title: Hippocampal replay reflects specific past experiences rather than a plan for subsequent choice

abstract: Executing memory-guided behavior requires both the storage of information about experience and the later recall of that information to inform choices. Awake hippocampal replay, when hippocampal neural ensembles briefly reactivate a representation related to prior experience, has been proposed to critically contribute to these memory-related processes. However, it remains unclear whether awake replay contributes to memory function by promoting the storage of past experiences, by facilitating planning based on an evaluation of those experiences, or both. We designed a dynamic spatial task which promotes replay before a memory-based choice and assessed how the content of replay related to past and future behavior. We found that replay content was decoupled from subsequent choice and instead was enriched for representations of previously rewarded locations and places that had not been recently visited, indicating a role in memory storage rather than in directly guiding subsequent behavior.


title: Comparative viral metagenomics from chicken feces and farm dust in the Netherlands

abstract: Farm animals may harbor many viral pathogens, some with zoonotic potential which can possibly cause severe clinical outcomes in animals and humans. Documenting viral content of dust may provide information of potential sources and movement of viruses. Here, we describe a dust sequencing strategy that provides detailed viral sequence characterization from farm dust samples and use this method to document the virus communities from chicken farm dust samples and paired feces collected at multiple time points during the production cycle in broiler farms in the Netherlands. From the sequencing data, Parvoviridae and Picornaviridae were the most prevalent families, detected in 85-100% of all feces and dust samples. Surprisingly large genomic diversity was identified in Picornaviridae and viruses from the Caliciviridae and Astroviridae were also obtained. This study provides a unique characterization of virus communities in farmed chickens and paired farm dust samples and our sequencing methodology enabled the recovery of viral genome sequences from farm dust, providing important tracking details for virus movement between livestock animals and their farm environment. This study serves as a proof of concept supporting that dust sampling could potentially be incorporated as part of viral metagenomic surveillance.

category: evolutionary biology


title: Establishing farm dust as a useful viral metagenomic surveillance matrix


title: Multivariate Pattern Analysis (MVPA) Reveals Distinct Neural Profiles of Frontoparietal Networks in Boys with Attention-Deficit/Hyperactivity Disorder and Boys with Persistent Depressive Disorder

abstract: Working memory deficits are common in attention-deficit/hyperactivity disorder (ADHD) and depression, two common neurodevelopmental disorders with overlapping cognitive profiles but distinct clinical presentation. Multivariate techniques have previously been utilized to understand working memory processes in functional brain networks in healthy adults, but have not yet been applied to investigate how working memory processes within the same networks differ within typical and atypical developing populations. We used multivariate pattern analysis (MVPA) to identify whether brain networks discriminated between spatial vs. verbal working memory processes in ADHD and Persistent Depressive Disorder (PDD). 36 male clinical participants and 19 typically developing (TD) boys participated in a fMRI scan while completing a verbal and a spatial working memory task. Within a priori functional brain networks (frontoparietal, default mode, salience) the TD group demonstrated differential response patterns to verbal and spatial working memory. The PDD group showed weaker differentiation than TD, with lower classification accuracies observed in primarily the left frontoparietal network. The neural profiles of the ADHD and PDD differed specifically in the SN where the ADHD groups neural profile suggests significantly less specificity in neural representations of spatial and verbal working memory. We highlight within-group classification as an innovative tool for understanding the neural mechanisms of how cognitive processes may deviate in clinical disorders, an important intermediary step towards improving translational psychiatry.

category: neuroscience


title: Distinct Neural Profiles of Frontoparietal Networks in Boys with ADHD and Boys with Persistent Depressive Disorder


title: DEVELOPMENT OF A SOYBEAN MATURITY PREDICTION MODEL FOR SOYBEAN GROWN IN AFRICAN ENVIRONMENTS

abstract: AO_SCPLOWBSTRACTC_SCPLOWTime-to-maturity (TTM) is an important trait in soybean breeding programs. However, soybean is a relatively new crop in Africa. As such, TTM information is not yet well defined as in other major producing areas. Multi Environment trials (MET) allow breeders to analyze crop performance across diverse conditions but also pose statistical challenges (e.g. unbalanced data). Modern statistical methods, e.g.. Generalized Additive Models (GAM), can flexibly smooth a range of responses while retaining observations that could be lost under other approaches. We leveraged 5 years of data from a MET breeding program in Africa to identify the best geographical and seasonal variables to explain site and genotypic differences in soybean TTM. Using soybean-cycle features (minimum temperature, daylength) along with trial geolocation (longitude, latitude), a GAM model predicted soybean TTM within {+/-} 10 days of the average observed TTM [[Formula] days post-planting]. Further, we found significant differences between cultivars (p<0.05) in TTM sensitivity to minimum temperature and daylength. Our results show promise to advance the design of maturity systems that enhance soybean planting and breeding decisions in Africa.

category: plant biology


title: Assessing the effectiveness of oxathiapiprolin towards Phytophthora agathidicida, the causal agent of kauri dieback disease

abstract: Phytophthora species cause disease and devastation of plants in ecological and horticultural settings worldwide. A recently identified species, P. agathidicida, infects and ultimately kills the treasured kauri trees that are endemic to New Zealand. Currently there are few options for controlling or treating P. agathidicida. In this study, we sought to assess the toxicity of the oomycide oxathiapiprolin against several lifecycle stages of two geographically distinct P. agathidicida isolates. Half maximal effective concentration (EC50) values were determined to be approximately 0.1 ng/ml for inhibiting mycelial growth, indicating that P. agathidicida mycelia are more sensitive to oxathiapiprolin than those from most other Phytophthora species that have been studied. Oxathiapiprolin was also highly effective at inhibiting the germination of zoospores (EC50 = 2-9 ng/ml for the two isolates) and oospores (complete inhibition at 100 ng/ml). In addition, oxathiapiprolin delayed the onset of detached kauri leaf infection in a dose-dependent manner. Collectively, the results presented here highlight the significant potential of oxathiapiprolin as a tool to aid in the control of kauri dieback disease.

category: microbiology


title: Coding Recognition of the Dose-Effect Interdependence of Small Biomolecules Encrypted on Paired Chromatographic-Based Microassay Arrays

abstract:
The discovery of small biomolecules suffers from the lack of a comprehensive framework to express the intrinsic correlation between bioactivity and contributing small molecules in complex samples with molecular and bioactivity diversity. Here, by mapping a samples 2D-HPTLC fingerprint to microplates, the paired chromatographic-based microassay arrays are created, which can be used as quasi-chip to characterize multiple attributes of chromatographic components; and as the array differential expression of the bioactivity and molecular attributes of irregular chromatographic spots for dose-effect interdependent encoding; and also as the automatic-collimated array mosaics of the multi-attributes of each component itself encrypted by its chromatographic fingerprint. Based on this homologous framework, we propose a correlating recognition strategy for small-biomolecules through their self-consistent chromatographic behavior characteristics. In the approach, the small-biomolecule recognition in diverse compounds is transformed into a constraint satisfaction problem, which is addressed through examining the dose-effect interdependence of the homologous 2D code pairs by array matching algorithm, instead of preparing diverse compound monomers of complex test sample for identifying item-by-item. Furtherly, considering the dose-effect interdependent 2D code pairs as links and the digital-specific quasimolecular ions as nodes, an extendable self-consistent framework that correlates mammalian cell phenotypic and target-based bioassays with small biomolecules is established. Therefore, the small molecule contributions and the correlations of bioactivities, as well as their pathway can be comprehensively revealed, so as to improve the reliability and efficiency of screening. This strategy was successfully applied to galangal, and practiced the high-throughput digital preliminary screening of small-biomolecules in a natural product.

HighlightRapid self-recognition of small biomolecules in diverse samples without pre-isolation Recognized by dose-effect interdependency developed from homologous TLC fingerprint Matching of HPTLC-based molecular imprinting and bioautography on microassay arrays Microarray-based differential expression of substance attributes instead of spot scan An array framework for combining phenotype-based and target-based assays with TLC-MS

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category: biochemistry


title: ExoBow: A transgenic strategy to study CD63 exosomes in vivo

abstract: Exosomes are described as central players in a myriad of biological processes. However, the available methodologies to study their function in complex biological systems in vivo are still very limited. The biodistribution of endogenously produced exosomes, the ability to trace their spontaneous flow in order to identify the cell types they interact with, remains a major challenge. New tools to identify comprehensive networks of communication established by exosomes originated in distinct cell types in vivo, are fundamental for a better understanding of their biology. Here, we describe the development of a genetically engineered mouse model that allows the expression of the mouse CD63 exosomal marker fused with one (monocolor) or up to four fluorescent proteins (multireporter), the ExoBow. The genetic design of the ExoBow transgene allows the conditional expression of the reporters in any tissue/cell-type in an inducible or non-inducible fashion. In addition, communication mediated by CD63 positive (CD63+) exosomes can be identified amongst the same tissue/cell types using the multireporter version of the model, in order to map intra-organ/tissue communication. We demonstrate the applicability of the ExoBow transgene in normal physiological conditions and in the context of cancer, using pancreas as a working model. The ExoBow comprises a unique strategy to identify intra- and inter-organ/cell-type communication mediated by CD63+ exosomes. We believe this tool will contribute for a better understanding of the complex interactions occurring in vivo that underly the biology of exosomes in health and disease.

category: cell biology


title: Differential expression of H2A isoforms contribute to tissue and lineage specificity with HIST2H2AC as a potential cancer biomarker

abstract: Recent advancements in the field of histone biology imply non-redundancy in the function of histone H2A isoforms; however, the expression of H2A isoforms in various normal tissue types, the correlation among organs and tumor/tumor type-specific expression remain poorly investigated. The profiling of sixteen H2A isoforms in eleven different normal human tissue types strongly suggests their tissue-specific or predominant expression. Further, clustering analysis shows a lineage-specific correlation of H2A isoforms. In continuation, the expression analysis in twelve human tumor types shows overexpression of HIST2H2AC. Moreover, overexpression was observed exclusively in tumor samples but not with fetal samples; highlighting the cancer-specific association of HIST2H2AC. Further, in silico analysis of TCGA pan-cancer data also showed tumor-specific over-expression of the HIST2H2AC isoform. Our findings provide insights into tissue-type-specificity of histone H2A isoforms expression patterns and advance our understanding of their importance in lineage specification and cancer.

