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Background: Echocardiography is the diagnostic modality for assessing cardiac systolic and diastolic function to diagnose and manage heart failure. However, manual interpretation of echocardiograms can be time consuming and subject to human error. Therefore, we developed a fully automated deep learning workflow to classify, segment, and annotate two-dimensional (2D) videos and Doppler modalities in echocardiograms. Methods: We developed the workflow using a training dataset of 1145 echocardiograms and an internal test set of 406 echocardiograms from the prospective heart failure research platform (Asian Network for Translational Research and Cardiovascular Trials; ATTRaCT) in Asia, with previous manual tracings by expert sonographers. We validated the workflow against manual measurements in a curated dataset from Canada (Alberta Heart Failure Etiology and Analysis Research Team; HEART; n=1029 echocardiograms), a real-world dataset from Taiwan (n=31 241), the US-based EchoNet-Dynamic dataset (n=10 030), and in an independent prospective assessment of the Asian (ATTRaCT) and Canadian (Alberta HEART) datasets (n=142) with repeated independent measurements by two expert sonographers. Findings: In the ATTRaCT test set, the automated workflow classified 2D videos and Doppler modalities with accuracies (number of correct predictions divided by the total number of predictions) ranging from 0·91 to 0·99. Segmentations of the left ventricle and left atrium were accurate, with a mean Dice similarity coefficient greater than 93% for all. In the external datasets (n=1029 to 10 030 echocardiograms used as input), automated measurements showed good agreement with locally measured values, with a mean absolute error range of 9–25 mL for left ventricular volumes, 6–10% for left ventricular ejection fraction (LVEF), and 1·8–2·2 for the ratio of the mitral inflow E wave to the tissue Doppler e' wave (E/e' ratio); and reliably classified systolic dysfunction (LVEF

Water pollution is one of the major global threats brought about by industrial, agricultural, and any other anthropogenic activity. Heavy metals represent a large group of water pollutants that can accumulate in the human body, causing cancer and mutagenic diseases. Technologies currently used to treat polluted wastewaters of heavy metals employ chemical, ion-exchange, and membrane purification methods. However, these techniques are energy-intensive due to high pressure and power requirements for membrane-based technologies, or highly selective, as in ion-exchange resins, making drinking water less affordable in developing countries. In this study, plant amyloid-carbon membranes consisting of sunflower and peanut amyloid fibrils were fabricated through a green and sustainable process and were used to remove toxic heavy metal pollutants to drinkable standards with negligible energy consumption. Protein-rich sunflower and peanut meals serve as low-cost raw materials, from which proteins were extracted, isolated, and self-assembled into functional amyloid fibrils for heavy metal removal. These amyloid fibrils were incorporated into hybrid carbon/amyloid membranes and used to filer Pt-, Cr-, and Pb-containing water to produce water of drinkable standards containing < 10 ppb heavy metals. This process can easily be upscaled due to its simplicity and minimal use of chemical reagents, pointing towards the future of low-cost yet efficient water treatment technologies., Chemical Engineering Journal, 445, ISSN:0300-9467, ISSN:1385-8947, ISSN:1873-3212, ISSN:0923-0467

Graphical abstract, Highlights • Corneal stromal dystrophies are a group of hereditary disorders caused by mutations in the TGFBI gene and affect the corneal stroma and epithelium. • The disease is characterized by the accumulation of insoluble deposits of the mutant TGFBIp leading to poor visual acuity in patients. • Mutations are hypothesized to disrupt the protein folding and stability, leading oligomerization of the mutant protein. • Current treatment relies on surgical intervention, either tissue removal or substitution, both of which are associated with disease recurrence. • The lead compounds reported here prevent/delay the atypical proteolysis of the mutant protein and the generation of amyloidogenic fragments., Corneal dystrophies are a group of genetically inherited disorders with mutations in the TGFBI gene affecting the Bowman’s membrane and the corneal stroma. The mutant TGFBIp is highly aggregation-prone and is deposited in the cornea. Depending on the type of mutation the protein deposits may vary (amyloid, amorphous powdery aggregate or a mixed form of both), making the cornea opaque and thereby decreases visual acuity. The aggregation of the mutant protein is found to be specific with a unique aggregation mechanism distinct to the cornea. The proteolytic processing of the mutant protein is reported to be different compared to the WT protein. The proteolytic processing of mutant protein gives rise to highly amyloidogenic peptide fragments. The current treatment option, available for patients, is tissue replacement surgery that is associated with high recurrence rates. The clinical need for a simple treatment option for corneal dystrophy patients has become highly essential either to prevent the protein aggregation or to dissolve the preformed aggregates. Here, we report the screening of 2500 compounds from the Maybridge RO3 fragment library using weak affinity chromatography (WAC). The primary hits from WAC were validated by 15N-HSQC NMR assays and specific regions of binding were identified. The recombinant mutant proteins (4th FAS-1 domain of R555W and H572R) were subjected to limited proteolysis by trypsin together with the lead compounds identified by NMR assays. The lead compounds (MO07617, RJF00203 and, BTB05094) were effective to delay/prevent the generation of amyloidogenic peptides in the R555W mutant and compounds (RJF00203 and BTB05094) were effective to delay/prevent the generation of amyloidogenic peptides in the H572R mutant. Thus the lead compounds reported here upon further validation and/or modification might be proposed as a potential treatment option to prevent/delay aggregation by inhibiting the formation of amyloidogenic peptides in TGFBI-corneal dystrophy.

