title: Predation Efficiency upon Clinical Isolates: Bdellovibrio bacteriovorus is Prey Specific and Origin Dependent

abstract:
The use of predatory bacteria as live antibiotics has been proposed for managing bacterial infections, especially for those caused by antibiotic multiresistant isolates for which there are few therapeutic options. However, the current knowledge in this field is scarce, with most of the available data based on environmental isolates, with a significant lack of human clinical samples. In this study, we evaluated the predatory spectrum of the reference strain Bdellovibrio bacteriovorus 109J on 13 Serratia marcescens (5 of which were carbapenemase producers) and 78 Pseudomonas aeruginosa clinical isolates from respiratory (colonizing the lungs of patients with cystic fibrosis) or bacteremic infections, differentiated by phenotype (mucoid or not), antibiotic resistance phenotype (including multidrug-resistant isolates), and genetic lineage (frequent and rare sequence types). The source of the isolates was significantly associated with predation efficiency (100% for S. marcescens, 67% for P. aeruginosa from cystic fibrosis, and 25% for P. aeruginosa from bacteremia). In contrast, no correlation with colonial morphotype, genetic background, or antibiotic susceptibility was found. To evaluate the influence of the predator on the predation event, we employed a more aggressive B. bacteriovorus mutant 109J preying upon the same 48 bacteremic P. aeruginosa isolates. The mutants predation efficiency was higher than that of their wild-type counterpart (43% vs. 25%), pointing out that predation is specific to each prey-predator pair of isolates. Our results provide the most extensive study of clinical prey susceptibility published to date and show that the prey-predator interaction is influenced by the origin of the isolates rather than by their genetic background or their antibiotic susceptibility phenotype.

IMPORTANCEThe potential usefulness of predatory bacteria in controlling human pathogens, particularly those that are multiresistant to antibiotics, is enormous. Although this possibility has long been suggested, there are still no data on predation susceptibility in clinical strains, and the possible presence of autochthonous predators of the human microbiota has not been investigated. In this study, we employed a reference predator with an environmental origin to study predation phenomena in 3 well-characterized collections of human clinical isolates. Our results demonstrated that predation is a specific consequence of each prey-predator interaction, with the origin of the strains the most relevant factor. In contrast, the genetic background, morphotype, and antibiotic resistance did not appear to influence the predation phenomenon. We also highlight the involvement of a putative polyhydroxyalkanoate depolymerase protein of B. bacteriovorus in determining prey susceptibility. To our knowledge, this study is the largest performed with strains of clinical origin, discriminating between various genera and including strains with multiresistance to antibiotics.


title: The E3 ligase RNF115 regulates phagosome maturation and host response to bacterial infection

abstract: Phagocytosis is a key process in innate immunity and homeostasis. After uptake, newly formed phagosomes mature by acquisition of endo-lysosomal enzymes. Macrophage activation by interferon-gamma (IFN-{gamma}) increases microbicidal activity, but delays phagosomal maturation by an unknown mechanism. Using quantitative proteomics, we show that phagosomal proteins harbour high levels of typical and atypical ubiquitin chain types. Moreover, phagosomal ubiquitylation of vesicle trafficking proteins is substantially enhanced upon IFN-{gamma} activation of macrophages, suggesting a role in regulating phagosomal functions. Furthermore, we identified the E3 ubiquitin ligase RNF115, which is enriched on phagosomes of IFN-{gamma} activated macrophages, as an important regulator of phagosomal maturation. Loss of RNF115 protein or ligase activity enhanced phagosomal maturation and increased cytokine responses to Staphylococcus aureus, suggesting that both innate immune signalling from the phagosome and phagolysosomal trafficking are controlled through ubiquitylation. RNF115 knock-out mice show less tissue damage in response to S. aureus infection, indicating a role of RNF115 in inflammatory responses in vivo. In conclusion, RNF115 and phagosomal ubiquitylation are important regulators of innate immune functions during bacterial infections.

category: biochemistry


title: SvAnna: efficient and accurate pathogenicity prediction for coding and regulatory structural variants in long-read genome sequencing

abstract: Structural variants (SVs) are implicated in the etiology of Mendelian diseases but have been systematically underascertained owing to limitations of existing technology. Recent technological advances such as long-read sequencing (LRS) enable more comprehensive detection of SVs, but approaches for clinical prioritization of candidate SVs are needed. Existing computational approaches do not specifically target LRS data, thereby missing a substantial proportion of candidate SVs, and do not provide a unified computational model for assessing all types of SVs. Structural Variant Annotation and Analysis (SvAnna) assesses all classes of SV and their intersection with transcripts and regulatory sequences in the context of topologically associating domains, relating predicted effects on gene function with clinical phenotype data. We show with a collection of 182 published case reports with pathogenic SVs that SvAnna places over 90% of pathogenic SVs in the top ten ranks. The interpretable prioritizations provided by SvAnna will facilitate the widespread adoption of LRS in diagnostic genomics.

category: bioinformatics


title: Predicting stable binding modes from simulated dimers of the D76N mutant of β2-microglobulin

abstract:
The D76N mutant of the {beta}2m protein is a biologically motivated model system to study protein aggregation. There is strong experimental evidence, supported by molecular simulations, that D76N populates a highly dynamic conformation (which we originally named I2) that exposes aggregation-prone patches as a result of the detachment of the two terminal regions. Here, we use Molecular Dynamics simulations to study the stability of an ensemble of dimers of I2 generated via protein-protein docking. MM-PBSA calculations indicate that within the ensemble of investigated dimers the major contribution to interface stabilization at physiological pH comes from hydrophobic interactions between apolar residues. Our structural analysis also reveals that the interfacial region associated with the most stable binding modes are particularly rich in residues pertaining to both the N- and C-terminus, as well residues from the BC- and DE-loops. On the other hand, the less stable interfaces are stabilized by intermolecular interactions involving residues from the CD- and EF-loops. By focusing on the most stable binding modes, we used a simple geometric rule to propagate the corresponding dimer interfaces. We found that, in the absence of any kind of structural rearrangement occurring at an early stage of the oligomerization pathway, some interfaces drive a self-limited growth process, while others can be propagated indefinitely allowing the formation of long, polymerized chains. In particular, the interfacial region of the most stable binding mode reported here falls in the class of self-limited growth.

Graphical Abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

HighlightsO_LIThe D76N mutant of protein {beta}2m populates an aggregation-prone monomer (I2) with unstructured terminal regions
C_LIO_LIMolecular Dynamics simulations and MM-PBSA calculations indicate that dimers of I2 are stabilized by hydrophobic interactions
C_LIO_LIThe N- and C-terminal regions, together with the BC- and DE-loops are prevalent in the most stable dimer interfaces, while the CD- and EF-loop appear in the less stable ones
C_LIO_LIThe most stable dimer interface has a limited potential to oligomerize in the absence of structural rearrangement
C_LI

category: biophysics


title: Modeling Allelic Diversity of Multi-parent Mapping Populations Affects Detection of Quantitative Trait Loci

abstract: The search for quantitative trait loci (QTL) that explain complex traits such as yield and flowering time has been ongoing in all crops. Methods such as bi-parental QTL mapping and genome-wide association studies (GWAS) each have their own advantages and limitations. Multi-parent advanced generation intercross (MAGIC) populations contain more recombination events and genetic diversity than bi-parental mapping populations and reduce the confounding effect of population structure that is an issue in association mapping populations. Here we discuss the results of using a MAGIC population of doubled haploid (DH) maize lines created from 16 diverse founders to perform QTL mapping. We compare three models that assume bi-allelic, founder, and ancestral haplotype allelic states for QTL. The three methods have different power to detect QTL for a variety of agronomic traits. Although the founder approach finds the most QTL, there are also QTL unique to each method, suggesting that each model has advantages for traits with different genetic architectures. A closer look at a well-characterized flowering time QTL, qDTA8, which contains vgt1, suggests a potential epistatic interaction and highlights the strengths and weaknesses of each method. Overall, our results reinforce the importance of considering different approaches to analyzing genotypic datasets, and show the limitations of binary SNP data for identifying multi-allelic QTL.9

category: plant biology


title: A CLEM approach to access to the ultrastructure at the graft interface in Arabidopsis thaliana

abstract: Despite recent progress in our understanding of the graft union formation, we still know little about the cellular events underlying the grafting process. This is partially due to the difficulty of reliably targeting the graft interface in electron microscopy to study its ultrastructure and three-dimensional architecture. To overcome this technological bottleneck, we developed a correlative light electron microscopy approach (CLEM) to study the graft interface with high ultrastructural resolution. Grafting hypocotyls of Arabidopsis thaliana lines expressing YFP or mRFP in the endoplasmic reticulum allowed the efficient targeting of the grafting interface for under light and electron microscopy. To explore the potential of our method to study sub-cellular events at the graft interface, we focused on the formation of secondary plasmodesmata (PD) between the grafted partners. We showed that 4 classes of PD were formed at the interface and that PD introgression into the call wall was initiated equally by both partners. Moreover, the success of PD formation appeared not systematic with a third of PD not spanning the cell wall entirely. Characterizing the ultrastructural characteristics of these failed PD gives us insights into the process of secondary PD biogenesis. We showed that the thinning of the cell wall and the endoplasmic reticulum-plasma membrane tethering seem to be required for the establishment of symplastic connections between the scion and the rootstock. The resolution reached in this work shows that our CLEM method offer a new scale to the study for biological processes requiring the combination of light and electron microscopy.


title: Alterations in leptin signaling in Amyotrophic Lateral Sclerosis (ALS)

abstract: Leptin has been suggested to play a role in amyotrophic lateral sclerosis (ALS), a fatal progressive and neurodegenerative disease. This adipokine has previously been shown to be associated with a lower risk of ALS disease and to confer a survival advantage in ALS patients. However, the role of leptin in the progression of ALS is unknown. Indeed, our understanding of the mechanisms underlying leptins effects in the pathogenesis of ALS is very limited, and it is fundamental to determine whether alterations in leptins actions take place in this neurodegenerative disease. To characterize the association between leptin signaling and the clinical course of ALS we assessed the mRNA and protein expression profiles of leptin, the long leptin receptor (Ob-Rb) and leptin-related signaling pathways over the time course of the disease (onset and end-stage of disease), in TDP-43A315T mice compared to age-matched WT littermates. In addition, at the selected time-points immunoassay analysis was conducted to characterize plasma levels of total ghrelin, the adipokines (resistin and leptin) and metabolic proteins (plasminogen activator inhibitor type 1 (PAI-1), gastric inhibitory peptide (GIP), glucagon like peptide 1 (GLP-1), insulin and glucagon) in TDP-43A315T mice compared to WT controls. Our results indicate alterations in leptin signaling in the spinal cord and the hypothalamus on the backdrop of TDP-43-induced deficits in mice, providing new evidence about the pathways that could link leptin signaling to ALS.