category: cancer biology


title: A Focused Small-Molecule Screen Identifies PHA-680626 as an Amphosteric Inhibitor Disrupting the Interaction between Aurora-A and N-Myc

abstract: Neuroblastoma is a severe childhood disease, accounting for ~10% of all infant cancers. The amplification of the MYCN gene, coding for the N-Myc transcriptional factor, is an essential marker correlated with tumor progression and poor prognosis. In neuroblastoma cells, the mitotic kinase Aurora-A (AURKA), also frequently overexpressed in cancer, prevents N-Myc degradation, by directly binding to a highly conserved N-Myc region, i.e. Myc Box I. As a result, elevated levels of N-Myc, which are required for the growth of MYCN amplified cells, are observed. During the last years, it has been demonstrated that the ATP competitive inhibitors of AURKA CD532, MLN8054 and Alisertib also cause essential conformational changes in the structure of the activation loop of the kinase that prevent N-Myc binding, thus impairing the formation of the AURKA/N-Myc complex. In this study, starting from a screening of crystal structures of AURKA in complex with known inhibitors, we identified additional compounds affecting the conformation of the kinase activation loop. We assessed the ability of such compounds to disrupt the interaction between AURKA and N-Myc in vitro, using Surface Plasmon Resonance competition assays, and in tumor cell lines overexpressing MYCN, by performing Proximity Ligation Assays. Finally, their effects on N-Myc cellular levels and cell viability were investigated. Our results, identifying PHA-680626 as an amphosteric inhibitor both in vitro and MYCN overexpressing cell lines, expand the repertoire of known conformational disrupting inhibitors of the AURKA/N-Myc complex, and confirm that altering the conformation of the activation loop of AURKA with a small molecule is an effective strategy to destabilize the AURKA/N-Myc interaction in neuroblastoma cancer cells.


title: A wing growth organizer in a hemimetabolous insect suggests wing origin

abstract: The origin and evolution of insect wings remain enigmatic after a century-long discussion. Molecular dissection of wing development in hemimetabolous insects, in which the first functional wings evolved, is key to understand genetic changes required for wing evolution. We investigated Drosophila wing marker genes in the cricket, Gryllus bimaculatus, and found apterous and vestigial show critical functions in nymphal tergal identity and margin formation, respectively. We further demonstrate that margin cells in the lateral-anterior tergal region constitute a growth organizer of wing blades. Transcriptome and RNAi analyses unveiled that Wnt, Fat-Dachsous, and Hippo pathways are involved in disproportional growth of Gryllus wings. Our data collectively support the idea that tergal margin cells of a wingless ancestor gave rise to the body wall extension required for evolution of the first powered flight.

category: developmental biology


title: TRANSFER ENTROPY BASED CAUSALITY FROM HEAD MOTION TO EYE MOVEMENT

abstract: Eye movement behavior, which provides the visual information acquisition and processing, plays an important role in performing sensorimotor tasks, such as driving, by human beings in everyday life. In the procedure of performing sensorimotor tasks, eye movement is contributed through a specific coordination of head and eye in gaze changes, with head motions preceding eye movements. Notably we believe that this coordination in essence indicates a kind of causality. In this paper, we investigate transfer entropy to set up a quantity for measuring an unidirectional causality from head motion to eye movement. A normalized version of the proposed measure, demonstrated by virtual reality based psychophysical studies, behaves very well as a proxy of driving performance, suggesting that quantitative exploitation of coordination of head and eye may be an effective behaviometric of sensorimotor activity.

category: bioinformatics


title: The level of synovial human VEGFA, IL-8 and MIP-1α correlate with truncation of lubricin glycans in osteoarthritis

abstract: Osteoarthrithis (OA) is an endemic disease due to the increase of the worlds elderly population. Previously thought to be a consequence of an imbalance between cartilage degradation and biosynthesis, it is now recognized as a disease also involving inflammation, hence influencing the level of inflammatory cytokines, growth factors and chemokines. Lubricin is a mucin type molecule where its OA induced glycosylation truncation propels a deteriorating lubrication of the articular cartilage. The objective of this study was to explore the OA driven truncation of O-linked glycosylation of synovial lubricin and its cross talk with systemic and local (synovial fluid, SF) inflammation. We compared the systemic level of cytokines/chemokine in OA patients and controls plasma with their local level in SF using a 44 plex screen. The level of 27 cytokines and chemokines was consistently measured in both plasma and SF. The data showed that the levels of cytokines and chemokines in OA plasma display limited correlation to their counterpart in SF. The level of synovial IL-8 and MIP-1 and VEGFA in OA patients, but not their plasma level, where the only cytokines that displayed a significant correlation to the observed lubricin O-linked glycosylation truncation. These cytokines were also shown to be upregulated exposing fibroblast like synoviocytes from healthy and OA patients to recombinant lubricin with truncated glycans mainly consisting of Tn-antigens, while lubricin with sialylated and non-sialylated T anigens did not have any effect. The data suggest that truncated glycans of lubricin, as found in OA, promotes the synovial cytokine production and exerebate the local synovial inflammation.

category: pathology


title: A tandem-repeat dimeric RBD protein-based COVID-19 vaccine ZF2001 protects mice and nonhuman primates

abstract: A safe, efficacious and deployable vaccine is urgently needed to control COVID-19 pandemic. We report here the preclinical development of a COVID-19 vaccine candidate, ZF2001, which contains tandem-repeat dimeric receptor-binding domain (RBD) protein with alum-based adjuvant. We assessed vaccine immunogenicity and efficacy in both mice and non-human primates (NHPs). ZF2001 induced high levels of RBD-binding and SARS-CoV-2 neutralizing antibody in both mice and NHPs, and also elicited balanced TH1/TH2 cellular responses in NHPs. Two doses of ZF2001 protected Ad-hACE2-transduced mice against SARS-CoV-2 infection, as detected by reduced viral RNA and relieved lung injuries. In NHPs, vaccination of either 25 g or 50 g ZF2001 prevented infection with SARS-CoV-2 in lung, trachea and bronchi, with milder lung lesions. No evidence of disease enhancement is observed in both models. ZF2001 is being evaluated in the ongoing international multi-center Phase 3 trials (NCT04646590) and has been approved for emergency use in Uzbekistan.

category: immunology


title: Dynamics of GLP-1R peptide agonist engagement are correlated with kinetics of G protein activation

abstract: The glucagon-like peptide-1 receptor (GLP-1R) has broad physiological roles and is a validated target for treatment of metabolic disorders. Despite recent advances in GLP-1R structure elucidation, detailed mechanistic understanding of how different peptides generate profound differences in G protein-mediated signalling is still lacking. Here we have combined cryo-electron microscopy, molecular dynamics simulations, receptor mutagenesis and pharmacological assays, to interrogate the mechanism and consequences of GLP-1R binding by four peptide agonists; glucagon-like peptide-1, oxyntomodulin, exendin-4 and exendin-P5. These data revealed that distinctions in peptide N-terminal interactions and dynamics with the GLP-1R transmembrane domain are reciprocally associated with differences in the allosteric coupling to G proteins. In particular, transient interactions with residues at the base of the binding cavity correlate with enhanced kinetics for G protein activation, providing a rationale for differences in G protein-mediated signalling efficacy from distinct agonists.


title: A dynamic equilibrium between TTP and CPEB4 controls mRNA stability and inflammation resolution

abstract: Temporal control of inflammation is critical to avoid pathological developments, and is largely defined through the differential stabilities of mRNAs. While TTP-directed mRNA deadenylation is known to destabilize ARE-containing mRNAs, this mechanism alone cannot explain the variety of mRNA expression kinetics observed during inflammation resolution. Here we show that inflammation resolution requires CPEB4 expression, in vitro and in vivo. Our results identify that CPEB4-directed polyadenylation and TTP-mediated deadenylation compete during the resolutive phase of the LPS response to uncouple the degradation of pro-inflammatory mRNAs from the sustained expression of anti-inflammatory mRNAs. The outcome of this equilibrium is quantitatively defined by the relative number of CPEs and AREs in each mRNA, and further shaped by the coordinated regulation by the MAPK signalling pathway of the levels and activities of their trans-acting factors, CPEB4 and TTP. Altogether, we describe a temporal- and transcript-specific regulatory network controlling the extent of the inflammatory response.

category: molecular biology


title: Acute myeloid leukemia cells are targeted by the naturally occurring CXCR4 antagonist EPI-X4

abstract: This manuscript has been withdrawn by the authors as no consent could be achieved with regard to data contribution. Based on this no agreement on authorship and/or listing in the acknowledgement section was reached. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.


title: Contribution of SARS-CoV-2 accessory proteins to viral pathogenicity in K18 hACE2 transgenic mice

abstract:
Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) is the viral pathogen responsible for the current coronavirus disease 2019 (COVID-19) pandemic. To date, it is estimated that over 113 million individuals have been infected with SARS-CoV-2 and over 2.5 million human deaths have been recorded worldwide. Currently, three vaccines have been approved by the Food and Drug Administration for emergency use only. However much of the pathogenesis observed during SARS-CoV-2 infection remains elusive. To gain insight into the contribution of individual accessory open reading frame (ORF) proteins in SARS-CoV-2 pathogenesis, we used our recently described reverse genetics system approach to successfully engineer recombinant (r)SARS-CoV-2, where we individually removed viral 3a, 6, 7a, 7b, and 8 ORF proteins, and characterized these recombinant viruses in vitro and in vivo. Our results indicate differences in plaque morphology, with ORF deficient ({Delta}ORF) viruses producing smaller plaques than those of the wild-type (rSARS-CoV-2/WT). However, growth kinetics of {Delta}ORF viruses were like those of rSARS-CoV-2/WT. Interestingly, infection of K18 human angiotensin converting enzyme 2 (hACE2) transgenic mice with the {Delta}ORF rSARS-CoV-2 identified ORF3a and ORF6 as the major contributors of viral pathogenesis, while {Delta}ORF7a, {Delta}ORF7b and {Delta}ORF8 rSARS-CoV-2 induced comparable pathology to rSARS-CoV-2/WT. This study demonstrates the robustness of our reverse genetics system to generate rSARS-CoV-2 and the major role for ORF3a and ORF6 in viral pathogenesis, providing important information for the generation of attenuated forms of SARS-CoV-2 for their implementation as live-attenuated vaccines for the treatment of SARS-CoV-2 infection and associated COVID-19.

