title: Antecedent effect models as an exploratory rather than predictive tool to understand the response of plant populations to climate drivers

abstract:
O_LIUnderstanding or predicting the responses of natural populations to climate is an urgent task for ecologists. However, studies linking the temporal dynamics of populations to climate remain limited. In population ecology, studies typically assume that populations respond only to the climate of the most recent growing season or year. However, evidence also exists that certain organisms respond to the climate in a lagged-response fashion.
C_LIO_LIAntecedent effect models are a set of statistical tools that help researchers select the past climatic factors that best predict a response (e.g., survival, reproduction). These models use the evidence provided by the data to select, for example, specific months, or time windows correlated with a response. Thus, antecedent effect models could improve our ability to perform exploratory analysis and to predict the effects of temporal climatic variation on population dynamics.
C_LIO_LIHere, we compare the predictive performance of antecedent effect models against simpler models. We fit three antecedent effect models: (1) weighted mean models (WMM), which weigh the importance of monthly anomalies based on a Gaussian curve, (2) stochastic antecedent models (SAM), which weigh the importance of monthly anomalies using a Dirichlet process, and (3) regularized regressions using the Finnish Horseshoe prior (FHM), which estimate a separate effect size for each monthly anomaly. We compare these approaches to a linear model using a yearly climatic predictor, and a null model with no predictors. We use high resolution demographic data from 34 plant species ranging between 7 and 36 years of length, which reflect the typical temporal grain employed to study the effects of climate on populations. We fit models to the overall asymptotic population growth rate ({lambda}), and to its underlying vital rates (survival, development, and reproduction) to examine the extent to which potential lagged effects occur.
C_LIO_LIAntecedent effect models do not consistently outperform the linear or null models. Average differences in performance are small among models, response variables, and across sample sizes. Surprisingly, ranked in order of decreasing predictive performance, the best approaches are: null model > linear model > FHM > SAM > WMMs. Development is on average easier to predict than survival and reproduction, and these have higher predictive power than the overall rate of growth of the population,{lambda} .
C_LIO_LISynthesis: In temporal datasets with limited sample size, antecedent effect models are better suited as exploratory tools. These models can help identify which single monthly anomalies drive population dynamics, while controlling the effect of noise on estimates. As such, antecedent effect models can be a useful tool for hypothesis generation, and to increase our understanding of the links between climate and plant population dynamics.
C_LI


title: Urbanization and green corridors influence reproductive success and pollinators of common milkweed

abstract: Urbanization exerts many pressures on species, yet little is known about how these pressures impact species interactions. Studies of urban plant-pollinator systems provide mounting evidence that urbanization impairs pollinator movement in fragmented urban landscapes, yet the consequences for pollinator-mediated plant reproduction remains unclear. In non-urban areas, habitat corridors can facilitate the movement of organisms including pollinators, but whether these corridors facilitate plant-pollinator interactions in urban areas remains understudied. To examine how urban environments and green corridors influence plant-pollinator interactions, we measured reproductive success in the native plant common milkweed (Asclepias syriaca), and the community structure of its pollinators, for two years along two urban-rural transects in the Greater Toronto Area, Canada, one of which followed a green corridor. We found that urbanization decreased male fitness (i.e., pollen removal), increased fruit set (i.e., mean no. of follicles per inflorescence), and inconsistently affected female fitness (i.e., no. of follicles) in A. syriaca. Urbanization simultaneously decreased pollinator abundance but increased pollinator richness. Proximity to a green corridor inconsistently affected male fitness but increased reproductive effort (i.e., no. of inflorescences) in A. syriaca, while pollinator diversity and richness was lower in corridors. Notably, there were no consistent relationships between pollinator community structure and reproductive success in A. syriaca in both the presence, and absence, of a green corridor. These results demonstrate the complexity with which urbanization, green corridors, and pollinator communities can shape the reproductive investment and fitness of native plant populations.

