bluuebunny/crossref_metadata_2025 huggingface dataset:
Different components of the RNAi machinery are required for conidiation, ascosporogenesis, virulence, DON production and fungal inhibition by exogenous dsRNA in the Head Blight pathogenFusarium graminearum
Authors: Gaffar Fatima Yousif , Imani Jafargholi , Karlovsky Petr , Koch Aline , Kogel Karl-Heinz
Published: May 2019

Gene silencing through RNA interference (RNAi) shapes many biological processes in filamentous fungi, including pathogenicity. In this study we explored the requirement of key components of fungal RNAi machinery, including DICER-like 1 and 2 (FgDCL1,FgDCL2), ARGONAUTE 1 and 2 (FgAGO1,FgAGO2), AGO-interacting proteinFgQIP (QDE2-interacting protein), RecQ helicase (FgQDE3), and four RNA-dependent RNA polymerases (FgRdRP1,FgRdRP2,FgRdRP3,FgRdRP4), in the ascomycete mycotoxin-producing fungal pathogenFusarium graminearum(Fg) for sexual and asexual multiplication, pathogenicity, and its sensitivity to double-stranded (ds)RNA. We corroborate and extend earlier findings that conidiation, ascosporogenesis and Fusarium Head Blight (FHB) symptom development require an operable RNAi machinery. The involvement of RNAi in conidiation is dependent on environmental conditions as it is detectable only under low light (< 2 µmol m−2s−1). Although both DCLs and AGOs partially share their functions, the sexual ascosporogenesis is mediated primarily byFgDCL1 andFgAGO2, whileFgDCL2 andFgAGO1 contribute to asexual conidia formation and germination.FgDCL1 andFgAGO2 also account for pathogenesis as their knock-out (KO) results in reduced FHB development. Apart from KO mutantsΔdcl2andΔago1, mutantsΔrdrp2, Δrdrp3, Δrdrp4, Δqde3andΔqipare strongly compromised for conidiation, while KO mutations in allRdPRs, QDE3andQIPstrongly affect ascosporogenesis. Analysis of trichothecenes mycotoxins in wheat kernels showed that the relative amount of deoxynivalenol (DON), calculated as [DON] per amount of fungal genomic DNA, was reduced in all spikes infected with RNAi mutants, suggesting the possibility that the fungal RNAi pathways affectFg’s DON production in wheat spikes. Moreover, gene silencing by exogenous target gene specific dsRNA (spray-induced gene silencing, SIGS) is dependent on fungal DCLs, AGOs, and QIP, but not on QDE3. Together these data show that inF. graminearumdifferent key components of the RNAi machinery are crucial in different steps of fungal development and pathogenicity.
KPHMMER: Hidden Markov Model generator for detecting KEGG PATHWAY-specific genes
Authors: Suetake Hirotaka , Kotera Masaaki
Published: May 2019

Motivation

Reinforcement of HMMER search for secondary metabolism-specific Pfam domains should contribute to discover novel biosynthetic machinery of clinically important natural products.

Results

Here we provide a Python-based command line tool, named as KPHMMER, to extract the Pfam domains that are specific in the user-defined set of pathways in the user-defined set of organisms registered in the KEGG database. KPHMMER outperformed the previous study in detecting secondary metabolism-specific Pfam domain set. Furthermore, it was proven that KPHMMER helps reduce the computational cost compared with the case using the whole Pfam-A HMM file. We believe that KPHMMER is a powerful tool enabling to deal with many other genome-sequenced species for more general purpose.

Availability

KPHMMER is implemented as a Python package freely available via the package management system “pip” and also at https://github.com/suecharo/KPHMMER

Contact

maskot@chemsys.t.u-tokyo.ac.jp
A genomic approach to inferring kinship reveals limited intergenerational dispersal in the yellow fever mosquito
Authors: Jasper Moshe , Schmidt Thomas L. , Ahmad Nazni W. , Sinkins Steven P. , Hoffmann Ary A
Published: May 2019

Understanding past dispersal and breeding events can provide insight into ecology and evolution, and can help inform strategies for conservation and the control of pest species. However, parent-offspring dispersal can be difficult to investigate in rare species and in small pest species such as mosquitoes. Here we develop a methodology for estimating parent-offspring dispersal from the spatial distribution of close kin, using pairwise kinship estimates derived from genome-wide single nucleotide polymorphisms (SNPs). SNPs were scored in 162Aedes aegypti(yellow fever mosquito) collected from eight close-set, high-rise apartment buildings in an area of Malaysia with high dengue incidence. We used the SNPs to reconstruct kinship groups across three orders of kinship. We transformed the geographical distances between all kin pairs within each kinship category into axial standard deviations of these distances, then decomposed these into components representing past dispersal events. From these components, we isolated the axial standard deviation of parent-offspring dispersal, and estimated neighbourhood area (129 m), median parent-offspring dispersal distance (75 m), and oviposition dispersal radius within a gonotrophic cycle (36 m). We also analysed genetic structure using distance-based redundancy analysis and linear regression, finding isolation by distance both within and between buildings and estimating neighbourhood size at 268 individuals. These findings indicate the scale required to suppress local outbreaks of arboviral disease and to target releases of modified mosquitoes for mosquito and disease control. Our methodology is readily implementable for studies of other species, including pests and species of conservation significance.
NGSEA: network-based gene set enrichment analysis for interpreting gene expression phenotypes with functional gene sets
Authors: Han Heonjong , Lee Sangyoung , Lee Insuk
Published: May 2019