IMPORTANCEDespite great efforts put forward worldwide to combat the current coronavirus disease 2019 (COVID-19) pandemic, Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) continues to be a human health and socioeconomic threat. Insights into the pathogenesis of SARS-CoV-2 and contribution of viral proteins to disease outcome remains elusive. Our study aims to determine the contribution of SARS-CoV-2 accessory open reading frame (ORF) proteins in viral pathogenesis and disease outcome, and develop a synergistic platform combining our robust reverse genetics system to generate recombinant (r)SARS-CoV-2 with a validated rodent model of infection and disease. We demonstrated that SARS-CoV-2 ORF3a and ORF6 contribute to lung pathology and ultimately disease outcome in K18 hACE2 transgenic mice, while ORF7a, ORF7b, and ORF8 have little impact on disease outcome. Moreover, our combinatory platform serves as the foundation to generate attenuated forms of the virus to develop live-attenuated vaccines for the treatment of SARS-CoV-2.


title: REPRODUCTIVE SENESCENCE IMPAIRS THE ENERGY METABOLISM OF HUMAN GRANULOSA CELLS

abstract: Female age is the single greatest factor influencing reproductive performance. It is widely known that mitochondrial dysfunction plays a key role in reproductive senescence. Ovarian bioenergetics includes a sophisticated metabolic synergism between oocytes and human mural granulosa cells (GCs), which is crucial for oocyte maturation during follicular growth. These cells are believed to be potential biomarkers of oocyte quality. It has been proposed that alterations in their energy metabolism could lead to infertility. We investigated if there is an age-related effect on the energy metabolism of human mural granulosa cells. We performed an observational prospective cohort and experimental study including 127 women that underwent in vitro fertilization cycles allocated to two groups: a control group comprising oocyte donors aged less than 35 years and a group of infertile women aged over 38 years. The bioenergetics of cumulus cells and purified mural GCs were determined from oxidative phosphorylation parameters, aerobic glycolysis and adenine nucleotide levels. We have found that human mural GCs and cumulus cells present a high glycolytic profile and that the follicular fluid is critical to sustain their energy metabolism. GCs from older women present lower mitochondrial respiration and glycolysis than those from young donors which is not accompanied by a lower respiratory capacity. The diminished energy metabolism leads to a decrease in the total cellular energy charge. We conclude that, as women age, mural granulosa cells exhibit a reduction in their energy metabolism that is likely to influence female reproductive potential.


title: Deeplasmid: Deep learning accurately separates plasmids from bacterial chromosomes

abstract:
Plasmids are mobile genetic elements that play a key role in microbial ecology and evolution by mediating horizontal transfer of important genes, such as antimicrobial resistance genes. Many microbial genomes have been sequenced by short read sequencers and have resulted in a mix of contigs that derive from plasmids or chromosomes. New tools that accurately identify plasmids are needed to elucidate new plasmid-borne genes of high biological importance. We have developed Deeplasmid, a deep learning tool for distinguishing plasmids from bacterial chromosomes based on the DNA sequence and its encoded biological data. It requires as input only assembled sequences generated by any sequencing platform and assembly algorithm and its runtime scales linearly with the number of assembled sequences. Deeplasmid achieves an AUC-ROC of over 93%, and it was much more precise than the state-of-the-art methods. Finally, as a proof of concept, we used Deeplasmid to predict new plasmids in the fish pathogen Yersinia ruckeri ATCC 29473 that has no annotated plasmids. Deeplasmid predicted with high reliability that a long assembled contig is part of a plasmid. Using long read sequencing we indeed validated the existence of a 102 Kbp long plasmid, demonstrating Deeplasmids ability to detect novel plasmids.

AvailabilityThe software is available with a BSD license: deeplasmid.sourceforge.io. A Docker container is available on DockerHub under: billandreo/deeplasmid.

Contactwandreopoulos@lbl.gov alevy@mail.huji.ac.il


title: Reconciliation of theoretical and empirical brain criticality via network heterogeneity

abstract: Inspired by heterogeneity in biological neural networks, we explore a heterogeneous network consisting of receipt, transmission and computation layers. It reconciles the dilemma that the data analysis scheme for empirical records yields non-power laws when applied to microscopic simulation of critical neural dynamics. Detailed analysis shows that the reconciliation is due to synchronization effect of the feedforward connectivity. The network favours avalanches with denser activity in the first half of life, and the result is consistent with the experimental observation. This heterogeneous structure facilitates robust criticality against external stimuli, which implies the inappropriateness of interpreting the subcritcality signature as an indication of subcrtical dynamics. These results propose the network heterogeneity as an essential piece for understanding the brain criticality.


title: Combination adjuvants enhance recombinant protein vaccine protection against fungal infection

abstract:
The development of effective vaccines against fungal infections requires the induction of protective, pathogen-specific cell mediated immune responses. Here, we asked whether combination adjuvants based on delta inulin (Advax) formulated with TLR agonists could improve vaccine protection mediated by a fungal recombinant protein, Bl-Eng2, which itself harbors an immunodominant antigen and Dectin-2 agonist/adjuvant. We found that Bl-Eng2 formulated with Advax3 containing TLR9 agonist or Advax8, containing TLR4 agonist, provided the best protection against pulmonary infection with Blastomyces dermatitidis, being more effective than Freunds complete adjuvant or Adjuplex. Advax3 was most efficient in inducing IFN-{gamma} and IL-17 producing antigen-specific T cells that migrated to the lung upon Blastomyces dermatitidis infection. Mechanistic studies revealed Bl-Eng2/Advax3 protection was tempered by neutralization of IL-17 and particularly IFN-{gamma}. Likewise, greater numbers of lung-resident T cells producing IFN-{gamma}, IL-17, or IFN-{gamma}+ and IL-17+ correlated with fewer fungi recovered from lung. Protection was maintained after depletion of CD4+ T cells, partially reduced by depletion of CD8+ T cells, and completely eliminated after depletion of both CD4+ and CD8+ T cells. We conclude that Bl-Eng2 formulated with Advax3 is promising for eliciting vaccine-induced antifungal immunity, through a previously uncharacterized mechanism involving CD8+ and also CD4+ T cells producing IFN-{gamma} and/or IL-17. Although no licensed vaccine exists as yet against any fungal disease, these findings indicate the importance of adjuvant selection for the development of effective fungal vaccines.

IMPORTANCEFungal disease remains a challenging clinical and public health problem. Despite medical advances, invasive fungal infections have skyrocketed over the last decade and pose a mounting health threat in immune-competent and -deficient hosts with worldwide mortality rates ranking 7th, even ahead of tuberculosis. The development of safe, effective vaccines remains a major hurdle for fungi. Critical barriers to progress include the lack of defined fungal antigens and suitable adjuvants. Our research is significant in identifying adjuvant combinations that elicit optimal vaccine-induced protection when formulated with a recombinant protective antigen and uncovering the mechanistic bases of the underlaying vaccine protection, which will foster the strategic development of anti-fungal vaccines.


title: Characterization of the utility of three nebulizers in investigating infectivity of airborne viruses

abstract:
Laboratory-generated bioaerosols are widely used in aerobiology studies of viruses, however few comparisons of alternative nebulizers exist. We compared aerosol production and virus survival for a Collison nebulizer, vibrating mesh nebulizer (VMN), and hydraulic spray atomizer (HAS). We also measured the dry size distribution of the aerosols produced, calculated the droplet sizes before evaporation and the dry size distribution from normal saline solution. Dry count median diameters of 0.25, 0.63 and 0.76 {micro}m were found for normal saline from the Collison nebulizer, VMN and HSA, respectively. The volume median diameters were 2.91, 3.2 and 2.43 {micro}m, respectively. The effect of nebulization on the viability of two influenza A viruses (IAVs) (H1N1, H3N2) and human rhinovirus (HRV)-16, was assessed by direct nebulization into an SKC Biosampler. The HSA had least impact on surviving fractions (SFs) of H1N1 and H3N2 (89{+/-}5%, 94{+/-}3%), followed by the Collison nebulizer (82{+/-}2%, 82{+/-}3%). The VMN yielded SFs of 78{+/-}2% and 76{+/-}2%, respectively. Conversely, for HRV-16, the VMN produced higher SFs (86{+/-}15%). Our findings indicate that although the VMN had the greatest impact on IAV survival, it produced higher aerosol concentrations within the airborne-size range making it more suitable where high aerosol mass production is required.

