Factors shaping community assemblages and species co-occurrence of different trophic levels

Species assemblages are the results of various processes, including dispersion and habitat filtering. Disentangling the effects of these different processes is challenging for statistical analysis, especially when biotic interactions should be considered. In this study, we used plants (producers) and leafhoppers (phytophagous) as model organisms, and we investigated the relative importance of abiotic versus biotic factors that shape community assemblages, and we infer on their biotic interactions by applying three-step statistical analysis. We applied a novel statistical analysis, that is, multiblock Redundancy Analysis (mbRA, step 1) and showed that 51.8% and 54.1% of the overall variation in plant and leafhopper assemblages are, respectively, explained by the two multiblock models. The most important blocks of variables to explain the variations in plant and leafhopper assemblages were local topography and biotic factors. Variation partitioning analysis (step 2) showed that pure abiotic filtering and pure biotic processes were relatively less important than their combinations, suggesting that biotic relationships are strongly structured by abiotic conditions. Pairwise co-occurrence analysis (step 3) on generalist leafhoppers and the most common plants identified 40 segregated species pairs (mainly between plant species) and 16 aggregated pairs (mainly between leafhopper species). Pairwise analysis on specialist leafhoppers and potential host plants clearly revealed aggregated patterns. Plant segregation suggests heterogeneous resource availability and competitive interactions, while leafhopper aggregation suggests host feeding differentiation at the local level, different feeding microhabitats on host plants, and similar environmental requirements of the species. Using the novel mbRA, we disentangle for the first time the relative importance of more than five distinct groups of variables shaping local species communities. We highlighted the important role of abiotic processes mediated by bottom-up effects of plants on leafhopper communities. Our results revealed that in-field structure diversification and trophic interactions are the main factors causing the co-occurrence patterns observed.Fil: Trivellone, Valeria. Swiss Federal Institute for Forest, Snow and Landscape Research; SuizaFil: Bougeard, Stephanie. French Agency for Food, Environmental and Occupational Health Safety; FranciaFil: Giavi, Simone. Swiss Federal Institute for Forest, Snow and Landscape Research; SuizaFil: Krebs, Patrik. Swiss Federal Institute for Forest, Snow and Landscape Research; SuizaFil: Balseiro, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Centro de Investigaciones en Ciencias de la Tierra. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Centro de Investigaciones en Ciencias de la Tierra; ArgentinaFil: Dray, Stephane. Université Claude Bernard Lyon 1; FranciaFil: Moretti, Marco. Swiss Federal Institute for Forest, Snow and Landscape Research; Suiz

THE SYNTHSEQ APPROACH TO PERSONAL GENOTYPING

Inspired by the Archon X Prize for Genomics, our research project involves implementing a novel strategy for sequencing the human genome. This prize worth $10 million will be awarded to the first company to sequence 100 human genomes with 99.999$10,000 each. However, the possibility of winning the X Prize is secondary to the prospect of revolutionizing medical diagnostics. Currently, the genomic state of‐the‐art involves identifying SNPs (single nucleotide polymorphisms) that are correlated to certain diseases. Compared to such existing diagnostics, the genome‐wide, sequence‐based biomarkers that will be made possible by fast and affordable human genome sequencing are staggering. After six months of thorough investigation and development, we are pleased to present SynthSeq, a cutting‐edge, whole‐genome sequencing venture based on the novel sequencing‐bysynthesis technology. In contrast to high‐priced competitors, our inexpensive and comparatively error‐free whole genome sequencing solution will prove to be an invaluable diagnostic resource, and it will only become more valuable as advances are made in the field of molecular diagnostics. At our intended retail price of $5,000, series A investors can expect a worst‐case MIRR of 22$700 thousand. We are confident that our innovative SynthSeq technology will deliver high‐fidelity, low‐cost whole genome sequencing to as many as 3,000 customers per year as currently envisioned, with the potential for scale‐up to millions