Gene set enrichment analysis (GSEA) is a popular tool to identify underlying biological processes in clinical samples using their gene expression phenotypes. GSEA measures the enrichment of annotated gene sets that represent biological processes for differentially expressed genes (DEGs) in clinical samples. GSEA may be suboptimal for functional gene sets, however, because DEGs from the expression dataset may not be functional genes per se but dysregulated genes perturbed by bona fide functional genes. To overcome this shortcoming, we developed network-based GSEA (NGSEA), which measures the enrichment score of functional gene sets using the expression difference of not only individual genes but also their neighbors in the functional network. We found that NGSEA outperformed GSEA in identifying pathway gene sets for matched gene expression phenotypes. We also observed that NGSEA substantially improved the ability to retrieve known anti-cancer drugs from patient-derived gene expression data using drug-target gene sets compared with another method, Connectivity Map. We also repurposed FDA-approved drugs using NGSEA and experimentally validated budesonide as a chemical with anti-cancer effects for colorectal cancer. We, therefore, expect that NGSEA will facilitate both pathway interpretation of gene expression phenotypes and anti-cancer drug repositioning. NGSEA is freely available at www.inetbio.org/ngsea.
Immune Profiling Panel: a proof of concept study of a new multiplex molecular tool to assess the immune status of critically-ill patients
Authors: Tawfik Dina M. , Vachot Laurence , Bocquet Adeline , Venet Fabienne , Rimmelé Thomas , Monneret Guillaume , Blein Sophie , Montogomery Jesse L. , Hemmert Andrew C. , Pachot Alexandre , Moucadel Virginie , Marcos Javier Yugueros , Brengel-Pesce Karen , Mallet François , Textoris Julien
Published: May 2019

Background

Critical illness such as sepsis is a life-threatening syndrome defined as a dysregulated host response to infection and is characterized by patients exhibiting various impaired immune profiles. In the field of diagnosis, a gap still remains in identifying the immune profile of critically-ill patients in the ICU. The availability of an immune profiling tool holds a great potential in providing patients at high risk with more accurate and precise management. In this study, a multiplex immune profiling panel prototype was assessed for its ability to semi-quantify immune markers directly from blood, using the FilmArray® System.

Results

The Immune Profiling Panel (IPP) prototype consists of 16 biomarkers that target both the innate and adaptive immune responses, pro- and anti-inflammatory mediators as well as genes involved in diverse regulatory pathways. The analytical studies carried out on healthy volunteers showed minimal inter- and intra-variability in testing the samples across the tested lots. The majority of the assays were linear with an R2 higher than 0.8. Results from the IPP pouch were comparable to qPCR and were within the limits of agreement. Finally, quantification cycle values of the target genes were normalized against reference genes to account for the different composition of cells among specimens. The use of the selected panel of markers in IPP demonstrated various gene modulations that could distinctly differentiate three profiles: healthy, borderline mHLA-DR septic shock patients and low mHLA-DR septic shock patients.

Conclusion

The Immune Profiling Panel allowed host transcriptomic analysis of immune response biomarkers directly from whole blood in less than an hour. The use of IPP showed great potential for the development of a fully automated, rapid and easy-to-use immune profiling tool, enabling the stratification of critically-ill patients at high risk in the ICU.
Manganese/iron-supported sulfate-dependent anaerobic oxidation of methane by archaea in lake sediments
Authors: Su Guangyi , Zopfi Jakob , Yao Haoyi , Steinle Lea , Niemann Helge , Lehmann Moritz F.
Published: May 2019

Anaerobic oxidation of methane (AOM) by methanotrophic archaea is an important sink of this greenhouse gas in marine sediments. However, evidence for AOM in freshwater habitats is rare, and little is known about the pathways, electron acceptors and microbes involved. Here, we show that AOM occurs in anoxic sediments of a lake in southern Switzerland (Lake Cadagno). Combined AOM-rate and 16S rRNA gene-sequencing data suggest thatCandidatusMethanoperedens archaea are responsible for the observed methane oxidation. Members of the Methanoperedenaceae family were previously reported to conduct nitrate- or iron/manganese-dependent AOM. However, we demonstrate for the first time that the methanotrophic archaea do not necessarily rely upon these oxidants as terminal electron acceptors directly, but mainly perform canonical sulfate-dependent AOM, which under sulfate-starved conditions can be supported by metal (Mn, Fe) oxides through oxidation of reduced sulfur species to sulfate. The correspondence of high abundances of Desulfobulbaceae andCandidatusMethanoperedens at the same sediment depth confirm the interdependence of anaerobic methane-oxidizing archaea and sulfate-reducing bacteria. The relatively high abundance and widespread distribution ofCandidatusMethanoperedens in lake sediments highlight their potentially important role in mitigating methane emissions from terrestrial freshwater environments to the atmosphere, analogous to ANME-1, -2 and -3 in marine settings.
Dose-dependent functions of SWI/SNF BAF in permitting and inhibiting cell proliferationin vivo
Authors: van der Vaart Aniek , Godfrey Molly , Portegijs Vincent , van den Heuvel Sander
Published: May 2019