ImportanceViral respiratory tract infections cause millions of lost days of work and physician visits globally, accounting for significant morbidity and mortality. Respiratory droplet and droplet nuclei from infected hosts are the substantial potential carriers of such viruses within indoor environments. Laboratory-generated bioaerosols are applied in understanding the transmission and infection of viruses, simulating the physiological aspects of bioaerosol generation in a controlled environment. However, little comparative characterization exists for nebulizers used in infectious disease aerobiology, including Collison nebulizer, Vibrating mesh nebulizer, and hydraulic spray atomizer. This study characterized the physical features of aerosols generated by laboratory nebulizers, and their performance in producing aerosols at a size relevant to airborne transmission used in infectious disease aerobiology. We also determined the impact of nebulization mechanisms of these nebulizers on the viability of human respiratory viruses, including IAV H1N1, IAV H3N2 and HRV-16.


title: DNA methylation aging and transcriptomic studies in horses

abstract: Human DNA methylation profiles have been used successfully to develop highly accurate biomarkers of aging ("epigenetic clocks"). Here, we describe epigenetic clocks for horses, based on methylation profiles of CpGs with flanking DNA sequences that are highly conserved between multiple mammalian species. Methylation levels of these CpGs were measured using a custom-designed Infinium array (HorvathMammalMethylChip40). We generated 336 DNA methylation profiles from 42 different horse tissues and body parts, which we used to develop five epigenetic clocks for horses: a multi-tissue clock, a blood clock, a liver clock and two dual-species clocks that apply to both horses and humans. Epigenetic age measured by these clocks show that while castration affects the basal methylation levels of individual cytosines, it does not exert a significant impact on the epigenetic aging rate of the horse. We observed that most age-related CpGs are adjacent to developmental genes. Consistently, these CpGs reside in bivalent chromatin domains and polycomb repressive targets, which are elements that control expression of developmental genes. The availability of an RNA expression atlas of these tissues allowed us to correlate CpG methylation, their corresponding contextual chromatin features and gene expression. This analysis revealed that while increased methylation of CpGs in enhancers is likely to repress gene expression, methylation of CpGs in bivalent chromatin domains on the other hand is likely to stimulate expression of the corresponding downstream loci, which are often developmental genes. This supports the notion that aging may be accompanied by increased expression of developmental genes. It is expected that the epigenetic clocks will be useful for identifying and validating anti-aging interventions for horses.


title: Long-term cross-scale comparison of grazing and mowing on plant diversity and community composition in a salt-marsh system

abstract:
O_LILand abandonment is increasing in recent decades in Europe, usually accompanied by a decline in biodiversity. Whether livestock grazing and mowing can safeguard biodiversity across spatial scales in the long term is unclear.
C_LIO_LIUsing a 48-year experiment in a salt marsh, we compared land abandonment (without grazing and mowing) and seven management regimes including cattle grazing, early season mowing, late season mowing, both early and late season mowing, and grazing plus each of the mowing regimes on plant diversity at the local (i.e. plot) and landscape scales (i.e. across plots). Also, we compared their effects on community composition (both in identities and abundances) in time and space.
C_LIO_LIUnder land abandonment, plant diversity declined in the local communities and this decline became more apparent at the landscape scale, particularly for graminoids and halophytes. All management regimes, except the late season mowing, maintained plant diversity at these scales.
C_LIO_LILocal plant communities under all treatments underwent different successional trajectories, in the end, diverged from their initial state except for that under grazing (a cyclic succession). Interannual composition change remained stable over time under land abandonment and grazing plus early season mowing. It increased over time under grazing and late season mowing, it increased in the second half of the experiment under other treatments. Vegetation homogenized in the landscape over time under land abandonment while vegetation was heterogeneous under all management regimes.
C_LIO_LISynthesis. Our experiment suggests that late season mowing may not be sustainable to conserve plant diversity in salt marshes. Other management regimes can maintain plant diversity across scales and vegetation heterogeneity in the landscape in the long term, but local community composition may change over time.
C_LI

category: ecology


title: Spatial Epigenome Sequencing at Tissue Scale and Cellular Level

abstract: Spatial biology is emerging as a new frontier of biomedical research in development and disease, but currently limited to transcriptome and a panel of proteins. Here we present spatial epigenome profiling for three histone modifications (H3K27me3, H3K4me3, H3K27ac) via next-generation sequencing by combining in-tissue CUT&Tag chemistry and microfluidic deterministic barcoding. Spatial chromatin states in mouse embryos or olfactory bulbs revealed tissue type-specific epigenetic regulations, in concordance with ENCODE reference data, but providing spatially resolved genome-wide profiles at tissue scale. Using fluorescence imaging to identify the tissue pixels (20m) each containing one nucleus allowed us to extract single-cell epigenomes in situ. Spatial chromatin state profiling in tissue may enable unprecedented opportunities to study epigenetic regulation, cell function and fate decision in normal physiology and pathogenesis.

category: genomics


title: Oligodendrocyte Precursor Cells Sculpt the Visual System by Regulating Axonal Remodeling

abstract: Many oligodendrocyte precursor cells (OPCs) do not differentiate to form myelin, suggesting additional roles of this cell population. The zebrafish optic tectum contains OPCs in regions devoid of myelin. Elimination of these OPCs impaired precise control of retinal ganglion cell axon arbor size during formation and maturation of retinotectal connectivity, and in consequence impaired visual acuity. Therefore, OPCs fine-tune neural circuit structure and function independently of their canonical role to make myelin.


title: Loss of TCF-1 regulates the production of noncanonical Tregs in a prion-like manner

abstract:
Regulatory T cells (Tregs) are suppressive immune cells used for a variety of clinical and therapeutic applications. Canonical Tregs express CD4, FOXP3, and CD25, which are considered definitive markers of Treg status when used together. However, a subset of noncanonical Tregs expressing only CD4 and FOXP3 have recently been described in some infection contexts. The transcriptional regulation of these cells is still unclear. We found that loss of TCF-1 in all T cells in mice leads to expansion of these cells in multiple tissues in a cell-intrinsic fashion. This effect was not due to aberrant expression of FOXP3, as other functional Treg markers were also expressed. In addition, presence of TCF-1-deficient cells in a chimeric mouse induced increased production of noncanonical Tregs from WT donor cells. Therefore, targeting of TCF-1 may remove suppression on this Treg lineage, increasing the yield of these cells for use in the clinic.

Summary sentenceLoss of TCF-1 causes expansion of CD25- FOXP3+ noncanonical Tregs, and TCF-1-deficient T cells induce increased production of CD25- Tregs from WT cells.


title: An Innovative antibody-based Plug-and-Play strategy for SARS-CoV-2

abstract: The novel and highly pathogenic coronavirus (SARS-CoV-2) remains a public health threat worldwide. SARS-CoV-2 enters human host lung cells via its spike protein binding to angiotensin-converting enzyme 2 (ACE2) in a process critical dependent on host protease-mediated fusion event. Thus, effective targeted therapies blocking the first step of viral fusion and cellular entry remains a critical unmet medical need to overcome disease pathology. Here we engineered and describe an antibody-based novel and targeted plug-and-play strategy, which directly competes with the proteolytic activation function of SAR-CoV-2 spike protein. The described strategy involves the engineering of furin substrate residues in IgG1 Fc-extended flexible region of spike targeting antibody. Our results with spike receptor-binding domain (RBD) targeting CR3022 antibody support blockade of the viral function using proof of concept ACE2 overexpressing cells. Our study reveals analytical, safe, and selective mechanistic insights for SARS-CoV-2 therapeutic design and is broadly applicable to the future coronaviridae family members (including mutant variants) exploiting the host protease system for cellular entry.


title: Confronting false discoveries in single-cell differential expression

abstract: Differential expression analysis in single-cell transcriptomics enables the dissection of cell-type-specific responses to perturbations such as disease, trauma, or experimental manipulation. While many statistical methods are available to identify differentially expressed genes, the principles that distinguish these methods and their performance remain unclear. Here, we show that the relative performance of these methods is contingent on their ability to account for variation between biological replicates. Methods that ignore this inevitable variation are biased and prone to false discoveries. Indeed, the most widely used methods can discover hundreds of differentially expressed genes in the absence of biological differences. Our results suggest an urgent need for a paradigm shift in the methods used to perform differential expression analysis in single-cell data.


title: Life-history evolution of class-structured populations in fluctuating environments

abstract: What is the influence of periodic environmental fluctuations on life-history evolution? We present a general theoretical framework to understand and predict the long-term evolution of lifehistory traits under a broad range of ecological scenarios. Specifically, we investigate how periodic fluctuations affect selection when the population is also structured in distinct classes. This analysis yields time-varying selection gradients that clarify the influence of the fluctuations of the environment on the competitive ability of a specific life-history mutation. We use this framework to analyse the evolution of key life-history traits of pathogens. We examine three different epidemiological scenarios and we show how periodic fluctuations of the environment can affect the evolution of virulence and transmission as well as the preference for different hosts. These examples yield new and testable predictions on pathogen evolution, and illustrate how our approach can provide a better understanding of the evolutionary consequences of time-varying environmental fluctuations in a broad range of scenarios.


title: Evolution of class-structured populations in fluctuating environments


title: The dynamic effect of regulatory genetic variation on the in vivo ER stress transcriptional response

abstract:
Genotype x Environment (GxE) interactions occur when environmental conditions drastically change the effect of a genetic variant. In order to truly understand the effect of genetic variation, we need to incorporate multiple environments into our analyses. Many variants, under steady state conditions, may be silent or even have the opposite effect under stress conditions. This study uses an in vivo mouse model to investigate how the effect of genetic variation changes with tissue type and cellular stress. Endoplasmic reticulum (ER) stress occurs when misfolded proteins accumulate in the ER. This triggers the unfolded protein response (UPR), a large transcriptional response which attempts to return the cell to homeostasis. This transcriptional response, despite being a well conserved, basic cellular process, is highly variable across different genetic backgrounds, making it an ideal system to study GxE effects. In this study, we sought to better understand how genetic variation alters expression across tissues, in the presence and absence of ER stress. The use of different mouse strains and their F1s allow us to also identify context specific cis- and trans-regulatory mechanisms underlying variable transcriptional responses. We found hundreds of genes that respond to ER stress in a tissue- and/or genotype-dependent manner. Genotype-dependent ER stress-responsive genes are enriched for processes such as protein folding, apoptosis, and protein transport, indicating that some of the variability occurs in canonical ER stress factors. The majority of regulatory mechanisms underlying these variable transcriptional responses derive from cis-regulatory variation and are unique to a given tissue or ER stress state. This study demonstrates the need for incorporating multiple environments in future studies to better elucidate the effect of any particular genetic factor in basic biological pathways, like the ER stress response.

