Development of a Prototype System for Archiving Integrative/Hybrid Structure Models of Biological Macromolecules

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Immunochemical comparison of membrane-associated and secreted arabinogalactan-proteins in rice and carrot

Arabinogalactan-proteins (AGPs) occurring in suspension-cultured rice (Oryza saliva L.) cells, their conditioned medium and at the rice root apex were investigated using monoclonal antibodies and the AGP-binding -glucosyl Yariv reagent ( GlcY). A monoclonal antibody, LM2, was generated that recognized an acidic carbohydrate epitope common to two soluble AGPs occurring in the conditioned medium of proliferating rice cells, membrane-associated AGPs (rmAGP) in the cultured cells and two AGPs at the rice root apex. In addition, LM2 recognized AGPs secreted by suspensioncultured carrot (Daucus carota L.) cells. The two AGPs of the rice culture medium, srAGP1 and srAGP2, were discriminated by their mobilities during sodium dodecyl sulfate-polyacrylamide gel electrophoresis, reaction with GlcY, the presence of arabinogalactan epitopes and anion-exchange chromatography. The association of rmAGP with the plasma membrane was investigated by Triton-X-114/aqueous partitioning of both microsomal and plasma-membrane preparations and rmAGP was found to partition into the detergent phase, indicating that AGPs are hydrophobic plasma-membrane proteins in rice. This was in contrast to plasma-membrane AGPs of suspension-cultured carrot cells that partitioned into the aqueous phase. At the rice root apex most of the AGP was associated with the microsomal fraction and also partitioned into the detergent phase, although a distinct highmolecular-mass AGP entered the aqueous phase.Abbreviations AGP arabinogalactan-protein - GlcY -glucosyl Yariv reagent - ELISA enzyme-linked immunosorbent assay We gratefully acknowledge support from the Leverhulme Trust, the UK Biotechnology and Biological Sciences Research Council and the Royal Society.     

Photosynthesis and respiration in Alocasia macrorrhiza following transfers to high and low light

Summary Photosynthetic capacities and respiration rates of Alocasia macrorrhiza leaves were measured for 4 weeks following reciprocal transfers between high (20% of full sun) and low (1% of full sun) light environments. Photosynthetic capacities and respiration rates of mature, high-light leaves were 1.7 and 4.5 times those of low-light leaves, respectively. Following transfer, respiration rates adjusted within 1 week to those characteristic of plants grown in the new environment. By contrast, photosynthetic capacities either did not adjust or changed only slowly following transfer. Most of the difference in respiration between high- and low-light leaves was related to the carbohydrate status as determined by the daily PFD and little was directly related to the maintenance costs of the photosynthetic apparatus. Leaf construction cost was directly proportional to maximum photosynthetic capacity. Consequently, although daily carbon gain per unit leaf area was the same for low-light and high to low-light transferred plants within a week after transfer, the carbon return per unit of carbon investment in the leaves remained lower in the high to low transfer plants throughout the 4 week measurement period. Conversely, in high-light, the low leaf construction cost of the low to high-light transferred plants resulted in carbon gain per unit investment just as high as that of the high-light plants.     

Meta-Fish-Lib: A generalised,dynamic DNA reference library pipeline for metabarcoding of fishes

The accuracy and reliability of DNA metabarcoding analyses depend on the breadth and quality of the reference libraries that underpin them. However, there are limited options available to obtain and curate the huge volumes of sequence data that are available on public repositories such as NCBI and BOLD. Here, we provide a pipeline to download, clean and annotate mitochondrial DNA sequence data for a given list of fish species. Features of this pipeline include (a) support for multiple metabarcode markers; (b) searches on species synonyms and taxonomic name validation; (c) phylogeny assisted quality control for identification and removal of misannotated sequences; (d) automatically generated coverage reports for each new GenBank release update; and (e) citable, versioned DOIs. As an example we provide a ready-to-use curated reference library for the marine and freshwater fishes of the U.K. To augment this reference library for environmental DNA metabarcoding specifically, we generated 241 new MiFish-12S sequences for 88 U.K. marine species, and make available new primer sets useful for sequencing these. This brings the coverage of common U.K. species for the MiFish-12S fragment to 93%, opening new avenues for scaling up fish metabarcoding across wide spatial gradients. The Meta-Fish-Lib reference library and pipeline is hosted at https://github.com/genner-lab/meta-fish-lib .     

Climate change alters temporal dynamics of alpine soil microbial functioning and biogeochemical cycling via earlier snowmelt

Soil microbial communities regulate global biogeochemical cycles and respond rapidly to changing environmental conditions. However, understanding how soil microbial communities respond to climate change, and how this influences biogeochemical cycles, remains a major challenge. This is especially pertinent in alpine regions where climate change is taking place at double the rate of the global average, with large reductions in snow cover and earlier spring snowmelt expected as a consequence. Here, we show that spring snowmelt triggers an abrupt transition in the composition of soil microbial communities of alpine grassland that is closely linked to shifts in soil microbial functioning and biogeochemical pools and fluxes. Further, by experimentally manipulating snow cover we show that this abrupt seasonal transition in wide-ranging microbial and biogeochemical soil properties is advanced by earlier snowmelt. Preceding winter conditions did not change the processes that take place during snowmelt. Our findings emphasise the importance of seasonal dynamics for soil microbial communities and the biogeochemical cycles that they regulate. Moreover, our findings suggest that earlier spring snowmelt due to climate change will have far reaching consequences for microbial communities and nutrient cycling in these globally widespread alpine ecosystems.Subject terms: Metagenomics, Climate-change ecology, Microbial ecology, Biogeochemistry, Soil microbiology     