SWI/SNF complexes regulate transcription through chromatin remodeling and opposing gene silencing by Polycomb-group (PcG) proteins. Genes that encode SWI/SNF subunits are frequently mutated in human cancer. The selective advantage, subunit bias, and common heterozygosity of such mutations remains poorly understood. Here, we characterized how functional loss of various SWI/SNF subunits and PcG EZH2 affect proliferation-differentiation decisionsin vivo, making use of the reproducible development of the nematodeC. elegans.We applied a lineage-specific genetics strategy to create partial or complete SWI/SNF subunit loss, as well as double gene knockout with PcG EZH2. Our data show that a high SWI/SNF BAF dosage is needed to oppose Polycomb-mediated transcriptional repression and to arrest cell division during differentiation. In contrast, even in the absence of the PcG EZH2-related methyltransferase, a low level of the SWI/SNF BAF complex is necessary and sufficient to sustain cell proliferation and hyperplasia. Our data provide experimental support for the theory that during carcinogenesis partial SWI/SNF BAF loss-of-function mutations are selected because they eliminate a tumor suppressor activity while maintaining an essential transcription regulatory function.
Deep-learning enables proteome-scale identification of phase-separated protein candidates from immunofluorescence images
Authors: Yu Chunyu , Shen Boyan , Huang Qi , Shi Minglei , You Kaiqiang , Wu Congying , Chen Yang , Li Tingting
Published: May 2019

Intrinsically disordered region (IDR) analysis has been widely used in the screening of phase-separated proteins. However, the precise sequences determining phase separation remain unclear. Furthermore, a large number of phase-separated proteins that exhibit relatively low IDR content remain uncharacterized. Phase-separated proteins appear as spherical droplet structures in immunofluorescence (IF) images, which renders them distinguishable from non-phase-separated proteins. Here, we transformed the problem of phase-separated protein recognition into a binary classification problem of image recognition. In addition, we established a method named IDeepPhase to identify IF images with spherical droplet structures based on convolutional neural networks. Using IDeepPhase on proteome-scale IF images from the Human Protein Atlas database, we generated a comprehensive list of phase-separated candidates which displayed spherical droplet structures in IF images, allowing nomination of proteins, antibodies and cell lines for subsequent phase separation study.
Genomic prediction including SNP-specific variance predictors
Authors: Mouresan E. F. , Selle M. , Rönnegård L.
Published: May 2019

The amount of available biological information on the markers is constantly increasing and provides valuable insight into the underlying biology of traits of interest. This information can also be used to inform the models applied for genomic selection to improve predictions. The objective of this study was to propose a general model for genomic selection using a link function approach within the hierarchical generalized linear model framework (hglm) that can include external information on the markers. These models can be fitted using the well-established hglm package in R. Furthermore, we also present an R package (CodataGS) to fit these models, which is significantly faster than the hglm package when the number of markers largely exceeds the number of individuals. Simulated data was used to validate the proposed model. Knowledge on the location of the QTLs on the genome, with varying degree of uncertainty, was used as external information on the markers. The proposed model showed improved accuracies from 3.8% up to 23.2% compared to the SNP-BLUP method, which assumes equal variances for all markers. The performance of the proposed models depended on the genetic architecture of the trait, as traits that deviate from the infinitesimal model benefited more from the external information. Also, the gain in accuracy depended on the degree of uncertainty of the external information provided to the model. The usefulness of these type of models is expected to increase with time as more accurate information on the markers becomes available.
Application of a novel force-field to manipulate the relationship between pelvis motion and step width in human walking
Authors: Heitkamp Lauren N. , Stimpson Katy H. , Dean Jesse C.
Published: May 2019

Motion of the pelvis throughout a step predicts step width during human walking. This behavior is often considered an important component of ensuring bipedal stability, but can be disrupted in populations with neurological injuries. The purpose of this study was to determine whether a novel force-field that exerts mediolateral forces on the legs can manipulate the relationship between pelvis motion and step width, providing proof-of-concept for a future clinical intervention. We designed a force-field able to: 1) minimize the delivered mediolateral forces (Transparent mode); 2) apply mediolateral forces to assist the leg toward mechanically-appropriate step widths (Assistive mode); and 3) apply mediolateral forces to perturb the leg away from mechanically-appropriate step widths (Perturbing mode). Neurologically-intact participants were randomly assigned to either the Assistive group (n=12) or Perturbing group (n=12), and performed a series of walking trials in which they interfaced with the force-field. We quantified the step-by-step relationship between mediolateral pelvis displacement and step width using partial correlations. Walking in the Transparent force-field had a minimal effect on this relationship. However, force-field assistance directly strengthened the relationship between pelvis displacement and step width, whereas force-field perturbations weakened this relationship. Both assistance and perturbations were followed by short-lived effects during a wash-out period, in which the relationship between pelvis displacement and step width differed from the baseline value. The present results demonstrate that the link between pelvis motion and step width can be manipulated through mechanical means, which may be useful for retraining gait balance in clinical populations.
Fluorescent Sp3 Defect-Tailored Carbon Nanotubes Enable NIR-II Single Particle Imaging in Live Brain Slices at Ultra-Low Excitation Doses
Authors: Mandal Amit Kumar , Wu Xiaojian , Ferreira Joana S. , Kim Mijin , Powell Lyndsey R. , Kwon Hyejin , Groc Laurent , Wang YuHuang , Cognet Laurent
Published: May 2019