Author SummaryThe effect of genetic variation is dependent on environmental context. Here we use genetically diverse mouse strains to understand how genetic variation interacts with stress state to produce variable transcriptional profiles. In this study, we take advantage of the endoplasmic reticulum (ER) stress response which is a large transcriptional response to misfolded proteins. Using this system, we uncovered tissue- and ER stress-specific effects of genetic variation on gene expression. Genes with genotype-dependent variable expression levels in response to ER stress were enriched for canonical ER stress functions, such as protein folding and transport. These variable effects of genetic variation are driven by unique sets of regulatory variation that are only active under context-specific circumstances. The results of this study highlight the importance of including multiple environments and genetic backgrounds when studying the ER stress response and other cellular pathways.

category: genetics


title: An ancient route towards salicylic acid and its implications for the perpetual Trichormus-Azolla symbiosis

abstract: Despite its small size, the water fern Azolla is a giant among plant symbioses. Within each of its leaflets, a specialized leaf cavity is home to a population of nitrogen-fixing cyanobacteria (cyanobionts). While examples of nitrogen fixing cyanobionts are found across the land plant tree of life, Azolla is unique in that its symbiosis is perpetual: the cyanobionts are inherited during sexual and vegetative propagation of the fern. What underpins the communication between the two partners? In angiosperms, the phytohormone salicylic acid (SA) is a well-known regulator of plant-microbe interactions. Using HPLC-MS/MS, we pinpoint the presence of SA in the fern; using comparative genomics and phylogenetics, we mined homologs of SA biosynthesis genes across Chloroplastida (Viridiplantae). While canonical isochorismate synthase (ICS) sequences are largely limited to angiosperms, homologs for the entire Phenylalanine ammonia-lyase (PAL)-dependent pathway likely existed in the last common ancestor of land plants. Indeed, A. filiculoides secondarily lost its ICS, but has the genetic competence to derive SA from benzoic acid. Global gene expression data from cyanobiont-containing and -free A. filiculoides unveil a putative feedback loop: SA appears to induce cyanobacterial proliferation, which in turn down-regulates genes in SA biosynthesis and its responses.


title: Associations Between Vocal Emotion Recognition and Socio-emotional Adjustment in Children

abstract: The human voice is a primary channel for emotional communication. It is often presumed that being able to recognise vocal emotions is important for everyday socio-emotional functioning, but direct empirical evidence for this remains scarce. Here, we examined relationships between vocal emotion recognition and socio-emotional adjustment in children. The sample included 6 to 8-year-old children (N = 141). The emotion tasks required them to categorise five emotions conveyed by nonverbal vocalisations (e.g., laughter, crying) and speech prosody: anger, disgust, fear, happiness, sadness, plus neutrality. Socio-emotional adjustment was independently evaluated by the childrens teachers using a multi-dimensional questionnaire of self-regulation and social behaviour. Based on frequentist and Bayesian analyses, we found that higher emotion recognition in speech prosody related to better general socio-emotional adjustment. This association remained significant even after accounting for the childrens general cognitive ability, age, sex, and parental education in multiple regressions. Follow-up analyses indicated that the advantages were particularly robust for the socio-emotional dimensions prosocial behaviour and cognitive and behavioural self-regulation. For emotion recognition in nonverbal vocalisations, no associations with socio-emotional adjustment were found. Overall, these results support the close link between childrens emotional prosody recognition skills and their everyday social behaviour.


title: Mitochondrial Phenotypes Distinguish Pathogenic MFN2 Mutations by Pooled Functional Genomics Screen

abstract:
Most human genetic variation is classified as VUS - variants of uncertain significance. While advances in genome editing have allowed innovation in pooled screening platforms, many screens deal with relatively simple readouts (viability, fluorescence) and cannot identify the complex cellular phenotypes that underlie most human diseases. In this paper, we present a generalizable functional genomics platform that combines high-content imaging, machine learning, and microraft isolation in a new method termed "Raft-Seq". We highlight the efficacy of our platform by showing its ability to distinguish pathogenic point mutations of the mitochondrial regulator MFN2, even when the cellular phenotype is subtle. We also show that our platform achieves its efficacy using multiple cellular features, which can be configured on-the-fly. Raft-Seq enables a new way to perform pooled screening on sets of mutations in biologically relevant cells, with the ability to physically capture any cell with a perturbed phenotype and expand it clonally, directly from the primary screen.

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=122 SRC="FIGDIR/small/434746v1_ufig1.gif" ALT="Figure 1">
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org.highwire.dtl.DTLVardef@1d1a431org.highwire.dtl.DTLVardef@72aba5org.highwire.dtl.DTLVardef@62feb1org.highwire.dtl.DTLVardef@13f2b2d_HPS_FORMAT_FIGEXP  M_FIG Graphical Abstract

Here, we address the need to evaluate the impact of a multitude of genetic variants. This manuscript depicts the methods of using machine learning on a biologically relevant phenotype to predict specific point mutations, followed by physically capturing those mutated cells.

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title: Phase and amplitude correlations change with disease progression in idiopathic Rapid eye-movement sleep behavior disorder patients

abstract:
Cognitive decline is a common trait of neurodegenerative diseases of central nervous system and one of the major risk factors associated with faster phenoconversion from prodromal stages. In the transition to full-blown clinical syndromes, increased phase synchronization in the theta, alpha or beta EEG rhythms is thought to reflect the activation of compensatory mechanisms that may counterbalance the cognitive decline of patients affected by Mild Cognitive Impairment (MCI). Patients suffering from idiopathic Rapid eye-movement sleep Behavior Disorder (iRBD) have high risk of developing Parkinson Disease (PD) or Dementia with Lewy Bodies (DLB) and cognitive impairment is among the strongest risk factors together with motor symptoms. Here we wanted to investigate whether altered phase synchronization and amplitude couplings of the brain oscillations could be linked to the balancing of cognitive decline in a longitudinal cohort (N=18) of iRBD patients. We measured high-density Electroencephalographic (HD-EEG) activity at baseline and follow-up and quantified power distribution, orthogonalized amplitude correlation and weighted phase lag index. Despite the overt neurodegenerative progression (three patients converted to PD and one to DLB), cognitive decline was not evident from Mini Mental State Examination (MMSE) or neuropsychological tests. On the other hand, alpha phase synchronization and delta amplitude correlations were significantly different at follow-up compared to baseline. In particular, alpha synchrony was enhanced while delta amplitude coupling was reduced. Those differences were more pronounced among central-posterior channels while frontal channels showed a reduced number of significant edges with respect to surrogates. Both large-scale amplitude and phase coupling significantly correlated with cognitive or neuropsychological scores but not with sleep quality indices. Altogether, these results suggest that increased alpha phase-synchronization and reduced delta amplitude correlation may be considered as electrophysiological signs of an active compensatory mechanism of the cognitive impairment in RDB patients. Large-scale functional modifications could thus be used as significant biomarker in the characterization of prodromal stages of PD.

Statement of SignificanceCognitive impairment and RBD emerge much earlier than the better-known motor symptoms distinctive of synucleinopathies. An improved investigation of RBD may constitute an important biomarker for an early diagnosis of the actual neurodegenerative diseases. For the first time, this preliminary study aims to quantify the large-scale network couplings as electrophysiological manifestation of the compensatory mechanism to the cognitive impairment in a longitudinal study of idiopathic RBD patients. Unfortunately, the small number of the subjects limits the generalizability of our observations, but this is only preliminary works in a larger project that aims to investigate advanced electrophysiological markers for an early diagnosis of the synucleinopathies.

category: bioengineering


title: How a sticky fluid facilitates prey retention in a carnivorous pitcher plant (Nepenthes rafflesiana)

abstract: Nepenthes pitcher plants live in nutrient-poor soils and produce large pitfall traps to obtain additional nutrients from animal prey. Previous research has shown that the digestive secretion in N. rafflesiana is a sticky viscoelastic fluid that is much more effective at retaining insects than water, even after significant dilution. Although the physical properties of the fluid are important for its retentive function, it is unclear how the fluid interacts with insect cuticle and how its sticky nature affects struggling insects. In this study, we investigated the mechanisms behind the efficient prey retention in N. rafflesiana pitcher fluid. By measuring the attractive forces exerted on insect body parts moving in and out of test fluids, we show that it costs insects significantly more energy to separate from pitcher fluid than from water. Moreover, both the maximum force and the energy required for retraction increase after the first contact with the pitcher fluid. We found that insects sink more easily into pitcher fluid than water and, accordingly, the surface tension of N. rafflesiana pitcher fluid was significantly lower than that of water (60.2 vs. 72.3 mN/m). By analysing the pitcher fluid dewetting behaviour, we demonstrate that it strongly resists dewetting from all surfaces tested, leaving behind residual films and filaments that can facilitate re-wetting. This inhibition of dewetting may be a further consequence of the fluids viscoelastic nature and likely represents a key mechanism underlying prey retention in Nepenthes pitcher plants.


title: Altered cortico-subcortical network after adolescent alcohol exposure mediates behavioral deficits in flexible decision-making

abstract: Behavioral flexibility, the ability to modify behavior according to changing conditions, is essential to optimize decision-making. Deficits in behavioral flexibility that persist into adulthood are one consequence of adolescent alcohol exposure, and another is decreased functional connectivity in brain structures involved in decision-making; however, a link between these two outcomes has not been established. We assessed effects of adolescent alcohol and sex on both Pavlovian and instrumental behaviors and functional connectivity in adult animals to determine associations between behavioral flexibility and resting-state functional connectivity. Alcohol exposure impaired attentional set reversals and decreased functional connectivity among cortical and subcortical regions-of-interest that underlie flexible behavior. Moreover, mediation analyses indicated that adolescent alcohol-induced reductions in functional connectivity within a subnetwork of affected brain regions mediated errors committed during reversal learning. These results provide a novel link between persistent reductions in brain functional connectivity and deficits in behavioral flexibility resulting from adolescent alcohol exposure.


title: MicroMator: Open and Flexible Software for Reactive Microscopy

abstract: Microscopy image analysis has recently made enormous progress both in terms of accuracy and speed thanks to machine learning methods. This greatly facilitates the online adaptation of microscopy experimental plans using real-time information of the observed systems and their environments. Here we report MicroMator, an open and flexible software for defining and driving reactive microscopy experiments, and present applications to single-cell control and single-cell recombination.

category: systems biology


title: Ozone nanobubble treatments improve survivability of Nile tilapia (Oreochromis niloticus) challenged with a pathogenic multidrug-resistant Aeromonas hydrophila

abstract:
Multidrug-resistant (MDR) bacteria has rapidly increased in aquaculture, which highlights the risk of production losses due to diseases and potential public health concerns. Previously, we reported that ozone nanobubbles (NB-O3) were effective at reducing concentrations of pathogenic bacteria in water and modulating fish immunity against pathogens; however, multiple treatments with direct NB-O3 exposures caused alterations to the gills of exposed-fish. Here, we set up a modified recirculation system (MRS) assembled with an NB-O3 device (MRS-NB-O3) to investigate whether MRS-NB-O3 were 1) safe for tilapia (Oreochromis niloticus), 2) effective at reducing bacterial load in rearing water, and 3) improved survivability of Nile tilapia following an immersion challenge with a lethal dose of MDR Aeromonas hydrophila. The results indicated no behavioral abnormalities or mortality of Nile tilapia during the 14 day study using the MRS-NB-O3 system. In the immersion challenge, although high bacterial concentration (~2 x 107 CFU/mL) was used, multiple NB-O3 treatments in the first two days reduced the bacteria between 15.9% to 35.6% of bacterial load in water while bacterial concentration increased 13.1% to 27.9% in the untreated control. There was slight up-regulation of non-specific immune-related genes in the gills of the fish receiving NB-O3 treatments. Most importantly, this treatment significantly improved survivability of Nile tilapia with relative percent survival (RPS) of 64.7 - 66.7% in treated fish and surviving fish developed specific antibody against MDR A. hydrophila. In summary, the result suggests that NB-O3 is a promising alternative to antibiotics to control bacterial diseases, including MDR bacteria, and has high potential for application in recirculation aquaculture system (RAS).