Defects in amorphous phase-change materials

Understanding the physical origin of threshold switching and resistance drift phenomena is necessary for making a breakthrough in the performance of low-cost nanoscale technologies related to nonvolatile phase-change memories. Even though both phenomena of threshold switching and resistance drift are often attributed to localized states in the band gap, the distribution of defect states in amorphous phase-change materials (PCMs) has not received so far, the level of attention that it merits. This work presents an experimental study of defects in amorphous PCMs using modulated photocurrent experiments and photothermal deflection spectroscopy. This study of electrically switching alloys involving germanium (Ge), antimony (Sb) and tellurium (Te) such as amorphous germanium telluride (a-GeTe), a-Ge15Te85 and a-Ge2Sb2Te5 demonstrates that those compositions showing a high electrical threshold field also show a high defect density. This result supports a mechanism of recombination and field-induced generation driving threshold switching in amorphous chalcogenides. Furthermore, this work provides strong experimental evidence for complex trap kinetics during resistance drift. This work reports annihilation of deep states and an increase in shallow defect density accompanied by band gap widening in aged a-GeTe thin film

Cell-specific occupancy of an extended repertoire of CREM and CREB binding loci in male germ cells

Background: CREB and CREM are closely related factors that regulate transcription in response to various stress, metabolic and developmental signals. The CREMτ activator isoform is selectively expressed in haploid spermatids and plays an essential role in murine spermiogenesis.Results: We have used chromatin immunoprecipitation coupled to sequencing (ChIP-seq) to map CREM and CREB target loci in round spermatids from adult mouse testis and spermatogonia derived GC1-spg cells respectively. We identify more than 9000 genomic loci most of which are cell-specifically occupied. Despite the fact that round spermatids correspond to a highly specialised differentiated state, our results show that they have a remarkably accessible chromatin environment as CREM occupies more than 6700 target loci corresponding not only to the promoters of genes selectively expressed in spermiogenesis, but also of genes involved in functions specific to other cell types. The expression of only a small subset of these target genes are affected in the round spermatids of CREM knockout animals. We also identify a set of intergenic binding loci some of which are associated with H3K4 trimethylation and elongating RNA polymerase II suggesting the existence of novel CREB and CREM regulated transcripts.Conclusions: We demonstrate that CREM and CREB occupy a large number of promoters in highly cell specific manner. This is the first study of CREM target promoters directly in a physiologically relevant tissue in vivo and represents the most comprehensive experimental analysis of CREB/CREM regulatory potential to date

Preoperative radiological characterization of hepatic angiomyolipoma using magnetic resonance imaging and contrast-enhanced ultrasonography: a case report

<p>Abstract</p> <p>Introduction</p> <p>A hepatic angiomyolipoma is a rare benign tumor of the liver composed of a mixture of smooth muscle cells, blood vessels and a variable amount of adipose tissue. Differentiating them from malignant liver tumors can often be very difficult.</p> <p>Case presentation</p> <p>We report the case of a 43-year-old Caucasian man presenting with a large liver mass in the right lobe. The results of magnetic resonance imaging and contrast-enhanced ultrasonography were consistent with a well-demarcated adipose tissue- containing tumor, showing prolonged hyperperfusion in comparison with the surrounding liver tissue. Surgery was performed and the diagnosis of hepatic angiomyolipoma was made with histopathology.</p> <p>Conclusion</p> <p>Preoperative radiological characterization using magnetic resonance imaging and contrast-enhanced ultrasonography may improve diagnostic accuracy of hepatic angiomyolipoma. Identification of smooth muscle cells, blood vessels and adipose tissue with a positive immunohistochemical reaction for HMB-45 is the final evidence for an angiomyolipoma.</p

Accumulation of mutations in antibody and CD8 T cell epitopes in a B cell depleted lymphoma patient with chronic SARS-CoV-2 infection