Cellular and tissue imaging in the second near-infrared window (NIR-II, ∼1000 - 1350 nm) is advantageous for in vivo studies because of low light extinction by biological constituents at these wavelengths. However, deep tissue imaging at the single molecule sensitivity has not been achieved in the NIR-II window due to lack of suitable bio-probes. Single-walled carbon nanotubes have emerged as promising near-infrared luminescent molecular bio-probes; yet, their inefficient photoluminescence (quantum yield ∼1%) drives requirements for sizeable excitation doses (∼1-10 kW/cm2) that are significantly blue-shifted from the NIR-II region (<850 nm) and may thus ultimately compromise live tissue. Here, we show that single nanotube imaging can be achieved in live brain tissue using ultralow excitation doses (∼100 W/cm2), an order of magnitude lower than those currently used. To accomplish this, we synthesized fluorescent sp3-defect tailored (6,5) carbon nanotubes which, when excited at their first order excitonic transition fluoresce brightly at ∼1160 nm. The biocompatibility of these functionalized nanotubes, which are wrapped by state-of-the-art encapsulation agents (phospholipid-polyethylene glycol), is demonstrated using standard cytotoxicity assays. Single molecule photophysical studies of these biocompatible nanotubes allowed us to identify the optimal luminescence properties in the context of biological imaging.
Bioresponsive Microspheres for On-demand Delivery of Anti-inflammatory Cytokines for Osteoarthritis
Authors: Park Eunjae , Hart Melanie , Rolauffs Bernd , Stegemann Jan P. , Annamalai Ramkumar T.
Published: May 2019

Despite innovations in surgical interventions, treatment of cartilage injury in osteoarthritic joints remains a challenge due to concomitant inflammation. Obstructing a single dominant inflammatory cytokine have shown remarkable clinical benefits in rheumatoid arthritis, and similar strategies are being suggested to target inflammatory pathways in osteoarthritis (OA). Here we describe the utility of gelatin microspheres that are responsive to arthritic flares, resulting in on-demand, and spatiotemporally controlled release of anti-inflammatory cytokines for cartilage preservation and repair. These microspheres had net negative charge potential to sequester cationic anti-inflammatory cytokines, and the magnitude of the negative charge potential increased with increase in crosslinking density. The enzymatic degradation of the microcarriers was concentration dependent. Release of anti-inflammatory cytokines from the loaded microspheres was directly correlated with the degradation of the gelatin matrix. Exposure of the IL-4 and IL-13 loaded microspheres reduced the inflammation of chondrocytes up to 80%. Hence, the delivery of these microspheres in an osteoarthritic joint can attenuate the stimulation of chondrocytes to secrete catabolic factors including proteinases and nitric oxide. The microsphere format also allows for minimally invasive delivery and is less susceptible to mechanically-induced drug release and are conformant to the intra-articular space. Consequently, bioresponsive microspheres are an effective tool for OA prevention and treatment.
Cell-Fate Determination from Embryo to Cancer Development: Genomic Mechanism Elucidated
Authors: Tsuchiya Masa , Giuliani Alessandro , Yoshikawa Kenichi
Published: May 2019

The elucidation of the how and when of a cell-fate change asks for a physically reasonable mechanism allowing to achieve a coordinated switching of thousands of genes within a small and highly packed cell nucleus. We previously demonstrated that whole genome expression is dynamically self-organized through the emergence of a critical point. Furthermore, it has been confirmed that this happens at both the cell-population and single-cell level through the physical principle of self-organized criticality.

In this paper, we further examine the genomic mechanism which determines cell-fate changes from embryo to cancer development. The state of the critical point, acting as the organizing center of cell-fate, determines whether the genome resides in a super- or sub-critical state. In the super-critical state, a specific stochastic perturbation can spread over the entire system through the ‘genome engine’ - an autonomous critical-control genomic system, whereas in the sub-critical state, the perturbation remains at a local level. We provide a consistent framework to develop a biological regulation transition theory demonstrating the cell-fate change.
The Pursuit of Pride: Outcomes achieved under Beliefs of Internal Control shape positive Affect and neural Dynamics in the vmPFC
Authors: Stolz David S , Müller-Pinzler Laura , Krach Sören , Paulus Frieder M
Published: May 2019

Experiencing events as controllable and attributing positive outcomes to own contributions is essential for human well-being. Based on classic psychological theory we test how internal control beliefs impact the affective valuation of task outcomes, neural dynamics and ensuing behavioral preferences. In three consecutive studies with independent samples we show that dynamics in self-evaluative affect specifically increase when agents believe they caused a given task outcome. We demonstrate that these outcomes engage brain networks processing self-referential information in the cortical midline. Here, activity in the ventromedial prefrontal cortex tracks outcome valence regarding both success as well as internal control, and covaries with self-evaluative affect. These affective dynamics also relate to increased functional coupling between the ventral striatum and cortical midline structures. Finally, we show that self-evaluative affect promotes preferences for control, even at a monetary cost. Our investigations extend recent models of positive affect and well-being, and emphasize that control beliefs drive intrinsic motivation.
Improved single-cell ATAC-seq reveals chromatin dynamics of in vitro corticogenesis
Authors: Mulqueen Ryan M. , DeRosa Brooke A. , Thornton Casey A. , Sayar Zeynep , Torkenczy Kristof A. , Fields Andrew J. , Wright Kevin M. , Nan Xiaolin , Ramji Ramesh , Steemers Frank J. , O’Roak Brian J. , Adey Andrew C.
Published: May 2019

