Search

Root exudates are well-known 'labile' sources of soil carbon that can prime microbial activity. Recent investigations suggest that the stability of labile carbon inputs in soil mostly depends upon the physical, chemical, and biological properties of the surroundings. Here, we propose that, in some ecosystems, such as forests and grasslands, root exudates can function as a source of soil organic carbon (SOC) that can be stabilized through various mechanisms leading to long-term sequestration. Increasing soil carbon sequestration is important for capturing atmospheric CO2 and combating climate change issues. Thus, there is an urgent need to preserve existing ecosystems and to adopt strategies such as afforestation, reforestation, and establishment of artificial grasslands to foster carbon sequestration through higher root exudate inputs in the soil.

The type species of the assimineid genus Acmella W.T. Blanford, 1869 is Cyclostoma tersum Benson, 1853, originally described from ‘Musmai’ [Mawsmai], Meghalaya, Northeast India. No specimens from B...

Sterility or subfertility of male hybrid offspring is commonly observed. This phenomenon contributes to reproductive barriers between the parental populations, an early step in the process of speciation. One frequent cause of such infertility is a failure of proper chromosome pairing during male meiosis. In subspecies of the house mouse, the likelihood of successful chromosome synapsis is improved by the binding of the histone methyltransferase PRDM9 to both chromosome homologs at matching positions. Using genetic manipulation, we altered PRDM9 binding to occur more often at matched sites, and find that chromosome pairing defects can be rescued, not only in an intersubspecific cross, but also between distinct species. Using different engineered variants, we demonstrate a quantitative link between the degree of matched homolog binding, chromosome synapsis, and rescue of fertility in hybrids between Mus musculus and Mus spretus. The resulting partial restoration of fertility reveals additional mechanisms at play that act to lock-in the reproductive isolation between these two species.

For the production and rederivation of mouse strains, pseudopregnant female mice are used for embryo transfer and serve as surrogate mothers to support embryo development to term. Vasectomized males are commonly used to render pseudopregnancy in females, generated by surgical procedures associated with considerable pain and discomfort. Genetically modified mouse strains with a sterility phenotype provide a non-surgical replacement and represent an important application of the 3Rs (Replacement, Reduction, Refinement). However, the maintenance of such genetically modified mouse strains requires extensive breeding and genotyping procedures, which are regulated procedures under national legislation. As an alternative, we have explored the use of sterile male hybrids that result when two wild-type mouse subspecies, Mus musculus musculus and Mus musculus domesticus, interbreed. We find the male STUSB6F1 hybrid, resulting from the mating of female STUS/Fore with male C57BL/6J, ideally suited and demonstrate that its performance for the production of oviduct and uterine transfer recipients is indistinguishable when compared to surgically vasectomized mice. The use of these sterile hybrids avoids the necessity for surgical procedures or the breeding of sterile genetically modified lines and can be generated by the simple mating of two wild-type laboratory strains—a non-regulated procedure. Furthermore, in contrast with the breeding of genetically sterile mice, all male offspring are sterile and suitable for the generation of pseudopregnancy, allowing their efficient production with minimal breeding pairs.

Skin lesions are commonly reported in farmed salmonids. Chinook salmon (Oncorhynchus tshawytscha), introduced from California USA, is the only salmonid species commercially farmed in New Zealand, although trout are cultured for release by Fish and Game New Zealand. There are several farming areas in New Zealand, including Marlborough Sounds, Canterbury and Stewart Island. While the industry has not been affected by any of the major production diseases seen internationally, skin lesions have been recorded with an increase in prevalence from 2012 onwards in the Marlborough Sounds and were associated with elevated summer mortalities on farms in 2015. Here we are proposing case definitions for different types of skin lesions for future monitoring and research. Based on our current understanding of the above skin conditions, we developed case definitions for spots, spreading spots, ulcerated spreading spots and Regular Outline Flank Ulcers defining a positive case for three study units, including individual fish, pen/unit and farm.

Gramene (http://www.gramene.org), a knowledgebase founded on comparative functional analyses of genomic and pathway data for model plants and major crops, supports agricultural researchers worldwide. The resource is committed to open access and reproducible science based on the FAIR data principles. Since the last NAR update, we made nine releases; doubled the genome portal's content; expanded curated genes, pathways and expression sets; and implemented the Domain Informational Vocabulary Extraction (DIVE) algorithm for extracting gene function information from publications. The current release, #63 (October 2020), hosts 93 reference genomes—over 3.9 million genes in 122 947 families with orthologous and paralogous classifications. Plant Reactome portrays pathway networks using a combination of manual biocuration in rice (320 reference pathways) and orthology-based projections to 106 species. The Reactome platform facilitates comparison between reference and projected pathways, gene expression analyses and overlays of gene–gene interactions. Gramene integrates ontology-based protein structure–function annotation; information on genetic, epigenetic, expression, and phenotypic diversity; and gene functional annotations extracted from plant-focused journals using DIVE. We train plant researchers in biocuration of genes and pathways; host curated maize gene structures as tracks in the maize genome browser; and integrate curated rice genes and pathways in the Plant Reactome.

CRISPR/Cas9 machinery delivered as ribonucleoprotein (RNP) to the zygote has become a standard tool for the development of genetically modified mouse models. In recent years, a number of reports have demonstrated the effective delivery of CRISPR/Cas9 machinery via zygote electroporation as an alternative to the conventional delivery method of microinjection. In this study, we have performed side-by-side comparisons of the two RNP delivery methods across multiple gene loci and conclude that electroporation compares very favourably with conventional pronuclear microinjection, and report an improvement in mutagenesis efficiency when delivering CRISPR via electroporation for the generation of simple knock-in alleles using single-stranded oligodeoxynucleotide (ssODN) repair templates. In addition, we show that the efficiency of knock-in mutagenesis can be further increased by electroporation of embryos derived from Cas9-expressing donor females. The maternal supply of Cas9 to the zygote avoids the necessity to deliver the relatively large Cas9 protein, and high efficiency generation of both indel and knock-in allele can be achieved by electroporation of small single-guide RNAs and ssODN repair templates alone. Furthermore, electroporation, compared to microinjection, results in a higher rate of embryo survival and development. The method thus has the potential to reduce the number of animals used in the production of genetically modified mouse models.

