Effects of Natural Habitat and Season on Cursorial Spider Assemblages in Mediterranean Vineyards

ABSTRACT: Spiders are potential natural enemies of insect pests in many crops, and their species composition in the crop may be influenced by nearby natural habitats. Here, we examined the effects of the habitat type (different sampling positions within the vineyard and in the nearby natural habitat) on spider assemblages in vineyards. Spider species richness, assemblage composition, and diversity were evaluated by means of pitfall traps in early and late summer, in three commercial vineyards and their adjacent natural habitats in a Mediterranean landscape in northern Israel. We collected 688 spiders, belonging to 25 families and 61 species and morphospecies. Spider richness differed in the two seasons; more species were documented in early summer (47) than in late summer (33). The natural habitat had the highest species richness, with 34 species, while three vineyard positions were inhabited by only 27–31 species each. The natural habitat assemblage differed from the vineyard assemblages, with 15 species that were found only in the natural habitat, yet 11 species were shared by both the natural habitat and all vineyard positions. Both season (early vs. late in the cropping season) and the habitat (vineyard vs. natural) affected the spider assemblage composition. The study documents the large diversity of spiders in a Mediterranean vineyard agroecosystem. The information that we provide here is critical in assessing the potential for conservation biocontrol, where natural habitats may be a source of natural enemies for nearby vineyards.info:eu-repo/semantics/publishedVersio

Genetic Divergence of Influenza A(H3N2) Amino Acid Substitutions Mark the Beginning of the 2016-2017 Winter Season in Israel

BACKGROUND: Influenza vaccine composition is reevaluated each year due to the frequency and accumulation of genetic changes that influenza viruses undergo. The beginning of the 2016-2017 influenza surveillance period in Israel has been marked by the dominance of influenza A(H3N2). OBJECTIVES: To evaluate the type, subtype, genetic evolution and amino acid substitutions of influenza A(H3N2) viruses detected among community patients with influenza-like illness (ILI) and hospitalized patients with respiratory illness in the first weeks of the 2016-2017 influenza season. STUDY DESIGN: Respiratory samples from community patients with influenza-like illness and from hospitalized patients underwent identification, subtyping and molecular characterization. Hemagglutinin sequences were compared to the vaccine strain, phylogenetic tree was created, and amino acid substitutions were determined. RESULTS: Influenza A(H3N2) predominated during the early stages of the 2016-2017 influenza season. Noticeably, approximately 20% of community patients and 36% of hospitalized patients, positive for influenza CONCLUSIONS: Characterization of the 2016-2017 A(H3N2) influenza viruses is imperative for determining the future influenza vaccine composition

Comprehensive Cancer-Predisposition Gene Testing in an Adult Multiple Primary Tumor Series Shows a Broad Range of Deleterious Variants and Atypical Tumor Phenotypes.

Multiple primary tumors (MPTs) affect a substantial proportion of cancer survivors and can result from various causes, including inherited predisposition. Currently, germline genetic testing of MPT-affected individuals for variants in cancer-predisposition genes (CPGs) is mostly targeted by tumor type. We ascertained pre-assessed MPT individuals (with at least two primary tumors by age 60 years or at least three by 70 years) from genetics centers and performed whole-genome sequencing (WGS) on 460 individuals from 440 families. Despite previous negative genetic assessment and molecular investigations, pathogenic variants in moderate- and high-risk CPGs were detected in 67/440 (15.2%) probands. WGS detected variants that would not be (or were not) detected by targeted resequencing strategies, including low-frequency structural variants (6/440 [1.4%] probands). In most individuals with a germline variant assessed as pathogenic or likely pathogenic (P/LP), at least one of their tumor types was characteristic of variants in the relevant CPG. However, in 29 probands (42.2% of those with a P/LP variant), the tumor phenotype appeared discordant. The frequency of individuals with truncating or splice-site CPG variants and at least one discordant tumor type was significantly higher than in a control population (χ2 = 43.642; p ≤ 0.0001). 2/67 (3%) probands with P/LP variants had evidence of multiple inherited neoplasia allele syndrome (MINAS) with deleterious variants in two CPGs. Together with variant detection rates from a previous series of similarly ascertained MPT-affected individuals, the present results suggest that first-line comprehensive CPG analysis in an MPT cohort referred to clinical genetics services would detect a deleterious variant in about a third of individuals.JW is supported by a Cancer Research UK Cambridge Cancer Centre Clinical Research Training Fellowship. Funding for the NIHR BioResource – Rare diseases project was provided by the National Institute for Health Research (NIHR, grant number RG65966). ERM acknowledges support from the European Research Council (Advanced Researcher Award), NIHR (Senior Investigator Award and Cambridge NIHR Biomedical Research Centre), Cancer Research UK Cambridge Cancer Centre and Medical Research Council Infrastructure Award. The University of Cambridge has received salary support in respect of EM from the NHS in the East of England through the Clinical Academic Reserve. The views expressed are those of the authors and not necessarily those of the NHS or Department of Health. DGE is an NIHR Senior Investigator and is supported by the all Manchester NIHR Biomedical Research Centre