category: neuroscience


title: An information theoretic method to resolve millisecond-scale spike timing precision in a comprehensive motor program

abstract: Sensory inputs in nervous systems are often encoded at the millisecond scale in a temporally precise code. There is now a growing appreciation for the prevalence of precise timing encoding in motor systems. Animals from moths to birds control motor outputs using precise spike timing, but we largely do not know at what scale timing matters in these circuits due to the difficulty of recording a complete set of spike-resolved motor signals and relatively few methods for assessing spike timing precision. We introduce a method to estimate spike timing precision in motor circuits using continuous MI estimation at increasing levels of added uniform noise. This method can assess spike timing precision at fine scales for encoding rich motor output variation. We demonstrate the advantages of this approach compared to a previously established discrete information theoretic method of assessing spike timing precision. We use this method to analyze a data set of simultaneous turning (yaw) torque output and EMG recordings from the 10 primary muscles of Manduca sexta as tethered moths visually tracked a robotic flower moving with a 1 Hz sinusoidal trajectory. We know that all 10 muscles in this motor program encode the majority of information about yaw torque in spike timings, but we do not know whether individual muscles receive information encoded at different levels of precision. Using the continuous MI method, we demonstrate that the scale of temporal precision in all motor units in this insect flight circuit is at the sub-millisecond or millisecond-scale, with variation in precision scale present between muscle types. This method can be applied broadly to estimate spike timing precision in sensory and motor circuits in both invertebrates and vertebrates.


title: Structure of bacterial communities in Japanese-style bathrooms: Comparative sequencing of bacteria in shower water and showerhead biofilms using a portable nanopore sequencer

abstract: Showers are one of the main exposure routes to diverse microbes for end users in built environments. Bacteria in water are responsible for biofilm formation on surfaces, and the inside of a showerhead is a specific niche. Here, for the purpose of microbial characterization, source estimation and possibility of infection, the bacterial compositions of both shower water and showerhead biofilms in the same bathroom were determined and compared using a portable nanopore sequencer. The results suggest that specific bacteria in source water would primarily adhere to the surface of the showerhead where they subsequently form biofilms, and the community compositions within biofilms largely vary depending on environmental factors. The relative abundance of several pathogenic bacterial genera in both water and biofilm samples was low. We suggest that it is important to manage risk of infection in each household, and rapid on-site analysis of microbial communities will allow the realization.

category: microbiology


title: HIF-dependent Neuropeptide Y Receptor Y1 and Y5 expression sensitizes hypoxic cells to NPY stimulation

abstract: Neuropeptide Y (NPY) is an abundant neurohormone in the central and peripheral nervous system involved in feeding behavior, energy balance, nociception, and anxiety. Several NPY receptor (NPYR) subtypes display elevated expression in many cancers including in breast cancer where this is exploited for imaging and diagnosis. Here, we show that NPY1R and NPY5R mRNA abundance is induced by hypoxia in a Hypoxia Inducible Factor (HIF)-dependent manner in breast cancer cell lines MCF7 and MDA-MB-231. The HIFs bind to several genomic regions upstream of the NPY1R and NPY5R transcription start sites. The MAPK/ERK pathway is activated more rapidly upon NPY5R stimulation in hypoxic cells compared to normoxic cells. This pathway requires IGF1R activity in normoxia, but not in hypoxic cells where they display resistance to the radiosensitizer and IGF1R inhibitor AG1024. Hypoxic cells proliferate and migrate more when stimulated with NPY relative to normoxic cells, with a more robust response observed with a Y5-specific agonist. Our data suggest that hypoxia induced NPYRs render hypoxic cells more sensitive to NPY stimulation. Considering that breast tissue receives a constant supply of NPY, and hypoxia is a common feature of the tumor microenvironment, breast tumors are the perfect storm for hyperactive NPYR. This study not only highlights a new relationship between the HIFs and NPYR expression and activity, but may inform the use of chemotherapeutics targeting NPYRs and hypoxic cells.

category: molecular biology


title: Ing4-deficiency enhances HSC quiescence and confers resistance to inflammatory stress

abstract: Hematopoiesis is tightly regulated by a network of transcription factors and complexes that are required for the development and maintenance of hematopoietic stem cells (HSCs). We recently identified the tumor suppressor, Ing4, as a critical regulator of HSC homeostasis. Though the Ing4 mechanism of action remains poorly characterized, it has been shown to promote stem-like cell characteristics in malignant cells. This activity is, in part, due to Ing4 mediated regulation of several major signaling pathways, including NF-{kappa}B and c-Myc. In murine hematopoiesis, Ing4 deficiency induces G0 arrest in HSCs, while simultaneously promoting gene expression signatures associated with differentiation. This results in a poised state for Ing4-deficient HSCs. Long term HSCs are unable to overcome this block, but short-term HSCs convert the poised state into regenerative capacity during hematopoietic challenges, including irradiation and transplantation. Overall, our findings suggest that Ing4 plays a crucial role in the regulation of hematopoiesis. Our model provides key tools for further identification and characterization of pathways that control quiescence and differentiation in HSCs.

category: cell biology


title: Increased intestinal permeability in an orally-reactive peanut allergy model identifies Angiopoietin like-4 as a biomarker

abstract: Peanut allergy reaction severity correlates with increased intestinal epithelial cell (IEC) barrier permeability. CC027/GeniUnc mice develop peanut allergy by intragastric administration of peanut proteins without adjuvant. We report that peanut-allergic CC027/GeniUnc mice showed increased IEC barrier permeability and systemic peanut allergen Ara h 2 after challenge. Jejunal epithelial cell transcriptomics showed effects of peanut allergy on IEC proliferation, survival, and metabolism, and revealed IEC-predominant angiopoietin like-4 (Angptl4) as a unique feature of CC027/GeniUnc peanut allergy. CC027/GeniUnc mice and peanut-allergic pediatric patients demonstrated significantly higher serum Angptl4 and ANGPTL4 compared to control C3H/HeJ mice and non-peanut-allergic but atopic patients, respectively, highlighting its potential as a biomarker of peanut allergy.


title: The myotendinous junction marker collagen XXII enables zebrafish postural control learning and optimal swimming performance through its force transmission activity

abstract: Although the myotendinous junction (MTJ) is essential for skeletal muscle integrity, its contribution to skeletal muscle function remains largely unknown. Here, we show that CRISPR-Cas9-mediated gene ablation of the MTJ marker col22a1 in zebrafish identifies two distinctive phenotypic classes: class 1 individuals reach adulthood with no overt muscle phenotype while class 2 display severe movement impairment and eventually dye before metamorphosis. Yet mutants that are unequally affected are all found to display defective force transmission attributed to a loss of ultrastructural integrity of the MTJ and myosepta, though with distinct degrees of severity. The behavior-related consequences of the resulting muscle weakness similarly reveal variable phenotypic expressivity. Movement impairment at the critical stage of swimming postural learning eventually causes class 2 larval death by compromising food intake while intensive exercise is required to uncover a decline in muscle performance in class 1 adults. By confronting MTJ gene expression compensation and structural, functional and behavioral insights of MTJ dysfunction, our work unravels variable expressivity of col22a1 mutant phenotype. This study also underscores COL22A1 as a candidate gene for myopathies associated with dysfunctional force transmission and anticipates a phenotypically heterogeneous disease.

category: developmental biology


title: Over-Representation of Potential SP4 Target Genes within Schizophrenia-Risk Genes

abstract: Reduction of Sp4 expression causes age-dependent hippocampal vacuolization and many other intermediate phenotypes of schizophrenia in Sp4 hypomorphic mice. Recent human genetic studies from both the Schizophrenia Exome Sequencing Meta-Analysis (SCHEMA) and the Genome-Wide Association Study (GWAS) validated SP4 as a schizophrenia-risk gene over the exome-wide or the genome-wide significance. Truncation of human SP4 gene has an odds ratio of 9.37 (3.38-29.7) for schizophrenia. Despite successful identification of many schizophrenia-risk genes, it is unknown whether and how these risk genes may interact with each other in the development of schizophrenia. By taking advantage of the specific localization of the GC-boxes bound by SP4 transcription factors, I analyzed the relative abundance of these GC-boxes in the proximal promoter regions of schizophrenia-risk genes. I found that the GC-box containing genes are significantly over-represented within schizophrenia-risk genes, suggesting that SP4 is not only a high-risk gene for schizophrenia, but may also act as a hub of network in regulation of many other schizophrenia-risk genes via these GC-boxes in the pathogenesis of schizophrenia.

category: genetics


title: An analytical pipeline for DNA Methylation Array Biomarker Studies

abstract:
DNA methylation is one of the most commonly studied epigenetic biomarkers, due to its role in disease and development. The Illumina Infinium methylation arrays still remains the most common method to interrogate methylation across the human genome, due to its capabilities of screening over 480, 000 loci simultaneously. As such, initiatives such as The Cancer Genome Atlas (TCGA) have utilized this technology to examine the methylation profile of over 20,000 cancer samples. There is a growing body of methods for pre-processing, normalisation and analysis of array-based DNA methylation data. However, the shape and sampling distribution of probe-wise methylation that could influence the way data should be examined was rarely discussed. Therefore, this article introduces a pipeline that predicts the shape and distribution of normalised methylation patterns prior to selection of the most optimal inferential statistics screen for differential methylation. Additionally, we put forward an alternative pipeline, which employed feature selection, and demonstrate its ability to select for biomarkers with outstanding differences in methylation, which does not require the predetermination of the shape or distribution of the data of interest.