Current commercial olive (Olea europaea) cultivars are susceptible to olive knot disease caused by Pseudomonas savastanoi pv. savastanoi. Here we report on the examination of the olive tree germplasm collection maintained at the USDA-ARS National Clonal Germplasm Repository (NCGR) in Winters, California for the incidence of olive knot disease. Over a two year period we evaluated olive knot disease incidence on 506 trees representing 144 unique accessions consisting of 104 named cultivars originating from the Mediterranean Basin, South America, and California, including several hybrids, and related subspecies e.g. Olea europaea ssp. cuspidata. All genotypes were replicated in four blocks with trees in these blocks ranging in age from 6 to 35 year old. The disease index was higher in 2014 (43.5%) than in 2013 (29.4%). The percentage of infection varied significantly (P

Research into the effects of soundscapes on aquaculture species in key production systems is sparse, despite potential impacts of sound on animal welfare and commercial yields. In the following study, 2 high-value global aquaculture species, whiteleg shrimp Litopenaeus vannamei and Atlantic salmon Salmo salar, were exposed to aquaculture production system soundscapes. For shrimp, sound recordings of a commercial recirculating aquaculture system (RAS) were played back at a sound pressure level (SPL) of 128 dB re 1 µPa, and for salmon, recordings from a commercial sea pen production system were played back at an SPL of 127 dB re 1 µPa for an 8 wk period. Effects of exposure on growth, survival, and indications of metabolic stress were measured as parameters of interest for aquaculture production. Mean growth performance and survival rates did not differ significantly between sound and control treatments for either species. Blood and haemolymph parameters from both species indicated no measurable change in metabolic status or stress levels. Slight, but non-significant, increases in total haemocyte count and, in particular, hyaline cell count were recorded in shrimp exposed to sound. Slight, but non-significant reductions in overall weight gain were recorded in sound-exposed salmon. Overall, the results indicate that sound exposure in current production systems does not negatively affect the early grow-out stage of these key species, either due to rapid habituation or higher hearing thresholds of hatchery-produced individuals, and that no measurable stress response occurs in sound-exposed animals. In future studies, response of the studied species to acute sound exposure and the response of earlier, and potentially more sensitive, life-stages will need to be determined to ensure optimal welfare and production performance.

RNA polymerase III (Pol III) promoters express short non-coding RNAs and have been adopted for expression of microRNA, interference RNA, and CRISPR single guide RNA (sgRNA). Vectors incorporating H1 and U6 Pol III promoters are being applied for therapeutic genome editing, including multiplexed CRISPR/Cas9 effects. We report a nucleosome-depleted, minimal U6 promoter, which when embedded within lentiviral long terminal repeat (LTR) regions, supports high level transcriptional activity. Furthermore, duplex minimal H1 & U6 promoters transcribed dual sgRNAs for simultaneous disruption of T cell receptor (TCR) and human leukocyte antigen (HLA) molecules, supporting efficient generation of ‘universal’ CAR T cells.

Background. Preclinical and observational evidence supports cancer prevention activity of non-steroidal anti-inflammatory drugs (NSAIDs) in the breast via suppression of prostaglandin E2 (PGE2) synthesis by cyclooxygenase-2 (COX2). Evidence includes linking of PGE2 to aromatase activity and estrogen synthesis in breast adipose tissue, as well as effects on collagen and breast density (BD). Methods. In an open-label trial, we evaluated the effect of the non-selective NSAID sulindac at 150 mg bid for 12 months on BD in 52 postmenopausal women taking adjuvant aromatase inhibitors (AIs) for breast cancer. BD was measured using a fat-water decomposition MRI based BD measure (MRD) previously shown to be more quantitative than mammographic density. A non-randomized observation cohort of 46 postmenopausal women on AI without NSAID use was conducted in parallel to assess the effect of AI on MRD over 12 months. Eligible participants were recruited at two study sites and included women with an intact, unaffected contralateral breast and BI-RADS ≥ 2. Each subject’s MRI_BD measures at baseline and at 6 and 12 months were included in linear mixed models for longitudinal data. Log-transformation was applied to the outcome of BD. Covariates included log-transformed baseline BD, time on AI, and baseline body mass index (BMI) and change in BMI. Breast tissue collagen fiber alignment for 30 women with paired breast biopsies, before and after 6 months on sulindac, was examined using Second-Harmonic Generation (SHG) microscopy and analysis of the distribution (histogram) of ‘straight’ fibers in three randomly selected areas of breast tissue. Straightness of individual fibers was calculated as the linear length of a fiber divided by the distance along the fiber. Results. Participants on sulindac intervention had a significant change in BD relative to baseline BD at 6 (p=0.05) and 12 months (p Citation Format: Patricia Thompson, Chuan Huang, Betsy Wertheim, Christina Preece, Jie Yang, Jessica Martinez, Denise Roe, Pavani Chalasani, Alison Stopeck. Sulindac reduces breast density and alters collagen alignment in patients on aromatase inhibitors [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr PD3-09.

Challenges to food security under conditions of global change are forcing us to increase global crop production. Focussing on belowground plant traits, especially root exudation, has great promise to meet this challenge. Root exudation is the release of a vast array of compounds into the soil. These exudates are involved in many biotic and abiotic interactions. Wild relatives of crops provide a large potential source of information and genetic material and have desirable traits that could be incorporated into modern breeding programs. However, root exudates are currently underexploited. Here, we highlight how the traits of root exudates of crop wild relatives could be used to improve agricultural output and reduce environmental impacts, particularly by decreasing our dependence on pesticides and fertilisers.

Global climate changes such as prolonged duration and intensity of drought can lead to adverse ecological consequences in forests. Currently little is known about soil microbial community responses to such drought regimes in tropical forests. In this study, we examined the resistance and resilience of topsoil prokaryotic communities to a prolongation of the dry season in terms of diversity, community structure and co-occurrence patterns in a French Guianan tropical forest. Through excluding rainfall during and after the dry season, a simulated prolongation of the dry season by five months was compared to controls. Our results show that prokaryotic communities increasingly diverged from controls with the progression of rain exclusion. Furthermore, prolonged drought significantly affected microbial co-occurrence networks. However, both the composition and co-occurrence networks of soil prokaryotic communities immediately ceased to differ from controls when precipitation throughfall returned. This study thus suggests modest resistance but high resilience of microbial communities to a prolonged drought in tropical rainforest soils.

Differences in the elemental composition of plants, mainly C, N, and P, have been shown to be related to differences in their nutritional status, and their morphological and functional traits. The relationship between morphological traits and micronutrients and trace elements, however, has been much less studied. Additionally, in bryophytes, research devoted to investigating these relationships is still very scarce. Here, we analysed 80 samples from 29 aquatic and semi-aquatic (hygrophytic) moss species living in Mediterranean springs to investigate the relationship between moss nutrient concentrations and their micro- and macroscopic morphological traits and growth forms. We found that, across species, the elemental concentration of mosses was more tightly linked to macroscopic traits than to microscopic traits. Growth forms could also be successfully explained by the concentration of elements in mosses. Apart from macronutrients and their stoichiometric ratios (C:N, C:P, and N:P), micronutrients and trace elements were also important variables predicting moss morphological traits and growth forms. Additionally, our results showed that microscopic traits were well related to macroscopic traits. Overall, our results clearly indicate that the elemental composition of mosses can be used to infer their morphological traits, and that elements other than macronutrients should be taken into account to achieve a good representation of their morphological and, potentially, functional traits when comparing the elemental composition across species.