category: ecology


title: Functional universality in slow-growing microbial communities arises from thermodynamic constraints

abstract: The dynamics of microbial communities is incredibly complex, determined by competition for metabolic substrates and cross-feeding of byproducts. Species in the community grow by harvesting energy from chemical reactions that transform substrates to products. In many anoxic environments, these reactions are close to thermodynamic equilibrium and growth is slow. To understand the community structure in these energy-limited environments, we developed a microbial community consumer-resource model incorporating energetic and thermodynamic constraints on an interconnected metabolic network. The central ingredient of the model is product inhibition, meaning that microbial growth may be limited not only by depletion of metabolic substrates but also by accumulation of products. We demonstrate that these additional constraints on microbial growth cause a convergence in the structure and function of the community metabolic network--independent of species composition and biochemical details--providing a possible explanation for convergence of community function despite taxonomic variation observed in many natural and industrial environments. Furthermore, we discovered that the structure of community metabolic network is governed by the thermodynamic principle of maximum heat dissipation. Overall, the work demonstrates how universal thermodynamic principles may constrain community metabolism and explain observed functional convergence in microbial communities.


title: Reproductive barriers and genomic hotspots of adaptation during allopatric species divergence

abstract: Theory predicts that in allopatric populations, genomic divergence and reproductive barriers will be driven largely by random genetic drift, and thereby evolve slowly in large populations. However, local adaptation and divergence under selection may also play important roles, which remain poorly characterised. Here we address three key questions in young allopatric species: (a) How widespread are genomic signatures of adaptive divergence?, (b) What is the functional space along which young sister species show divergence at the genomic level?, and (c) How quickly might prezygotic and postzygotic reproductive barriers evolve? Analysis of 82 re-sequenced genomes of the Oriental Papilio polytes species group revealed surprisingly widespread hotspots of intense selection and selective sweeps at hundreds of genes unique to each species, and spanning all chromosomes, rather than divergence only in a few genomic islands. These genes perform diverse ecologically important adaptive functions such as wing development, colour patterning, courtship behaviour, mimicry, pheromone synthesis and olfaction, and host plant use and digestion of secondary metabolites, that could contribute to local adaptation and subsequent reproductive isolation. Divergence at such functional genes appeared to have reproductive consequences: behavioural and hybridisation experiments revealed strong assortative mate preference (prezygotic barriers) as well as postzygotic barriers to hybridisation in timespans as short as 1.27 my, indicating that speciation was already complete, rather than incipient. Our study thus demonstrates an underappreciated role of intense selection and potential local adaptation in creating genome-wide hotspots of rapid molecular evolution and divergence, during differentiation and speciation in young allopatric species.

category: evolutionary biology


title: A self-adjusting, progressive shock magnitude procedure to investigate resistance to punishment: characterization in male and female rats

abstract: Indifference to harmful consequences is one of the main characteristics of compulsive behaviors and addiction. Animal models that provide a rapid and effective measure of resistance to punishment could be critical for the investigation of mechanisms underlying these maladaptive behaviors. Here, analogous to the progressive ratio (PR) procedure widely used to evaluate appetitive motivation as the response requirement is increased, we developed a self-adjusting, progressive shock magnitude (PSM) procedure. The PSM provides, within a single session, a break point that quantifies the propensity to work for a reward in spite of receiving electric footshock that progressively increases in duration. In both male and female rats, the PSM break point was sensitive to 1) the hunger drive; and 2) changes in the qualitative, but not quantitative, incentive value of the reward. In systematic comparisons between PSM and PR procedures in the same rats, we found that both measures are sensitive to manipulations of motivational states, but they are not correlated, suggesting that they measure overlapping but distinct processes. Importantly, the PSM procedure represents a refinement in the 3Rs principles of animal research because animals can control the magnitude of shock that they are willing to tolerate. This self-adjusting PSM procedure may represent a useful tool to investigate mechanisms underlying maladaptive behavior that persists in certain individuals despite harmful consequences.