Antibodies against the spike protein of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) can drive adaptive evolution in immunocompromised patients with chronic infection. Here we longitudinally analyze SARS-CoV-2 sequences in a B cell-depleted, lymphoma patient with chronic, ultimately fatal infection, and identify three mutations in the spike protein that dampen convalescent plasma-mediated neutralization of SARS-CoV-2. Additionally, four mutations emerge in non-spike regions encoding three CD8 T cell epitopes, including one nucleoprotein epitope affected by two mutations. Recognition of each mutant peptide by CD8 T cells from convalescent donors is reduced compared to its ancestral peptide, with additive effects resulting from double mutations. Querying public SARS-CoV-2 sequences shows that these mutations have independently emerged as homoplasies in circulating lineages. Our data thus suggest that potential impacts of CD8 T cells on SARS-CoV-2 mutations, at least in those with humoral immunodeficiency, warrant further investigation to inform on vaccine design

Multiparameter toxicity assessment of novel DOPO-derived organophosphorus flame retardants

Halogen-free organophosphorus flame retardants are considered as replacements for the phased-out class of polybrominated diphenyl ethers (PBDEs). However, toxicological information on new flame retardants is still limited. Based on their excellent flame retardation potential, we have selected three novel 9,10- dihydro-9-oxa-10-phosphaphenanthrene-10-oxide (DOPO) derivatives and assessed their toxicological profile using a battery of in vitro test systems in order to provide toxicological information before their large-scale production and use. PBDE-99, applied as a reference compound, exhibited distinct neuroselective cytotoxicity at concentrations ≥10 μM. 6-(2-((6-Oxidodibenzo[1,2]oxaphosphinin-6-yl)amino)ethoxydibenzo[1,2]oxaphosphinine-6-oxide) (ETA-DOPO) and 6,6′-(ethane-1,2-diylbis(oxy))bis(dibenzo[1,2]oxaphosphinine-6-oxide) (EG-DOPO) displayed adverse effects at concentrations >10 μM in test systems reflecting the properties of human central and peripheral nervous system neurons, as well as in a set of non-neuronal cell types. DOPO and its derivative 6,6′-(ethane-1,2-diylbis(azanediyl))bis(6H-dibenzo[1,2]oxaphosphine-6-oxide) (EDA-DOPO) were neither neurotoxic, nor did they exhibit an influence on neural crest cell migration, or on the integrity of human skin equivalents.The two compounds furthermore displayed no inflammatory activation potential, nor did they affect algae growth or daphnia viability at concentrations ≤400 μM. Based on the superior flame retardation properties,biophysical features suited for use in polyurethane foams, and low cytotoxicity of EDA-DOPO, our results suggest that it is a candidate for the replacement of currently applied flame retardants

Allelic Imbalance of Recurrently Mutated Genes in Acute Myeloid Leukaemia

The patho-mechanism of somatic driver mutations in cancer usually involves transcription, but the proportion of mutations and wild-type alleles transcribed from DNA to RNA is largely unknown. We systematically compared the variant allele frequencies of recurrently mutated genes in DNA and RNA sequencing data of 246 acute myeloid leukaemia (AML) patients. We observed that 95% of all detected variants were transcribed while the rest were not detectable in RNA sequencing with a minimum read-depth cut-off (10x). Our analysis focusing on 11 genes harbouring recurring mutations demonstrated allelic imbalance (AI) in most patients. GATA2, RUNX1, TET2, SRSF2, IDH2, PTPN11, WT1, NPM1 and CEBPA showed significant AIs. While the effect size was small in general, GATA2 exhibited the largest allelic imbalance. By pooling heterogeneous data from three independent AML cohorts with paired DNA and RNA sequencing (N = 253), we could validate the preferential transcription of GATA2-mutated alleles. Differential expression analysis of the genes with significant AI showed no significant differential gene and isoform expression for the mutated genes, between mutated and wild-type patients. In conclusion, our analyses identified AI in nine out of eleven recurrently mutated genes. AI might be a common phenomenon in AML which potentially contributes to leukaemogenesis.Peer reviewe