HighlightsO_LIMultiple treatments of NB-O3 in a modified recirculation system (MRS) were relatively safe for juvenile Nile tilapia
C_LIO_LINB-O3 treatments in MRS significantly improved survivability of Nile tilapia challenged with multidrug-resistant (MDR) A. hydrophila with RPS of 64.7 - 66.7%
C_LIO_LIConcentration of MDR A. hydrophila in MRS was reduced by 15.9 to 35.6% following each NB-O3 treatment, and increased by 13.1 to 27.9 % in untreated control
C_LIO_LISurviving fish developed specific antibody IgM against MDR A. hydrophila
C_LIO_LINB-O3 is a promising non-antibiotic approach to control diseases caused by MDR A. hydrophila
C_LI


title: A potential SARS-CoV-2 variant of interest (VOI) harboring mutation E484K in the Spike protein was identified within lineage B.1.1.33 circulating in Brazil

abstract: The SARS-CoV-2 epidemic in Brazil was dominated by two lineages designated as B.1.1.28 and B.1.1.33. Two SARS-CoV-2 variants harboring mutations at the receptor-binding domain of the Spike (S) protein, designated as lineages P.1 and P.2, evolved within lineage B.1.1.28 and are rapidly spreading in Brazil. Lineage P.1 is considered a Variant of Concern (VOC) because of the presence of multiple mutations in the S protein (including K417T, E484K, N501Y), while lineage P.2 only harbors mutation S:E484K and is considered a Variant of Interest (VOI). Here we report the identification of a new SARS-CoV-2 VOI within lineage B.1.1.33 that also harbors mutation S:E484K and was detected in Brazil between November 2020 and February 2021. This VOI displayed four non-synonymous lineage-defining mutations (NSP3:A1711V, NSP6:F36L, S:E484K, and NS7b:E33A) and was designated as lineage N.9. The VOI N.9 probably emerged in August 2020 and has spread across different Brazilian states from the Southeast, South, North and Northeast regions.


title: Discovery of indole-modified aptamers for highly specific recognition of protein glycoforms

abstract: Glycosylation is one of the most abundant forms of post-translational modification, and can have a profound impact on a wide range of biological processes and diseases. Unfortunately, efforts to characterize such modifications in the context of basic and clinical research are severely hampered by the lack of affinity reagents that can differentiate protein glycoforms. This lack of reagents is largely due to the challenges associated with generating affinity reagents that can bind to particular glycan epitopes with robust affinity and specificity. In this work, we use a fluorescence-activated cell sorting (FACS)-based approach to generate and screen aptamers with indole-modified bases in an effort to isolate reagents that can differentiate between protein glycoforms. Using this approach, we were able to select multiple aptamers that exhibit strong selectivity for specific glycoforms of two different proteins, with the capacity to discriminate between molecules with identical tertiary structures that differ only in terms of their glycan modifications.


title: The hidden effects of agrochemicals on plant metabolism and root-associated microorganisms

abstract:
Agrochemicals are commonly used in agriculture to protect crops and ensure yields. Several of them are mobile within the plant and, being perceived as xenobiotics regardless of their protective/curative roles, they induce a reprogramming of secondary metabolism linked to the detoxification processes even in the absence of phenotype symptoms. Moreover, it is well documented that plants, thanks to the root exudation of different metabolites, are able to shape the microbial population at the rhizosphere and to significantly affect the processes occurring therein. Here we show that plant metabolic response to foliarly-applied pesticides is much broader than what previously thought and includes diverse and compound-specific hidden processes. Among others, stress-related metabolism and phytohormones profile underwent a considerable reorganization. Moreover, a distinctive microbial rearrangement of the rhizosphere was recorded following foliar application of pesticides. Such effects have unavoidably energetic and metabolic costs for the plant paving the way to both positive and negative aspects. The understanding of these effects is crucial for an increasingly sustainable use of pesticides in agriculture.

HighlightThe foliar application of pesticides induces a broad metabolic reprogramming in plant and shapes the microbial population of the rhizosphere.


title: Cryo-EM structure of an elusive pre-transport intermediate of the multidrug transporter BmrCD reveals modes of asymmetric drug binding

abstract:
Vectorial substrate efflux by ATP binding cassette (ABC) transporters, which play a major role in multidrug resistance, entails the ATP-powered interconversion of the transporter between stable intermediates. Despite recent progress in structure elucidation of ABC transporters, a number of such intermediates have yet to be visualized and mechanistically interpreted. Here, we combine single particle cryo-EM, Double Electron Electron Resonance (DEER) spectroscopy with Molecular Dynamics simulations to profile and mechanistically frame the conformation of a hitherto unobserved intermediate in the context of BmrCD, a heterodimeric multidrug ABC exporter from Bacillus subtilis. In our cryo-EM structure, BmrCD adopts an inward-facing architecture bound to both ATP and the substrate Hoechst-33342 and is capped by an extracellular domain which undergoes ATP-dependent conformational changes. A striking feature of the structure is a symmetric arrangement of the nucleotide-binding domain (NBD) in the presence of ATP whereas binding of Hoechst at two distinct sites in an acidic pocket stabilizes an asymmetric arrangement of the transmembrane domain architecture (TMD). Mutation of residues coordinating Hoechst in the structure abrogates the cooperative stimulation of ATP hydrolysis. In conjunction with previous studies, our findings suggest a mechanistic role for symmetry mismatch between NBDs and TMDs in the conformational cycle of ABC transporters. Moreover, the resolved structures of bimodally-bound drugs are of notable importance for future rational design and optimization of molecules for targeted transport inhibition of ABC transporters.

ONE SENTENCE SUMMARYCryo-EM and EPR analysis reveal cooperative substrate binding in BmrCD in an architecture primed for transport.

category: biophysics


title: Preferential selection and contribution of non-structural protein 1 (NS1) to the efficient transmission of the panzootic avian influenza H5N8 2.3.4.4 clades A and B viruses in chickens and ducks

abstract:
Highly pathogenic avian influenza viruses H5N8 clade 2.3.4.4 caused outbreaks in poultry at an unprecedented global scale. The virus was spread by wild birds in Asia in two waves: clade-2.3.4.4A in 2014/2015 and clade-2.3.4.4B since 2016 up to today. Both clades were highly virulent in chickens, but only clade-B viruses exhibited high virulence in ducks. Viral factors which contribute to virulence and transmission of these panzootic H5N8 2.3.4.4 viruses are largely unknown. The NS1 protein, typically composed of 230 amino acids (aa), is a multifunctional protein which is also a pathogenicity factor. Here, we studied the evolutionary trajectory of H5N8 NS1 proteins from 2013 to 2019 and their role in the fitness of H5N8 viruses in chickens and ducks. Sequence analysis and in-vitro experiments indicated that clade-2.3.4.4A and clade-2.3.4.4B viruses have a preference for NS1 of 237-aa and 217-aa, respectively over NS1 of 230-aa. NS217 was exclusively seen in domestic and wild birds in Europe. The extension of the NS1 C-terminus of clade-B virus reduced virus transmission and replication in chickens and ducks and partially impaired the systemic tropism to the endothelium in ducks. Conversely, lower impact on fitness of clade-A virus was observed. Remarkably, the NS1 of clade-A and clade-B, regardless of length, was efficient to block interferon induction in infected chickens and changes in the NS1 C-terminus reduced the efficiency for interferon antagonism. Together, the NS1 C-terminus contributes to the efficient transmission and high fitness of H5N8 viruses in chickens and ducks.

ImportanceThe panzootic H5N8 highly pathogenic avian influenza viruses of clade 2.3.4.4A and 2.3.4.4B devastated poultry industry globally. Clade 2.3.4.4A was predominant in 2014/2015 while clade 2.3.4.4B was widely spread in 2016/2017. Both clades exhibited different pathotypes in ducks. Virus factors contributing to virulence and transmission are largely unknown. The NS1 protein is typically composed of 230 amino-acids (aa) and is an essential interferon (IFN) antagonist. Here, we found that the NS1 protein of clade 2.3.4.4A preferentially evolved toward long NS1 with 237-aa, while clade 2.3.4.4B evolved toward shorter NS1 with 217-aa (exclusively found in Europe) due stop-codons in the C-terminus (CTE). We showed that the NS1 CTE of H5N8 is required for efficient virus replication, transmission and endotheliotropism in ducks. In chickens, H5N8 NS1 evolved toward higher efficiency to block IFN-response. These findings may explain the preferential pattern for short NS1 and high fitness of the panzootic H5N8 in birds.