AvailabilityThe Distribution test and the feature selection pipelines are available for download at: https://github.com/uqjlu8/DistributionTest


title: Population model of Temnothorax albipennis as a distributed dynamical system II: secret of "chemical reaction" in collective house-hunting in ant colonies is unveiled by operator methods

abstract: The collective intelligence of animal groups is a complex algorithm for computer scientist and a many-body problem for physics of living system. We show how the time evolution of features in such a system, like number of ants in particular state for colonies, can be mapped to many-body problems in non-equilibrium statistical mechanics. There exist role transitions of active and passive ant between distributed functions, including exploration, assessing, recruiting and transportation in the house-hunting process. Theoretically, such a process can be approximately described as birth-death process where large number of particles living in the Fock space and particles of one sub-type transfer to a different sub-type with some probability. Started from the master equation with constrain of the quorum criterion, we express the evolution operator as a functional integral mapping from operators acting on Fock space in number representation to functional space in coherent state representation. We then read out the action from the evolution operator, and we use least action principal equations of motion, which are the number field equations. The equations we get are couple ordinary differential equations, which can faithfully describe the original master equation, and hence fully describe the system. This method provides us differential equation-based algorithm, which allow us explore parameter space with respect to more complicated agent-based algorithm. The algorithm also allows exploring stochastic process with memory in a Markovian way, which provide testable prediction on collective decision making.


title: Nucleotide Biosynthesis Links Glutathione Metabolism to Ferroptosis Sensitivity

abstract: Nucleotide synthesis is a metabolically demanding process essential for cell division. Several anti-cancer drugs that inhibit nucleotide metabolism induce apoptosis. How inhibition of nucleotide metabolism impacts non-apoptotic cell death is less clear. Here, we report that inhibition of nucleotide metabolism by the p53 pathway is sufficient to suppress the non-apoptotic cell death process of ferroptosis. Mechanistically, stabilization of wild-type p53 and induction of the p53 target gene CDKN1A (p21) leads to decreased expression of the ribonucleotide reductase (RNR) subunits RRM1 and RRM2. RNR is the rate-limiting enzyme of de novo nucleotide synthesis that reduces ribonucleotides to deoxyribonucleotides in a glutathione-dependent manner. Direct inhibition of RNR conserves glutathione which can then be used to limit the accumulation of toxic lipid peroxides, preventing the onset of ferroptosis. These results support a mechanism linking p53-dependent regulation of nucleotide metabolism to non-apoptotic cell death.

category: cancer biology


title: Cellular Pharmacology of Curcumin With and Without Piperine

abstract: Prior reports have suggested that piperine enhances curcumins anti-carcinogenesis. We tested the hypothesis that piperine increases the intracellular concentrations of curcumin by improving intracellular uptake or reducing curcumin efflux or metabolism in breast cells. We incubated SUM149, MCF10A, primary normal human breast cells, ALDH+, and ALDH-CD44+24- SUM149 cells with curcumin {+/-} piperine at concentrations 1 M to 15 M for time periods of 15 minutes to 24 hours. We assayed cell viability by MTT assay and proliferation by primary mammosphere assay. Curcumin and its metabolites were assayed using liquid chromatography mass spectroscopy. Curcumin, but not piperine, showed significantly higher effects on the viability of breast cancer SUM149 cells than in non-tumorigenic MCF10A cells. Curcumin + piperine synergistically reduced viability of SUM149 cells but had a concentration dependent effect upon MCF10A cell viability. Cellular uptake of curcumin in SUM149 is significantly higher, while the efflux in SUM149 is significantly lower than in MCF10A, which correlated with cell viability. Piperine did not alter curcumin cellular uptake, efflux, or metabolism in any of the cell models. The observed synergism of piperine+curcumin in reducing breast stem cell self renewal is likely due to independent anti-carcinogenesis effects rather than any effects upon intracellular curcumin concentrations.

category: pharmacology and toxicology


title: Long-Term Protective Effects of Single-Dose infusion of Warm Blood Cardioplegic Solution in a mini-pig model on the background of intraoperative anemia

abstract:
ObjectivesThe tolerable ischemic time for many cardioplegia solutions has not been established yet. The aim of this study was to estimate the effect of a single-dose of cardioplegia solution Normacor (solution No. 1) and to establish the tolerable ischemic time in a normothermic cardiopulmonary bypass mini-pig model on the background of intraoperative anemia.

MethodsFive female mini-pigs (34{+/-}3 kg, 6-month-old) were subjected to 180 min or 210 min of cardiac arrest by single-dose 400 ml Normacor cardioplegia (solution No. 1). A needle biopsy was taken from the left ventricle before the aortic cross-clamping and every 30 minutes after it. The restoration of left ventricle contractility was assessed by the clinical indicators, catecholamine support, morphological and immunohistochemical examination.

ResultsThe morphological signs of cardiomyocytes ischemia were found after 120 minutes of aortic cross-clamping. According to the content of succinate dehydrogenase and hypoxia-inducible factor, the signs of the cardiomyocytes ischemic injury onset were detected at the same time point. During the entire period of aortic cross-clamping atrial activity was observed in all cases. The proposed single-dose ischemic time for re-dosing of cardioplegia is 120 minutes or ventricular activity onset.

ConclusionsSafe and effective cardioprotection can be achieved with warm blood cardioplegia Normacor (solution No. 1) within 120 minutes for a single-dose infusion.

Graphical Abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

category: physiology


title: The DocMaps Framework for representing assertions on research products in an extensible, machine-readable, and discoverable format

abstract: Peer review of a research product varies widely depending on the publishers and platforms involved in the process. As scholarly publishing is disrupted by new innovations, peer review processes become more heterogeneous, placing an increasing burden on the researcher in understanding how they can communicate their scholarship. New ways to model such processes, and increase transparency, trust, and experimentation in scholarly publishing are needed. Many are emerging but can tend to focus on the needs of creators, and not those of readers, funders, and the whole scholarly publishing ecosystem. They may not place focus on representing editorial practices in ways that can be reliably aggregated, surfaced, and queried; are often limited to traditional peer review processes; and cannot capture the full range of editorial practices and events needed to accommodate alternative publication, review, and curation models. To support researchers in a world of experimentation in scholarly publishing, we propose a machine-readable, extensible, and discoverable framework for representing and surfacing review and editorial processes. Working with a Technical Committee composed of interested parties by employing a modified Delphi Method, we developed initial guiding principles and proposals towards an object-level editorial metadata framework compatible with a broad range of possible futures for scholarly publishing. We present the results of this process with a proposal and example use cases for DocMaps, a framework for representing object-level assertions.

category: scientific communication and education


title: Exploring the metabolic landscape of pancreatic ductal adenocarcinoma cells using genome-scale metabolic modeling

abstract:
Pancreatic ductal adenocarcinoma (PDAC) is a major research focus due to its poor therapy response and dismal prognosis. PDAC cells adapt their metabolism efficiently to the environment to which they are exposed, often relying on diverse fuel sources depending on availability. Since traditional experimental techniques appear exhaustive in the search for a viable therapeutic strategy against PDAC, in this study, a highly curated and omics-informed genome-scale metabolic model of PDAC was reconstructed using patient-specific transcriptomic data. From the analysis of the model-predicted metabolic changes, several new metabolic functions were explored as potential therapeutic targets against PDAC in addition to the already known metabolic hallmarks of pancreatic cancer. Significant downregulation in the peroxisomal fatty acid beta oxidation pathway reactions, flux modulation in the carnitine shuttle system, and upregulation in the reactive oxygen species detoxification pathway reactions were observed. These unique metabolic traits of PDAC were then correlated with potential drug combinations that can be repurposed for targeting genes with poor prognosis in PDAC. Overall, these studies provide a better understanding of the metabolic vulnerabilities in PDAC and will lead to novel effective therapeutic strategies.

Author summaryPancreatic ductal adenocarcinoma (PDAC) is the most common type of pancreatic cancer, with late diagnosis, early metastasis, insufficient therapy response, and very low survival rates. Due to these challenges associated with the diagnosis and treatment of PDAC, it has been a research area of interest. With the goal of understanding the metabolic reprogramming in proliferating PDAC cells, we reconstructed healthy and PDAC models by incorporating patient transcriptomic data into a genome-scale global human metabolic model. Comparing the metabolic flux space for the reactions in the two context-specific models, we identified significantly divergent pathways in PDAC. These results allowed us to further investigate growth-limiting genes in PDAC and identify potential drug combinations that can be repositioned for treatment of PDAC.

category: systems biology


title: The Antimicrobial Efficacy Of Plasma Activated Water Is Modulated By Reactor Design And Water Composition

abstract:
Plasma activated water (PAW) contains a cocktail of reactive oxidative species and free radicals and has demonstrated efficacy as a sanitizer for fresh produce, however there is a need for further optimization. The antimicrobial efficacy of PAW produced by a bubble spark discharge (BSD) reactor and a dielectric barrier discharge-diffuser (DBDD) reactor operating at atmospheric conditions with air, discharge frequencies of 500, 1000 and 1500 Hz, and MilliQ and tap water, was investigated with model organisms Listeria innocua and Escherichia coli. Optimal conditions were subsequently employed for pathogenic bacteria Listeria monocytogenes, E. coli and Salmonella enterica. PAW generated with the DBDD reactor reduced more than 6-log CFU of bacteria within 1 minute of treatment. The BSD-PAW, while attaining high CFU reduction was less effective, particularly for L. innocua. Analysis of physicochemical properties revealed BSD-PAW had a greater variety of reactive species than DBDD-PAW. Scavenger assays were employed to specifically sequester reactive species, including the short-lived superoxide ({middle dot}O2-) radical that could not be directly measured in the PAW. This demonstrated a critical role of superoxide for the inactivation of both E. coli and L. innocua by DBDD-PAW, while in BSD-PAW it had a role in L. innocua inactivation only. Overall, this study demonstrates the potential of DBDD-PAW in fresh produce, where there is a need for sterilization while minimizing chemical inputs and residues and maintaining food quality. Highly effective PAW was generated using air as a processing gas and tap water, making this a feasible and cost-effective option.