Summary The endoplasmic reticulum (ER) stress is defined by the accumulation of unfolded proteins at the ER and perturbation at the ER membrane, known as lipid bilayer stress (LBS). In turn, ER stress triggers the unfolded protein response (UPR) to restore ER homeostasis. Here, we provide a modified protocol based on the synthetic genetic array analysis in Saccharomyces cerevisiae to identify genetic perturbations that induce the UPR by LBS. This method is adaptable to other canonical stress pathways. For complete details on the use and execution of this protocol, please refer to Ho et al. (2020), Jonikas et al. (2009) and Baryshnikova et al. (2010)., Graphical abstract, Highlights • Generation and validation of IRE1 and IRE1ΔLD query strains with a UPR reporter • Detailed protocol of query strains mated to the yeast deletion library using SGA • High-throughput measurement of reporter fluorescence levels by flow cytometry • Data analysis to identify gene deletions activating the UPR by lipid bilayer stress, The endoplasmic reticulum (ER) stress is defined by the accumulation of unfolded proteins at the ER and perturbation at the ER membrane, known as lipid bilayer stress (LBS). In turn, ER stress triggers the unfolded protein response (UPR) to restore ER homeostasis. Here, we provide a modified protocol based on the synthetic genetic array analysis in Saccharomyces cerevisiae to identify genetic perturbations that induce the UPR by LBS. This method is adaptable to other canonical stress pathways.

Recent research on the SARS-CoV-2 pandemic has exploded around the furin-cleavable polybasic insert PRRAR↓S, found within the spike protein. The insert and the receptor-binding domain, (RBD), are vital clues in the Sherlock Holmes-like investigation into the origin of the virus and in its zoonotic crossover. Based on comparative analysis of the whole genome and the sequence features of the insert and the RBD domain, the bat and the pangolin have been proposed as very likely intermediary hosts. In this study, using the various databases, in-house developed tools, sequence comparisons, structure-guided docking, and molecular dynamics simulations, we cautiously present a fresh, theoretical perspective on the SARS-CoV-2 virus activation and its intermediary host. They are a) the SARS-CoV-2 has not yet acquired a fully optimal furin binding site or this seemingly less optimal sequence, PRRARS, has been selected for survival; b) in structural models of furin complexed with peptides, PRRAR↓S binds less well and with distinct differences as compared to the all basic RRKRR↓S; c) these differences may be exploited for the design of virus-specific inhibitors; d) the novel polybasic insert of SARS-CoV-2 may be promiscuous enough to be cleaved by multiple enzymes of the human airway epithelium and tissues which may explain its unexpected broad tropism; e) the RBD domain of the feline coronavirus spike protein carries residues that are responsible for high-affinity binding of the SARS-CoV-2 to the ACE 2 receptor; f) en route zoonotic transfer, the virus may have passed through the domestic cat whose very human-like ACE2 receptor and furin may have played some role in optimizing the traits required for zoonotic transfer., Highlights • Polybasic insert of the SARS-CoV-2 spike protein is rare among several hundred proteins with a motif ‘RRARS’. • SARS CoV-2 shares furin-like site and RBD interface residues including hotspot sites, with some of the lethal form of Feline coronavirus spike protein and those from the healthy cats. • Polybasic sequence PRRARS binds less well to furin in structural models. • SARS-CoV-2 may have passed through the domestic cat during zoonotic transfer.

Plants respond to bacterial infection acutely with actin remodeling during plant immune responses. The mechanisms by which bacterial virulence factors (VFs) modulate plant actin polymerization remain enigmatic. Here, we show that plant-type-I formin serves as the molecular sensor for actin remodeling in response to two bacterial VFs: Xanthomonas campestris pv. campestris (Xcc) diffusible signal factor (DSF), and pathogen-associated molecular pattern (PAMP) flagellin in pattern-triggered immunity (PTI). Both VFs regulate actin assembly by tuning the clustering and nucleation activity of formin on the plasma membrane (PM) at the nano-sized scale. By being integrated within the cell-wall-PM-actin cytoskeleton (CW-PM-AC) continuum, the dynamic behavior and function of formins are highly dependent on each scaffold layer's composition within the CW-PM-AC continuum during both DSF and PTI signaling. Our results reveal a central mechanism for rapid actin remodeling during plant-bacteria interactions, in which bacterial signaling molecules fine tune plant formin nanoclustering in a host mechanical-structure-dependent manner. Ministry of Education (MOE) Nanyang Technological University Published version S.M. is supported by a Margdarshi Fellowship (IA/M/15/1/502018) from the DBT-Wellcome Trust Alliance and the Department of Atomic Energy (Government of India) under project no. RTI 4006 to National Centre for Biological Sciences, India. This study was supported by an NTU startup grant (M4081533) and the Singapore Ministry of Education (MOE) tiers 1 (RG32/20) and 3 (MOE2019-T3-1-012) to Y.M.