Key message The growth of UCB-1 pistachio rootstock seedlings in the earliest years is a poor predictor of subsequent growth. Therefore, rogueing during the 1st years of growth is not effective. Abstract The UCB-1 hybrid, produced from a controlled cross between Pistacia atlantica (female) and P. integerrima (male), is the main pistachio rootstock used in the USA. Variation has been observed in orchards planted with seedling UCB-1 rootstocks for over 20 years. Reduced vigor and stunting of some trees are of particular concern to growers due to decreased nut yield. This study was conducted to better understand the growth of non-grafted UCB-1, as well as between UCB-1 rootstock and Pistacia vera scions in commercial orchards. Phenotypic traits were evaluated in the non-grafted orchard. Grafted tree data were collected for both P. vera female scions and their UCB-1 seedling rootstocks in commercial orchards. The uniformity of tree height, trunk caliper, and canopy volume decreased annually during the first 5 years of growth. Individual tree growth was not linear and was poorly synchronized among siblings, causing the population to become increasingly less uniform as it aged. Consequently, growth in the earliest years is a poor predictor of subsequent growth. The strongest correlation was between growth parameters during the later years. There was a significant correlation between rootstock and scion caliper of the grafted trees in commercial orchards, with the least vigorous rootstocks producing the least vigorous scions. These data confirm the need to reliably rogue out seedlings that later will not be vigorous; however, our data show that rogueing based on the 1st years of growth is ineffective. This study suggests the need to develop predictive molecular markers for rootstock vigor.

Plant Reactome (https://plantreactome.gramene.org) is an open-source, comparative plant pathway knowledgebase of the Gramene project. It uses Oryza sativa (rice) as a reference species for manual curation of pathways and extends pathway knowledge to another 82 plant species via gene-orthology projection using the Reactome data model and framework. It currently hosts 298 reference pathways, including metabolic and transport pathways, transcriptional networks, hormone signaling pathways, and plant developmental processes. In addition to browsing plant pathways, users can upload and analyze their omics data, such as the gene-expression data, and overlay curated or experimental gene-gene interaction data to extend pathway knowledge. The curation team actively engages researchers and students on gene and pathway curation by offering workshops and online tutorials. The Plant Reactome supports, implements and collaborates with the wider community to make data and tools related to genes, genomes, and pathways Findable, Accessible, Interoperable and Re-usable (FAIR).

We review recent approaches and challenges in monitoring and estimating recruitment for the main commercial tuna species managed under the auspices of the five tuna Regional Fisheries Management Organizations (tRFMOs), including: (i) the stock assessment and management context, (ii) fisheries-independent recruitment monitoring successes, failures and future options, (iii) recruitment estimation methods within statistical population models and (iv) recruitment in projections for traditional stock assessment and management strategy evaluation. Despite the diversity in tuna populations and tRFMO scientific processes, there are many common recruitment themes, including: (i) fisheries-independent recruitment monitoring is difficult and rare (the aerial surveys for juvenile southern bluefin tuna, Thunnus maccoyi, and juvenile eastern Atlantic bluefin tuna stocks, T. thynnus, are the only time series used in assessments), (ii) most statistical models estimate lognormal recruitment deviations around a stationary Beverton-Holt relationship using a penalized likelihood approach, (iii) the degree of compensation in the stock-recruitment relationship and the variance is difficult to estimate (steepness is usually fixed at 0.7 ≤ h ≤ 1.0, and the CV is most often fixed with σR = 0.6 for lognormal recruitment deviations), and (iv) estimated recruitment time series often deviate systematically from the mean relationship, but it is unclear the extent to which this reflects reality (e.g. environmental change) or estimation artefacts (e.g. incorrect model assumptions or biased data). There is a trend toward the use of model ensembles to represent recruitment (and other sources of) uncertainty, both in the context of traditional assessments and management strategy evaluation. Recommendations include: i) continued development of fisheries-independent recruitment monitoring methods, including adopting emerging technologies (e.g. genetics-based mark-recapture or abundance monitoring with a network of acoustic FADs), and (ii) the management paradigm should be designed to be robust to future recruitment uncertainties (e.g. recognize that recruitment compensation might be much lower than model-based estimates or assumptions, and be prepared to respond to substantial serially-correlated recruitment deviations, e.g. regime shifts). Following a history of over-exploitation and difficulties in reaching international scientific and management consensus, the CCSBT now provides a leading example of how tuna recruitment issues might be addressed through innovative monitoring, comprehensive modelling of uncertainty, and management with simulation-tested management procedures.

Transport And Golgi Organization protein 2 (TANGO2) deficiency has recently been identified as a rare metabolic disorder with a distinct clinical and biochemical phenotype of recurrent metabolic crises, hypoglycemia, lactic acidosis, rhabdomyolysis, arrhythmias, and encephalopathy with cognitive decline. We report nine subjects from seven independent families, and we studied muscle histology, respiratory chain enzyme activities in skeletal muscle and proteomic signature of fibroblasts. All nine subjects carried autosomal recessive TANGO2 mutations. Two carried the reported deletion of exons 3 to 9, one homozygous, one heterozygous with a 22q11.21 microdeletion inherited in trans. The other subjects carried three novel homozygous (c.262C>T/p.Arg88*; c.220A>C/p.Thr74Pro; c.380+1G>A), and two further novel heterozygous (c.6_9del/p.Phe6del); c.11‐13delTCT/p.Phe5del mutations. Immunoblot analysis detected a significant decrease of TANGO2 protein. Muscle histology showed mild variation of fiber diameter, no ragged‐red/cytochrome c oxidase‐negative fibers and a defect of multiple respiratory chain enzymes and coenzyme Q10 (CoQ10) in two cases, suggesting a possible secondary defect of oxidative phosphorylation. Proteomic analysis in fibroblasts revealed significant changes in components of the mitochondrial fatty acid oxidation, plasma membrane, endoplasmic reticulum‐Golgi network and secretory pathways. Clinical presentation of TANGO2 mutations is homogeneous and clinically recognizable. The hemizygous mutations in two patients suggest that some mutations leading to allele loss are difficult to detect. A combined defect of the respiratory chain enzymes and CoQ10 with altered levels of several membrane proteins provides molecular insights into the underlying pathophysiology and may guide rational new therapeutic interventions., Agència de Gestió d'Ajuts Universitaris i de Recerca (AGAUR), Grant/Award Number: 2014: SGR 393; Association Française contre les Myopathies (FR), Grant/Award Number: 21644; CERCA Programme/ Generalitat de Catalunya, the Hesperia Foundation, the Secretariat for Universities and Research of the Ministry of Business and Knowledge of the Government of Catalonia, Grant/Award Number: [2017SGR1206]; European Research Council, Grant/Award Number: 309548; FEuropean Union Seventh Framework Programme, Grant/Award Number: (FP7/2007‐2013); Instituto de la Marató de TV3, Grant/Award Number: 345/C/2014rm Care (CA); Instituto de Salud Carlos III, Grant/Award Number: grants PI17‐01286, PI17/00109, PI16/00579, PI16/01048, PI14/00581 and CP09/00011; Medical Research Council, Grant/Award Number: MR/N025431/1; Mitochondrial Disease Patient Cohort (UK) , Grant/Award Number: (G0800674); National Institute for Health Research (NIHR) doctoral fellowship, Grant/Award Number: NIHR‐HCS‐D12‐03‐04; Newton Fund, Grant/Award Number: MR/N027302/1; Wellcome Centre for Mitochondrial Research, Grant/Award Number: (203105/Z/16/Z); Wellcome Investigator fund, Grant/Award Number: 109915/Z/15/Z; Wellcome Trust Pathfinder Scheme, Grant/Award Number: 201064/Z/16/Z