category: animal behavior and cognition


title: Strength-mass scaling law governs mass distribution inside honey bee swarms

abstract: To survive during colony reproduction, bees create dense clusters of thousands of suspended individuals. How can this swarm, which is orders of magnitude larger than the size of an individual, maintain mechanical stability? We hypothesize that the internal structure in the bulk of the swarm, about which there is little prior information, plays a key role in mechanical stability and thermoregulation. Here, we provide the first-ever 3D reconstructions of the positions of the bees in the bulk of the swarm using x-ray computed tomography. We find that the mass of bees in a layer decreases with distance from the attachment surface. By quantifying the distribution of bees within swarms varying in size (made up of 4000-10000 bees), we find that the same power law governs the smallest and largest swarms, with the weight supported by each layer scaling with the mass of each layer to the {approx} 1.5 power. This arrangement ensures that each layer exerts the same fraction of its total strength, and on average a bee supports a lower weight than its maximum grip strength. This illustrates the extension of the scaling law relating weight to strength of single organisms to the weight distribution within a superorganism made up of thousands of individuals.


title: GRAPE: Genomic Relatedness Detection Pipeline

abstract: Classifying the degree of relatedness between pairs of individuals has both scientific and commercial applications. As an example, GWAS may suffer from high rates of false positive results due to unrecognized population structure. This problem becomes especially relevant with recent increases in large-cohort studies. Accurate relationship classification is also required for genetic linkage analysis to identify disease-associated loci. Additionally, DNA relatives matching service is one of the leading drivers for the direct-to-consumer genetic testing market. Despite the availability of scientific and research information on the methods for determining kinship and the accessibility of relevant tools, the assembly of the pipeline, that stably operates on a real-world genotypic data, requires significant research and development resources. Currently, there is no open-source end-to-end solution for relatedness detection in genomic data, that is fast, reliable and accurate for both close and distant degrees of kinship, combines all the necessary processing steps to work on real data, and is ready for production integration. To address this, we developed GRAPE: Genomic RelAtedness detection PipelinE. It combines data preprocessing, identity-by-descent (IBD) segments detection, and accurate relationship estimation. The project uses software development best practices, as well as GA4GH standards and tools. Pipeline efficiency is demonstrated on both simulated and real-world datasets.

category: bioinformatics


title: Tension anisotropy drives phenotypic transitions of cells via two-way cell-ECM feedback

abstract: Mechanical factors such as stress in the extracellular environment are known to affect phenotypic commitment of cells. However, the stress fields experienced by cells in tissues are multiaxial, and the ways that cells integrate this multiaxial information are largely unknown. Here, we report that the anisotropy of these stress fields is a critical factor triggering phenotypic transition in fibroblast cells, outweighing the previously reported role of stress amplitude. Using a combined experimental and computational approach, we discovered a self-reinforcing mechanism in which cellular protrusions interact with collagen fibers to develop tension anisotropy, which in turn stabilizes protrusions and amplifies their contractile forces. Disruption of this self-reinforcing process, either by reducing tension anisotropy or by inhibiting contractile protrusions, prevented phenotypic conversion of fibroblasts to contractile myofibroblasts.

category: biophysics


title: Generative and interpretable machine learning for aptamer design and analysis of in vitro sequence selection

abstract: Selection protocols such as SELEX, where molecules are selected over multiple rounds for their ability to bind to a target molecule of interest, are popular methods for obtaining binders for diagnostic and therapeutic purposes. With the increasing amount of such high-throughput experimental data available, machine learning techniques have become increasingly popular for molecular datasets analysis. Here, we show that Restricted Boltzmann Machines (RBMs), a two-layer neural network architecture, can successfully be trained on sequence ensembles from SELEX experiments for thrombin aptamers, and used to estimate the fitness of the sequences obtained through the experimental protocol. As a direct consequence, we show that trained RBMs can be exploited to classify as well as generate novel molecules. To confirm our findings, we experimentally verify the generated sequences from RBM.


title: Automated patch clamp screening of amiloride and 5-N,N-hexamethyleneamiloride (HMA) analogs identifies 6-iodoamiloride as a potent acid-sensing ion channel inhibitor.