ImportanceThere is a growing demand for fresh food produced with minimal processing, however guaranteeing microbial safety in the absence of a thermal kill step is challenging. Plasma-activated water (PAW) is a promising novel antimicrobial but its use in high-risk applications like the sanitization of fresh produce requires further optimization. This study demonstrated the importance of reactor design in the production of reactive species in PAW with capacity to kill bacteria. Very effective PAW was generated using a dielectric barrier discharge-diffuser (DBDD) system, with antimicrobial activity attributed to the presence of superoxide radicals. The DBBD reactor used air as a processing gas and tap water, highlighting the potential of this approach as a cost-effective and green alternative to chemical treatment methods that are currently used in food decontamination.


title: DNA double strand break position leads to distinct gene expression changes and regulates VSG switching pathway choice.

abstract: Antigenic variation is an immune evasion strategy used by Trypanosoma brucei that results in the periodic exchange of the surface protein coat. Underlying this process is the movement of variant surface glycoprotein genes in or out of a specialized locus known as bloodstream form expression site by homologous recombination, facilitated by blocks of repetitive sequence known as the 70-bp repeats, that provide homology for gene conversion events. DNA double strand breaks are potent drivers of antigenic variation, however where these breaks must fall to elicit a switch is not well understood. To understand how the position of a break influences antigenic variation we established a series of cell lines to study the effect of an I-SceI meganuclease break in the active expression site. We found that a DNA break within repetitive regions is not productive for VSG switching, and show that the break position leads to a distinct gene expression profile and DNA repair response which dictates how antigenic variation proceeds in African trypanosomes.


title: Reciprocal regulation of Shh trafficking and H2O2 levels via a noncanonical BOC-Rac1 pathway

abstract: Among molecules that bridge environment, cell metabolism, and cell signaling, H2O2 recently appeared as an emerging but central player. Its level depends on cell metabolism and environment and was recently shown to play key roles during embryogenesis, contrasting with its long-established role in disease progression. We decided to explore whether the secreted morphogen Sonic hedgehog (Shh), known to be essential in a variety of biological processes ranging from embryonic development to adult tissue homeostasis and cancers, was part of these interactions. Here, we report that H2O2 levels control key steps of Shh delivery and that physiological in vivo modulation of H2O2 levels changes Shh distribution and tissue patterning. A feedback loop exists in which Shh trafficking controls H2O2 synthesis via a non-canonical BOC-Rac1 pathway, leading to cytoneme growth. Our findings reveal that Shh directly impacts its own distribution, thus providing a molecular explanation for the robustness of morphogenesis to both environmental insults and individual variability.


title: Differential requirements for mitochondrial electron transport chain components in the adult murine liver

abstract: Mitochondrial electron transport chain (ETC) dysfunction is a common cause of metabolic disease in humans, but the mechanisms underlying tissue specific phenotypes are not understood. Complex I (cI) is classically considered the entry point for electrons into the ETC, and in vitro experiments indicate that cI is required for maintenance of the NAD+/NADH ratio, an indicator of cellular redox status. This finding has largely not been tested in vivo. Here, we report that mitochondrial complex I (cI) is dispensable for homeostasis of the adult mouse liver; animals with hepatocyte-specific loss of cI function display no overt phenotypes or signs of liver damage, and maintain liver function and redox status. Further analysis of cI-deficient livers did not reveal significant proteomic or metabolic changes, indicating little to no compensation is required in the setting of complex I loss. In contrast, complex IV (cIV) dysfunction in adult hepatocytes results in decreased liver function, steatosis, and liver damage, accompanied by significant metabolomic and proteomic perturbations. Correspondingly, we find that complex I-deficient livers are reliant on an alternative pathway, whereby electrons are donated to the ETC via dihydroorotate dehydrogenase, to maintain redox status. Our results support a model whereby complex I loss is tolerated in the mouse liver because hepatocytes make use of alternative electron donors to fuel the mitochondrial ETC.


title: An efficient polymer cocktail-based transportation method for cartilage tissue, yielding chondrocytes with enhanced hyaline cartilage expression during in vitro culturing

abstract: Chondrocytes are used in cell-based therapies such as autologous chondrocyte implantation (ACI) and matrix-associated cartilage implantation (MACI). To transport the cartilage tissue to the laboratory for in vitro culturing, phosphate-buffered saline (PBS), Euro-Collins solution (ECS) and Dulbeccos Modified Eagles Medium (DMEM) are commonly employed at 4-8 {degrees}C. In this study, eight samples of human cartilage biopsy tissues from elderly patients with severe osteoarthritis undergoing arthroscopy, which would otherwise have been discarded, were used. The cartilage tissue samples were compared to assess the cell yield between two transportation groups: i) a thermo-reversible gelation polymer (TGP) based method without cool preservation (~25 {degrees}C) and ii) ECS transport at 4 {degrees}C. These samples were subjected to in vitro culture in a two-dimensional (2D) monolayer for two weeks and subsequently in a three-dimensional (3D) TGP scaffold for six weeks. The cell count obtained from the tissues transported in TGP was higher (0.2 million cells) than those transported in ECS (0.08 million cells) both after initial processing and after in vitro culturing for 2 weeks in 2D (18 million cells compared with 10 million cells). In addition, mRNA quantification demonstrated significantly higher expression of Col2a1 and SOX-9 in 3D-TGP cultured cells and lower expression of COL1a1 in RT-PCR, characteristic of the hyaline cartilage phenotype, than in 2D culture. This study confirms that the TGP cocktail is suitable for both the transport of human cartilage tissue and for in vitro culturing to yield better-quality cells for use in regenerative therapies.


title: Calcium signaling mediates mechanotransduction at the multicellular stage of Dictyostelium discoideum

abstract:
Calcium acts as a second messenger and regulates cellular functions, including cell motility. In Dictyostelium discoideum, the cytosolic calcium level oscillates synchronously, and calcium signal waves propagate in the cell population during the early stages of development, including aggregation. At the unicellular phase, the calcium response through Piezo channels also functions in mechanosensing. However, calcium signaling dynamics during multicellular morphogenesis is still unclear. Here, live-imaging of cytosolic calcium levels revealed that calcium wave propagation, depending on cAMP relay, temporarily disappeared at the onset of multicellular body formation. Alternatively, the occasional burst of calcium signals and their propagation were observed in both anterior and posterior regions of migrating multicellular bodies. Calcium signaling in multicellular bodies occurred in response to mechanical stimulation. Both pathways, calcium release from the endoplasmic reticulum via IP3 receptor and calcium influx from outside the cell, were involved in calcium waves induced by mechanical stimuli. These show that calcium signaling works on mechanosensing in both the unicellular and multicellular phases of Dictyostelium using different molecular mechanisms during development.

Summary statementFluorescence imaging revealed that calcium signaling via both endoplasmic reticulum and extracellular pathways plays an important role in mechanosensing during the multicellular stage of Dictyostelium.


title: Gene Evolutionary Trajectories in M. tuberculosis Reveal Temporal Signs of Selection

abstract: Genetic differences between different Mycobacterium tuberculosis complex (MTBC) strains determine their ability to transmit within different host populations, their latency times, and their drug-resistance profiles. Said differences usually emerge through de novo mutations and are maintained or discarded by the balance of evolutionary forces. Using a dataset of ~5,000 strains representing global MTBC diversity, we determined the past and present selective forces that have shaped the current variability observed in the pathogen population. We identified regions that have evolved under changing types of selection since the time of the MTBC common ancestor. Our approach highlighted striking differences in the genome regions relevant for host-pathogen interaction and, in particular, suggested an adaptive role for the sensor protein of two-component systems. In addition, we applied our approach to successfully identify potential determinants of resistance to drugs administered as second-line tuberculosis treatments.

category: evolutionary biology


title: Phylogeny, evolution, and classification of the ant genus Lasius, the tribe Lasiini, and the subfamily Formicinae (Hymenoptera: Formicidae)

abstract:
Within the Formicidae, the higher classification of nearly all subfamilies has been recently revised due to the findings of molecular phylogenetics. Here, we integrate morphology and molecular data to holistically address the evolution and classification of the ant genus Lasius, its tribe Lasiini, and their subfamily Formicinae. We accomplish this through a critical re-examination of morphology of extant and fossil taxa, molecular phylogenetic analyses, total-evidence dating under fossilized birth-death process, phylogeography, and ancestral state estimation. We use these results to provide revised taxonomic definitions for the Lasiini and select genera, and we provide a key to the genera of the Lasiini with emphasis on the Lasius genus group. We find that the crown Lasiini originated around the end of the Cretaceous on the Eurasian continent and is divisible into four morphologically distinct clades: Cladomyrma, the Lasius genus group, the Prenolepis genus group, and a previously undetected lineage we name XXX gen. n. The crown of the Lasius genus group is considerably younger than that of the Prenolepis genus group, indicating that extinction has played a major role in the evolution of the former clade. Lasius itself is divided into two well-supported monophyletic groups which are approximately equally speciose. We present evidence that temporary social parasitism and fungiculture arose in Lasius two times independently. Additionally, we recover the paraphyly of three Lasius subgenera and propose replacing all subgenera with an informal species group classification: Lasius = Acanthomyops syn. rev., = Austrolasius syn. n., = Cautolasius syn. n., = Chthonolasius syn. n., = Dendrolasius syn. n. Total-evidence analysis reveals that the Baltic-region amber fossil species {dagger}Lasius pumilus and {dagger}Pseudolasius boreus are misplaced to genus; we therefore designate {dagger}XXX gen. n. for the former and {dagger}XXX gen. n. for the latter. Further, we transfer {dagger}XXX and {dagger}Glaphyromyrmex out of the tribe, considering the former to be incertae sedis in the subfamily, and the latter a member of the Formicini (tribal transfer). Two final taxonomic actions are deemed necessary: synonymy of Lasius escamole Reza, 1925 with Liometopum apiculatum Mayr, 1870 syn. n. (subfamilial transfer), and transfer of Paratrechina kohli to Anoplolepis (tribal transfer, forming A. kohli (Forel, 1916) n. comb.).