Summary TACI (transmembrane activator and calcium modulator and cyclophilin ligand interactor) plays critical roles in B cells by promoting immunoglobulin class switching and plasma cell survival. However, its expression and function in T cells remain controversial. We show here that TACI expression can be strongly induced in murine CD4+ T cells in vitro by cytokines responsible for TH17 but not TH1 or TH2 differentiation. Frequencies and numbers of TH17 cells were elevated in TACI−/− compared with wild-type mice as well as among TACI−/− versus wild-type CD4+ T cells in mixed bone marrow chimeras, arguing for a T cell-intrinsic effect in the contribution of TACI deficiency to TH17 cell accumulation. TACI−/− mice were more susceptible to severe colitis induced by dextran sodium sulfate or adoptive T cell transfer, suggesting that TACI negatively regulates TH17 function and limits intestinal inflammation in a cell-autonomous manner. Finally, transcriptomic and biochemical analyses revealed that TACI−/− CD4+ T cells exhibited enhanced activation of TH17-promoting transcription factors NFAT, IRF4, c-MAF, and JUNB. Taken together, these findings reveal an important role of TACI in constraining TH17 pathogenicity and protecting against gut disease., Graphical Abstract, Highlights • TACI expression is induced in TH17 but not TH1 or TH2 cells differentiated in vitro • TACI−/− mice have expanded TH17 and Treg populations in various organs • TACI−/− mice have enhanced susceptibility to intestinal disease • Activation of TH17-promoting transcription factors is enhanced in TACI−/− CD4+ T cells, Immunology

Summary Southeast Asia has been the hotbed for the development of drug-resistant malaria parasites, including those with resistance to artemisinin combination therapy. While mutations in the kelch propeller domain (K13 mutations) are associated with artemisinin resistance, a range of evidence suggests that other factors are critical for the establishment and subsequent transmission of resistance in the field. Here, we perform a quantitative analysis of DNA damage and repair in the malaria parasite Plasmodium falciparum and find a strong link between enhanced DNA damage repair and artemisinin resistance. This experimental observation is further supported when variations in seven known DNA repair genes are found in resistant parasites, with six of these mutations being associated with K13 mutations. Our data provide important insights on confounding factors that are important for the establishment and spread of artemisinin resistance and may explain why resistance has not yet arisen in Africa., Graphical Abstract, Highlights • High-throughput MalariaCometChip to measure DNA damage level in P. falciparum • Subpopulation of Cambodian isolates possess enhanced DNA damage repair • Important link between enhanced DNA damage repair and artemisinin resistance, Southeast Asia (SEA) has been the breeding ground for malaria drug resistance, including resistance to artemisinin, the first-line anti-malarial drug. In this study, Xiong et al. find a relationship between DNA damage repair and artemisinin resistance in SEA, leading to insights on the establishment and spread of current artemisinin resistance.

Early-life stress causes anxiogenesis and sensitivity of stress endocrine axis, facilitated by changes in the basolateral amygdala and hippocampal neurogenesis. In this report, we examined if male-like relationship between early-life stress and anxiety was recapitulated in female rats, along with related neurobiological substrates of the amygdala and the hippocampus. Maternal separation, a paradigm consistently utilized in male rats in most previously published scripts, did not cause similar behavioral consequences in females. Maternal separation caused an increase in adult hippocampal neurogenesis in females without causing substantial differences in dendritic arbors of the basolateral amygdala. Thus, female rats displayed remarkable resilience in the emotional consequences of early-life stress., Amygdala, Anxiety, Gender, Hypertrophy, Neurogenesis, Behavioral neuroscience, Nervous system, Cellular neuroscience, Neuroanatomy, Mental disorder.

For more than 40 years, metformin has been used before and during pregnancy. However, it is important to note that metformin can cross the placenta and circulate in the developing foetus. Recent studies reported that the concentration of metformin in foetal cord blood ranges from half to nearly the same concentration as in the maternal plasma. Since metformin has anti-cell growth and pro-apoptotic effects, there are persistent concerns over the use of metformin in early pregnancy. Current human studies are limited by sample size, lack of controls or, short follow-up durations. In this review, we examine the settings in which metformin can be passed on from mother to child during pregnancy and address the current controversies relating to the cellular and molecular mechanisms of metformin. Our efforts highlight the need for more data on the effects of metformin on general offspring health as well as further scrutiny into foetal development upon exposure to metformin. NRF (Natl Research Foundation, S’pore) ASTAR (Agency for Sci., Tech. and Research, S’pore) NMRC (Natl Medical Research Council, S’pore) MOH (Min. of Health, S’pore) Published version