Development is a complex process that requires the precise modulation of regulatory gene networks controlled through dynamic changes in the epigenome. Single-cell-omic technologies provide an avenue for understanding the mechanisms of these processes by capturing the progression of epigenetic cell states during the course of cellular differentiation using in vitro or in vivo models1. However, current single-cell epigenomic methods are limited in the information garnered per individual cell, which in turn limits their ability to measure chromatin dynamics and state shifts. Single-cell combinatorial indexing (sci-) has been applied as a strategy for identifying single-cell-omic originating libraries and removes the necessity of single-cell, single-compartment chemistry2. Here, we report an improved sci-assay for transposase accessible chromatin by sequencing (ATAC-seq), which utilizes the small molecule inhibitor Pitstop 2™ (scip-ATAC-seq)3. We demonstrate that these improvements, which theoretically could be applied to any in situ transposition method for single-cell library preparation, significantly increase the ability of transposase to enter the nucleus and generate highly complex single-cell libraries, without altering biological signal. We applied sci-ATAC-seq and scip-ATAC-seq to characterize the chromatin dynamics of developing forebrain-like organoids, an in vitro model of human corticogenesis4. Using these data, we characterized novel putative regulatory elements, compared the epigenome of the organoid model to human cortex data, generated a high-resolution pseudotemporal map of chromatin accessibility through differentiation, and measured epigenomic changes coinciding with a neurogenic fate decision point. Finally, we combined transcription factor motif accessibility with gene activity (GA) scores to directly observe the dynamics of complex regulatory programs that regulate neurogenesis through developmental pseudotime. Overall, scip-ATAC-seq increases information content per cell and bolsters the potential for future single-cell studies into complex developmental processes.
Evaluation of radioprotective effect of chickpea (Cicer arietinum) in the survival of Lasioderma serricorne (Fabricius, 1792) (Coleoptera, Anobìidae) irradiated with 60Co
Authors: Barros Adilson C. , Okazaki Kayo , Arthur Valter
Published: May 2019

We investigated the presence of natural radioprotectors in food using a new technical modality that utilizes the insect Lasioderma serricorne as a radiosensitivity bioindicator to check radioprotection properties in minimally processed chickpeas. The insects were obtained from the entomological biotherium of the Laboratory of Radiobiology and Environment of CENA-USP. They were fed with an experimental diet and just when the first generation hatched completely, the experiments were conducted. The randomly chosen control diet, consisted of three parts of wheat germ, one part of brewer’s yeast, and a slice of French bread toasted in an oven previously set up for humidity control. The diet of chickpeas consists only of whole grains crushed in a mechanical grinder to obtain flour. The result was significant for the survival of insects (p<0.0001) reared on a diet of chickpeas compared to those reared on control diet irradiated with gamma rays from 60Co in the range of 5.0 to 1500 Gy. We presented statistical evidence that the chickpea diet has radioprotective properties in the insect for gamma rays.

SUMMARY STATEMENT

The study is important because it shows that chickpea has protective properties against ionizing radiation, how to act against its biological effects and minimize them.
Elaborate expansion of syntenic V1R hotspots correlates with high species diversity in nocturnal mouse and dwarf lemurs
Authors: Hunnicutt Kelsie E. , Tiley George P. , Williams Rachel C. , Larsen Peter A. , Blanco Marina B. , Rasoloarison Rodin M. , Campbell C. Ryan , Zhu Kevin , Weisrock David W. , Matsunami Hiroaki , Yoder Anne D.
Published: May 2019

Sensory gene families are of special interest, both for what they can tell us about molecular evolution, and for what they imply as mediators of social communication. The vomeronasal type-1 receptors (V1Rs) have often been hypothesized as playing a fundamental role in driving or maintaining species boundaries given their likely function as mediators of intraspecific mate choice, particularly in nocturnal mammals. Here, we employ a comparative genomic approach for revealing patterns of V1R evolution within primates, with a special focus on the small-bodied nocturnal mouse and dwarf lemurs of Madagascar (generaMicrocebusandCheirogaleus, respectively). By doubling the existing genomic resources for strepsirrhine primates (i.e., the lemurs and lorises), we find that the highly-speciose and morphologically-cryptic mouse lemurs have experienced an elaborate proliferation of V1Rs that we argue is functionally related to their capacity for rapid lineage diversification. Contrary to a previous study that found equivalent degrees of V1R diversity in diurnal and nocturnal lemurs, our study finds a strong correlation between nocturnality and V1R elaboration, with nocturnal lemurs showing elaborate V1R repertoires and diurnal lemurs showing less diverse repertoires. Recognized subfamilies among V1Rs show unique signatures of diversifying positive selection, as might be expected if they have each evolved to respond to specific stimuli. Further, a detailed syntenic comparison of mouse lemurs with mouse (genusMus) and other mammalian outgroups shows that orthologous mammalian subfamilies, predicted to be of ancient origin, tend to cluster in a densely populated region across syntenic chromosomes that we refer to as V1R “hotspots.”
Power-law behaviour of transcription factor dynamics at the single-molecule level implies a continuum affinity model
Authors: Garcia David A. , Fettweis Gregory , Presman Diego M. , Paakinaho Ville , Jarzynski Christopher , Upadhyaya Arpita , Hager Gordon L.
Published: May 2019

