acute asthma model). Immunohistochemical analysis showed that Smad 7 immunoreactivity in the airways was increased after the development of acute and chronic asthma models and mainly detected in bronchial epithelial cells. Interestingly, Smad 7 immunoreactivity was significantly less in the airways of chronic asthma model than in those of acute asthma model, which was also confirmed by real-time PCR analysis of Smad 7. In consistent with decreased Smad 7 expression in the airways of chronic asthma model, phosphorylation of Smad 2, a marker of active TGF-β signaling, was increased in bronchial epithelial cells of chronic asthma model when compared with acute asthma model. These results suggest that decreased Smad 7 expression and Smad 2 upregulation in bronchial epithelial cells might result in increased TGF-β activity and contribute to the development of airway remodeling seen in chronic asthma

Mapping the H2 resistance effective against Globodera pallida pathotype Pa1 in tetraploid potato

This work was supported by the Rural & Environment Science & Analytical Services Division of the Scottish Government, the BBSRC, through the joint projects CRF/2009/SCRI/SOP 0929, BB/L008025/1 and BB/K018299/1. Additional funding was obtained through the James Hutton Institute SEEDCORN initiative, AHDB Potato, the Perry Foundation and The Felix Cobbold Trust. Amanpreet Kaur was supported by the Commonwealth Scholarship Commission through a Commonwealth split-site Ph.D. grant.Key message: The nematode resistance gene H2 was mapped to the distal end of chromosome 5 in tetraploid potato. The H2 resistance gene, introduced into cultivated potatoes from the wild diploid species Solanum multidissectum, confers a high level of resistance to the Pa1 pathotype of the potato cyst nematode Globodera pallida. A cross between tetraploid H2-containing breeding clone P55/7 and susceptible potato variety Picasso yielded an F1 population that segregated approximately 1:1 for the resistance phenotype, which is consistent with a single dominant gene in a simplex configuration. Using genome reduction methodologies RenSeq and GenSeq, the segregating F1 population enabled the genetic characterisation of the resistance through a bulked segregant analysis. A diagnostic RenSeq analysis of the parents confirmed that the resistance in P55/7 cannot be explained by previously characterised resistance genes. Only the variety Picasso contained functionally characterised disease resistance genes Rpi-R1, Rpi-R3a, Rpi-R3b variant, Gpa2 and Rx, which was independently confirmed through effector vacuum infiltration assays. RenSeq and GenSeq independently identified sequence polymorphisms linked to the H2 resistance on the top end of potato chromosome 5. Allele-specific KASP markers further defined the locus containing the H2 gene to a 4.7 Mb interval on the distal short arm of potato chromosome 5 and to positions that correspond to 1.4 MB and 6.1 MB in the potato reference genome.Publisher PDFPeer reviewe

Cellular Hypertrophy and Increased Susceptibility to Spontaneous Calcium-Release of Rat Left Atrial Myocytes Due to Elevated Afterload

Atrial remodeling due to elevated arterial pressure predisposes the heart to atrial fibrillation (AF). Although abnormal sarcoplasmic reticulum (SR) function has been associated with AF, there is little information on the effects of elevated afterload on atrial Ca2+-handling. We investigated the effects of ascending aortic banding (AoB) on Ca2+-handling in rat isolated atrial myocytes in comparison to age-matched sham-operated animals (Sham). Myocytes were either labelled for ryanodine receptor (RyR) or loaded with fluo-3-AM and imaged by confocal microscopy. AoB myocytes were hypertrophied in comparison to Sham controls (P<0.0001). RyR labeling was localized to the z-lines and to the cell edge. There were no differences between AoB and Sham in the intensity or pattern of RyR-staining. In both AoB and Sham, electrical stimulation evoked robust SR Ca2+-release at the cell edge whereas Ca2+ transients at the cell center were much smaller. Western blotting showed a decreased L-type Ca channel expression but no significant changes in RyR or RyR phosphorylation or in expression of Na+/Ca2+ exchanger, SR Ca2+ ATPase or phospholamban. Mathematical modeling indicated that [Ca2+]i transients at the cell center were accounted for by simple centripetal diffusion of Ca2+ released at the cell edge. In contrast, caffeine (10 mM) induced Ca2+ release was uniform across the cell. The caffeine-induced transient was smaller in AoB than in Sham, suggesting a reduced SR Ca2+-load in hypertrophied cells. There were no significant differences between AoB and Sham cells in the rate of Ca2+ extrusion during recovery of electrically-stimulated or caffeine-induced transients. The incidence and frequency of spontaneous Ca2+-transients following rapid-pacing (4 Hz) was greater in AoB than in Sham myocytes. In conclusion, elevated afterload causes cellular hypertrophy and remodeling of atrial SR Ca2+-release

Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake.