abstract: Acid-sensing ion channels (ASICs) are transmembrane sensors of extracellular acidosis and potential drug targets in several disease indications, including neuropathic pain and cancer metastasis. The K+-sparing diuretic amiloride is a moderate non-specific inhibitor of ASICs and has been widely used as a probe for elucidating ASIC function. In this work, we screened a library of 6-substituted and 5,6-disubstituted amiloride analogs using a custom-developed automated patch-clamp protocol and identified 6-iodoamiloride as a more potent ASIC1 inhibitor. Follow-up IC50 determinations in tsA-201 cells confirmed higher ASIC1 inhibitory potency for 6-iodoamiloride 97 (hASIC1 97 IC50 88 nM cf. amiloride 11 IC50 1.7 M). A similar improvement in activity was observed in ASIC3-mediated currents from rat small diameter dorsal root ganglion neurons (rDRG single-concentration 97 IC50 230 nM cf. 11 IC50 2.7 M). 6-iodoamiloride represents the amiloride analogue of choice for studying the effects of ASIC inhibition on cell physiology.

category: pharmacology and toxicology


title: Is Melanopsin Activation Affecting Large Field Color Matching Functions?

abstract: Color theory is based on the exclusive activation of cones. However, since the discovery of melanopsin expressing cells in the human retina, evidence of its intrusion in brightness and color vision is increasing. We aimed to assess if differences between peripheral or large field and foveal color matches can be accounted for melanopsin activation or rod intrusion. Photopic color matches by young observers showed that differences between extrafoveal and foveal results cannot be explained by rod intrusion. Furthermore, statistical analyses on existing color matching functions suggest a role of melanopsin activation, particularly, in Large Field S Fundamentals.

category: physiology


title: Phyllochron duration and changes through rice development shape the vertical leaf size profile

abstract:
O_LIWell-irrigated aerobic rice (Oryza sativa L.) plants are often shorter with smaller leaves, and the leaf appearance rate is slower in well-irrigated than in flooded environments. This observation questions the functional relationship between the leaf appearance rate, which is correlated with the apical cell production rate, and leaf length that is in turn correlated with the leaf division zone length.
C_LIO_LIMeristem size, blade size, and appearance were monitored for all leaves from leaf 6 on the main stem of rice plants in field experiments using two varieties, two watering systems, and three sowing dates.
C_LIO_LILeaf blade and division zone lengths were correlated in all leaves of the main stem of rice plants. New stable linear relationships were found between the leaf division zone growth duration and internal cell production rate, which changed after leaf 11. These stable relationships imply a stable link between the rates of cell production in the stem apex and leaf meristem, explaining the vertical leaf size profile.
C_LIO_LIOverall, faster leaf appearance leads to shorter leaves and organs in rice because of a functional link, which is counterbalanced by additional acclimation in transplanted plants.
C_LI

category: plant biology


title: Impairments in fear extinction memory and basolateral amygdala plasticity in the TgF344-AD rat model of Alzheimer's disease are distinct from non-pathological aging.

abstract:
Fear-based disorders such as posttraumatic stress disorder (PTSD) steepen age-related cognitive decline and doubles the risk for developing Alzheimers disease. Due to the seemingly hyperactive properties of fear memories, PTSD symptoms can worsen with age. Perturbations in the synaptic circuitry supporting fear memory extinction are key neural substrates of PTSD. The basolateral amygdala (BLA) is a medial temporal lobe structure critical in the encoding, consolidation, and retrieval of fear memories. As little is known about fear extinction memory and BLA synaptic dysfunction within the context of aging and AD, the goal of this study was to investigate how fear extinction memory deficits and basal amygdaloid nucleus (BA) synaptic dysfunction differentially associate in non-pathological aging and AD in the TgF344AD (TgAD) rat model of AD. Young, middle-aged, and older-aged WT and TgAD rats were trained on a delay fear conditioning and extinction procedure prior to ex vivo extracellular field potential recording experiments in the BA. Relative to young WT rats, long-term extinction memory was impaired, and in general, associated with a hyperexcitable BA and impaired LTP in TgAD rats at all ages. In contrast, long-term extinction memory was impaired in aged WT rats and associated with impaired LTP but not BA hyperexcitability. Interestingly, the middle-aged TgAD rats showed intact short-term extinction and BA LTP, suggestive of a compensatory mechanism, whereas differential neural recruitment in older-aged WT rats may have facilitated short-term extinction. As such, associations between fear extinction memory and amygdala deficits in non-pathological aging and AD are dissociable.