Subject categoryAnimal, RNA Viruses


title: A malaria parasite phospholipid flippase safeguards midgut traversal of ookinetes for mosquito transmission

abstract: Mosquito midgut epithelium traversal is an essential component of transmission of malaria parasites. Phospholipid flippases are eukaryotic type IV ATPases (P4-ATPases), which in association with CDC50 cofactors, translocate phospholipids across lipid bilayers to maintain the membrane asymmetry. In this study, we investigated the function of a putative P4-ATPase, ATP7, from the rodent malaria parasite P. yoelii. Disruption of ATP7 results in block of parasite infection of mosquitoes. ATP7 is localized on the ookinete plasma membrane. While ATP7-depleted ookinetes are motile and capable of invading the midgut, they are quickly eliminated within the epithelial cells by a process that is independent from the mosquito complement-like immunity. ATP7 colocalizes and interacts with the flippase co-factor CDC50C. Importantly, depletion of CDC50C phenocopies ATP7 deficiency. ATP7-depleted ookinetes fail to translocate phosphatidylcholine (PC) across the plasma membrane, resulting in PC exposure at the ookinete surface. Lastly, ookinete microinjection into the mosquito hemocoel reverses the ATP7 deficiency phenotype. Our study identifies Plasmodium flippase as a novel mechanism of parasite survival in the midgut epithelium that is required for mosquito transmission.


title: Dissolved oxygen minimally affects magnetic susceptibility in biologically relevant conditions

abstract:
PurposeTo investigate the potential of quantitative susceptibility mapping (QSM) with MRI as a biomarker for tissue oxygenation in fat-water mixture. Oxygen molecules (O2) are paramagnetic. This suggests that dissolved O2 in tissue should affect the measured magnetic susceptibility. However, direct measurements of dissolved O2 in tissues is challenging with QSM as the induced change in susceptibility is below the sensitivity of existing algorithms. QSM in regions that contain fat could be sensitive enough to be used as a marker of tissue oxygenation as oxygen has a larger solubility in fat than in water.

MethodsThe relationship between dissolved O2 concentration and magnetic susceptibility was investigated based on MRI measurements using phantoms made of fat-water emulsions. Dairy cream was used to approximate fat-containing biological tissues. Phantoms based on dairy cream with 35 % fat were designed with controlled concentrations of dissolved O2. O2 was bubbled into the dairy cream to reach O2 concentrations above the concentration at atmospheric pressure, while nitrogen was bubbled in cream to obtain O2 concentrations below atmospheric pressure. Magnetic susceptibility was expected to increase, becoming more paramagnetic, as O2 concentration was increased.

ResultsMagnetic susceptibility from MRI-based QSM measurements did not reveal a dependence on O2 concentration in fat-water mixture phantoms. The relationship between susceptibility and O2 was weak and inconsistent among the various phantom experiments.

ConclusionQSM in fat-water mixture appears to be minimally sensitive to dissolved O2 based on phantom experiments. This suggests that QSM is not likely to be sensitive enough to be proposed as a marker for tissue oxygenation, as the change in magnetic susceptibility induced by the change in dissolved O2 concentration is below the current detection limit, even in the presence of fat.


title: Rational engineering of low temperature activity in thermoalkalophilic Geobacillus thermocatenulatus lipase

abstract: While thermophilic enzymes have thermostability desired for broad industrial applications, they can lose activity at ambient temperatures far from their optimal. Engineering cold activity into thermophilic enzymes has the potential to broaden the range of temperatures resulting in significant activity (i.e., decreasing the temperature dependence of kcat). Even though it has been widely suggested that cold temperature enzyme activity results from active flexibility that is at odds with the rigidity necessary for thermostable enzymes; however, directed evolution experiments have shown us these properties are not mutually exclusive. In this study, rational protein engineering was used to introduce flexibility inducing mutations around the active sites of Geobacillus thermocatenulatus lipase (GTL). Two mutants were found to have enhanced specific activity compared to wild-type at temperatures between 283 K to 363 K with p-nitrophenol butyrate but not with larger substrates. Kinetics assay revealed both mutations resulted in psychrophilic traits, such as lower activation enthalpy and more negative entropy values compared to wild type in all substrates. Furthermore, the mutants had significantly improved thermostability compared to wild type enzyme, which proves that it is feasible to improve the cold activity without trade-off. Our study provides insight into the enzyme cold adaptation mechanism and design principles for engineering cold activity into thermostable enzymes.


title: Detection of Chronic Wasting Disease prions in fetal tissues of free-ranging white-tailed deer

abstract: The transmission of chronic wasting disease (CWD) has largely been attributed to contact with infectious prions shed in excretions (saliva, urine, feces, blood) by direct animal-to-animal exposure or indirect contact with the environment. Less-well studied has been the role mother-to-offspring transmission may play in the facile transmission of CWD. We asked whether such extensive spread may also be due to mother-to-offspring transmission, perhaps before birth. We thereby focused on a population of white-tailed deer from West Virginia, USA, in which CWD has been detected. Fetal tissues, ranging from 113 to 158 days of gestation, were harvested from the uteri of CWD+ dams in the asymptomatic phase of infection. Using serial protein misfolding amplification (sPMCA), we detected evidence of prion seeds in 6 of 14 in utero harvested fetuses, with earliest detection at 113 gestational days. This is the first report of CWD detection in free ranging white-tailed deer fetal tissues. Further investigation within cervid populations across North America will help define the role and impact of mother-to-offspring vertical transmission of CWD.


title: Differential gene expression by RNA-Seq in Sigma-2 Receptor/TMEM97 knockout cells reveals its role in complement activation and SARS-CoV-2 viral uptake

abstract: Our lab has recently shown that the Sigma-2 Receptor/Transmembrane Protein 97 (sigma-2R/TMEM97) interacts with the low-density lipoprotein receptor (LDLR) and facilitates the enhanced uptake of various ligands including lipoproteins and intrinsically disordered proteins. TMEM97 has been recently been shown to interact with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral proteins, highlighting its potential involvement with viral entry into the cell. We hypothesized that sigma-2R/TMEM97 may play a role in facilitating viral uptake, and with the regulation of inflammatory and thrombotic pathways that are involved with viral infection. In this study, we identified the top differentially expressed genes upon the knockout of sigma-2R/TMEM97, and analyzed the genes involved with the inflammatory and thrombotic cascades, effects that are observed in patients infected with SARS-CoV-2. We found that the ablation of sigma-2R/TMEM97 resulted in an increase in Complement Component 4 Binding Protein (C4BP) proteins, at both the translational and transcriptional levels. We also showed that sigma-2R/TMEM97 interacts with the cellular receptor for SARS-CoV-2, the human angiotensin-converting enzyme 2 (ACE2) receptor, forming a protein complex, and that disruption of this complex results in the inhibition of viral uptake. The results of this study suggest that sigma-2R/TMEM97 may be a novel therapeutic target to inhibit SARS-CoV-2 viral uptake, as well as to decrease inflammatory and thrombotic effects through the modulation of the complement cascade.


title: A General LSTM-based Deep Learning Method for Estimating Neuronal Models and Inferring Neural Circuitry

abstract: Computational neural models are essential tools for neuroscientists to study the functional roles of single neurons or neural circuits. With the recent advances in experimental techniques, there is a growing demand to build up neural models at single neuron or large-scale circuit levels. A long-standing challenge to build up such models lies in tuning the free parameters of the models to closely reproduce experimental recordings. There are many advanced machine-learning-based methods developed recently for parameter tuning, but many of them are task-specific or requires onerous manual interference. There lacks a general and fully-automated method since now. Here, we present a Long Short-Term Memory (LSTM)-based deep learning method, General Neural Estimator (GNE), to fully automate the parameter tuning procedure, which can be directly applied to both single neuronal models and large-scale neural circuits. We made comprehensive comparisons with many advanced methods, and GNE showed outstanding performance on both synthesized data and experimental data. Finally, we proposed a roadmap centered on GNE to help guide neuroscientists to computationally reconstruct single neurons and neural circuits, which might inspire future brain reconstruction techniques and corresponding experimental design. The code of our work will be publicly available upon acceptance of this paper.

category: neuroscience


title: Amplitude and phase coupling optimize information transfer between brain networks that function at criticality

abstract: Brain function depends on segregation and integration of information processing in brain networks often separated by long-range anatomical connections. Neuronal oscillations orchestrate such distributed processing through transient amplitude and phase coupling, yet surprisingly little is known about local network properties facilitating these functional connections. Here, we test whether criticality--a dynamical state characterized by scale-free oscillations--optimizes the capacity of neuronal networks to couple through amplitude or phase, and transfer information. We coupled in silico networks with varying excitatory and inhibitory connectivity, and found that phase coupling emerges at criticality, and that amplitude coupling, as well as information transfer, are maximal when networks are critical. Importantly, regulating criticality through neuromodulation of synaptic strength showed that critical dynamics--as opposed to a static ratio of excitatory and inhibitory connections--optimize network coupling and information transfer. Our data support the idea that criticality is important for local and global information processing and may help explain why brain disorders characterized by local alterations in criticality also exhibit impaired long-range synchrony, even prior to degeneration of axonal connections.


title: Paratransgenic manipulation of tsetse miR275 alters the physiological homeostasis of the flys midgut environment

abstract:
Tsetse flies are vectors of parasitic African trypanosomes (Trypanosoma spp.). Current disease control methods include fly-repelling pesticides, trapping flies, and chemotherapeutic treatment of infected people. Inhibiting tsetses ability to transmit trypanosomes by strengthening the flys natural barriers can serve as an alternative approach to reduce disease. The peritrophic matrix (PM) is a chitinous and proteinaceous barrier that lines tsetses midgut. It protects the epithelial cells from the gut lumen content such as food and invading trypanosomes, which have to overcome this physical barrier to establish an infection. Bloodstream form trypanosomes shed variant surface glycoproteins (VSG) into tsetses gut lumen early during the infection establishment. The VSG molecules are internalized by the flys PM-producing cardia, which results in a reduction in tsetse miR275 expression and a sequential molecular cascade that compromises the PM integrity. In the present study, we investigated the role(s) of miR275 in tsetses midgut physiology and trypanosome infection processes by developing a paratransgenic expression system. We used tsetses facultative bacterial endosymbiont Sodalis glossinidius to express tandem antagomir-275 repeats (or miR275 sponge) that constitutively reduce miR275 transcript abundance. This paratransgenic system successfully knocked down miR275 levels in the flys midgut, which consequently obstructed blood digestion and modulated infection outcomes with an entomopathogenic bacteria and with trypanosomes. RNA sequencing of cardia and midgut tissues from the paratransgenic tsetse confirmed that miR275 regulates processes related to the expression of PM-associated proteins and digestive enzymes as well as genes that encode abundant secretory proteins. Our study demonstrates that paratransgenesis can be employed to study microRNA-regulated pathways in arthropods housing symbiotic bacteria.