Summary: Dendritic cells (DCs) and macrophages (Mϕs) share close developmental pathways and functional features, leading to blurring of the boundaries between these two cell lineages. However, a deeper understanding of DC and Mϕ ontogeny and more refined phenotypic and functional characterizations have helped to delineate pre-DC-derived conventional DCs (cDCs), including cDC1s and cDC2s, from monocyte-derived Mϕs. Here, we further refine DC/Mϕ cell classification and report that classically defined cDC2s contain a discrete population of monocyte-derived migratory antigen-presenting cells with Mϕ phenotype but functional DC features, including cross-presentation. : Sheng et al. describe a distinct subset of migratory antigen-presenting cells that share features characteristic of both cDC2s and macrophages. Their numbers are markedly increased in tumors, where they are able to cross-present tumor antigens, thus representing an important addition to the arsenal of known antigen-presenting cells. Keywords: dendritic cells, antigen-presenting cell, monocyte derived, cross-priming, migration, tumor microenvironment, macrophages, hybrid

Cancer cell migration and invasion involves temporal and spatial regulation of actin cytoskeleton reorganization, which is regulated by the WASP family of proteins such as N-WASP (Neural- Wiskott Aldrich Syndrome Protein). We have previously shown that expression of N-WASP was increased under hypoxic conditions. In order to characterize the regulation of N-WASP expression, we constructed an N-WASP promoter driven GFP reporter construct, N-WASPpro-GFP. Transfection of N-WASPpro-GFP construct and plasmid expressing HiF1α (Hypoxia Inducible factor 1α) enhanced the expression of GFP suggesting that increased expression of N-WASP under hypoxic conditions is mediated by HiF1α. Sequence analysis of the N-WASP promoter revealed the presence of two hypoxia response elements (HREs) characterized by the consensus sequence 5′-GCGTG-3′ at -132 bp(HRE1) and at -662 bp(HRE2) relative to transcription start site (TSS). Site-directed mutagenesis of HRE1(-132) but not HRE2(-662) abolished the HiF1α induced activation of N-WASP promoter. Similarly ChIP assay demonstrated that HiF1α bound to HRE1(-132) but not HRE2(-662) under hypoxic condition. MDA-MB-231 cells but not MDA-MB-231KD cells treated with hypoxia mimicking agent, DMOG showed enhanced gelatin degradation. Similarly MDA-MB-231KD(N-WASPpro-N-WASPR) cells expressing N-WASPR under the transcriptional regulation of WT N-WASPpro but not MDA-MB-231KD(N-WASPproHRE1-N-WASPR) cells expressing N-WASPR under the transcriptional regulation of N-WASPproHRE1 showed enhanced gelatin degradation when treated with DMOG. Thus indicating the importance of N-WASP in hypoxia induced invadopodia formation. Thus, our data demonstrates that hypoxia-induced activation of N-WASP expression is mediated by interaction of HiF1α with the HRE1(-132) and explains the role of N-WASP in hypoxia induced invadopodia formation., Highlights • Expression of N-WASP expression is enhanced under hypoxia conditions. • N-WASP is essential for hypoxia induced invasion. • HiF1α binds to hypoxia response element (HRE) in N-WASP promoter. • HRE1 is essential for hypoxia induced invadopodia activity

Recent years have seen a renaissance in the research linking inflammation and cancer with immune cells playing a central role in smouldering inflammation in the tumor microenvironment. Diverse immune cell types infiltrate the tumor microenvironment, and the dynamic tumor-immune cell interplay gives rise to a rich milieu of cytokines and growth factors. Fundamentally, this intricate cross-talk creates the conducive condition for tumor cell proliferation, survival and metastasis. Interestingly, the prominent impact of immune cells is expounded in their contrary pro-tumoral role, as well as their potential anti-cancer cellular weaponry. The latter is known as immunotherapy, a concept born out of evidence that tumors are susceptible to immune defence and that by manipulating the immune system, tumor growth can be successfully restrained. Naturally, a deeper understanding of the multifaceted roles of various immune cell types thus contributes toward developing innovative anti-cancer strategies. Therefore, in this review we first outline the roles played by the major immune cell types, such as macrophages, neutrophils, natural killer cells, T cells and B cells. We then explain the recently-explored strategies of immunomodulation and discuss some important approaches via an immunology perspective. Keywords: Cancer, Immunotherapy, Nanoparticles, Immune checkpoint, Inflammation