Summary of taxonomic actionsO_LISubgenera of Lasius synonymized: Lasius = Acanthomyops syn. rev. = Austrolasius syn. n. = Cautolasius syn. n. = Chthonolasius syn. n. = Dendrolasius syn. n.
C_LIO_LILasius myrmidon transferred to XXX gen. n. (Lasiini, XXX genus group).
C_LIO_LI{dagger}Lasius pumilus transferred to {dagger}XXX gen. n. (Lasiini, XXX genus group).
C_LIO_LI{dagger}Pseudolasius boreus transferred to {dagger}XXX gen. n. (incertae sedis in Formicinae) (tribal transfer).
C_LIO_LI{dagger}Glaphyromyrmex transferred to the Formicini from the Lasiini (tribal transfer).
C_LIO_LILasius escamole Reza, 1925 synonymized with Liometopum apiculatum Mayr, 1870, syn. n. (subfamilial transfer).
C_LIO_LIParatrechina kohli (Forel, 1916) transferred to Anoplolepis (Plagiolepidini) (genus and tribal transfer).
C_LI


title: Challenges and costs of asexuality: Variation in premeiotic genome duplication in gynogenetic hybrids from Cobitis taenia complex.

abstract: The transition from sexual reproduction to asexuality is often triggered by hybridization. The gametogenesis of many hybrid asexuals involves a stage of premeiotic genomic endoreduplication leading to the production of clonal gametes and bypassing genomic incompatibilities that would normally cause hybrid sterility. However, it is still not clear at what gametogenic stage the endoreplication occurs, how many gonial cells it affects and whether its rate differs among clonal lineages. Here, we investigated meiotic and premeiotic cells of diploid and triploid hybrids of spined loaches (Cypriniformes: Cobitis) that reproduce by gynogenesis. We found that naturally as well as experimentally produced F1 hybrid strains undergo an obligatory genome duplication event to achieve asexuality, occurring in the gonocytes just before entering meiosis or, rarely, one or few divisions before meiosis. Surprisingly however, the genome endoreplication was observed only in a minor fraction of the hybrids gonocytes, while the vast majority were unable to duplicate their genomes and consequently could not proceed beyond pachytene due to defects in pairing and bivalent formation. We also noted that the rate of endoreplication was significantly higher among gonocytes of hybrids from successful natural clones than of experimentally produced F1 hybrids, indicating that interclonal selection may favour lineages which maximize the rate of premeiotic endoreduplication. We conclude that asexuality and hybrid sterility are intimately related phenomena and the transition from sexual reproduction to asexuality must overcome significant problems with genome incompatibilities with possible impact on reproductive potential.


title: Inhibitory control performance is repeatable across years and contexts in a wild bird population

abstract: Inhibitory control is one of several cognitive mechanisms required for self-regulation, decision making and attention towards tasks. Linked to a variety of maladaptive behaviours in humans, inhibitory control is expected to influence behavioural plasticity in animals in the context of foraging, social interaction, or responses to sudden changes in the environment. One widely used cognitive assay, the  detour task, putatively tests inhibitory control. In this task, subjects must avoid impulsively touching transparent barriers positioned in front of food, and instead access the food by an alternative but known route. Recently it has been suggested that the detour task is unreliable and measures factors unrelated to inhibitory control, including motivation, previous experience and persistence. Consequently, there is growing uncertainty as to whether this task leads to erroneous interpretations about animal cognition and its links with socio-ecological traits. To address these outstanding concerns, we designed a variant of the detour task for wild great tits (Parus major) and deployed it at the nesting site of the same individuals across two spring seasons. This approach eliminated the use of food rewards, limited social confounds, and maximised motivation. We compared task performance in the wild with their performance in captivity when tested using the classical cylinder detour task during the non-breeding season. Task performance was temporally and contextually repeatable, and none of the confounds had any significant effect on performance, nor did they drive any of the observed repeatable differences among individuals. These results support the hypothesis that our assays captured intrinsic differences in inhibitory control. Instead of  throwing the detour task out with the bathwater, we suggest confounds are likely system and experimental-design specific, and that assays for this potentially fundamental but largely overlooked source of behavioural plasticity in animal populations, should be validated and refined for each study system.

category: animal behavior and cognition


title: Influence of Strain Post-Processing on Brain Injury Prediction

abstract:
Finite element head models are a tool to better understand brain injury mechanisms. Many of the models use strain as output but with different percentile values such as 100th, 95th, 90th, and 50th percentiles. Some use the element value, whereas other use the nodal average value for the element. Little is known how strain post-processing is affecting the injury predictions and evaluation of different prevention systems. The objective of this study was to evaluate the influence of strain output on injury prediction and ranking.

Two models with different mesh densities were evaluated (KTH Royal Institute of Technology head model and the Total Human Models for Safety (THUMS)). Pulses from reconstructions of American football impacts with and without a diagnosis of mild traumatic brain injury were applied to the models. The value for 100th, 99th, 95th, 90th, and 50th percentile for element and nodal averaged element strain was evaluated based on peak values, injury risk functions, injury predictability, correlation in ranking, and linear correlation.

The injury risk functions were affected by the post-processing of the strain, especially the 100th percentile element value stood out. Meanwhile, the area under the curve (AUC) value was less affected, as well as the correlation in ranking (Kendalls tau 0.71-1.00) and the linear correlation (Pearsons r2 0.72-1.00). With the results presented in this study, it is important to stress that the same post-processed strain should be used for injury predictions as the one used to develop the risk function.

category: bioengineering


title: Large-scale identification of viral quorum sensing systems reveal convergent evolution of density-dependent sporulation-hijacking in bacteriophages

abstract:
Communication between viruses supported by quorum sensing systems (QSSs) were found to optimize the fitness of temperate bacteriophages of Bacilli by guiding the transition from the host-destructive lytic cycle to the host-protective lysogenic cycle in a density-dependent manner. All known phage-encoded QSSs consist of a communication propeptide and a cognate intracellular receptor that regulates the expression of adjacent target genes upon recognition of the matured peptide, a signature known as RRNPP and found in chromosomes, plasmids and phages of Firmicutes bacteria. Recently, we have introduced the RRNPP_detector software to detect novel genetic systems matching the RRNPP signature, which unearthed many novel phage-encoded candidate QSSs. Here, by looking at the adjacent genes likely regulated by these viral candidate QSSs, we identified an unsuspected clustering of viral QSSs with viral genes whose bacterial homologs are key regulators of the last-resort bacterial sporulation initiation pathway (rap, spo0E or abrB). Consistently, we found evidence in published data that certain of these QSSs encoded by prophages (phage genomes inserted within a bacterial genome) dynamically manipulate the timing of sporulation in the host. Because these viral QSSs are genetically diverse and are found associated with different sporulation regulators, this suggests a convergent evolution in bacteriophages of density-dependent sporulation-hijacking mechanisms.

SIGNIFICANCECommunication between viruses supported by quorum sensing systems (QSSs) is a brand new research area that has transformed our views of viral adaptation and virus-host co-evolution. The viral QSSs discovered so far were found to guide the lysis-lysogeny decision in temperate bacteriophages as a function of phage density. Here, we identified that quorum sensing-mediated communication between phages can not only guide the regulation of viral processes but also the manipulation of the bacterial sporulation pathway. Our finding introduces the new view that not only bacteria decide when it is time to sporulate, some bacteriophages are also key stakeholders in this dynamical decision-making process. Considering that spores are the transmissive form of many pathogens, these new insights have important applied implications.

category: bioinformatics


title: Large-scale identification of viral quorum sensing systems reveals density-dependent sporulation-hijacking mechanisms in bacteriophages


title: ACORBA: Automated workflow to measure Arabidopsis thaliana root tip angle dynamic

abstract:
Plants respond to the surrounding environment in countless ways. One of these responses is their ability to sense and orient their root growth toward the gravity vector. Root gravitropism is studied in many laboratories as a hallmark of auxin-related phenotypes. However, manual analysis of images and microscopy data is known to be subjected to human bias. This is particularly the case for manual measurements of root bending as the selection lines to calculate the angle are set subjectively. Therefore, it is essential to develop and use automated or semi-automated image analysis to produce reproducible and unbiased data. Moreover, the increasing usage of vertical-stage microscopy in plant root biology yields gravitropic experiments with an unprecedented spatiotemporal resolution. To this day, there is no available solution to measure root bending angle over time for vertical-stage microscopy. To address these problems, we developed ACORBA (Automatic Calculation Of Root Bending Angles), a fully automated software to measure root bending angle over time from vertical-stage microscope and flatbed scanner images. Moreover, the software can be used semi-automated for camera, mobile phone or stereomicroscope images. ACORBA represents a flexible approach based on both traditional image processing and deep machine learning segmentation to measure root angle progression over time. By its automated nature, the workflow is limiting human interactions and has high reproducibility. ACORBA will support the plant biologist community by reducing time and labor and by producing quality results from various kinds of inputs.

Significance statementACORBA is implementing an automated and semi-automated workflow to quantify root bending and waving angles from images acquired with a microscope, a scanner, a stereomicroscope or a camera. It will support the plant biology community by reducing time and labor and by producing trustworthy and reproducible quantitative data.


title: Age-Related Changes in the Rhesus Macaque Eye

abstract:
PurposeTo assess age-related changes in the rhesus macaque eye and evaluate them to corresponding human age-related eye disease.

MethodsData from eye exams and imaging tests including intraocular pressure (IOP), lens thickness, axial length, and retinal optical coherence tomography (OCT) images were evaluated from 142 individuals and statistically analyzed for age-related changes. Quantitative autofluorescence (qAF) was measured as was the presence of macular lesions as related to age.

ResultsAges of the 142 rhesus macaques ranged from 0.7 to 29 years (mean=16.4 years, stdev=7.5 years). Anterior segment measurements such as IOP, lens thickness, and axial length were acquired. Advanced retinal imaging in the form of optical coherence tomography and qAF were obtained. Quantitative assessments were made and variations by age groups were analyzed to compare with established age-related changes in human eyes. Quantitative analysis of data revealed age-related increase in intraocular pressure, ocular biometry (lens thickness and axial length), and presence of macular lesions. Age-related changes in thicknesses of retinal layers on OCT were observed and quantified. Age was correlated with increased qAF.