Farmed New Zealand Chinook salmon Oncorhynchus tshawytscha Walbaum have been found to be infected by rickettsia-like organisms (NZ-RLO). While these Gram-negative intra-cellular bacteria are closely related to Piscirickettsia salmonis, a significant pathogen for farmed salmon globally, the pathogenicity of NZ-RLO is unknown. The aim of the present study was to determine if one strain, NZ-RLO2, causes disease in Chinook salmon. Post-smolt salmon were inoculated with NZ-RLO2 by intraperitoneal injection at high, medium and low doses and observed for 30 d. All fish in the high and medium dosed groups died by the end of the study and 63% of the low dose group died within 30 d of inoculation. Necropsy revealed the fish inoculated with NZ-RLO2 had internal multifocal haemorrhages. The most consistent histological finding in fish inoculated with NZ-RLO2 was neutrophilic and necrotizing pancreatitis and steatitis with intra-cytoplasmic organisms often visible within areas of inflammation. Other histological lesions included multifocal hepatic necrosis, haematopoietic cell necrosis and splenic and renal lymphoid depletion. The presence of NZ-RLO2 within the inoculated fish was confirmed by replication in cell culture and qPCR. The results suggest NZ-RLO2 can cause disease in Chinook salmon and therefore could be a significant pathogen in farmed Chinook salmon.

Background Pomegranate (Punica granatum L.) - a delicious fruit once used in Ayurvedic medicine - is now largely known for the antioxidant properties of its juice, which has also been considered to have health benefits against diseases such as cancer and cardiovascular diseases. These beneficial effects are associated with the fruit's high content of polyphenolic compounds. High demand and lower production levels drive pomegranate prices up, which leads to the possibility of pomegranate products being adulterated, diluted or substituted. To ensure the presence of pomegranate in various preparations labeled as containing pomegranate, a simple method was developed to screen and quantify the specific punicalagins by mass spectrometry. Results The present method was used to analyze several pure and mixed beverages from the US market, and also to quantify punicalagins in the juice of 14 pomegranate cultivars. Punicalagins were detected in all cultivars, with higher concentrations in whole fruit juices compared with aril juices. Amongst the 20 commercial beverages, punicalagins were not detected in four preparations. Conclusion The liquid chromatographic-mass spectrometric method presented herein enables an easy and rapid quantification of the specific punicalagins. The latter was detected in all cultivar samples, thus supporting that punicalagin is a suitable marker of these 14 pomegranate cultivars in commercial juices. Absence of the specific marker in four commercial preparations shows the necessity of having simple and rapid methods to evaluate the presence of pomegranate in preparations. © 2019 Society of Chemical Industry.

Characterising the pathology of skeletal anomalies in farmed finfish is key to elucidating the underlying causes. Spinal curvature is frequently observed in farmed New Zealand king salmon (Oncorhynchus tshawytscha), but its cause is currently unknown and knowledge about its pathology is limited. Dual-energy X-ray absorptiometry (DXA) was used to investigate the relationship between spinal curvature and body composition in farmed adult New Zealand king salmon. Differences in fat mass (FM), lean mass (LM) and bone mineral content (BMC) between harvest-sized fish affected and unaffected by spinal curvature were evaluated. As there is presently no evidence of an association between spinal curvature and vertebral mineral loss, between-group differences in BMC were not anticipated. Conversely, as spinal anomalies can alter the swimming and feeding of affected fish, and existing research suggests a role for soft tissues in spinal curvature development, differences in FM and LM were expected. Whole-body and regional (cranial, trunco-cranial, trunco-caudal and caudal spine) measurements of percent FM, LM and BMC were obtained from lateral DXA scans of size-matched adult female king salmon (1890–6903 g) affected (n = 31) and unaffected (n = 31) by spinal curvature. Repeatability was comparable to previous DXA studies. Measurements of FM and LM by DXA and chemical carcass analysis (CCA) were highly similar. As frequently reported in previous animal-based studies, DXA-derived BMC values were significantly lower than those obtained from CCA. Contrary to the overarching hypothesis, there were no significant between-group differences in whole-body or regional FM, LM or BMC, suggesting that there was no relationship between body composition and spinal curvature. Though the relationship between soft tissue changes and spinal curvature remains to be determined, DXA appears to be a viable tool for non-invasive assessment of king salmon body composition. However, studying end-stage disease has recognised limitations, so future investigations should utilise longitudinal designs.

Sea spray aerosol (SSA) is responsible for the large-scale transfer of particles from the sea to the land, leading to significant deposition of a range of ions, predominantly Na+, K+, Mg2+, Ca2+, and Cl−. Up to now, there has been little research into the effects of SSA on spring water chemistry. Therefore, we sampled 303 semi-natural springs across Catalonia (NE Iberian Peninsula) and analysed the concentrations of 20 different ions and elements, and determined the impact of SSA (using distance to the coast as a proxy) as well as climate, lithology and human disturbances. We found that distance to the coast had a clear effect on the water chemical composition of springs, while accounting for potentially confounding factors such as anthropogenic water pollution (nitrate, NO3−), differences in lithology and annual rainfall. Our results showed that springs located closer to the coast had higher Cl−, SO42−, Na+, Mg2+, K+ and Ca2+ concentrations than those of springs located further away. Precipitation was generally negatively correlated with the concentration of almost all elements analysed. The concentration of NO3− increased with distance to the coast, concurrently with farming activities, located mainly inland in the study area. These results demonstrate that SSA has an important effect on the groundwater of coastal zones, up to a distance of around 70 km from the coastline. This analysis reveals the main natural and human processes that influence spring water chemistry in this Mediterranean region, information that could be helpful in similar regions for ecological studies, water quality policies, and for the improvement of predictions in the current context of global change.