Summary Patients with an HNF1BS148L/+ mutation (MODY5) typically exhibit pancreatic hypoplasia. However, the molecular mechanisms are unknown due to inaccessibility of patient material and because mouse models do not fully recapitulate MODY5. Here, we differentiated MODY5 human-induced pluripotent stem cells (hiPSCs) into pancreatic progenitors, and show that the HNF1BS148L/+ mutation causes a compensatory increase in several pancreatic transcription factors, and surprisingly, a decrease in PAX6 pancreatic gene expression. The lack of suppression of PDX1, PTF1A, GATA4, and GATA6 indicates that MODY5-mediated pancreatic hypoplasia is mechanistically independent. Overexpression studies demonstrate that a compensatory increase in PDX1 gene expression is due to mutant HNF1BS148L/+ but not wild-type HNF1B or HNF1A. Furthermore, HNF1B does not appear to directly regulate PAX6 gene expression necessary for glucose tolerance. Our results demonstrate compensatory mechanisms in the pancreatic transcription factor network due to mutant HNF1BS148L/+ protein. Thus, patients typically develop MODY5 but not neonatal diabetes despite exhibiting pancreatic hypoplasia., Graphical Abstract, Highlights • HNF1BS148L/+ mutation elicits a compensatory increase in DE and pancreatic genes • MODY5-mediated pancreatic hypoplasia is independent of PDX1, PTF1A, GATA4, and GATA6 • HNF1BS148L mutation directly causes a compensatory increase in PDX1 gene expression • HNF1BS148L/+ mutation limits PAX6 expression and consequently leads to MODY5, Kulkarni, Teo, and colleagues differentiated MODY5-hiPSCs into pancreatic progenitors and demonstrated that HNF1BS148L/+ mutation elicits a compensatory mechanism in the pancreatic transcription factor network. They report that MODY5-mediated pancreatic hypoplasia is independent of PDX1, PTF1A, GATA4, and GATA6. In addition, a decrease in PAX6 gene expression may lead to MODY5 development.

In this year there is the 40th anniversary of the first publication of plant nitric oxide (NO) emission by Lowell Klepper. In the decades since then numerous milestone discoveries have revealed that NO is a multifunctional molecule in plant cells regulating both plant development and stress responses. Apropos of the anniversary, these authors aim to review and discuss the developments of past concepts in plant NO research related to NO metabolism, NO signaling, NO's action in plant growth and in stress responses and NO's interactions with other reactive compounds. Despite the long-lasting research efforts and the accumulating experimental evidences numerous questions are still needed to be answered, thus future challenges and research directions have also been drawn up., Financial background of this work was provided by the National Research, Development and Innovation Fund (Grant no. NKFI-6, K120383 and NKFI-8, KH129511). ZSK was supported by the János Bolyai Research Scholarship of the Hungarian Academy of Sciences (Grant no. BO/00751/16/8) and by UNKP-18-4 New National Excellence Program of the Ministry of Human Capacities.

International audience; Enteric viruses represent a global public health threat and are implicated in numerous foodborne andwaterborne disease outbreaks. Nonetheless, relatively little is known of their fate and stability in the environment. In this studywe used carefully validatedmethods tomonitor enteric viruses, namely adenovirus (AdV), JC polyomavirus (JCV), noroviruses (NoVs), sapovirus (SaV) and hepatitis A and E viruses (HAV and HEV) fromwastewater source to beaches and shellfish beds. Wastewater influent and effluent, surface water, sediment and shellfish samples were collected in the Conwy catchment (North Wales, UK) once a month for one year. High concentrations of AdV and JCV were found in the majority of samples, and no seasonal patterns were observed. No HAV and HEVwere detected and no related illnesses were reported in the area during the period of sampling. Noroviruses and SaV were also detected at high concentrations in wastewater and surface water, and their presence correlated with local gastroenteritis outbreaks during the spring and autumn seasons. Noroviruses were also found in estuarine sediment and in shellfish harvested for human consumption. As PCR-based methods were used for quantification, viral infectivity and degradation was estimated using a NoV capsid integrity assay. The assay revealed low-levels of viral decay in wastewater effluent compared to influent, and more significant decay in environmental waters and sediment. Results suggest that AdV and JCV may be suitable markers for the assessment of the spatial distribution of wastewater contamination in the environment; and pathogenic viruses can be directly monitored during and after reported outbreaks to prevent further environment-derived illnesses.

Summary Heterochromatin-dependent gene silencing is central to the adaptation and survival of Plasmodium falciparum malaria parasites, allowing clonally variant gene expression during blood infection in humans. By assessing genome-wide heterochromatin protein 1 (HP1) occupancy, we present a comprehensive analysis of heterochromatin landscapes across different Plasmodium species, strains, and life cycle stages. Common targets of epigenetic silencing include fast-evolving multi-gene families encoding surface antigens and a small set of conserved HP1-associated genes with regulatory potential. Many P. falciparum heterochromatic genes are marked in a strain-specific manner, increasing the parasite's adaptive capacity. Whereas heterochromatin is strictly maintained during mitotic proliferation of asexual blood stage parasites, substantial heterochromatin reorganization occurs in differentiating gametocytes and appears crucial for the activation of key gametocyte-specific genes and adaptation of erythrocyte remodeling machinery. Collectively, these findings provide a catalog of heterochromatic genes and reveal conserved and specialized features of epigenetic control across the genus Plasmodium., Graphical Abstract, Highlights • Multi-gene families are common targets of heterochromatin in malaria parasites • Conserved heterochromatic genes are rare and tend to have regulatory function • Heterochromatin is stable during asexual replication but variable between strains • Gametocyte differentiation is linked to changes in the heterochromatin landscape, Fraschka, Filarsky et al. performed a genome-wide characterization of heterochromatin organization across multiple species, strains, and life cycle stages of malaria parasites. This revealed that heterochromatic gene silencing is a conserved strategy to drive clonal variation of surface antigens and to control life cycle stage transitions and cell differentiation.

