Exome sequencing and arrayCGH detection of gene sequence and copy number variation between ILS and ISS mouse strains

It has been well documented that genetic factors can influence predisposition to develop alcoholism. While the underlying genomic changes may be of several types, two of the most common and disease associated are copy number variations (CNVs) and sequence alterations of protein coding regions. The goal of this study was to identify CNVs and single-nucleotide polymorphisms that occur in gene coding regions that may play a role in influencing the risk of an individual developing alcoholism. Toward this end, two mouse strains were used that have been selectively bred based on their differential sensitivity to alcohol: the Inbred long sleep (ILS) and Inbred short sleep (ISS) mouse strains. Differences in initial response to alcohol have been linked to risk for alcoholism, and the ILS/ISS strains are used to investigate the genetics of initial sensitivity to alcohol. Array comparative genomic hybridization (arrayCGH) and exome sequencing were conducted to identify CNVs and gene coding sequence differences, respectively, between ILS and ISS mice. Mouse arrayCGH was performed using catalog Agilent 1 × 244 k mouse arrays. Subsequently, exome sequencing was carried out using an Illumina HiSeq 2000 instrument. ArrayCGH detected 74 CNVs that were strain-specific (38 ILS/36 ISS), including several ISS-specific deletions that contained genes implicated in brain function and neurotransmitter release. Among several interesting coding variations detected by exome sequencing was the gain of a premature stop codon in the alpha-amylase 2B (AMY2B) gene specifically in the ILS strain. In total, exome sequencing detected 2,597 and 1,768 strain-specific exonic gene variants in the ILS and ISS mice, respectively. This study represents the most comprehensive and detailed genomic comparison of ILS and ISS mouse strains to date. The two complementary genome-wide approaches identified strain-specific CNVs and gene coding sequence variations that should provide strong candidates to contribute to the alcohol-related phenotypic differences associated with these strains.     

Biomass harvest of invasive Typha promotes plant diversity in a Great Lakes coastal wetland

Ecological and financial constraints limit restoration efforts, preventing the achievement of desired ecological outcomes. Harvesting invasive plant biomass for bioenergy has the potential to reduce feedback mechanisms that sustain invasion, while alleviating financial limitations. Typha × glauca is a highly productive invasive wetland plant that reduces plant diversity, alters ecological functioning, its impacts increase with time, and is a suitable feedstock for bioenergy. We sought to determine ecological effects of Typha utilization for bioenergy in a Great Lakes coastal wetland by testing plant community responses to harvest‐restoration treatments in stands of 2 age classes and assessing community resilience through a seed bank study. Belowground harvesting increased light penetration, diversity, and richness and decreased Typha dominance and biomass in both years post‐treatment. Aboveground harvesting increased light and reduced Typha biomass in post‐year 1 and in post‐year 2, increased diversity and richness and decreased Typha dominance. Seed bank analysis revealed that young stands (<20 years) had greater diversity, richness, seedling density, and floristic quality than old stands (>30 years). In the field, stand‐age did not affect diversity or Typha dominance, but old stands had greater Typha biomass and slightly higher richness following harvest. Harvesting Typha achieved at least 2 desirable ecological outcomes: reducing Typha dominance and increasing native plant diversity. Younger stands had greater potential for native recovery, indicated by more diverse seed banks. In similar degraded wetlands, a single harvest of Typha biomass would likely result in significant biodiversity and habitat improvements, with the potential to double plant species richness.     

A bacterial effector counteracts host autophagy by promoting degradation of an autophagy component

Beyond its role in cellular homeostasis, autophagy plays anti‐ and promicrobial roles in host–microbe interactions, both in animals and plants. One prominent role of antimicrobial autophagy is to degrade intracellular pathogens or microbial molecules, in a process termed xenophagy. Consequently, microbes evolved mechanisms to hijack or modulate autophagy to escape elimination. Although well‐described in animals, the extent to which xenophagy contributes to plant–bacteria interactions remains unknown. Here, we provide evidence that Xanthomonas campestris pv. vesicatoria (Xcv) suppresses host autophagy by utilizing type‐III effector XopL. XopL interacts with and degrades the autophagy component SH3P2 via its E3 ligase activity to promote infection. Intriguingly, XopL is targeted for degradation by defense‐related selective autophagy mediated by NBR1/Joka2, revealing a complex antagonistic interplay between XopL and the host autophagy machinery. Our results implicate plant antimicrobial autophagy in the depletion of a bacterial virulence factor and unravel an unprecedented pathogen strategy to counteract defense‐related autophagy in plant–bacteria interactions.     