Author SummaryTsetse flies transmit African trypanosomes, which are the parasites that cause sleeping sickness in human in sub-Saharan Africa. When tsetse ingests a blood meal containing trypanosomes, the expression level of a microRNA (miR275) decreases in the flys gut. This process results in a series of events that interrupt the physiological homeostasis of the gut environment. To further understand the function of miR275 in tsetse fly, we genetically modified a tsetses native bacterial symbiont, reintroduced the genetically modified bacterium back into the fly, and successfully knocked down the miR275 expression in tsetses midgut. These  paratransgenic flies (which house genetically modified bacteria) presented impaired digestive processes and were highly susceptible to infection with trypanosomes. Lastly, we discovered that miR275 regulates tsetse secretory pathways. Our novel paratransgenic expression system can be applied to study the function of other microRNAs and how they regulate disease transmission in tsetse and other insect systems.


title: BNT162b2 mRNA COVID-19 vaccine induces antibodies of broader cross-reactivity than natural infection but recognition of mutant viruses is up to 10-fold reduced

abstract:
BackgroundSeveral new variants of SARS-CoV-2 have emerged since fall 2020 which have multiple mutations in the receptor binding domain (RBD) of the spike protein.

ObjectiveWe aimed to assess how mutations in RBD affected recognition of immune sera by antibodies induced by natural infection versus immunization with BNT162b2, a mRNA-based vaccine against COVID-19.

MethodsWe produced SARS-CoV-2 RBD mutants with single mutations in the receptor binding domain (RBD) region (E484K, K417N, N501Y) or with all 3 mutations combined, as occurring in the newly emerged variants B.1.351 (South Africa) and P.1 (Brazil). Using standard and avidity ELISAs, we determined the binding capacities to mutant RBDs of antibodies induced by infection versus vaccination.

ResultsThese binding assays showed that vaccination induced antibodies recognize both wildtype and mutant RBDs with higher avidities than those raised by infection. Nevertheless, recognition of mutants RBDK417N and RBDN501Y was 2.5-3-fold reduced while RBDE484K and the triple mutant were 10-fold less well recognized, demonstrating that the mutation at position 484 was key for the observed loss in cross-reactivity.

ConclusionOur binding data demonstrate improved recognition of mutant viruses by BNT162b2-induced antibodies compared to those induced by natural infection. Recognition may, however, be 10-fold reduced for the variants B.1.351/P.1, suggesting that the development of a new vaccine is warranted. The E484K mutation is an key hurdle for immune recognition, convalescent plasma and monoclonal antibody therapy as well as serological assays based on the wildtype sequence may therefore seriously impaired.

Capsule summaryBNT162b2 mRNA COVID-19 vaccine-induced antibodies recognize mutant viruses with up to 10-fold lower efficiency


title: Borrelia infection in rodent host has dramatic effects on the microbiome of ticks

abstract:
BackgroundVector-borne diseases remain major causes of human morbidity and mortality. It is increasingly recognized that the community of microbes inhabiting arthropods can strongly affect their vector competence, but the role of the tick microbiome in Borrelia transmission - the cause of Lyme disease - remains unclear.

ResultsHere, we use a large-scale experiment to clarify the reciprocal interactions between Borrelia afzelii and the microbiome of Ixodes ricinus, its primary vector. In contrast to other reports, we find that depletion of the bacterial microbiome in larval ticks has no effect on their subsequent acquisition of B. afzelii during blood feeding on infected mice. Rather, exposure to B. afzelii-infected hosts drives pervasive changes to the tick microbiome, decreasing overall bacterial abundance, shifting bacterial community composition, and increasing bacterial diversity. These effects appear to be independent of the acquisition of B. afzelii by ticks, suggesting they are mediated by physiological or immunological aspects of B. afzelii infection in the rodent host.

ConclusionsManipulation of the microbiome of I. ricinus larvae had no effect on their ability to acquire B. afzelii. In contrast, B. afzelii infection in the mouse had dramatic effects on the composition of the gut microbiome in I. ricinus nymphs. Our study demonstrates that vector-borne infections in the vertebrate host shape the microbiome of the arthropod vector.


title: A simple coloring method to distinguish colonies of the yeasts Lachancea thermotolerans and Saccharomyces cerevisiae on agar media

abstract: The yeast Lachancea thermotolerans converts consumed sugar partly to lactic acid instead of ethanol and is therefore used together with Saccharomyces cerevisiae to produce wines with a lower alcohol content. Being able to distinguish these yeasts is important for quality control and quantitative assessment of the contributions of both yeasts to wine fermentations. Commonly used methods to routinely distinguish these organisms are indirect or rely on commercial products of undisclosed composition. Here we describe that adding bromocresol purple to agar media induces Lachancea colonies to develop a brown color, whereas Saccharomyces colonies remain white.


title: A biomechanical comparison of the jerk, back jerk, vertical jump and jump squat.

abstract: Although weightlifting exercises and their pulling and catching derivatives have been well studied, less is known about the group of weightlifting overhead pressing derivatives (WOPDs). There were two purposes of the present study. Above all, it was to compare WOPDs (i.e. jerk and back jerk) with jump squat in enhancing sport performance such as vertical jump in the perspective of biomechanics. Furthermore, it was to gain a better understanding of the biomechanical difference between jerk and back jerk. The study compared the kinetics, kinematics, and muscle activation of the jerk, back jerk, vertical jump and jump squat. Ground reaction forces, joint angle data and electromyography were collected from 20 track and field athletes while they performed the four movements. The joint coordination pattern and EMG characters of the jump squat were more similar to those of the vertical jump. WOPDs, especially jerk, exhibited less similarity with vertical jump in joint coordination, as well as the subsequent peak activation. The electromyography data demonstrated significant differences in rectus femoris and gluteus maximus in the relative timing of peak activations and the maximum activation. Jump squat was greater in peak force (2211N) than jerk (P < .005), greater peak power (4749W) than jerk and back jerk (P < .001) and no significant difference with WOPDs in rate of force development. Back jerk produced a greater peak force (2223 N), peak power (3767W) and eccentric RFD (15965 N{middle dot}s-1) than jerk (2061N)(P < .001) (3364W)(P < .05) (12280 N{middle dot}s-1)(P < .01)and the opposite in concentric RFD that jerk (7702 N{middle dot}s-1) was greater than back jerk (5972 N{middle dot}s-1)(P < .05). We can conclude that for runner and jumpers, jump squat was better for improving vertical jump than WOPDs and back jerk is better than jerk in power training.

category: scientific communication and education


title: Tracing evolution history of 100 whole genome sequences of diffuse stem brain tumor

abstract: Diffuse intrinsic pontine glioma (DIPG) is a deadly disease among young children. The evolution path and mutational processes giving rise to DIPG remain elusive. We analyzed 100 whole genome sequences (WGS) from 60 DIPG patients. This revealed 25% DIPGs acquired whole-genome duplications (WGD) early during tumor evolution. WGD samples are associated with loss of TP53 and poorer survival. In addition, almost all WGD samplers harbor complex structural variations (SVs) and show characteristic short microhomology at SV breakpoints. Mutation analysis revealed that H3K27M driver mutation is acquired early during tumor clonal evolution. Mutation signature analysis identified a unique mutational process at a late stage of tumor evolution. This study revealed that tumor evolution of DIPG is characterized by chromosomal instability shaped by DNA repair defects and dynamic mutational processes. Our work shed new insights on the disease pathogenesis of DIPG and provided rationale for designing novel therapy for this deadly disease.


title: Cytotoxic efficiency of human CD8+ T cell memory subtypes

abstract: Immunological memory is an important concept to protect humans against recurring diseases. Memory CD8+ T cells are required for quick expansion into effector cells but also provide immediate cytotoxicity against their targets. Whereas many functions of the two main cytotoxic subtypes, effector memory CD8+ T cells (TEM) and central memory CD8+ T cells (TCM), are relatively well defined, single TEM and TCM cell cytotoxicity has not been quantified. Here, we analyze human CD8+ subtype distribution following SEA stimulation and quantify the expression of death mediators, including perforin, granzyme B, FasL and TRAIL. We find higher perforin, granzyme B and FasL expression in TEM and compared to TCM. To quantify single TEM and TCM cytotoxicity, we develop a FRET-based fluorescent assay with NALM6 target cells stably transfected with a GFP-RFP FRET construct based on a caspase-cleavage sequence (apoptosis sensor Casper-GR). Applying this assay, TEM or TCM induced target cell apoptosis or necrosis can be quantified. We find that single TEM are much more effective than TCM in killing their targets mainly by apoptosis and secondary necrosis. The reason for this is the higher perforin expression and on a more efficient lytic immunological synapse during TEM-target contact compared to TCM-target contact. Defining and quantifying single TEM and TCM cytotoxicity and the respective mechanism should be helpful to optimize future subset-based immune therapies.


title: Antibiotic Resistance in Bacillus-based Biopesticide Products

abstract:
The crisis of antibiotic resistant bacterial infections is one of the most pressing public health issues. Common agricultural practices have been implicated in the generation of antibiotic resistant bacteria. Biopesticides, live bacteria used for pest control, are non-pathogenic and considered safe for consumption. Application of bacteria-based pesticides to crops in high concentrations raises the possibility of unintentional contributions to the movement and generation of antibiotic resistance genes in the environment. However, the presence of clinically relevant antibiotic resistance genes and their resistance phenotypes are currently unknown. Here we use a combination of multiple bioinformatic and microbiological techniques to define resistomes of widely used biopesticides and determine how the presence of suspected antibiotic resistance genes translates to observable resistance phenotypes in several biopesticide products. Our results demonstrate that biopesticide products are reservoirs of clinically relevant antibiotic resistance genes and bear resistance to multiple drug classes.

ImportanceThis is the first study to specifically address antibiotic resistance in widely distributed bacterial strains used as commercial biopesticides. Safety assessments of commercial live bacterial biopesticide products do not include antibiotic resistance phenotype identification. We identify antibiotic resistance genes in all live bacterial strains examined, and resistant phenotypes in all strains tested for antibiotic susceptibility. This work demonstrates that biopesticides potentially play a critical role as reservoirs and vectors of antibiotic resistance in the broader environmental resistome that is to date, unstudied.

category: microbiology