Long non-coding RNAs (lncRNAs) play important roles in cancer. They are involved in chromatin remodeling, as well as transcriptional and post-transcriptional regulation, through a variety of chromatin-based mechanisms and via cross-talk with other RNA species. lncRNAs can function as decoys, scaffolds, and enhancer RNAs. This review summarizes the characteristics of lncRNAs, including their roles, functions, and working mechanisms, describes methods for identifying and annotating lncRNAs, and discusses future opportunities for lncRNA-based therapies using antisense oligonucleotides. NRF (Natl Research Foundation, S’pore) MOE (Min. of Education, S’pore) Published version

Much remains unknown concerning the mechanism by which the splicing machinery pinpoints short exons within intronic sequences and how splicing factors are directed to their pre-mRNA targets. One probable explanation lies in differences in chromatin organization between exons and introns. Proteomic, co-immunoprecipitation, and sedimentation analyses described here indicate that SF3B1, an essential splicing component of the U2 snRNP complex, is strongly associated with nucleosomes. ChIP-seq and RNA-seq analyses reveal that SF3B1 specifically binds nucleosomes located at exonic positions. SF3B1 binding is enriched at nucleosomes positioned over short exons flanked by long introns that are also characterized by differential GC contentbetween exons and introns. Disruption of SF3B1 binding to such nucleosomes affects splicing of these exons similarly to SF3B1 knockdown. Ourfindings suggest that the association of SF3B1 with nucleosomes is functionally important for splice-site recognition and that SF3B1 conveys splicing-relevant information embedded in chromatin structure. Published version

Embryonic stem cells (ESCs) possess a distinct chromatin conformation maintained by specialized chromatin proteins. To identify chromatin regulators in ESCs, we developed a simple biochemical assay named D-CAP (differential chromatin-associated proteins), using brief micrococcal nuclease digestion of chromatin, followed by liquid chromatography tandem mass spectrometry (LC-MS/MS). Using D-CAP, we identified several differentially chromatin-associated proteins between undifferentiated and differentiated ESCs, including the chromatin remodeling protein SMARCD1. SMARCD1 depletion in ESCs led to altered chromatin and enhanced endodermal differentiation. Gene expression and chromatin immunoprecipitation sequencing (ChIP-seq) analyses suggested that SMARCD1 is both an activator and a repressor and is enriched at developmental regulators and that its chromatin binding coincides with H3K27me3. SMARCD1 knockdown caused H3K27me3 redistribution and increased H3K4me3 around the transcription start site (TSS). One of the identified SMARCD1 targets was Klf4. In SMARCD1-knockdown clones, KLF4, as well as H3K4me3 at the Klf4 locus, remained high and H3K27me3 was abolished. These results propose a role for SMARCD1 in restricting pluripotency and activating lineage pathways by regulating H3K27 methylation. Published version

Here, we provide data related to the research article entitled “Quantitative proteomics study of Aspergillus fumigatus secretome revealed deamidation of secretory enzymes” by Adav et al. (J. Proteomics (2015) [1]). Aspergillus sp. plays an important role in lignocellulosic biomass recycling. To explore biomass hydrolyzing enzymes of A. fumigatus, we profiled secretome under different carbon sources such as glucose, cellulose, xylan and starch by high throughput quantitative proteomics using isobaric tags for relative and absolute quantification (iTRAQ). The data presented here represents the detailed comparative abundances of diverse groups of biomass hydrolyzing enzymes including cellulases, hemicellulases, lignin degrading enzymes, and peptidases and proteases; and their post translational modification like deamidation. MOE (Min. of Education, S’pore) Published version

International audience; Ecological network analysis (ENA) provides a mechanistic framework for describing complex species interactions, quantifying ecosystem services, and examining the impacts of environmental change on ecosystems. In this chapter, we highlight the importance and potential of ENA in future biomonitoring programs, as current biomonitoring indicators (e.g. species richness, population abundances of targeted species) are mostly descriptive and unable to characterize the mechanisms that underpin ecosystem functioning. Measuring the robustness of multilayer networks in the long term is one way of integrating ecological metrics more generally into biomonitoring schemes to better measure biodiversity and ecosystem functioning. Ecological networks are nevertheless difficult and labour-intensive to construct using conventional approaches, especially when building multilayer networks in poorly studied ecosystems (i.e. many tropical regions). Next-generation sequencing (NGS) provides unprecedented opportunities to rapidly build highly resolved species interaction networks across multiple trophic levels, but are yet to be fully exploited. We highlight the impediments to ecologists wishing to build DNA-based ecological networks and discuss some possible solutions. Machine learning and better data sharing between ecologists represent very important areas for advances in NGS-based networks. The future of network ecology is very exciting as all the tools necessary to build highly resolved multilayer networks are now within ecologists reach.