Single-molecule tracking (SMT) allows the study of transcription factor (TF) dynamics in the nucleus, giving important information regarding the search and binding behaviour of these proteins in the nuclear environment. Dwell time distributions for most TFs have been described by SMT to follow bi-exponential behaviour. This is consistent with the existence of two discrete populations bound to chromatin in vivo, one non-specifically bound to chromatin (i.e. searching mode) and another specifically bound to target sites, as originally defined by decades of biochemical studies. However, alternative models have started to emerge, from multiple exponential components to power-law distributions. Here, we present an analytical pipeline with an unbiased model selection approach based on different statistical metrics to determine the model that best explains SMT data. We found that a broad spectrum of TFs (including glucocorticoid receptor, oestrogen receptor, FOXA1, CTCF) follow a power-law distribution, blurring the temporal line between non-specific and specific binding, and suggesting that productive binding may involve longer binding events than previously thought. We propose a continuum of affinities model to explain the experimental data, consistent with the movement of TFs through complex interactions with multiple nuclear domains as well as binding and searching on the chromatin template.
Interactions between the gut microbiome and mucosal immunoglobulins A, M and G in the developing infant gut
Authors: Janzon Anders , Goodrich Julia K. , Koren Omry ,   the TEDDY Study Group, Waters Jillian L. , Ley Ruth E.
Published: May 2019

Objective

Interactions between the gut microbiome and immunoglobulin (Ig) A in infancy are important for future health. IgM and IgG are also present, however, their interactions with the microbiome in the developing infant are less understood.

Design

We employed stool samples sampled 15 times in infancy from 32 healthy subjects at 4 locations in 3 countries (from the TEDDY study). We characterized patterns of microbiome development in relation to levels of IgA, IgG and IgM. For 8 infants from a single location, we FACS-sorted microbial cells from stool by Ig status. We used 16S rRNA gene profiling on full and sorted microbiomes to assess patterns of antibody coating in relation to age and other factors.

Results

All antibodies decreased in concentration with age, but were augmented by breastmilk feeding regardless of infant age. Levels of IgA correlated with the relative abundances of OTUs belonging to the Bifidobacteria and Enterobacteriaceae, which dominated the early microbiome, and IgG levels correlated with Haemophilus. The diversity of Ig-coated microbiota was influenced by breastfeeding and age, but birth mode. IgA and IgM coated the same microbiota, while IgG targeted a different subset. Blautia generally evaded antibody coating, while members of the Bifidobacteria and Enterobacteriaceae were high in IgA/M.

Conclusion

IgA/M have similar dynamics with respect to microbiome development with age, and their interactions with the microbiome are influenced by breastfeeding status. IgG generally does not coat the commensal microbiota.

What is already known on this subject?

Secretory IgA coats ~50% of microbiota in the gut

IgM and IgG are less prevalent and coat a lower fraction in the adult, dynamics in the infant gut are not well characterized.

Breastmilk is a source of IgA to the infant gut and decreases with time.

IgA coating of microbial cells in infant gut microbiome decreases over time.

What are the new findings?

Breastfeeding augments the IgA coating of the microbiome at all ages.

IgA and IgM coat many of the same cells, whereas few are coated by IgG alone.

Bifidobacteria, Enterobacteriaceae, Ruminococcus gnavus are enriched in IgA/M-coated cell fraction, Blautia is enriched in uncoated fraction.

IgG levels correlated with Haemophilus.

How might it impact on clinical practice in the foreseeable future?

Ig-coated fraction of the gut microbiome could serve as a useful tool for tracking development of the infant gut microbiome, and/or identifying aberrations to immune sensing of the microbiome.
Unveiling the multi-step solubilization mechanism of single vesicles by detergents
Authors: Dalgarno Paul A. , Juan-Colás José , Hedley Gordon J. , Piñeiro Lucas , Novo Mercedes , Gonzalez Cibran Perez , Samuel Ifor D. W. , Leake Mark C. , Johnson Steven , Al-Soufi Wajih , Penedo J. Carlos , Quinn Steven D.
Published: May 2019

The solubilization of membranes by detergents is critical for many technological applications and has become widely used in biochemistry research to induce cell rupture, extract cell constituents, and to purify, reconstitute and crystallize membrane proteins. The thermodynamic details of solubilization have been extensively investigated, but the kinetic aspects remain poorly understood. Here we used a combination of single-vesicle Förster resonance energy transfer (svFRET), fluorescence correlation spectroscopy and quartz-crystal microbalance with dissipation monitoring to access the real-time kinetics and elementary solubilization steps of sub-micron sized vesicles, which are inaccessible by conventional diffraction-limited optical methods. Real-time injection of a non-ionic detergent, Triton X, induced biphasic solubilization kinetics of surface-immobilized vesicles labelled with the Dil/DiD FRET pair. The nanoscale sensitivity accessible by svFRET allowed us to unambiguously assign each kinetic step to distortions of the vesicle structure comprising an initial fast vesicle-swelling event followed by slow lipid loss and micellization. We expect the svFRET platform to be applicable beyond the sub-micron sizes studied here and become a unique tool to unravel the complex kinetics of detergent-lipid interactions.
Degree and site of chromosomal instability define its oncogenic potential
Authors: Hoevenaar W.H.M. , Janssen A. , Quirindongo A.I. , Ma H. , Klaasen S. , Teixeira A. , Offerhaus G.J.A. , Medema R.H. , Kops G.J.P.L. , Jelluma N.
Published: May 2019