SignificanceAdults with fear-based disorders like post-traumatic stress disorder are at an increased risk for developing age-related cognitive decline and Alzheimers disease (AD). Moreover, negative emotional affect is an early marker of AD. The link between fear-based disorders and AD creates a disadvantage for achieving positive outcomes later in life. Central to the circuitry underlying fear disorders are medial temporal lobe structures like the basal amygdaloid nucleus (BA). However, the role of the BA in fear-based disorders exacerbated by aging and AD is not well understood. Using the TgF344AD rat model of AD, we investigated how fear extinction memory impairments and BA synaptic function are impacted by aging and AD and whether these processes differentially associate in non-pathological aging and AD.

category: neuroscience


title: Associations between locus coeruleus MRI contrast and physiological responses to acute stress in younger and older adults

abstract: Acute stress robustly activates the brains noradrenergic system, the hub of which is the locus coeruleus (LC). Recent studies have indicated that structural integrity of the LC, assessed through magnetic resonance imaging (MRI), is associated with better cognitive outcomes in later life. However, no studies have examined whether MRI-assessed LC integrity is related to arousal responses to acute stress in either younger or older adults, despite the LCs documented role in promoting physiological arousal as part of the acute stress response. In this study, 102 younger and 51 older adults completed an acute stress induction task while we assessed multiple measures of physiological arousal (heart rate, breathing rate, systolic and diastolic blood pressure, sympathetic tone, and heart rate variability, HRV). We used turbo spin echo MRI scans to quantify LC MRI contrast as a measure of LC integrity. Using univariate and multivariate approaches, we assessed how LC MRI contrast was associated with arousal at rest and during acute stress reactivity and recovery. We found that in older adults, having higher caudal LC MRI contrast was associated with greater stress-related increases in systolic blood pressure and decreases in HRV, as well as lower HRV during recovery from acute stress. These results suggest that having higher caudal LC integrity in older adulthood is associated with more pronounced physiological responses to acute stress. Further work is needed to confirm these patterns in larger samples of older adults.


title: Examination of diurnal variation and sex differences in hippocampal neurophysiology and spatial memory

abstract:
Circadian rhythms are biological processes that cycle across 24 hours and regulate many facets of neurophysiology, including learning and memory. Circadian variation in performance on spatial memory tasks is well-documented; however, the effect of sex across circadian time remains unclear. Additionally, little is known regarding the impact of time-of-day on hippocampal neuronal physiology. Here, we investigated the influence of both sex and time-of-day on hippocampal neurophysiology and memory.

Performance on the object location memory (OLM) task depended on both circadian time and sex, with memory enhanced at night in males but during the day in females. Long-term synaptic potentiation (LTP) magnitude at CA3-CA1 synapses was greater at night compared to day in both sexes. Next, we measured spontaneous synaptic excitation and inhibition onto CA1 pyramidal neurons. Frequency and amplitude of inhibition was greater during the day compared to night, regardless of sex. Frequency and amplitude of excitation was larger in females, compared to males, independent of time-of-day, although both time-of-day and sex influenced presynaptic release probability. At night, CA1 pyramidal neurons showed enhanced excitability (action potential firing and/or baseline potential) that was dependent on synaptic excitation and inhibition, regardless of sex. This study emphasizes the importance of sex and time-of-day in hippocampal physiology, especially given that many neurological disorders impacting the hippocampus are linked to circadian disruption and present differently in men and women. Knowledge about how sex and circadian rhythms affect hippocampal physiology can improve the translational relevancy of therapeutics and inform the appropriate timing of existing treatments.