SARS-CoV-2 virus is the causative agent of COVID-19. Here we demonstrate that non-infectious SARS-CoV-2 virus like particles (VLPs) can be assembled by co-expressing the viral proteins S, M and E in mammalian cells. The assembled SARS-CoV-2 VLPs possess S protein spikes on particle exterior, making them ideal for vaccine development. The particles range in shape from spherical to elongated with a characteristic size of 129 ± 32 nm. We further show that SARS-CoV-2 VLPs dried in ambient conditions can retain their structural integrity upon repeated scans with Atomic Force Microscopy up to a peak force of 1 nN.

Purpose: To evaluate the effect of sulindac, a nonselective anti-inflammatory drug (NSAID), for activity to reduce breast density (BD), a risk factor for breast cancer. Experimental Design: An open-label phase II study was conducted to test the effect of 12 months' daily sulindac at 150 mg twice daily on change in percent BD in postmenopausal hormone receptor–positive breast cancer patients on aromatase inhibitor (AI) therapy. Change in percent BD in the contralateral, unaffected breast was measured by noncontrast magnetic resonance imaging (MRI) and reported as change in MRI percent BD (MRPD). A nonrandomized patient population on AI therapy (observation group) with comparable baseline BD was also followed for 12 months. Changes in tissue collagen after 6 months of sulindac treatment were explored using second-harmonic generated microscopy in a subset of women in the sulindac group who agreed to repeat breast biopsy. Results: In 43 women who completed 1 year of sulindac (86% of those accrued), relative MRPD significantly decreased by 9.8% [95% confidence interval (CI), −14.6 to −4.7] at 12 months, an absolute decrease of −1.4% (95% CI, −2.5 to −0.3). A significant decrease in mean breast tissue collagen fiber straightness (P = 0.032), an investigational biomarker of tissue inflammation, was also observed. MRPD (relative or absolute) did not change in the AI-only observation group (N = 40). Conclusions: This is the first study to indicate that the NSAID sulindac may reduce BD. Additional studies are needed to verify these findings and determine if prostaglandin E2 inhibition by NSAIDs is important for BD or collagen modulation.

Ecological stoichiometry and studies of biogeochemical niches have mainly focused on plankton and vascular plants, but the phenotypically closest modern relatives of early plants, bryophytes, have been largely neglected. We analysed C:N:P stoichiometries and elemental compositions (K, Na, Mg, Ca, S, Fe) of 35 widely distributed bryophyte species inhabiting springs. We estimated bryophyte C:N:P ratios and their biogeochemical niches, investigated how elementomes respond to the environment and determined whether they tend to diverge more for coexisting than non-coexisting individuals and species. The median C:N:P was 145:8:1, intermediate between Redfield's ratio for marine plankton and those for vascular plants. Biogeochemical niches were differentiated amongst species and were phylogenetically conserved. Differences in individual and species-specific elementomes increased with coexistence between species. Our results provide an evolutionary bridge between the ecological stoichiometries of algae and vascular plants and suggest that differences in elementomes could be used to understand community assemblages and functional diversity.

Nutrient economy and plant nutrient concentrations have been suggested as important selective pressures of reproductive traits in vascular plants. However, evidence supporting that the reproduction of bryophytes and their reproductive traits have also been conditioned by nutrient availability is lacking. We here analysed the nutrient (N, P, K, and Fe) concentration of 35 aquatic and semi-aquatic bryophytes and the chemistry of the spring water in which they lived to determine whether bryophyte nutrient concentrations were correlated with the frequency of sexual reproduction, main reproductive mode (sexual vs. asexual), dioicy, and spore diameter, while controlling for climate and nutrient concentrations in the spring water. Water nutrient concentrations, except for K, had a small but positive influence on bryophyte nutrient concentrations. P-rich and K-poor species produced sporophytes more often and were more likely to reproduce sexually and be monoicous. Spore diameter was smaller in P- and Fe-rich mosses but larger in N-rich mosses living in humid climates. P-rich species thus produced more and smaller spores and were able to propagate more extensively. Overall, our results suggest that nutrient economy, especially P economy, has played an important role in shaping the reproductive traits of bryophytes.

Background: Rhizodeposition is the release of organic compounds from plant roots into soil. Positive relationships between rhizodeposition and soil microbial biomass are commonly observed. Rhizodeposition may be disrupted by increasing drought however the effects of water stress on this process are not sufficiently understood. Scope: We aimed to provide a synthesis of the current knowledge of drought impacts on rhizodeposition. The current scarcity of well-defined studies hinders a quantitative meta-analysis, but we are able to identify the main effects of water stress on this process and how changes in the severity of drought may produce different responses. We then give an overview of the links between rhizodeposition and microbial communities, and describe how drought may disrupt these interactions. Conclusions: Overall, moderate drought appears to increase rhizodeposition per gram of plant, but under extreme drought rhizodeposition is more variable. Concurrent decreases in plant biomass may lessen the total amount of rhizodeposits entering the soil. Effects on rhizodeposition may be strongly species-dependant therefore impacts on soil communities may also vary, either driving subsequent changes or conferring resilience in the plant community. Advances in the study of rhizodeposition are needed to allow a deeper understanding of this plant-soil interaction and how it will respond to drought.

The abstract is available here: https://uscholar.univie.ac.at/o:1603267

Bryophytes are some of the most sensitive biological indicators of environmental change. Springs have a significant presence of bryophytes and so are ideal habitats for studying their relationship with the environment. We tested whether bryophyte assemblages can be explained with macro-, meso- and micro-ecological variables (i.e. seasonal climate, altitude, water pH and conductivity) sampling bryophytes from 198 semi-natural springs distributed along montane regions in the north-eastern Iberian Peninsula. We tested the influence of environmental variables on bryophyte assemblages in springs using sparse Partial Least Squares. Our results show that variability in bryophyte assemblages is explained by seasonal climate (temperature and precipitation from winter, spring, summer and autumn and temperature and precipitation seasonality), altitude and water conductivity. The results obtained by the present study will be useful for predicting bryophyte diversity in springs using simple and easy to obtain variables such as climate, water pH and conductivity.