11 páginas, 4 tablas, 5 figuras.-- Paula Méndez Fernández ... et al., Concentrations of thirty two polychlorinated biphenyls (PCBs) were determined in the blubber of five sympatric species of odontocetes stranded or by-caught along the Northwest coast of the Iberian Peninsula: common dolphin (Delphinus delphis), long-finned pilot whale (Globicephala melas), harbour porpoise (Phocoena phocoena), striped dolphin (Stenella coeruleoalba) and bottlenose dolphin (Tursiops truncatus). Multivariate analyses were applied to evaluate the ability of PCB patterns to discriminate these sympatric species and to determine which eco-biological factors influence these patterns, thus evaluating the relevance of PCB concentrations as biogeochemical tracers of feeding ecology. The five species could be separated according to their PCB patterns. Different exposure to these contaminants, a consequence of their different dietary preferences or habitats, together with potentially dissimilar metabolic capacities, likely explain these results; sex, age, habitat and the type of prey eaten were the most important eco-biological parameters of those tested. Although, no single congener has been specifically identified as a tracer of feeding ecology, 4 congeners from the 22 analysed seemed to be the most useful and around 12 congeners appear to be enough to achieve good discrimination of the cetaceans studied. Therefore, this study suggests that PCB patterns can be used as tracers for studying the feeding ecology, sources of contamination or even population structure of cetacean species from the Northwest Iberian Peninsula, P. Méndez- Fernandez was supported during the research period through a PhD grant from the Fundação do Ministério de Ciência e Tecnologia de Portugal and ANIMATE project (SFRH/BD/36766/2007) and through a Science Without Borders (CSF) young talent postdoctoral grant of the Brazilian government. G. J. Pierce acknowledges support from the EU ANIMATE project (MEXC-CT-2006-042337), University of Aveiro and Caixa Geral de Depósitos (Portugal).

Mitochondrial pathology is a seminal pathogenic hallmark of familial amyotrophic lateral sclerosis (FALS) which is extensively manifested by human patients and mutant SOD1G93A mammalian models. Rodents expressing human FALS-associated mutations successfully mimic several human disease features; although they are not as amenable to genetic and therapeutic compound screenings as non-mammalian models. In this study, we report a newly generated and characterized Drosophila model that expresses human SOD1G93A in muscle fibers. Presence of SOD1G93A in thoracic muscles causes mitochondrial pathology and impairs normal motor behavior in these flies. Use of this new FALS-24B-SOD1G93A fly model holds promise for better understanding of the mitochondrial affectation process in FALS and for the discovery of novel therapeutic compounds able to reverse mitochondrial dysfunction in this fatal disease. Accepted version

Development of DNA aptamer screens that are both simple and informative can increase the success rate of DNA aptamer selection and induce greater adoption. High eIF4e levels contribute to malignancies, thus eIF4e presents itself as a valuable target for DNA aptamer-based inhibition screen. Here, we demonstrate a method for the rapid selection of looped DNA aptamers against eIF4e by combining negative selection and purification in a single step, followed by characterization with high throughput sequencing. The resulting aptamers show functional binding to eIF4e and inhibit translation initiation in biochemical assays. When transfected into cells, eIF4e aptamers cause a dramatic loss of cell proliferation in tumor cells as seen with eIF4e knockdown with antisense oligonucleotides, shRNAs, and siRNAs, hinting at therapeutic possibilities. With the large data set provided by high throughput sequencing, we demonstrate that selection happens in waves and that sequencing data can be used to infer aptamer structure. Lastly, we show that ligation of looped aptamers can enhance their functional effects. These results demonstrate a rapid protocol to screen and optimize aptamers against macromolecules of interest. ASTAR (Agency for Sci., Tech. and Research, S’pore) Published version

Flexas, Jaume et al.-- 14 páginas, 9 figuras, 157 referencias.-- cmartin@irnase.csic.es, Mesophyll diffusion conductance to CO 2 is a key photosynthetic trait that has been studied intensively in the past years. The intention of the present review is to update knowledge of g m, and highlight the important unknown and controversial aspects that require future work. The photosynthetic limitation imposed by mesophyll conductance is large, and under certain conditions can be the most significant photosynthetic limitation. New evidence shows that anatomical traits, such as cell wall thickness and chloroplast distribution are amongst the stronger determinants of mesophyll conductance, although rapid variations in response to environmental changes might be regulated by other factors such as aquaporin conductance.Gaps in knowledge that should be research priorities for the near future include: how different is mesophyll conductance among phylogenetically distant groups and how has it evolved? Can mesophyll conductance be uncoupled from regulation of the water path? What are the main drivers of mesophyll conductance? The need for mechanistic and phenomenological models of mesophyll conductance and its incorporation in process-based photosynthesis models is also highlighted., The study was financially supported by the Estonian Ministry of Science and Education (grant SF1090065s07), the Spanish Ministry of Science and Innovation through projects BFU2008-01072 (MEFORE), AGL2009-11310/AGR, BFU2011-23294 (MECOME) and CGL2009- 13079-C02-01 (PALEOISOTREE), and the European Commission through European Regional Fund (the Estonian Center of Excellence in Environmental Adaptation), and the Marie Curie project MCERG- 246725 (FP7). J.P.F. is supported by the Ramón y Cajal program (RYC-2008-02050). A.G. had a Swiss National Science Fellowship (PA00P3 126259). M.M.B. and C.R.W are supported by Future Fellowships from the Australian Research Council (FT0992063 and FT100100024). C.D. was supported by a grant from the French government and by the cooperation project Tranzfor (Transferring Research between EU and Australia–New Zealand on Forestry and Climate Change, PIRSES-GA-2008-230793) funded by the European Union.