title: Sample size requirement for achieving multisite harmonization using structural brain MRI features

abstract: When data is pooled across multiple sites, the extracted features are confounded by site effects. Harmonization methods attempt to correct these site effects while preserving the biological variability within the features. However, little is known about the sample size requirement for effectively learning the harmonization parameters and their relationship with the increasing number of sites. In this study, we performed experiments to find the minimum sample size required to achieve multisite harmonization (using neuroHarmonize) using volumetric and surface features by leveraging the concept of learning curves. Our first two experiments show that site-effects are effectively removed in a univariate and multivariate manner; however, it is essential to regress the effect of covariates from the harmonized data additionally. Our following two experiments with actual and simulated data showed that the minimum sample size required for achieving harmonization grows with the increasing average Mahalanobis distances between the sites and their reference distribution. We conclude by positing a general framework to understand the site effects using the Mahalanobis distance. Further, we provide insights on the various factors in a cross-validation design to achieve optimal inter-site harmonization.


title: E-cigarette vapour from base components propylene glycol and vegetable glycerine inhibits inflammatory response in macrophages and epithelial cells

abstract: E-cigarettes are a highly popular nicotine replacement therapy in the process of smoking cessation. Despite this, research on the effects of E-vapours to human health remains limited. The popularity of vaping and mass production of cheap E-liquids has led to compromised safety regulations, with contaminants such as heavy metals and alkaloids detected in multiple liquids. Vaporised E-liquids increase cellular ROS generation and inflammatory cytokine release from pulmonary macrophages. This suggests that E-cigarette usage might activate inflammasomes. Common food additives vegetable glycerine (VG) and propylene glycol (PG) form the base of all E-liquids, but little is known about their inflammatory potential once inhaled. Here, the effect of base components PG and VG on inflammasome activation and cytokine release was investigated in macrophages and epithelial cells exposed to E-liquids and vaporised E-liquid extract (E-vapour). Base E-liquid and E-vapour did not induce cellular cytotoxicity and non-vapourised E-liquid had no effect on IL-8 release. However, basic PG/VG E-vapour inhibited both IL-8 release and conventional inflammasome activation by known inflammatory activators in macrophages and epithelial cells. These results propose a novel inhibitory effect of basic E-vapour components to inflammatory challenges.

category: immunology


title: A minimal growth medium for Pseudomonas azotoformans associated with insect gut

abstract: Pseudomonas spp. can be found associated with several insect hosts. Some of these strains play a crucial role in helping their hosts overcome biotic challenges such as plant defence effectors. Defined media and optimally minimal media are instrumental in studying the physiology and metabolic pathways of microorganisms. In the case of the insect-associated Pseudomonas azotoformans isolated from Galeruca laticollis gut, we tested six previously designed defined/minimal media. To determine the optimal medium, we compared the bacteriums growth performances on the different defined/minimal media to its growth performance on a rich medium using the Dynamic Time Warping Algorithm. The growth results at both 25{degrees}C and 30{degrees}C indicated the SMM as the optimal medium, with bacterial growth performances being the closest to a rich medium. Therefore, this medium would be highly suitable to study the catabolic pathways for the degradation of some xenobiotics in P. azotoformans.

category: microbiology


title: Molecular architecture of the TasA biofilm scaffold in Bacillus subtilis

abstract: Many bacteria in nature exist in multicellular communities termed biofilms. Cells within biofilms are embedded in a primarily self-secreted extracellular polymeric matrix that provides rigidity to the biofilm and protects cells from chemical and mechanical stresses. In the Gram-positive model biofilm-forming bacterium Bacillus subtilis, TasA is the major protein component of the biofilm matrix, where it has been reported to form functional amyloid fibres contributing to biofilm structure and stability. The structure of TasA fibres, however, and how fibres scaffold the biofilm at the molecular level, is not known. Here, we present electron cryomicroscopy structures of TasA fibres, which show that rather than forming amyloid fibrils, TasA monomers assemble into filaments through donor strand complementation, with each subunit donating a {beta}-strand to complete the fold of the next subunit along the filament. Combining electron cryotomography, atomic force microscopy, and mutational studies, we show how TasA filaments congregate in three dimensions to form abundant fibre bundles that are essential for B. subtilis biofilm formation. This study explains the previously observed biochemical properties of TasA and shows, for the first time, how a bacterial extracellular globular protein can assemble from monomers into {beta}-sheet-rich fibres, and how such fibres assemble into bundles in biofilms. We establish a hierarchical, atomic-level assembly mechanism of biofilm scaffolding that provides a structural framework for understanding bacterial biofilm formation.