GWAS meta-analysis of intrahepatic cholestasis of pregnancy implicates multiple hepatic genes and regulatory elements

Intrahepatic cholestasis of pregnancy (ICP) is a pregnancy-specific liver disorder affecting 0.5–2% of pregnancies. The majority of cases present in the third trimester with pruritus, elevated serum bile acids and abnormal serum liver tests. ICP is associated with an increased risk of adverse outcomes, including spontaneous preterm birth and stillbirth. Whilst rare mutations affecting hepatobiliary transporters contribute to the aetiology of ICP, the role of common genetic variation in ICP has not been systematically characterised to date. Here, we perform genome-wide association studies (GWAS) and meta-analyses for ICP across three studies including 1138 cases and 153,642 controls. Eleven loci achieve genome-wide significance and have been further investigated and fine-mapped using functional genomics approaches. Our results pinpoint common sequence variation in liver-enriched genes and liver-specific cis-regulatory elements as contributing mechanisms to ICP susceptibility

Ovarian steroid levels in Salamandra salamandra infraimmaculata during the reproductive cycle. Gen Comp Endocrinol

Gonadal steroid levels were determined in the ovary of Salamandra salamandra infraimmaculata during the reproductive cycle in populations from a xeric region in northern Israel. Varying proportions of previtellogenic and vitellogenic oocytes were present throughout the year, and mature oocytes were present in winter and spring. The numbers of mature oocytes were greater between December and April, after parturition. The levels of 17b-estradiol and testosterone rose during oocyte vitellogenesis and maturation. Levels of progesterone and 17a-hydroxy progesterone appeared to be related to the level of vitellogenesis. Gravid females contained greater quantities of all four steroids than did nongravid females. r 1997 Academic Pres

The Adenovirus E4orf4 Protein Provides a Novel Mechanism for Inhibition of the DNA Damage Response.

The DNA damage response (DDR) is a conglomerate of pathways designed to detect DNA damage and signal its presence to cell cycle checkpoints and to the repair machinery, allowing the cell to pause and mend the damage, or if the damage is too severe, to trigger apoptosis or senescence. Various DDR branches are regulated by kinases of the phosphatidylinositol 3-kinase-like protein kinase family, including ataxia-telangiectasia mutated (ATM) and ATM- and Rad3-related (ATR). Replication intermediates and linear double-stranded genomes of DNA viruses are perceived by the cell as DNA damage and activate the DDR. If allowed to operate, the DDR will stimulate ligation of viral genomes and will inhibit virus replication. To prevent this outcome, many DNA viruses evolved ways to limit the DDR. As part of its attack on the DDR, adenovirus utilizes various viral proteins to cause degradation of DDR proteins and to sequester the MRN damage sensor outside virus replication centers. Here we show that adenovirus evolved yet another novel mechanism to inhibit the DDR. The E4orf4 protein, together with its cellular partner PP2A, reduces phosphorylation of ATM and ATR substrates in virus-infected cells and in cells treated with DNA damaging drugs, and causes accumulation of damaged DNA in the drug-treated cells. ATM and ATR are not mutually required for inhibition of their signaling pathways by E4orf4. ATM and ATR deficiency as well as E4orf4 expression enhance infection efficiency. Furthermore, E4orf4, previously reported to induce cancer-specific cell death when expressed alone, sensitizes cells to killing by sub-lethal concentrations of DNA damaging drugs, likely because it inhibits DNA damage repair. These findings provide one explanation for the cancer-specificity of E4orf4-induced cell death as many cancers have DDR deficiencies leading to increased reliance on the remaining intact DDR pathways and to enhanced susceptibility to DDR inhibitors such as E4orf4. Thus DDR inhibition by E4orf4 contributes both to the efficiency of adenovirus replication and to the ability of E4orf4 to kill cancer cells

ATM and ATR inhibit Ad replication whereas E4orf4 enhances it.