Root exudation is an important input of carbon into soils and affects plant and soil communities, but little is known about the effect of climatic factors such as drought on exudation, and its ability to recover. We studied the impact of increasing drought on root exudation and its subsequent recovery in the Mediterranean tree species Quercus ilex L. in a greenhouse study by measuring the amount of total organic carbon in exudates. The amount of exudation per unit root area increased with drought duration and was 21% higher under the most extreme drought scenario compared with the non-droughted control. The amount of root exudation did not differ between the treatments following 6 weeks of re-watering, indicating a strong capacity for recovery in this species. We concluded that drought could affect the amount of root exudation, which could in turn have a large impact on microbial activity in the rhizosphere, and alter these microbial communities, at least in the short term. This tree species may be able to return to normal levels of root exudation after a drought event, but long-term exudate-mediated impacts on Mediterranean forest soils may be an unforeseen effect of drought.

Aims: Secondary forests are expanding rapidly in tropical regions and could play an important role in conserving native biodiversity and stabilising global climate. The recovery rate of plant communities in secondary forests varies considerably due to mechanisms associated with seed dispersal and recruitment dynamics. We explored these mechanisms along a chronosequence of tropical secondary forests in an agricultural landscape that was extensively cleared. Location: We explored these mechanisms along a chronosequence of secondary forests in tropical Australia. Methods: We used selected plant traits to characterise plant species and compared community composition between demographic stages (i.e. soil seedbank, understorey and overstorey) and forest age categories. We collected soil samples to assess seedbank composition and used quadrants and transects to assess understorey and overstorey plant community composition at each site. Results: For all demographic stages, we found that young (4-12 years) and intermediate-aged forests (16-20 years) were dominated by early successional, small-seeded species and traits associated with disturbed forests. In old secondary forest (23-34 years) some traits associated with late successional stages were present (e.g. large seeds, trees). However, the traits and species composition of mature forests remained distinct from all secondary forests. Across the chronosequence, forest age and demographic stage were significant factors in discriminating species and trait composition between forest sites. We found clear plant community similarities within demographic stages, despite the forest age differences. This suggests stronger limitations to dispersal and recruitment between demographic stages than between forest ages. Conclusions: Our results show that secondary forests in this region assemble slowly with dispersal and recruitment limitations constraining their recovery. Although a successional transition in species and plant traits composition along the chronosequence is clear, similarities to mature forests remain low. The slow recovery of late successional and large-seeded species in these secondary forests suggests that active restoration of such species may be necessary if we want to enhance the capacity of these forests to conserve native biodiversity.

Tick bites in Australia are linked to the transmission of a variety of infectious diseases in humans, livestock and wildlife. Despite this recognition, little is currently known about the variety of potential pathogens that are carried and transmitted by Australian ticks. In this study, we attempted to expand knowledge of Australian tick-borne bacterial pathogens by analyzing various tick species from the state of Queensland for potential human pathogens belonging to the Rickettsia, Coxiella and Borrelia genera. A total of 203 ticks, comprising of four genera and nine different tick species, were screened by specific qPCR assays. An overall Rickettsia qPCR positivity of 6.4% (13/203) was detected with rickettsial DNA found in four tick species (Ixodes holocyclus, I. tasmani, Amblyommatriguttatum, and Haemaphysalis longicornis). Amplification and analysis of several rickettsial genes from rickettsial qPCR positive samples identified sequences closely related to but genetically distinct from several previously described cultured and uncultured rickettsial species in the Rickettsia spotted fever subgroup. No ticks were positive for either Coxiella or Borrelia DNA. This work suggests that a further diversity of rickettsiae remain to be described in Australian ticks with the full importance of these bacteria to human and animal health yet to be elucidated.

SARS-CoV-2 is a novel coronavirus which has caused the COVID-19 pandemic. Other known coronaviruses show a strong pattern of seasonality, with the infection cases in humans being more prominent in winter. Although several plausible origins of such seasonal variability have been proposed, its mechanism is unclear. SARS-CoV-2 is transmitted via airborne droplets ejected from the upper respiratory tract of the infected individuals. It has been reported that SARS-CoV-2 can remain infectious for hours on surfaces. As such, the stability of viral particles both in liquid droplets as well as dried on surfaces is essential for infectivity. Here we have used atomic force microscopy to examine the structural stability of individual SARS-CoV-2 virus like particles at different temperatures. We demonstrate that even a mild temperature increase, commensurate with what is common for summer warming, leads to dramatic disruption of viral structural stability, especially when the heat is applied in the dry state. This is consistent with other existing non-mechanistic studies of viral infectivity, provides a single particle perspective on viral seasonality, and strengthens the case for a resurgence of COVID-19 in winter.Statement of Scientific SignificanceThe economic and public health impact of the COVID-19 pandemic are very significant. However scientific information needed to underpin policy decisions are limited partly due to novelty of the SARS-CoV-2 pathogen. There is therefore an urgent need for mechanistic studies of both COVID-19 disease and the SARS-CoV-2 virus. We show that individual virus particles suffer structural destabilization at relatively mild but elevated temperatures. Our nanoscale results are consistent with recent observations at larger scales. Our work strengthens the case for COVID-19 resurgence in winter.

Funder: Max-Planck-Gesellschaft (Max Planck Society); doi: https://doi.org/10.13039/501100004189, Funder: Heinz L. Krekeler Foundation, Large brains and behavioural innovation are positively correlated, species-specific traits, associated with the behavioural flexibility animals need for adapting to seasonal and unpredictable habitats. Similar ecological challenges would have been important drivers throughout human evolution. However, studies examining the influence of environmental variability on within-species behavioural diversity are lacking despite the critical assumption that population diversification precedes genetic divergence and speciation. Here, using a dataset of 144 wild chimpanzee (Pan troglodytes) communities, we show that chimpanzees exhibit greater behavioural diversity in environments with more variability — in both recent and historical timescales. Notably, distance from Pleistocene forest refugia is associated with the presence of a larger number of behavioural traits, including both tool and non-tool use behaviours. Since more than half of the behaviours investigated are also likely to be cultural, we suggest that environmental variability was a critical evolutionary force promoting the behavioural, as well as cultural diversification of great apes.

Previous activity classification studies have typically been performed on normal weight individuals. Therefore, it is unclear whether a generic classification algorithm could be developed that would perform consistently across individuals who fall within different BMI categories. Acceleration data were collected from the hip and ankle joints of 50 individuals: 17 normal weight, 14 overweight and 19 obese. Each participant performed a set of 10 dynamic tasks, which included activities of daily living and gym-based exercises. The performance of a generic classification algorithm, developed using linear discriminant analysis, was compared across the three separate BMI groups for each sensor. Higher classification accuracies (92-95%) were observed for the ankle sensor; however, both sensors demonstrated consistent performance across the three groups. This is the first study to demonstrate the effectiveness of a generic classification algorithm across individuals with different BMI and may be a first step towards automated activity profiling in weight-loss programmes.