ConclusionsThe rhesus macaque has age-related ocular changes similar to humans. IOP increases with age while retinal ganglion cell layer thickness decreases. Macular lesions develop in some aged animals. Our findings support the concept that rhesus macaques may be useful for the study of important age-related diseases such as glaucoma, macular diseases, and cone disorders, and for development of therapies for these diseases.


title: Large-scale all-optical dissection of motor cortex connectivity reveals a segregated functional organization of mouse forelimb representations

abstract: In rodent motor cortex, the rostral forelimb area (RFA) and the caudal forelimb area (CFA) are major actors in orchestrating the control of forelimb complex movements. However, their intrinsic connections and reciprocal functional organization are still unclear, limiting our understanding of how the brain coordinates and executes voluntary movements. Here we causally probed cortical connectivity and activation patterns triggered by transcranial optogenetic stimulation of ethologically relevant complex movements exploiting a novel large-scale all-optical method in awake mice. Results show specific activation features for each movement class, providing evidence for a segregated functional organization of CFA and RFA. Importantly, we identified a second discrete lateral grasping representation area, namely lateral forelimb area (LFA), with unique connectivity and activation patterns. Therefore, we propose the LFA as a distinct motor representation in the forelimb somatotopic motor map.


title: Size-dependent susceptibility of lake phytoplankton to light stress: An implication for succession of large green algae in a deep oligotrophic lake

abstract: Field observations of the population dynamics and measurements of photophysiology in Lake Biwa were conducted by size class (< vs. > 30 m) from early summer to autumn to investigate the relationships between susceptibility to light stress and cell size. Also, a nutrient bioassay was conducted to clarify whether the growth rate and photosystem II (PSII) photochemistry of small and large phytoplankton are limited by nutrient availability. Large phytoplankton, which have lower intracellular Chl-a concentrations, had higher maximum PSII photochemical efficiency (Fv/Fm) but lower non-photochemical quenching (NPQNSV) than small phytoplankton under both dark and increased light conditions. The nutrient bioassay revealed that the PSII photochemistry of small phytoplankton was restricted by N and P deficiency at the pelagic site even at the end of the stratification period, while that of large phytoplankton was not. These results suggest that large phytoplankton have lower susceptibility to PSII photodamage than small phytoplankton due to lower intracellular Chl-a concentrations. The size dependency of susceptibility to PSII photoinactivation may play a key role in large algal blooms in oligotrophic water.


title: Effect of Geobacter metallireducens nanowire on electron transfer efficiency in MFC

abstract: The inhibitory effect of electron mediator 2,6-anthraquinone disulphonate (AQDS) on Geobacter metallireducens nanowire in the microbial fuel cell (MFC) was studied. In the culture process of G.metallireducens with Fe(OH)3 as an electron acceptor, the concentration of reduction product Fe (II) in solution without AQDS was higher than that with AQDS after 10 days, due to the formation of microbial nanowires. The effects of nanowire on electron transfer efficiency and electrical current characteristic were studied using a double chamber MFC reactor. The transfer efficiency between biofilm and electrodes was increased by nanowire, which increased the maximum output voltage of MFC was 442 mV. The nanowire biofilm electrode had a bigger cyclic voltammetry curve peak, smaller activation resistance, and a stronger current response signal through electrochemical measurement, which indicates that the nanowire enhanced the electrochemical activity of the electrode.


title: RAD51AP1 compensates for the loss of RAD54 in homology-directed DNA repair

abstract:
Homologous recombination (HR) is a complex DNA damage repair pathway and an attractive target of inhibition in anti-cancer therapy. To help guide the development of efficient HR inhibitors, it is critical to identify compensatory sub-pathways.

In this study, we describe a novel synthetic interaction between RAD51AP1 and RAD54, two structurally unrelated proteins that function downstream of the RAD51 recombinase in HR. We show that deletion of both RAD51AP1 and RAD54 synergistically sensitizes human cancer cell lines to treatment with a Poly(adenosine 5 s-diphosphate-ribose) polymerase inhibitor, to the DNA inter-strand crosslinking agent mitomycin C, and to hydroxyurea, which stalls the progression of DNA replication forks. We infer that HR-directed anti-cancer treatment modalities shall consider this intra-pathway functional overlap, and we hypothesize that in cancerous cells the simultaneous inactivation of both RAD54 and RAD51AP1 will accentuate tumor kill.


title: RAD51AP1 and RAD54 underpin two distinct RAD51-dependent routes of DNA damage repair via homologous recombination


title: Late-acting self-incompatible system, preferential allogamy and delayed selfing in the heterostylous invasive populations of Ludwigia grandiflora subsp. hexapetala

abstract: AO_SCPLOWBSTRACTC_SCPLOWBreeding system influences local population genetic structure, effective size, offspring fitness and functional variation. Determining the respective importance of self- and cross-fertilization in hermaphroditic flowering plants is thus important to understand their ecology and evolution. The worldwide invasive species, Ludwigia grandiflora subsp. hexapetala (Lgh) presents two floral morphs: one self-compatible short-styled morph (S-morph) and one self-incompatible long-styled morph (L-morph). In this study, we identified the breeding systems of western European experimental and natural populations of Lgh by comparing structural characteristics of pollen and style, by studying self- and cross-pollen tube elongations and the viability of the resulting seeds and seedlings in both floral morphs. Our results showed no differences in pollen shape and stigma surfaces no matter the floral morph. In the self-incompatible L-morph flowers, self-pollen tubes were stopped tardily, in the ovarian area, and were unable to fertilize the ovules. This first formal identification of a late-acting, prezygotic self-incompatible system (LSI) in Ludwigia genus contributes a case of LSI in an additional family within the Myrtales order. In the self-compatible S-morph flowers, self-pollen always succeeded to self-fertilize the ovules that nearly all developed into viable seedlings. However, cross-pollen tubes always elongated faster than self-pollen tubes in both morphs. S-morph individuals may thus advantage preferential allogamy over selfing when cross-pollen is available despite its self-compatibility. As expected in late-acting self-incompatible systems, L-morph flowers authorised 0.2{per thousand} of selfed seeds during the uppermost flowering season, that increased to 1{per thousand} at the end of the flowering season. Such delayed selfing resulted in a significant quantity of viable floating seeds. They may contribute to the local regeneration, seed bank and propagation of the L-morph, which may contribute to explain its invasion success worldwide. Management plans of Lgh would gain to consider the breeding systems we identified.

category: ecology


title: Late-acting self-incompatible system, preferential allogamy and delayed selfing in the heteromorphic invasive populations of Ludwigia grandiflora subsp. hexapetala


title: Evolution of DNA methylation across Ecdysozoa

abstract: DNA methylation is a crucial, abundant mechanism of gene regulation in vertebrates. It is less prevalent in many other metazoan organisms and completely absent in some key model species, such as D. melanogaster and C. elegans. We report here a comprehensive study of the presence and absence of DNA methyltransferases (DNMTs) in 138 Ecdysozoa, covering Arthropoda, Nematoda, Priapulida, Onychophora, and Tardigrada. Three of these phyla have not been investigated for the presence of DNA methylation before. We observe that the loss of individual DNMTs independently occurred multiple times across ecdysozoan phyla. We computationally predict the presence of DNA methylation based on CpG rates in coding sequences using an implementation of Gaussian Mixture Modelling, MethMod. Integrating both analysis we predict two previously unknown losses of DNA methylation in Ecdysozoa, one within Chelicerata (Mesostigmata) and one in Tardigrada. In the early-branching Ecdysozoa Priapulus caudatus we predict the presence of a full set of DNMTs and the presence of DNA methylation. We are therefore showing a very diverse and independent evolution of DNA methylation in different ecdysozoan phyla spanning a phylogenetic range of more than 700 million years.


title: Reviewing the consequences of genetic purging on the success of rescue programs

abstract: Genetic rescue is increasingly considered a promising and underused conservation strategy to reduce inbreeding depression and restore genetic diversity in endangered populations, but the empirical evidence supporting its application is limited to a few generations. Here we discuss on the light of theory the role of inbreeding depression arising from partially recessive deleterious mutations and of genetic purging as main determinants of the medium to long-term success of rescue programs. This role depends on two main predictions: (1) The inbreeding load hidden in populations with a long stable demography increases with the effective population size; and (2) After a population shrinks, purging tends to remove its (partially) recessive deleterious alleles, a process that is slower but more efficient for large populations than for small ones. We also carry out computer simulations to investigate the impact of genetic purging on the medium to long term success of genetic rescue programs. For some scenarios, it is found that hybrid vigor followed by purging will lead to sustained successful rescue. However, there may be specific situations where the recipient population is so small that it cannot purge the inbreeding load introduced by migrants, which would lead to increased fitness inbreeding depression and extinction risk in the medium to long term. In such cases, the risk is expected to be higher if migrants came from a large non-purged population with high inbreeding load, particularly after the accumulation of the stochastic effects ascribed to repeated occasional migration events. Therefore, under the specific deleterious recessive mutation model considered, we conclude that additional caution should be taken in rescue programs. Unless the endangered population harbors some distinctive genetic singularity whose conservation is a main concern, restoration by continuous stable gene flow should be considered, whenever feasible, as it reduces the extinction risk compared to repeated occasional migration and can also allow recolonization events.


title: Oncogenic truncations of ASXL1 enhance a motif for BRD4 ET-domain binding

abstract: Proper regulation of gene-expression relies on specific protein-protein interactions between a myriad of epigenetic regulators. As such, mutation of genes encoding epigenetic regulators often drive cancer and developmental disorders. Additional sex combs-like protein 1 (ASXL1) is a key example, where mutations frequently drive haematological cancers and can cause developmental disorders. It has been reported that nonsense mutations in ASXL1 promote an interaction with BRD4, another central epigenetic regulator. Here we provide a molecular mechanism for the BRD4-ASXL1 interaction, demonstrating that a motif near to common truncation breakpoints of ASXL1 contains an epitope that binds the ET domain within BRD4. Binding-studies show that this interaction is analogous to common ET-binding modes of BRD4-interactors, and that all three ASX-like protein orthologs (ASXL1-3) contain a functional ET-domain-binding epitope. Crucially, we observe that BRD4-ASXL1 binding is markedly increased in the prevalent ASXL1Y591X truncation that maintains the BRD4-binding epitope, relative to full-length ASXL1 or truncated proteins that delete the epitope. Together, these results show that ASXL1 truncation enhances BRD4 recruitment to transcriptional complexes via its ET domain, which could misdirect regulatory activity of either BRD4 or ASXL1 and may inform potential therapeutic interventions.

category: biochemistry


title: Potato juice, a starch industry waste, as a cost-effective medium for the biosynthesis of bacterial cellulose

abstract:
The unique properties of bacterial cellulose (BC) make it of great interest for numerous branches of industry. Nevertheless, the high cost of the dedicated, microbiological medium used for BC production significantly hinders possibility of widespread use. Searching for an alternative, we turned our attention to potato tuber juice (PJ), a major waste product of the potato starch industry. We verified the possibility of using PJ as a cost-effective, ecological-friendly medium that yielded BC with properties equivalent to those from conventional commercial Hestrin-Schramm medium. The BC yield from PJ medium (>4 g/L) was comparable, despite the lack of any pre-treatment. Likewise, the macro- and microstructure, physicochemical parameters, and chemical composition showed no significant differences between PJ and control BC. Importantly, BC obtained from PJ was not cytotoxic against fibroblast cell line L929 in vitro and did not contain any hard-to-remove impurities. These are very important aspects from an application standpoint, particularly in biomedicine. Therefore, we conclude that using PJ for BC biosynthesis is a path towards significant valorization of an environmentally problematic waste product of the starch industry and can help ultimately lower BC production costs.