<p>(<b>A</b>) ATM-deficient A-T cells, reconstituted with WT ATM or with an empty vector, were infected with the Ad mutants <i>dl366*</i> and <i>dl366*+E4orf4</i> (30 ffu/cell), or were mock infected. An ATR inhibitor (ATRi) was added to parallel cell samples as described in the methods section. The cells were visualized 24 hrs post infection using a Zeiss Axioskop at a magnification of 100. Representative pictures of two independent experiments are shown. The percent of area covered with cells out of the total field area (ce) was determined using Image-Pro Premier 9.1 and the percent of area covered with cell clusters larger than 6000 pixels² out of total cell area (cl), was calculated using FIJI. (B) Viruses from two independent experiments performed as described in A were collected from infected cells 24 hrs post infection and their titer was determined. Data is displayed in box plots as previously described [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005420#ppat.1005420.ref072" target="_blank">72</a>] and black dots represent outliers. Statistical significance was calculated using unpaired t-test and p values of significant differences between <i>dl366*</i> and <i>dl366*+E4orf4</i> viruses are shown.</p

Loss of ATM and expression of E4orf4 accelerate Ad infection.

<p>(<b>A</b>) A-T cells and matching WT control cells were infected with the Ad mutants <i>dl366*</i> and <i>dl366*+E4orf4</i> (100 ffu/cell) or were mock infected. The cells were visualized at the indicated times post infection (p.i.) using a Zeiss Axioskop at a magnification of 100. Mock infected samples are from the 24 hrs time point. Representative pictures of two independent experiments are shown. The percent of area covered with cells out of the total field area (ce) was determined using Image-Pro Premier 9.1 and the percent of area covered with cell clusters larger than 1000 pixels² out of total cell area (cl), was calculated using FIJI. (<b>B</b>) Production of viruses in cells infected as described in A was determined by a titer assay. p.i.: post infection. Data is displayed in box plots as previously described [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005420#ppat.1005420.ref072" target="_blank">72</a>]. Statistical significance was calculated using unpaired t-test and p values of significant differences between <i>dl366*</i> and <i>dl366*+E4orf4</i> viruses are shown.</p

The effect of ATM and ATR inactivation and E4orf4 expression on various stages of Ad replication.

<p>(<b>A</b>) ATM-deficient A-T cells, reconstituted with WT ATM or with an empty vector, were infected with the Ad mutants <i>dl366*</i> and <i>dl366*+E4orf4</i>, or were mock infected. An ATR inhibitor (ATRi) was added to parallel cell samples as described in the methods section. Proteins were harvested 24 hrs later and Western blot analysis was carried out with the indicated antibodies. Three different exposures of the blot stained with a capsid-specific antibody are shown (long, short, very short). Protein levels were quantified by densitometry. Values of virus protein levels obtained by densitometry were normalized to the Tubulin loading control. The value for <i>dl366*</i> infection of A-T + VECTOR cells was defined as 1 and relative protein levels are shown beneath the relevant protein bands. (<b>B</b>) Virus DNA levels were quantified by quantitative PCR and normalized to cellular DNA represented by the <i>PRPH2</i> gene. The viral DNA level in a <i>dl366*</i> infection of A-T + WT ATM cells was defined as 1 and relative DNA levels are shown.</p

DDR inhibition by E4orf4 is PP2A-dependent.

<p>(<b>A</b>) L11 cells in which a PP2A-B55 shRNA can be transiently expressed following Dox induction were induced with Dox (+) or left untreated (-). 48 hrs later, the cells were transfected with an empty vector (-), or with a vector expressing shRNA-resistant PP2A-B55-HA (+). One day later, <i>dl366*</i> and <i>dl366*+E4orf4</i> mutant viruses were used to infect the transfected cells, and some of the cells were left uninfected (Mock). Protein extracts were prepared 24 hrs post-infection and subjected to Western blot analysis with the indicated antibodies. Quantitation and normalization were performed as described in the legend to <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005420#ppat.1005420.g001" target="_blank">Fig 1</a>. (<b>B</b>) HEK293-derived clone 13 cells containing Dox-inducible WT E4orf4 or clone 3 cells expressing an E4orf4 mutant unable to bind PP2A (R81F84A: E4orf4-mut) were induced with Dox for three hrs (+E4orf4)) or were left uninduced (-E4orf4), and were then treated with 4 μM hydroxyurea (HU) or with 25 ng per ml neocarzinostatin (NCS), or were left untreated (Control). Protein extracts were prepared after 3 hrs incubation with the drugs and subjected to Western blot analysis, using antibodies to phosphorylated and non-phosphorylated Chk1 and to E4orf4. Quantitation and normalization were performed as described above.</p