Targeting T cell malignancies using chimeric antigen receptor (CAR) T cells is hindered by ‘T v T’ fratricide against shared antigens such as CD3 and CD7. Genome-editing can overcome such hurdles through targeted disruption of problematic shared antigens. Base editing offers the possibility of seamless disruption of gene expression through the creation of stop codons or elimination of splice donor or acceptor sites. We describe the generation of fratricide resistant, T cells by orderly removal of shared antigens such as TCR/CD3 and CD7 ahead of lentiviral mediated expression of CARs specific for CD3 or CD7. Molecular interrogation of base edited cells confirmed virtual elimination of chromosomal translocation events detected in conventional Cas9 treated cells. Interestingly, co-culture of 3CAR and 7CAR cells resulted in ‘self-enrichment’ yielding populations that were 99.6% TCR-/CD3/-CD7-. 3CAR or 7CAR cells were able to exert specific cytotoxicity against their relevant target antigen in leukaemia lines with defined CD3 and/or CD7 expression as well as primary T-ALL cells. Co-cultured 3CAR/7CAR cells exhibited the highest level of cytotoxicity against T-ALL targets expressing both target in vitro and an in vivo human:murine chimeric model. While APOBEC editors can reportedly exhibit guide-independent deamination of both DNA and RNA, we found no evidence of promiscuous base conversion activity affecting CAR antigen specific binding regions which may otherwise redirect T cell specificity. Combinational infusion of fratricide resistant anti-T CAR T cells may enable enhanced molecular remission ahead of allogeneic haematopoietic stem cell transplantation for T cell malignancies.

High-throughput phenotyping systems are powerful, dramatically changing our ability to document, measure, and detect biological phenomena. Here, we describe a cost-effective combination of a custom-built imaging platform and deep-learning-based computer vision pipeline. A minimal version of the maize ear scanner was built with low-cost and readily available parts. The scanner rotates a maize ear while a cellphone or digital camera captures a video of the surface of the ear. Videos are then digitally flattened into two-dimensional ear projections. Segregating GFP and anthocyanin kernel phenotype are clearly distinguishable in ear projections, and can be manually annotated using image analysis software. Increased throughput was attained by designing and implementing an automated kernel counting system using transfer learning and a deep learning object detection model. The computer vision model was able to rapidly assess over 390,000 kernels, identifying male-specific transmission defects across a wide range of GFP-marked mutant alleles. This includes a previously undescribed defect putatively associated with mutation of Zm00001d002824, a gene predicted to encode a vacuolar processing enzyme (VPE). We show that by using this system, the quantification of transmission data and other ear phenotypes can be accelerated and scaled to generate large datasets for robust analyses.One sentence summaryA maize ear phenotyping system built from commonly available parts creates images of the surface of ears and identifies kernel phenotypes with a deep-learning-based computer vision pipeline.

Mammalian genomes are subdivided into large (50-2000 kb) regions of chromatin referred to as Topologically Associating Domains (TADs or sub-TADs). Chromatin within an individual TAD contacts itself more frequently than with regions in surrounding TADs thereby directing enhancer-promoter interactions. In many cases, the borders of TADs are defined by convergently orientated boundary elements associated with CCCTC-binding factor (CTCF), which stabilises the cohesin complex on chromatin and prevents its translocation. This delimits chromatin loop extrusion which is thought to underlie the formation of TADs. However, not all CTCF-bound sites act as boundaries and, importantly, not all TADs are flanked by convergent CTCF sites. Here, we examined the CTCF binding sites within a ∼70 kb sub-TAD containing the duplicated mouse α-like globin genes and their five enhancers (5’-R1-R2-R3-Rm-R4-α1-α2-3’). The 5’ border of this sub-TAD is defined by a pair of CTCF sites. Surprisingly, we show that deletion of the CTCF binding sites within and downstream of the α-globin locus leaves the sub-TAD largely intact. The predominant 3’ border of the sub-TAD is defined by a steep reduction in contacts: this corresponds to the transcribed α2-globin gene rather than the CTCF sites at the 3’-end of the sub-TAD. Of interest, the almost identical α1- and α2-globin genes interact differently with the enhancers, resulting in preferential expression of the proximal α1-globin gene which behaves as a partial boundary between the enhancers and the distal α2-globin gene. Together, these observations provide direct evidence that actively transcribed genes can behave as boundary elements.Significance StatementMammalian genomes are complex, organised 3D structures, partitioned into Topologically Associating Domains (TADs): chromatin regions that preferentially self-interact. These chromatin interactions are thought to be driven by a mechanism that continuously extrudes chromatin loops, forming structures delimited by chromatin boundary elements and reflecting the activity of enhancers and promoters. Boundary elements bind architectural proteins such as CCCTC-binding factor (CTCF). Previously, an overlap between the functional roles of enhancers and promoters has been shown. However, whether there is overlap between enhancers/promoters and boundary elements is not known. Here, we show that actively transcribed genes can also behave as boundary elements, similar to CTCF boundaries. In both cases, multi-protein complexes bound to these regions may stall the process of chromatin loop extrusion.

It is widely held that clinical isolates of human cytomegalovirus (HCMV) are highly cell associated, and mutations affecting the UL128-131 and RL13 loci that arise in culture lead to the appearance of a cell-free spread phenotype. The bacterial artificial chromosome (BAC) clone Merlin (ME) expresses abundant UL128-131, is RL13 impaired, and produces low infectivity virions in fibroblasts, whereas TB40/e (TB) and TR are low in UL128-131, are RL13 intact, and produce virions of much higher infectivity. Despite these differences, quantification of spread by flow cytometry revealed remarkably similar spread efficiencies in fibroblasts. In epithelial cells, ME spread more efficiently, consistent with robust UL128-131 expression. Strikingly, ME spread far better than did TB or TR in the presence of neutralizing antibodies on both cell types, indicating that ME is not simply deficient at cell-free spread but is particularly efficient at cell-to-cell spread, whereas TB and TR cell-to-cell spread is poor. Sonically disrupted ME-infected cells contained scant infectivity, suggesting that the efficient cell-to-cell spread mechanism of ME depends on features of the intact cells such as junctions or intracellular trafficking processes. Even when UL128-131 was transcriptionally repressed, cell-to-cell spread of ME was still more efficient than that of TB or TR. Moreover, RL13 expression comparably reduced both cell-free and cell-to-cell spread of all three strains, suggesting that it acts at a stage of assembly and/or egress common to both routes of spread. Thus, HCMV strains can be highly specialized for either for cell-free or cell-to-cell spread, and these phenotypes are determined by factors beyond the UL128-131 or RL13 loci. IMPORTANCE Both cell-free and cell-to-cell spread are likely important for the natural biology of HCMV. In culture, strains clearly differ in their capacity for cell-free spread as a result of differences in the quantity and infectivity of extracellular released progeny. However, it has been unclear whether “cell-associated” phenotypes are simply the result of poor cell-free spread or are indicative of particularly efficient cell-to-cell spread mechanisms. By measuring the kinetics of spread at early time points, we were able to show that HCMV strains can be highly specialized to either cell-free or cell-to-cell mechanisms, and this was not strictly linked the efficiency of cell-free spread. Our results provide a conceptual approach to evaluating intervention strategies for their ability to limit cell-free or cell-to-cell spread as independent processes.