Most human cancers are aneuploid, due to a chromosomal instability (CIN) phenotype. Despite being hallmarks of cancer, however, the roles of CIN and aneuploidy in tumor formation have not unequivocally emerged from animal studies and are thus still unclear. CIN can both promote and suppress tumorigenesis, but variances in mechanisms and timings of CIN induction in different oncogenic backgrounds and associated tissues limit interpretation of the contributions of CIN. Using a novel conditional mouse model for diverse degrees of CIN, we find that a particular range is sufficient to drive very early onset spontaneous adenoma formation in the intestine, showing that CIN can act as a much more potent oncogenic driver than was previously reported. In mice predisposed to intestinal cancer (ApcMin/+), moderate but not low CIN causes a remarkable increase in adenoma burden in the entire intestinal tract, especially in the distal colon, more closely modelling human disease. Strikingly, high levels of CIN promote adenoma formation in the distal colon even more than moderate CIN does, but have no effect in the small intestine. Our results thus show that CIN can be potently oncogenic, but that certain levels of CIN can have contrasting effects in distinct tissues.
ChIP-seq of plasma cell-free nucleosomes identifies cell-of-origin gene expression programs
Authors: Sadeh Ronen , Sharkia Israa , Fialkoff Gavriel , Rahat Ayelet , Gutin Jenia , Chappleboim Alon , Nitzan Mor , Fox-Fisher Ilana , Neiman Daniel , Meler Guy , Kamari Zahala , Yaish Dayana , Peretz Tamar , Hubert Ayala , Cohen Jonatan E , Azzam Salach , Temper Mark , Grinshpun Albert , Maoz Myriam , Abu-Gazala Samir , Ya’acov Ami Ben , Shteyer Eyal , Safadi Rifaat , Kaplan Tommy , Shemer Ruth , Planer David , Galun Eithan , Glaser Benjamin , Zick Aviad , Dor Yuval , Friedman Nir
Published: May 2019

Genomic DNA is packed by histone proteins that carry a multitude of post-translational modifications that reflect cellular transcriptional state. Cell-free DNA (cfDNA) is derived from fragmented chromatin in dying cells, and as such it retains the histones markings present in the cells of origin. Here, we pioneer chromatin immunoprecipitation followed by sequencing of cell-free nucleosomes (cfChIP-seq) carrying active chromatin marks. Our results show that cfChIP-seq provides multidimensional epigenetic information that recapitulates the epigenetic and transcriptional landscape in the cells of origin. We applied cfChIP-seq to 268 samples including samples from patients with heart and liver pathologies, and 135 samples from 56 metastatic CRC patients. We show that cfChIP-seq can detect pathology-related transcriptional changes at the site of the disease, beyond the information on tissue of origin. In CRC patients we detect clinically-relevant, and patient-specific information, including transcriptionally active HER2 amplifications. cfChIP-seq provides genome-wide information and requires low sequencing depth. Altogether, we establish cell-free chromatin immunoprecipitation as an exciting modality with potential for diagnosis and interrogation of physiological and pathological processes using a simple blood test.

One Sentence Summary

ChIP-seq of plasma-circulating nucleosomes (cfChIP-seq) from a simple blood test provides detailed information about gene expression programs in human organs, and cancer.
Genetic screening for single-cell variability modulators driving therapy resistance
Authors: Torre Eduardo A. , Arai Eri , Bayatpour Sareh , Beck Lauren E. , Emert Benjamin L. , Shaffer Sydney M. , Mellis Ian A. , Fane Mitchell , Alicea Gretchen , Budinich Krista A. , Weeraratna Ashani , Shi Junwei , Raj Arjun
Published: May 2019

Cellular plasticity describes the ability of cells to transition from one set of phenotypes to another. In the context of cancer therapeutics, plasticity refers to transient fluctuations in the molecular state of tumor cells, driving the formation of rare cells primed to survive drug treatment and ultimately reprogram into a stably resistant fate. However, the biological processes governing this cellular plasticity remain unknown. We used CRISPR/Cas9 genetic screens to reveal genes that affect cell fate decisions by altering cellular plasticity across a range of functional categories. We found that cellular plasticity and cell fate decision making can be decoupled in that factors can affect cell fate decisions in both plasticity-dependent and independent manners. We discovered a novel mode of altering resistance based on cellular plasticity that, contrary to known mechanisms, pushes cells towards a more differentiated state. We further confirmed our prediction that manipulating cellular plasticity before the addition of the main therapy would result in changes in therapy resistance more than concurrent administration. Together, our results indicate that identifying pathways modulating cellular plasticity has the potential to alter cell fate decisions and may provide a new avenue for treating drug resistance.
CD38 is a good predictor of anti-PD-1 immunotherapy responsiveness in hepatocellular carcinoma
Authors: Goh Siting , Ng Harry Ho Man , Chew Valerie , Sim Xin Ni , Li Huihua , Lim Sherlly , Lim Jeffrey Chun Tatt , Loh Josh Jie Hua , Sabai Khin , Ong Clara Chong Hui , Loh Tracy , Leow Wei Qiang , Xin Joycelyn Lee Jie , Toh Han Chong , Malavasi Fabio , Tai David Wai Meng , Lee Ser Yee , Chow Pierce , Newell Evan , Choo Su Pin , Yeong Joe , Lim Tony Kiat Hon
Published: May 2019

Hepatocellular carcinoma (HCC) is the fourth leading cause of cancer-associated mortality in the world. However, with the associated low five-year survival and high recurrence rates, alternative treatment modalities specifically immunotherapy have been researched. A correlation between CD38+tumour-infiltrating leukocyte (TIL) density and improved prognosis was found in a recent study. However, studies relating to CD38 expression in immune infiltrates within tumours are limited. In the present study, we confirmed the expression of CD38 on macrophages in HCC and determined the relationship between CD38+leukocytes and lymphocytes and patient response to immunotherapy. Using immunohistochemistry, we analysed tissue samples obtained from 20 patients from Singapore with HCC prior to immunotherapy. Tumour infiltrating leukocytes expression within tumour were correlated to the responsiveness of patients to immunotherapy.

