Investigating the beneficial traits of Trichoderma hamatum GD12 for sustainable agriculture-insights from genomics.

This is the final version of the article. Available from the publisher via the DOI in this record.Trichoderma hamatum strain GD12 is unique in that it can promote plant growth, activate biocontrol against pre- and post-emergence soil pathogens and can induce systemic resistance to foliar pathogens. This study extends previous work in lettuce to demonstrate that GD12 can confer beneficial agronomic traits to other plants, providing examples of plant growth promotion in the model dicot, Arabidopsis thaliana and induced foliar resistance to Magnaporthe oryzae in the model monocot rice. We further characterize the lettuce-T. hamatum interaction to show that bran extracts from GD12 and an N-acetyl-β-D-glucosamindase-deficient mutant differentially promote growth in a concentration dependent manner, and these differences correlate with differences in the small molecule secretome. We show that GD12 mycoparasitises a range of isolates of the pre-emergence soil pathogen Sclerotinia sclerotiorum and that this interaction induces a further increase in plant growth promotion above that conferred by GD12. To understand the genetic potential encoded by T. hamatum GD12 and to facilitate its use as a model beneficial organism to study plant growth promotion, induced systemic resistance and mycoparasitism we present de novo genome sequence data. We compare GD12 with other published Trichoderma genomes and show that T. hamatum GD12 contains unique genomic regions with the potential to encode novel bioactive metabolites that may contribute to GD12's agrochemically important traits.This work was supported by a Biotechnology and Biological Sciences Research Council grant BB/I014691/1 to Murray Grant and Chris R. Thornto

Patterns of BAP1 protein expression provide insights into prognostic significance and the biology of uveal melanoma

Uveal melanoma (UM) is a rare aggressive intraocular tumour with a propensity for liver metastases, occurring in ∼50% of patients. The tumour suppressor BAP1 is considered to be key in UM progression. Herein, we present the largest study to date investigating cellular expression patterns of BAP1 protein in 165 UMs, correlating these patterns to prognosis. Full clinical, histological, genetic, and follow‐up data were available for all patients. BAP1 gene sequencing was performed on a subset of 26 cases. An independent cohort of 14 UMs was examined for comparison. Loss of nuclear BAP1 (nBAP1) protein expression was observed in 54% (88/165) UMs. nBAP1 expression proved to be a significant independent prognostic parameter: it identified two subgroups within monosomy 3 (M3) UM, which are known to have a high risk of metastasis. Strikingly, nBAP1‐positiveM3 UMs were associated with prolonged survival compared to nBAP1‐negative M3 UMs (Log rank, p = 0.014). nBAP1 protein loss did not correlate with a BAP1 mutation in 23% (6/26) of the UMs analysed. Cytoplasmic BAP1 protein (cBAP1) expression was also observed in UM: although appearing ‘predominantly diffuse’ in most nBAP1‐negative UM, a distinct ‘focal perinuclear’ expression pattern – localized immediately adjacent to the cis Golgi – was seen in 31% (18/59). These tumours tended to carry loss‐of‐function BAP1 mutations. Our study demonstrates loss of nBAP1 expression to be the strongest prognostic marker in UM, confirming its importance in UM progression. Our data suggest that non‐genetic mechanisms account for nBAP1 loss in a small number of UMs. In addition, we describe a subset of nBAP1‐negative UM, in which BAP1 is sequestered in perinuclear bodies, most likely within Golgi, warranting further mechanistic investigation

Metal-macrofauna interactions determine microbial community structure and function in copper contaminated sediments

Peer reviewedPublisher PD

TRY plant trait database - enhanced coverage and open access

Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives

Maltreated children use more grammatical negations

Many studies reveal a strong impact of childhood maltreatment on language development, mainly resulting in shorter utterances, less rich vocabulary, or a delay in grammatical complexity. However, different theories suggest the possibility for resilience – a positive adaptation to an otherwise adverse environment – in children who experienced childhood maltreatment. Here, we investigated different measures for language development in spontaneous speech, examining whether childhood maltreatment leads to a language deficit only or whether it can also result in differences in language use due to a possible adaptation to a toxic environment. We compared spontaneous speech during therapeutic peer-play sessions of 32 maltreated and 32 non-maltreated children from the same preschool and equivalent in gender, age (2 to 5 years), home neighborhood, ethnicity, and family income. Maltreatment status was reported by formal child protection reports, and corroborated by independent social service reports. We investigated general language sophistication (i.e., vocabulary, talkativeness, mean length of utterance), as well as grammatical development (i.e., use of plurals, tense, grammatical negations). We found that maltreated and non-maltreated children showed similar sophistication across all linguistic measures, except for the use of grammatical negations. Maltreated children used twice as many grammatical negations as non-maltreated children. The use of this highly complex grammatical structure shows an advanced linguistic skill, which shows that childhood maltreatment does not necessarily lead to a language deficit. The result might indicate the development of a negativity bias in the structure of spontaneous language due to an adaptation to their experiences

A new investigation of electron neutrino appearance oscillations with improved sensitivity in the MiniBooNE+ experiment