Predictors of Remission in Depression to Individual and Combined Treatments (PReDICT): Study Protocol for a Randomized Controlled Trial

ABSTRACT: BACKGROUND: Limited controlled data exist to guide treatment choices for clinicians caring for patients with major depressive disorder (MDD). Although many putative predictors of treatment response have been reported, most were identified through retrospective analyses of existing datasets and very few have been replicated in a manner that can impact clinical practice. One major confound in previous studies examining predictors of treatment response is the patient's treatment history, which may affect both the predictor of interest and treatment outcomes. Moreover, prior treatment history provides an important source of selection bias, thereby limiting generalizability. Consequently, we initiated a randomized clinical trial designed to identify factors that moderate response to three treatments for MDD among patients never treated previously for the condition. METHODS: Treatment-naive adults aged 18-65 years with moderate-to-severe, non-psychotic MDD are randomized equally to one of three 12-week treatment arms: 1) cognitive behavior therapy (CBT, 16 sessions), 2) duloxetine (30-60 mg/d), or 3) escitalopram (10-20 mg/d). Prior to randomization, patients undergo multiple assessments, including resting state functional magnetic resonance imaging (fMRI), immune markers, DNA and gene expression products, and dexamethasone-corticotropin releasing hormone (Dex/CRH) testing. Prior to or shortly after randomization, patients also complete a comprehensive personality assessment. Repeat assessment of the biological measures (fMRI, immune markers, and gene expression products) occur at an early time-point in treatment, and upon completion of 12-week treatment, when a a second Dex/CRH test is also conducted, Patients remitting by the end of this acute treatment phase are then eligible to enter a 21-month follow-up phase, with quarterly visits to monitor for recurrence. Non-remitters are offered augmentation treatment for a second 12-week course of treatment, during which they receive a combination of CBT and antidepressant medication. Predictors of the primary outcome, remission, will be identified for overall and treatment-specific effects, and a statistical model incorporating multiple predictors will be developed to predict outcomes. DISCUSSION: The PReDICT study's evaluation of biological, psychological, and clinical factors that may differentially impact treatment outcomes represents a sizeable step toward developing personalized treatments for MDD. Identified predictors should help guide the selection of initial treatments, and identify those patients most vulnerable to recurrence, who thus warrant maintenance or combination treatments to achieve and maintain wellness.     

When to start and when to stop: Effects of climate on breeding in a multi‐brooded songbird

Climate warming has been shown to affect the timing of the onset of breeding of many bird species across the world. However, for multi‐brooded species, climate may also affect the timing of the end of the breeding season, and hence also its duration, and these effects may have consequences for fitness. We used 28 years of field data to investigate the links between climate, timing of breeding, and breeding success in a cooperatively breeding passerine, the superb fairy‐wren (Malurus cyaneus). This multi‐brooded species from southeastern Australia has a long breeding season and high variation in phenology between individuals. By applying a “sliding window” approach, we found that higher minimum temperatures in early spring resulted in an earlier start and a longer duration of breeding, whereas less rainfall and more heatwaves (days > 29°C) in late summer resulted in an earlier end and a shorter duration of breeding. Using a hurdle model analysis, we found that earlier start dates did not predict whether or not females produced any young in a season. However, for successful females who produced at least one young, earlier start dates were associated with higher numbers of young produced in a season. Earlier end dates were associated with a higher probability of producing at least one young, presumably because unsuccessful females kept trying when others had ceased. Despite larger scale trends in climate, climate variables in the windows relevant to this species’ phenology did not change across years, and there were no temporal trends in phenology during our study period. Our results illustrate a scenario in which higher temperatures advanced both start and end dates of individuals’ breeding seasons, but did not generate an overall temporal shift in breeding times. They also suggest that the complexity of selection pressures on breeding phenology in multi‐brooded species may have been underestimated.     

Seasonal variability in the grazing potential of the invasive amphipod Gammarus tigrinus and the native amphipod Gammarus salinus (Amphipoda: Crustacea) in the northern Baltic Sea

Mesograzers are known to reduce the biomass of their host plant and modify the structure of the whole macrophyte community in many ecosystems. Thus, the introduction of an efficient mesograzer may destabilize macrophyte community and also affect the native grazers. We estimated how large proportion of macrophyte production are consumed by the alien gammarid G. tigrinus and the native gammarid G. salinus in the species poor ecosystem of the northern Baltic Sea. We analysed whether G. tigrinus consumes different diet as the native G. salinus and whether the effect of G. tigrinus on the survival of the native G. salinus is macrophyte species specific. Grazing experiments showed that there was a clear difference in the grazing rates of gammarids among the studied macrophyte species in summer and autumn but not in spring. The grazing rates were significantly higher in the prevailing macrophyte Pilayella littoralis as compared to other macrophytes. The grazing was inversely related to the diurnal net photosynthetic values of macrophytes. The gammarid amphipods potentially removed only a minor part of plant primary production except for summer and autumn when grazing of a few perennial species exceeded macrophyte production. Macrophyte species and presence of G. salinus had no effect on the survival of G. tigrinus. The presence of G. tigrinus, however, reduced the survival of the native gammarids within P. littoralis in summer. To conclude it is likely that both native and alien gammarid amphipods do not exert significant pressure on the macroalgal communities in the northern Baltic Sea. Competitive interactions between G. tigrinus and G. salinus within the prevailing macrophyte P. littoralis is the likely explanation of the decline of the native gammarid amphipods after the establishment of G. tigrinus in the northern Baltic Sea.