The genomic causes and effects of divergent ecological selection during speciation are still poorly understood. Here we report the discovery and detailed characterization of early-stage adaptive divergence of two cichlid fish ecomorphs in a small (700 meters in diameter) isolated crater lake in Tanzania. The ecomorphs differ in depth preference, male breeding color, body shape, diet, and trophic morphology. With whole-genome sequences of 146 fish, we identified 98 clearly demarcated genomic "islands" of high differentiation and demonstrated the association of genotypes across these islands with divergent mate preferences. The islands contain candidate adaptive genes enriched for functions in sensory perception (including rhodopsin and other twilight-vision-associated genes), hormone signaling, and morphogenesis. Our study suggests mechanisms and genomic regions that may play a role in the closely related mega-radiation of Lake Malawi.The work was funded by Royal Society-Leverhulme Trust Africa Awards AA100023 and AA130107 (M.J.G., B.P.N. and G.F.T.), a Wellcome Trust PhD studentship grant 097677/Z/11/Z (M.M.), Wellcome Trust grant WT098051 (S.S. and R.D.), Wellcome Trust and Cancer Research UK core support and a Wellcome Trust Senior Investigator Award (E.A.M.), a Leverhulme Trust Research Fellowship RF-2014-686 (M.J.G.), a University of Bristol Research Committee award (M.G.), a Bangor University Anniversary PhD studentship (to A.M.T.) and a Fisheries Society of the British Isles award (G.F.T.). Raw sequencing reads are in the SRA nucleotide archive: RAD sequencing (BioProject: PRJNA286304; accessions SAMN03768857 to SAMN03768912) and whole genome sequencing (BioProject PRJEB1254: sample accessions listed in Table S16). The RAD based phylogeny and alignments have been deposited in TreeBase (TB2:S18241). Whole genome variant calls in the VCF format, phylogenetic trees, and primer sequences for Sequenom genotyping are available from the Dryad Digital Repository (http://dx.doi.org/10.5061/dryad.770mc). RD declares his interests as a founder and non-executive director of Congenica Ltd., that he owns stock in Illumina from previous consulting, and is a scientific advisory board member of Dovetail Inc. We thank R. Schley for generating pharyngeal jaw data; S. Mzighani, J. Kihedu and staff of the Tanzanian Fisheries Research Institute for logistical support; A. Smith, H. Sungani, A. Shechonge, P. Parsons, J. Swanstrom, G. Cooke and J. Bridle for contributions to sampling and aquarium maintenance, the Sanger Institute sequencing core for DNA sequencing and Dr. H. Imai (Kyoto University) for the use of spectrometer in his laboratory.This is the author accepted manuscript. The final version is available from AAAS via http://dx.doi.org/10.1126/science.aac992

Revealing the Mechanism for Covalent Inhibition of Glycoside Hydrolases by Carbasugars at an Atomic Level

Mechanism-based glycoside hydrolase inhibitors are carbohydrate analogs that mimic the natural substrate’s structure. Their covalent bond formation with the glycoside hydrolase makes these compounds excellent tools for chemical biology and potential drug candidates. Here we report the synthesis of cyclohexene-based α-galactopyranoside mimics and the kinetic and structural characterization of their inhibitory activity toward an α-galactosidase from Thermotoga maritima (TmGalA). By solving the structures of several enzyme-bound species during mechanism-based covalent inhibition of TmGalA, we show that the Michaelis complexes for intact inhibitor and product have half-chair (2H3) conformations for the cyclohexene fragment, while the covalently linked intermediate adopts a flattened half-chair (2H3) conformation. Hybrid QM/MM calculations confirm the structural and electronic properties of the enzyme-bound species and provide insight into key interactions in the enzyme-active site. These insights should stimulate the design of mechanism-based glycoside hydrolase inhibitors with tailored chemical properties

Roles of Dicer-Like Proteins 2 and 4 in Intra- and Intercellular Antiviral Silencing

RNA silencing is an innate antiviral mechanism conserved in organisms across kingdoms. Such cellular defense involves DICER or DICER-LIKEs (DCLs) that process viral RNAs into small interfering (vsi)RNAs. Plants encode four DCLs which play diverse roles in cell-autonomous virus-induced RNA silencing (known as VIGS) against viral invasion. However, intracellular VIGS can spread between cells, and the genetic basis and involvement of vsiRNAs in non-cell autonomous VIGS remains poorly understood. Here using GFP as a reporter gene together with a suite of DCL RNAi transgenic lines, we show that in addition to well-established activities of DCLs in intracellular VIGS and vsiRNA biogenesis, DCL4 inhibits intercellular VIGS whilst DCL2 is required, likely along with DCL2-processed/dependent vsiRNAs and their precursor RNAs, for efficient VIGS trafficking from epidermal to adjacent cells. DCL4 imposed an epistatic effect on DCL2 to impede cell-to-cell spread of VIGS. Our results demonstrate previously unknown functions for DCL2 and DCL4 which may form a dual defensive frontier for intra- and intercellular silencing to double-protect cells from virus infection in Nicotiana benthamiana