HighlightsO_LIPotato juice (PJ) was used as a culture medium for cellulose-synthesizing bacteria.
C_LIO_LIPJ was suitable as source of nutrients and did not required any pre-treatment.
C_LIO_LIYield of BC from PJ was equivalent to that obtained from conventional HS.
C_LIO_LIPJ-BC did not differ from conventionally produced HS-BC in terms of its properties.
C_LIO_LIPJ-BC can be used in the same applications as commercially produced BC.
C_LI

Graphical abstract

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title: INFIMA leverages multi-omics model organism data to identify effector genes of human GWAS variants

abstract: Genome-wide association studies have revealed many non-coding variants associated with complex traits. However, model organism studies have largely remained as an untapped resource for unveiling the effector genes of non-coding variants. We develop INFIMA, Integrative Fine-Mapping, to pinpoint causal SNPs for Diversity Outbred (DO) mice eQTL by integrating founder mice multi-omics data including ATAC-seq, RNA-seq, footprinting, and in silico mutation analysis. We demonstrate INFIMAs superior performance compared to alternatives with human and mouse chromatin conformation capture datasets. We apply INFIMA to identify novel effector genes for GWAS variants associated with diabetes. The results of the application are available at http://www.statlab.wisc.edu/shiny/INFIMA/


title: Fatty Alcohols, a Minor Component of the Tree Tobacco Surface Wax, Reduce Insect Herbivory

abstract: Despite decades of research resulting in a comprehensive understanding of epicuticular wax biosynthesis and metabolism, the function of these almost ubiquitous metabolites in plant-herbivore interactions remains unresolved. To develop a better understanding of this role, we investigated plant-herbivore interactions in four Nicotiana glauca (tree tobacco) genome edited mutants. This included [eceriferum1 (cer1), eceriferum3 (cer3), {beta}-ketoacyl-coA synthase6 (kcs6), and fatty acyl-coA reductase (far)] displaying a wide range of alkane and fatty alcohol abundances. Three interaction classes were examined: chewing herbivory with seven caterpillar and one snail species, phloem feeding with Myzus persicae (green peach aphid), and egg laying with Bemisia tabaci (sweet potato whitefly). We found that high wax load and alkane abundance did not reduce caterpillar or snail herbivory. However, fatty alcohol content was negatively correlated with caterpillar growth, suggesting a role in reducing insect herbivory despite its lower levels. Aphid reproduction and feeding activity were not correlated with wax load and composition but are potentially affected by altered cutin composition of cer1 mutants. When examining non-feeding activities, wax crystal morphology could explain the preference of B. tabaci to lay eggs on wildtype plants relative to cer1 and far mutants. Accordingly, the fatty alcohol wax component reduces caterpillar herbivory on the chemical level, but oviposition is increased when wax crystals are dense. The results suggest that this varied response between herbivore classes and species, at times displaying increased and at times reduced fitness in response to altered wax composition is in part a consequence of co-evolution that shaped the specific effects of different N. glauca metabolites such as anabasine and fatty alcohols in plant-herbivore interactions.

category: plant biology


title: IRAK1-dependent Regnase-1-14-3-3 complex formation controls Regnase-1-mediated mRNA decay

abstract: Regnase-1 is an endoribonuclease crucial for controlling inflammation by degrading mRNAs encoding cytokines and inflammatory mediators in mammals. However, it is unclear how Regnase-1-mediated mRNA decay is controlled in interleukin (IL)-1{beta} or Toll-like receptor (TLR) ligand-stimulated cells. Here, by analyzing the Regnase-1 interactome, we found that IL-1{beta} or TLR stimulus dynamically induced the formation of Regnase-1-{beta}-transducin repeat-containing protein ({beta}TRCP) complex. Importantly, we also uncovered a novel interaction between Regnase-1 and 14-3-3 in both mouse and human cells. Strikingly, both interactions occur in a mutually exclusive manner, underscoring the importance of modulating Regnase-1s activity. Additionally, we show that in IL-1R/TLR-stimulated cells, the Regnase-1-14-3-3 interaction is mediated by IRAK1 through a previously uncharacterized C-terminal structural domain. Phosphorylation of Regnase-1 at S494 and S513 is critical for Regnase-1-14-3-3 interaction, while a different set of phosphorylation sites of Regnase-1 are known to be required for the recognition by {beta}TRCP and proteasome-mediated degradation. 14-3-3 stabilizes Regnase-1 but abolishes its activity by inhibiting Regnase-1-mRNA association. Furthermore, nuclear-cytoplasmic shuttling of Regnase-1 is abrogated by 14-3-3 interaction. Taken together, the results suggest that a novel inflammation-induced interaction of 14-3-3 with Regnase-1 stabilizes inflammatory mRNAs by sequestering Regnase-1 in the cytoplasm to prevent mRNA recognition.

category: immunology


title: Phenotypic and genomic diversification in complex carbohydrate degrading human gut bacteria

abstract: Symbiotic bacteria are responsible for the majority of complex carbohydrate digestion in the human colon. Since the identities and amounts of dietary polysaccharides directly impact the gut microbiota, determining which microorganisms consume specific nutrients is central to defining the relationship between diet and gut microbial ecology. Using a custom phenotyping array, we determined carbohydrate utilization profiles for 354 members of the Bacteroidetes, a dominant saccharolytic phylum. There was wide variation in the numbers and types of substrates degraded by individual bacteria, but phenotype-based clustering grouped members of the same species indicating that each species performs characteristic roles. The ability to utilize dietary polysaccharides and endogenous mucin glycans was negatively correlated, suggesting exclusion between these niches. By analyzing related Bacteroides ovatus/xylanisolvens strains that vary in their ability to utilize mucin glycans, we addressed whether gene clusters that confer this complex, multi-locus trait are being gained or lost in individual strains. Pangenome reconstruction of these strains revealed a remarkably mosaic architecture in which genes involved in polysaccharide metabolism are highly variable and bioinformatics data provide evidence of interspecies gene transfer that might explain this genomic heterogeneity. Global transcriptomic analyses suggest that the ability to utilize mucin has been lost in some lineages of B. ovatus and B. xylanisolvens, which still harbor residual gene clusters that are involved in mucin utilization by strains that still actively express this phenotype. Our data provide insight into the breadth and complexity of carbohydrate metabolism in the microbiome and the underlying genomic events that shape these behaviors.

category: microbiology


title: High-resolution single cell transcriptome analysis of zebrafish sensory hair cell regeneration

abstract: Loss of sensory hair cells in the mammalian inner ear leads to permanent hearing and vestibular defects, whereas loss of hair cells in zebrafish results in their regeneration. We used scRNA-Seq to characterize the transcriptional dynamics of hair cell regeneration in zebrafish at unprecedented spatio-temporal resolution. We uncovered three, sequentially activated modules. First, an injury/inflammatory response and downregulation of progenitor/stem cell maintenance genes within minutes after hair cell loss. Second, the transient activation of regeneration-specific genes. And third, a robust reactivation of developmental gene programs, including hair cell specification, cell cycle activation, ribosome biogenesis, and a metabolic switch to oxidative phosphorylation. The results are not only relevant for our understanding of hair cell regeneration and how we might be able to trigger it in mammals but also for regenerative processes in general. The data is searchable and publicly accessible via a web-based interface.


title: Phylogenomic and mitogenomic data can accelerate inventorying of tropical beetles during the current biodiversity crisis

abstract: Conservation efforts must be evidence-based, so rapid and economically feasible methods should be used to quantify diversity and distribution patterns. We have attempted to overcome current impediments to the gathering of biodiversity data by using integrative phylogenomic and three mtDNA fragment analyses. As a model, we sequenced the Metriorrhynchini beetle fauna, sampled from [~]700 localities in three continents. The species-rich dataset included [~]6,500 terminals, >2,300 putative species, more than a half of them unknown to science. The phylogenomic backbone enabled the integrative delimitation of robustly defined natural units that will inform future research. Using constrained mtDNA analysis, we identified the spatial structure of -diversity, very high species-level endemism, a biodiversity hotspot in New Guinea, and high phylogenetic diversity in the Sundaland. We suggest that [~]20 person months of focused field research and subsequent laboratory and bioinformatic workflow steps would substantially accelerate the inventorying of any hyperdiverse tropical group with several thousand species. The outcome would be a scaffold for the incorporation of further data. The database of sequences could set a benchmark for the spatiotemporal evaluation of biodiversity, would support evidence-based conservation planning, and would provide a robust framework for systematic, biogeographic, and evolutionary studies.