Expression of CD38 was found within the tumour cells and surrounding immune infiltrates including lymphocytes and macrophages. We then ask whether CD38 expression by the distinct cell populations may acquire theranostic relevance. Patients with higher level of CD38+immune infiltrate subsets had significantly better response to anti-PD-1 immunotherapy, and this is also true for CD38+lymphocytes within the tumour microenvironment. In particular, a cut-off of 13.0% positive out of total leukocytes and 12.4% positive out of total lymphocytes is found to be of strong predictive value of responsiveness to immunotherapy treatment, thus a strong theranostic impact is seen by using CD38 as a biomarker for anti-PD-1 therapy.

The establishment of an association between CD38 expression and the response to anti-PD-1 immunotherapy in HCC, could be applied to a larger cohort outside Singapore. These may eventually change the routine testing in clinical practice to identify HCC patients suitable for immunotherapy.
Prediction of risk scores for colorectal cancer patients from the concentration of proteins involved in mitochondrial apoptotic pathway
Authors: Lathwal Anjali , Arora Chakit , Raghava Gajendra P. S.
Published: May 2019

One of the major challenges in managing the treatment of colorectal cancer (CRC) patients is to predict risk scores or level of risk for CRC patients. In past, several biomarkers, based on concentration of proteins involved in type-2/intrinsic/mitochondrial apoptotic pathway, have been identified for prognosis of colorectal cancer patients. Recently, a prognostic tool DR MOMP has been developed that can discriminate high and low risk CRC patients with reasonably high accuracy (Hazard Ratio, HR = 5.24 and p-value = 0.0031). This prognostic tool showed an accuracy of 59.7% when used to predict favorable/unfavorable survival outcomes. In this study, we developed knowledge based models for predicting risk scores of CRC patients. Models were trained and evaluated on 134 stage III CRC patients. Firstly, we developed multiple linear regression based models using different techniques and achieved a maximum HR value of 6.34 with p-value = 0.0032 for a model developed using LassoLars technique. Secondly, models were developed using a parameter optimization technique and achieved a maximum HR value of 38.13 with p-value 0.0006. We also predicted favorable/unfavorable survival outcomes and achieved maximum prediction accuracy value of 71.64%. The performance of our models were evaluated using five-fold cross-validation technique. For providing service to the community we also developed a web server ‘CRCRpred’, to predict risk scores of CRC patients, which is freely available at https://webs.iiitd.edu.in/raghava/crcrpred.
Nociception testing during fixed-wing ambulance flights. An interventional pilot study on the effects of flight-related environmental changes on the nociception of healthy volunteers
Authors: Prottengeier Johannes , Elsner Stefan , Wehrfritz Andreas , Moritz Andreas , Schmidt Joachim , Meyer Michael
Published: May 2019

Background

The effects of environmental changes on the somato-sensory system during long-distance air ambulance flights need to be further investigated. Changes in nociceptive capacity are conceivable in light of previous studies performed under related environmental settings. We used standardized somato-sensory testing to investigate nociception in healthy volunteers during air-ambulance flights.

Methods

Twenty-five healthy individuals were submitted to a test compilation analogous to the quantitative sensory testing battery – performed during actual air-ambulance flights. Measurements were paired around the major changes of external factors during take-off/climb and descent/landing. Bland-Altman-Plots were calculated to identify possible systemic effects.

Results

Bland-Altman-analyses suggest that the thresholds of stimulus detection and pain as well as above-threshold pain along critical waypoints of travel are not subject to systemic effects but instead demonstrate random variations.

Conclusions

We provide a novel description of a real-life experimental setup and demonstrate the general feasibility of performing somato-sensory testing during ambulance flights. No systematic effects on the nociception of healthy individuals were apparent from our data. Our findings open up the possibility of future investigations into potential effects of ambulance flights on patients suffering acute or chronic pain.
CREB down-regulation in the laterodorsal thalamic nucleus deteriorates memory consolidation in rats
Authors: Xiang Wenxi , Li Tingting , Gao Tianhang , Wang Bin
Published: May 2019

The laterodorsal thalamic nucleus (LD) is believed to play roles in learning and memory, especially spatial tasks. However, the molecular mechanism that underlies the cognitive process in the LD remains unclear and needs to be investigated. So far, there is plenty of evidence indicating that plasticity has been in some of the cortical or subcortical regions closely related to the LD, particularly stimulated by external learning tasks. Therefore, the present study aimed to test the hypothesis that similar effect exists in the LD. The transcription factor, cAMP-response element binding protein (CREB), works essentially in brain plasticity by tightly regulating the transcriptional level of memory-related target genes, and the increase of activated CREB (phosphorylated CREB, p-CREB) could facilitate memory consolidation. In this study, the siRNA against CREB was synthesized to down-regulate the CREB mRNA in the LD. After Morris water maze behavioral training, CREB siRNA rats exhibited a memory deficiency, significantly diverging from the control groups. In subsequent detection, the expression of p-CREB of these memory impairment rats attenuated. These results support the hypothesis that CREB-mediated plasticity contributes to memory facilitation and consolidation in the LD.