BackgroundPeanut allergy affects 3% of Australian children and has a higher risk of anaphylaxis than most food allergies. Predicting who is likely to develop anaphylaxis is still an inexact science. The fraction of exhaled nitric oxide (FeNO) shows promise as a biomarker involved in peanut allergy, as nitric oxide plays a role in inhibiting mast cell degranulation which is relevant in anaphylaxis, where mast cell degranulation plays a mediator role. The aim of this study was to assess the change in FeNO in children during peanut challenge.MethodsThirty-six children aged from 5 to 17 years were recruited for open-labelled peanut challenge. Participants had skin prick test to peanut performed, and serum collected for Ara h2 specific IgE and peanut specific IgE. FeNO was measured by portable device (NIOX VERO) prior to and throughout the peanut challenge.ResultsWhen grouped according to reaction type at peanut challenge (anaphylaxis, clinical allergy not anaphylaxis and tolerant), there were significant differences in the mean change in FeNO measurement between the anaphylaxis group and the clinical allergy, not anaphylaxis group (p = 0.005), and between the anaphylaxis group and tolerant group (p ConclusionsFeNO decreased more significantly in those who subsequently developed anaphylaxis than in those with clinical allergy, not anaphylaxis or negative peanut challenge (tolerance). As a bedside test that can be used in children, it has potential for further research into mechanisms of anaphylaxis in food allergy and potentially assists in predicting an imminent anaphylactic reaction in some patients.Trial registrationClinicalTrials.gov: PEAnut Anaphylaxis Predictors (PEAAP) NCT02424136.

Understanding the mitotic DNA damage response (DDR) is critical to our comprehension of cancer, premature aging and developmental disorders which are marked by DNA repair deficiencies. In this study we use a micro-focused-laser to induce DNA damage in selected mitotic chromosomes to study the subsequent repair response. Our findings demonstrate that (1) mitotic cells are capable of DNA repair as evidenced by DNA synthesis at damage sites, (2) Repair is attenuated when DNA-PKcs and ATM are simultaneously compromised, (3) Laser damage may permit the observation of previously undetected DDR proteins when damage is elicited by other methods in mitosis, and (4) Twenty five percent of mitotic DNA-damaged cells undergo a subsequent mitosis. Together these findings suggest that mitotic DDR is more complex than previously thought and may involve factors from multiple repair pathways that are better understood in interphase.

Anthropogenic activities and intensive farming arc causing nitrate pollution in groundwater bodies. These aquifers are drained by springs which, in the Mediterranean region, act as refugia for preserving biodiversity of species that need continuous water. Some springs are also used for drinking water for wild animals, livestock and humans, so if their water quality is compromised it can become a threat to public health. However, the impact of nitrate pollution on these biotic communities remains unknown. We sampled 338 assemblages of aquatic and semi-aquatic bryophytes (i.e., hygrophytic mosses and liverworts) growing in springs in a gradient of water conductivity, nitrate concentration and climate and distributed across the north-east of the Iberian Peninsula to investigate the impact of nitrate pollution on the diversity of bryophytes and moss functional traits in Mediterranean springs. Based on previous literature suggesting that increased nitrogen load decreases biodiversity in grasslands and freshwater ecosystems, we hypothesised that water nitrate pollution in springs decreases bryophyte diversity at the local and regional scales. Our results indicated that, at the local scale (spring), nitrate pollution reduced the number and the likelihood of finding a rare species in springs. Rare species were found in 4% of the springs with nitrate above 50 mg but in 32% of the springs with nitrate below 50 mg L-1. Moss, liv- erwort and overall bryophyte diversity were not directly affected by nitrate at the local scale but nitrate consistently decreased diversity of mosses, liverworts and rare bryophyte species at the regional scale. We also found that warmer and drier springs presented fewer bryophyte species. Our results show that the combination of nitrate pollution, increasing temperature and drought could severely threaten bryophyte diversity Mediterranean springs. Our results indicate that the absence of rare bryophytes could be used as a bioindicator of nitrate pollution in springs. (C) 2018 Elsevier B.V. All rights reserved.

The drivers of global change, such as increasing drought and nutrient deposition, are affecting soils and their microbial communities in many different habitats, but how these factors interact remains unclear. Quercus ilex and Pinus sylvestris are two important tree species in Mediterranean montane areas that respond differently to drought, which may be associated with the soils in which they grow. We measured soil respiration and physiologically profiled microbial communities to test the impact of drought and subsequent recovery on soil function and diversity for these two species. We also tested whether the addition of nitrogen and phosphorus modified these effects. Drought was the stronger driver of changes to the soil communities, decreasing diversity (Shannon index), and evenness for both species and decreasing soil respiration for Q. ilex when N was added. Soil respiration for P. sylvestris during the drought period was positively affected by N addition but was not affected by water stress. P addition during the drought period did not affect soil respiration for either tree species but did interact with soil-water content to affect community evenness for P. sylvestris. The two species also differed following the recovery from drought. Soil respiration for Q. ilex recovered fully after the drought treatment ended but decreased for P. sylvestris, whereas the soil community was more resilient for P. sylvestris than Q. ilex. Nutrient addition did not affect respiration or community composition or diversity during the recovery period. Soil respiration was generally weakly positively correlated with soil diversity. We demonstrate that short-term water stress and nutrient addition can have variable effects on the soil communities associated with different tree species and that the compositions of the communities can become uncoupled from soil respiration. Overall, we show that drought may be a stronger driver of changes to soil communities than nitrogen or phosphorus deposition.

The growth and spread of breast cancer are influenced by the composition and structural properties of collagen in the extracellular matrix of tumors. Straight alignment of collagen has been attributed to tumor cell migration, which is correlated with tumor progression and metastasis in breast cancer. Thus, there is a need to characterize collagen alignment to study its value as a prognostic biomarker. We present a framework to characterize the curliness of collagen fibers in breast cancer images from DUET (DUal-mode Emission and Transmission) studies on hematoxylin and eosin (H&E) stained tissue samples. Our novel approach highlights the characteristic fiber gradients using a standard ridge detection method before feeding into the convolutional neural network. Experiments were performed on patches of breast cancer images containing straight or curly collagen. The proposed approach outperforms in terms of area under the curve against transfer learning methods trained directly on the original patches. We also explore a feature fusion strategy to combine feature representations of both the original patches and their ridge filter responses.