title: Assessing the matrix effects of pigmented and non-pigmented salmon during multi-residue antibiotic analysis with liquid chromatography coupled to tandem mass spectrometry

abstract: Several validated methods exist for the quantitation of antibiotics in seafood with ultra-high pressure liquid chromatography coupled with tandem spectrometry (UPLC-MS/MS). To our knowledge, none have explored the effects of co-eluting matrix components on the accuracy of quantitation. Such matrix effects could disproportionally change the ionization of analytes and their respective surrogate/internal standards during UPLC-MS/MS analysis, resulting in over-or under-estimation of antibiotic values. In this study, we measured matrix effects, alongside extraction recoveries for 30 antibiotics and their respective class-specific surrogate standards in Sockeye, King and Ivory (non-pigmented) salmon extracted using the QUEChERS method. A modified QUEChERS method involving dispersive or hydrophilic-lipophilic balance (HLB) solid phase extraction (SPE) was also tested on Sockeye salmon. Despite acceptable extraction recoveries for most antibiotics extracted using the QUEChERS method, significant matrix effects were observed for most antibiotic standards. Dispersive or HLB SPE clean-up did not improve analyte recoveries from Sockeye salmon, and in some cases, increased matrix effects. Accuracy and sensitivity were reduced when matrix effects were high. Our results demonstrate that matrix components in salmon cause matrix effects on antibiotics during UPLC-MS/MS analysis which could impact the accuracy and sensitivity of the analysis.


title: Mining bacterial NGS data vastly expands the complete genomes of temperate phages

abstract: Temperate phages (active prophages induced from bacteria) help control pathogenicity, modulate community structure, and maintain gut homeostasis1. Complete phage genome sequences are indispensable for understanding phage biology. Traditional plaque techniques are inapplicable to temperate phages due to the lysogenicity of these phages, which curb the identification and characterization of temperate phages. Existing in silico tools for prophage prediction usually fail to detect accurate and complete temperate phage genomes2-5. In this study, by a novel computational method mining both the integrated active prophages and their spontaneously induced forms (temperate phages), we obtained 192,326 complete temperate phage genomes from bacterial next-generation sequencing (NGS) data, hence expanded the existing number of complete temperate phage genomes by more than 100-fold. The reliability of our method was validated by wet-lab experiments. The experiments demonstrated that our method can accurately determine the complete genome sequences of the temperate phages, with exact flanking sites (attP and attB sites), outperforming other state-of-the-art prophage prediction methods. Our analysis indicates that temperate phages are likely to function in the evolution of microbes by 1) cross-infecting different bacterial host species; 2) transferring antibiotic resistance and virulence genes; and 3) interacting with hosts through restriction-modification and CRISPR/anti-CRISPR systems. This work provides a comprehensive complete temperate phage genome database and relevant information, which can serve as a valuable resource for phage research.


title: Plumage balances camouflage and thermoregulation in Horned Larks (Eremophila alpestris)

abstract: Animal coloration serves many biological functions and must therefore balance potentially competing selective pressures. For example, many animals have camouflage, in which coloration matches the visual background against which predators scan for prey. However, different colors reflect different amounts of solar radiation and may therefore have thermoregulatory implications as well. In this study, we examined geographic variation in dorsal patterning, color, and solar reflectance among Horned Larks (Eremophila alpestris) of the western United States. We found associations between dorsal plumage brightness, hue, and patterning relative to the soil conditions where specimens were collected. Specifically, brighter dorsal plumage corresponded to brighter soil, while redder, more saturated hues in dorsal plumage corresponded to redder soils. Furthermore, backs with more high-contrast patterning were more common among females and also associated with soil that had coarser soil fragments, suggesting that lark plumage has been selected to optimize background matching in different environments. We also found that larks exhibited higher solar reflectance in hotter and more arid environments, which lowers the water requirements for homeothermy. Taken together, these findings suggest that natural selection has balanced camouflage and thermoregulation in Horned Larks across a wide variety of soil types and abiotic conditions.

category: zoology


title: Novel municipal sewage-associated bacterial genomes and their potential in source tracking

abstract: Little is known about the genomic diversity of raw municipal wastewater (sewage) microbial communities, including to what extent sewage-specific populations exist and how they can be used to improve source attribution and partitioning in sewage-contaminated waters. Herein, we used the influent of three wastewater treatment plants in Atlanta, Georgia (USA) as inoculum in multiple controlled laboratory mesocosms to simulate sewage contamination events and followed these perturbed freshwater microbial communities with metagenomics over a 7-day observational period. We describe 15 abundant non-redundant bacterial metagenome-assembled genomes (MAGs) ubiquitous within all sewage inoculum yet absent from the unperturbed freshwater control at our analytical limit of detection. Tracking the dynamics of populations represented by these MAGs revealed varied decay kinetics, depending on (inferred) phenotypes, e.g., anaerobes decayed faster under the well-aerated incubation conditions. Notably, a portion of these populations show decay patterns similar to common markers, Enterococcus and HF183. Comparisons against MAGs from different sources such as human and animal feces, revealed low cross-reactivity, indicating how genomic collections could be used to sensitively identify sewage contamination and partition signal among multiple sources. Overall, our results indicate the usefulness of metagenomic approaches for assessing sewage contamination in waterbodies and provides needed methodologies for doing so.


title: Chromatin alterations in the aging lung change progenitor cell activity

abstract: The lung contains multiple progenitor cell types that respond to damage, but how their responses are choreographed and why they decline with age is poorly understood. We report that histone H3 lysine 9 di-methylation (K9me2), mediated by histone methyltransferase G9a, regulates the dynamics of lung epithelial progenitor cells, and this regulation deteriorates with age. In aged mouse lungs, K9me2 loss coincided with lower frequency and activity of alveolar type 2 (AT2) cell progenitors. In contrast, K9me2 loss resulted in increased frequency and activity of multipotent progenitor cells with bronchiolar and alveolar potential (BASCs) and bronchiolar progenitors. K9me2 depletion in young mice through deletion or inhibition of G9a decreased AT2 progenitor activity and impaired alveolar injury regeneration. Conversely, K9me2 depletion increased chromatin accessibility of bronchiolar cell genes, increased BASC frequency and accelerated bronchiolar repair. K9me2 depletion also resulted in increased bronchiolar cell expression of the SARS-CoV2 receptor Ace2 in aged lungs. These data point to K9me2 and G9a as a critical regulator of the balance of lung progenitor cell regenerative responses and prevention of susceptibility to age-related lung diseases. These findings indicate that epigenetic regulation coordinates progenitor cell populations to expedite regeneration in the most efficient manner and disruption of this regulation presents significant challenges to lung health.

category: molecular biology


title: Induced Membrane Curvature Bypasses Clathrin's Essential Endocytic Function

abstract:
During membrane trafficking, flat membrane is rapidly remodeled to produce nanometer-scale vesicles. The mechanisms underlying this shape change are not completely understood, but coat proteins such as clathrin are implicated. Clathrins ability to bind to membranes of many different geometries casts uncertainty on its specific role in curvature generation and stabilization. Here, we used nanopatterning to produce substrates of ideal optical properties for live-cell imaging, with U-shaped features that bend a cells ventral plasma membrane into shapes characteristic of the energetically-unfavorable intermediate of clathrin- mediated endocytosis (CME). This induced plasma membrane curvature recruits the endocytic machinery, promoting productive endocytosis. Upon clathrin or AP2 disruption, CME sites on flat substrates are diminished. However, induced curvature rescues the localization, turnover and transferrin cargo uptake activities of CME sites after clathrin, but not AP2, disruption. These data establish that clathrins essential function during CME is to facilitate the evolution of membrane curvature rather than to scaffold CME protein recruitment.

SummaryCail et al. demonstrate that induced nanoscale membrane curvature recruits endocytic sites and produces vesicles in cells lacking the coat protein clathrin, while the adaptor protein AP2 is still required, showing that clathrins essential function is to facilitate curvature development of the nascent vesicle.

category: cell biology


title: Tuned to Learn: An anticipatory hippocampal convergence state conducive to memory formation revealed during midbrain activation

abstract: The hippocampus has been a focus of memory research since H.Ms surgery in 1953 abolished his ability to form new memories, yet its mechanistic role in memory is still debated. Here, we identify a novel, systems-level candidate memory mechanism: an anticipatory hippocampal "convergence state", observed while awaiting valuable information, that both predicts later memory, and accounts for the relationship between midbrain activation and enhanced learning. To reveal this state, we leveraged endogenous neuromodulation associated with motivation: During fMRI, participants viewed trivia questions eliciting high or low curiosity, each followed seconds later by its answer. We reasoned that memory encoding success requires a convergence of factors, and as such, hippocampal states associated with remembered trials would be less variable than forgotten ones. Using a novel multivariate approach, we measured convergence by quantifying the typicality of spatially distributed patterns. We found that during anticipation of trivia answers, hippocampal states showed greater convergence under high than low curiosity. Crucially, convergence in the hippocampus increased with greater midbrain activation and uniquely accounted for the association between midbrain activation and subsequent memory recall. We propose that this novel convergence state in the hippocampus reflects a mechanism of its contribution to long term memory formation and that engagement of this convergence state completes the cascade from motivation to midbrain activity to memory enhancement.

category: neuroscience


title: Single cell profiling of T and B cell repertoires following SARS-CoV-2 mRNA vaccine

abstract: mRNA based vaccines for SARS-CoV-2 have shown exceptional clinical efficacy providing robust protection against severe disease. However, our understanding of transcriptional and repertoire changes following full vaccination remains incomplete. We used single-cell RNA sequencing and functional assays to compare humoral and cellular responses to two doses of mRNA vaccine with responses observed in convalescent individuals with asymptomatic disease. Our analyses revealed enrichment of spike-specific B cells, activated CD4 T cells, and robust antigen-specific polyfunctional CD4 T cell responses in all vaccinees. On the other hand, CD8 T cell responses were both weak and variable. Interestingly, clonally expanded CD8 T cells were observed in every vaccinee, as observed following natural infection. TCR gene usage, however, was variable, reflecting the diversity of repertoires and MHC polymorphism in the human population. Natural infection induced expansion of larger CD8 T cell clones occupied distinct clusters, likely due to the recognition of a broader set of viral epitopes presented by the virus not seen in the mRNA vaccine. Our study highlights a coordinated adaptive immune response where early CD4 T cell responses facilitate the development of the B cell response and substantial expansion of effector CD8 T cells, together capable of contributing to future recall responses.