Submitted as whitepaper for Snowmass'13 proceedings - 8 pages, 3 figures; version 2: Minor change to title and author listSubmitted as whitepaper for Snowmass'13 proceedings - 8 pages, 3 figures; version 2: Minor change to title and author listWe propose the addition of scintillator to the existing MiniBooNE detector to allow a test of the neutral-current/charged-current (NC/CC) nature of the MiniBooNE low-energy excess. Scintillator will enable the reconstruction of 2.2 MeV $\gamma$s from neutron-capture on protons following neutrino interactions. Low-energy CC interactions where the oscillation excess is observed should have associated neutrons with less than a 10% probability. This is in contrast to the NC backgrounds that should have associated neutrons in approximately 50% of events. We will measure these neutron fractions with $\nu_\mu$ CC and NC events to eliminate that systematic uncertainty. This neutron-fraction measurement requires $6.5\times10^{20}$ protons on target delivered to MiniBooNE with scintillator added in order to increase the significance of an oscillation excess to over $5\sigma$. This new phase of MiniBooNE will also enable additional important studies such as the spin structure of nucleon ($\Delta s$) via NC elastic scattering, a low-energy measurement of the neutrino flux via \numu ^{12}C \rightarrow \mu^{-} ^{12}N_\textrm{g.s.} scattering, and a test of the quasielastic assumption in neutrino energy reconstruction. These topics will yield important, highly-cited results over the next 5 years for a modest cost, and will help to train Ph.D. students and postdocs. This enterprise offers complementary information to that from the upcoming liquid Argon based MicroBooNE experiment. In addition, MicroBooNE is scheduled to receive neutrinos in early 2014, and there is minimal additional cost to also deliver beam to MiniBooNE

Exploring the predation of UK bumblebees (Apidae, Bombus spp.) by the invasive pitcher plant Sarracenia purpurea: examining the effects of annual variation, seasonal variation, plant density and bumblebee gender

Invasive carnivorous plant species can impact the native invertebrate communities on which they prey. This article explores the predation of native UK bumblebees (Bombus spp.) by the invasive pitcher plant species Sarracenia purpurea and discusses the potential effect of S. purpurea on native bumblebees. Specifically, it evaluates whether the extent to which bumblebees are captured varies (i) over successive years, (ii) across June and July, (iii) with density of distribution of pitchers or (iv) with bumblebee gender. Pitcher contents were examined from an established population of Sarracenia purpurea growing in Dorset, UK. Results show that the total extent to which bumblebees were captured differed over the years 2012–2014 inclusive. A 1-year study in 2013 showed that more bumblebees were caught in July than in June and more bumblebees were captured when pitchers grew at high density. Results from 2013 also showed that more pitchers caught more than one bumblebee than would be expected based on a normal probability distribution and that this phenomenon affects female and male bumblebees equally. We discuss possible reasons for these results including that the bumblebees may be using S. purpurea as a resource. Further work is required to establish the exact underpinning mechanisms and the relative roles of plant and bumblebee behaviour within the relationship. Such interaction complexity may have consequences for consideration in invasive carnivorous plant management

Protein kinase C and cardiac dysfunction: a review

Heart failure (HF) is a physiological state in which cardiac output is insufficient to meet the needs of the body. It is a clinical syndrome characterized by impaired ability of the left ventricle to either fill or eject blood efficiently. HF is a disease of multiple aetiologies leading to progressive cardiac dysfunction and it is the leading cause of deaths in both developed and developing countries. HF is responsible for about 73,000 deaths in the UK each year. In the USA, HF affects 5.8 million people and 550,000 new cases are diagnosed annually. Cardiac remodelling (CD), which plays an important role in pathogenesis of HF, is viewed as stress response to an index event such as myocardial ischaemia or imposition of mechanical load leading to a series of structural and functional changes in the viable myocardium. Protein kinase C (PKC) isozymes are a family of serine/threonine kinases. PKC is a central enzyme in the regulation of growth, hypertrophy, and mediators of signal transduction pathways. In response to circulating hormones, activation of PKC triggers a multitude of intracellular events influencing multiple physiological processes in the heart, including heart rate, contraction, and relaxation. Recent research implicates PKC activation in the pathophysiology of a number of cardiovascular disease states. Few reports are available that examine PKC in normal and diseased human hearts. This review describes the structure, functions, and distribution of PKCs in the healthy and diseased heart with emphasis on the human heart and, also importantly, their regulation in heart failure

Оценка качества образования на основе компетентностного подхода

В работе представлен практический опыт оценки качества образования в новом формате компетентностного подход

Sexual dimorphism in cancer.

The incidence of many types of cancer arising in organs with non-reproductive functions is significantly higher in male populations than in female populations, with associated differences in survival. Occupational and/or behavioural factors are well-known underlying determinants. However, cellular and molecular differences between the two sexes are also likely to be important. In this Opinion article, we focus on the complex interplay that sex hormones and sex chromosomes can have in intrinsic control of cancer-initiating cell populations, the tumour microenvironment and systemic determinants of cancer development, such as the immune system and metabolism. A better appreciation of these differences between the two sexes could be of substantial value for cancer prevention as well as treatment