SummaryHigher-order chromosomal organization for transcription regulation is poorly understood in eukaryotes. Using genome-wide Chromatin Interaction Analysis with Paired-End-Tag sequencing (ChIA-PET), we mapped long-range chromatin interactions associated with RNA polymerase II in human cells and uncovered widespread promoter-centered intragenic, extragenic, and intergenic interactions. These interactions further aggregated into higher-order clusters, wherein proximal and distal genes were engaged through promoter-promoter interactions. Most genes with promoter-promoter interactions were active and transcribed cooperatively, and some interacting promoters could influence each other implying combinatorial complexity of transcriptional controls. Comparative analyses of different cell lines showed that cell-specific chromatin interactions could provide structural frameworks for cell-specific transcription, and suggested significant enrichment of enhancer-promoter interactions for cell-specific functions. Furthermore, genetically-identified disease-associated noncoding elements were found to be spatially engaged with corresponding genes through long-range interactions. Overall, our study provides insights into transcription regulation by three-dimensional chromatin interactions for both housekeeping and cell-specific genes in human cells.

Julian Gutt ... et al. -- 10 pages, 5 figures, 1 table, supplementary data https://doi.org/10.1016/j.dsr2.2010.05.024, The marine ecosystem on the eastern shelf of the Antarctic Peninsula was surveyed 5 and 12 years after the climate-induced collapse of the Larsen A and B ice shelves. An impoverished benthic fauna was discovered, that included deep-sea species presumed to be remnants from ice-covered conditions. The current structure of various ecosystem components appears to result from extremely different response rates to the change from an oligotrophic sub-ice-shelf ecosystem to a productive shelf ecosystem. Meiobenthic communities remained impoverished only inside the embayments. On local scales, macro- and mega-epibenthic diversity was generally low, with pioneer species and typical Antarctic megabenthic shelf species interspersed. Antarctic Minke whales and seals utilised the Larsen A/B area to feed on presumably newly established krill and pelagic fish biomass. Ecosystem impacts also extended well beyond the zone of ice-shelf collapse, with areas of high benthic disturbance resulting from scour by icebergs discharged from the Larsen embayments, Financial supportofANTXXIII/8 Polarstern expedition by CAML, BIANZOII, UMAC, DFGandof L.M. Gould and N.B. Palmer expeditions by NSF.Additional species identification by E.Cano (E.C.), C.DeBroyer (C.D.B.), J.-M.Gili (J.-M.G.), C.M.Lopez-Fedela Cuadra (C.M.L.), C. McClelland (C.M.), E.Rodríguez (E.R.), M.Roux (M.R.), V.Siegel, N.Teixido, H.Wägele (H.W.), helpful comments by A. Van reuse land two anonymous referees. ROV provided by MARUM/University of Bremen, oceanographic equipment by D. Gerdes.This is CAML contribution #39

E-mail addresses: fleur_ponton@hotmail.com, fponton@sydney.edu.au; International audience; Drosophila melanogaster is one of the most important genetic models and techniques such as reverse transcription quantitative real-time PCR (RT-qPCR) are being employed extensively for deciphering the genetics basis of physiological functions. In RT-qPCR, the expression levels of target genes are estimated on the basis of endogenous controls. The purpose of these reference genes is to control for variations in RNA quantity and quality. Although determination of suitable reference genes is essential to RT-qPCR studies, reports on the evaluation of reference genes in D. melanogaster studies are lacking. We analyzed the expression levels of seven candidate reference genes (Actin, EF1, Mnf, Rps20, Rpl32, Tubulin and 18S) in flies that were injured, heat-stressed, or fed different diets. Statistical analyses of variation were determined using three established software programs for reference gene selection, geNorm, NormFinder and BestKeeper. Best-ranked references genes differed across the treatments. Normalization candidacy of the selected candidate reference genes was supported by an analysis of gene expression values obtained from microarray datasets available online. The differences between the experimental treatments suggest that assessing the stability of reference gene expression patterns, determining candidates and testing their suitability is required for each experimental investigation.