The effects of ambient flow velocity,colony size,and upstream colonies on the feeding success of bryozoa. I. Bugula stolonifera Ryland,an arborescent species

The effects of ambient flow velocity, colony size, and the presence of upstream colonies on the feeding success of the arborescent bryozoan, Bugula stolonifera (Ryland), were studied. Faster ambient flow velocities were found to reduce feeding of zooids of small colonies but not of large colonies. Zooids from different regions of colonies dominated in feeding at different ambient flow velocities: upstream zooids dominated in feeding from slow ambient flow: zooids from central regions dominated in feeding from fast ambient flow. These results are interpreted with respect to the branching morphology of colonies. Finally, evidence that upstream colonies interfere with the feeding success of zooids of colonies downstream was obtained.     

Benthic macrofaunal communities in intermittent estuaries during a drought: Comparisons with permanently open estuaries

Drought conditions have prevailed in many areas of NSW since 2002. On the mid-north coast, below-average rainfall resulted in reduced riverine flows and the extended closure of intermittent estuaries within the Solitary Islands Marine Park. Patterns of structure of benthic infaunal communities were evaluated at the height of the drought to determine if they differed between closed, intermittent estuaries and permanently open estuaries within the region. Replicate van Veen grab samples were taken in the upper, mid- and lower reaches of six intermittent and three permanently open estuaries and sieved to retain the macrofauna. A range of physico-chemical measures was also taken at each sampling time. Multivariate analyses of assemblage data revealed a significant difference between the structure of the two estuary types and also among estuaries within each type. Differences between estuary types were attributable to small differences in the abundance of a number of taxa but also to the absence of the amphipod Urohaustorius metungi from most of the intermittent estuaries. In contrast, these small amphipods dominated communities in the lower reaches of the permanently open estuaries. Physico-chemical variables were highly variable among estuaries and were not strongly correlated with assemblage patterns. Correlations with catchment size were the strongest and, as most of the intermittent estuaries in the region are smaller than the permanently open estuaries, this confounds the interpretation of assemblage patterns in this preliminary study. In order to differentiate between the effects of catchment size and entrance status, the same estuaries need to be resurveyed during periods when at least some of the intermittent estuaries are open.     

Anti-MRSA agent discovery using Caenorhabditis elegans -based high-throughput screening

Staphylococcus aureus is a leading cause of hospital- and community-acquired infections. Despite current advances in antimicrobial chemotherapy, the infections caused by S. aureus remain challenging due to their ability to readily develop resistance. Indeed, antibiotic resistance, exemplified by methicillin-resistant S. aureus (MRSA) is a top threat to global health security. Furthermore, the current rate of antibiotic discovery is much slower than the rate of antibiotic-resistance development. It seems evident that the conventional in vitro bacterial growth-based screening strategies can no longer effectively supply new antibiotics at the rate needed to combat bacterial antibiotic-resistance. To overcome this antibiotic resistance crisis, screening assays based on host–pathogen interactions have been developed. In particular, the free-living nematode Caenorhabditis elegans has been used for drug screening against MRSA. In this review, we will discuss the general principles of the C. elegans-based screening platform and will highlight its unique strengths by comparing it with conventional antibiotic screening platforms. We will outline major hits from high-throughput screens of more than 100,000 small molecules using the C. elegans–MRSA infection assay and will review the mode-of-action of the identified hit compounds. Lastly, we will discuss the potential of a C. elegans-based screening strategy as a paradigm shift screening platform.     

Substrate binding to Src: A new perspective on tyrosine kinase substrate recognition from NMR and molecular dynamics

Most signal transduction pathways in humans are regulated by protein kinases through phosphorylation of their protein substrates. Typical eukaryotic protein kinases are of two major types: those that phosphorylate‐specific sequences containing tyrosine (~90 kinases) and those that phosphorylate either serine or threonine (~395 kinases). The highly conserved catalytic domain of protein kinases comprises a smaller N lobe and a larger C lobe separated by a cleft region lined by the activation loop. Prior studies find that protein tyrosine kinases recognize peptide substrates by binding the polypeptide chain along the C‐lobe on one side of the activation loop, while serine/threonine kinases bind their substrates in the cleft and on the side of the activation loop opposite to that of the tyrosine kinases. Substrate binding structural studies have been limited to four families of the tyrosine kinase group, and did not include Src tyrosine kinases. We examined peptide‐substrate binding to Src using paramagnetic‐relaxation‐enhancement NMR combined with molecular dynamics simulations. The results suggest Src tyrosine kinase can bind substrate positioning residues C‐terminal to the phosphoacceptor residue in an orientation similar to serine/threonine kinases, and unlike other tyrosine kinases. Mutagenesis corroborates this new perspective on tyrosine kinase substrate recognition. Rather than an evolutionary split between tyrosine and serine/threonine kinases, a change in substrate recognition may have occurred within the TK group of the human kinome. Protein tyrosine kinases have long been therapeutic targets, but many marketed drugs have deleterious off‐target effects. More accurate knowledge of substrate interactions of tyrosine kinases has the potential for improving drug selectivity.