title: Gram-negative Antimicrobial spectrum of Ulmus pumila

abstract:
PurposeThis study explores the antimicrobial spectrum of Ulmus pumila by screening commonly infectious gram-negative bacteria for susceptibility. Currently, many gram-negative bacteria are developing resistance to recommended antibiotic therapies used in clinical practice. It is imperative that we continue to explore new antimicrobial compounds in order to help combat the global health issue of antibiotic resistance.

Method3g of freshly harvested leaves and flower samples of Ulmus pumila were extracted in 15 ml of 95% ethanol. The mixture was filtered to remove the debris and sterile blank discs were soaked in the clear filtrate (samples) or the extraction solvent (as background controls) for 20 minutes. Glycerol stocks of bacteria were scaled in LB broth and Muller Hinton agar was prepared with 38g of agar in a liter of water. A 100-microliter suspension of the scaled bacteria was diluted with 9 ml of 1% saline solution and 100 microliters of this saline dilution was plated. Sterile paper discs that were infused with extracts (samples) or vehicle control (95% ethanol) were placed on the freshly plated bacterial plates and incubated at 37 degree Celsius overnight. Zones of inhibition were recorded as a measure of antibacterial activity.

ResultUlmus pumila demonstrated antimicrobial activity against the following gram-negative bacteria: E. coli (16 mm mean zone of clearing), P. vulgaris (15 mm mean zone of clearing), E. cloacae (20.5 mm mean zone of clearing), and K. pneumoniae (16 mm mean zone of clearing).

ConclusionUlmus pumila displayed antimicrobial activity against various species of gram-negative bacteria including E. coli, P. vulgaris, K. pneumonaie, and E. cloacae. Ulmus pumila has also previously demonstrated activity against some species of gram-positive bacteria. By this discovery, Ulmus pumila has the potential to serve as a broad-spectrum antimicrobial agent with activity against both gram-positive and gram-negative bacteria.


title: Inorganic sulfur fixation via a new homocysteine synthase allows yeast cells to cooperatively compensate for methionine auxotrophy

abstract:
The assimilation, incorporation, and metabolism of sulfur is a fundamental process across all domains of life, yet how cells deal with varying sulfur availability is not well understood. We studied an unresolved conundrum of sulfur fixation in yeast, in which an organosulfur-auxotrophy caused by deletion of homocysteine synthase Met17p is overcome when cells are inoculated at high cell density. We discovered that an uncharacterized gene YLL058Wp, herein named Hydrogen sulfide utilizing-1 (HSU1), acts as a homocysteine synthase and allows the cells to substitute for Met17p by re-assimilating hydrosulfide ions leaked from met17{Delta} cells into O-acetyl-homoserine and forming homocysteine. Our results show that cells can cooperate to achieve sulfur fixation, indicating that the collective properties of microbial communities facilitate their basic metabolic capacity.

SummarySulfur limitation activates a dormant hydrogen sulfide fixation route via a novel homocysteine synthase Hsu1p (YLL058Wp).

category: molecular biology


title: Diffusional variance-determined stochastic translation efficiency

abstract: Full-transcriptome methods have brought versatile power to protein biosynthesis research, but remain difficult to apply for the quantification of absolute protein synthesis rates. Here we propose and, using modified translation complex profiling, confirm co-localisation of ribosomes on messenger(m)RNA resulting from their diffusional dynamics. We demonstrate that these stochastically co-localised ribosomes are linked with the translation initiation rate and provide a robust variable to model and quantify specific protein output from mRNA.


title: Not1 and Not4 inversely determine mRNA solubility that sets the dynamics of co-translational events

abstract:
BackgroundThe Ccr4-Not complex is most well known as the major eukaryotic deadenylase. However, several studies have uncovered roles of the complex, in particular of the Not subunits, unrelated to deadenylation and relevant for translation. In particular, the existence of Not condensates that regulate translation elongation dynamics have been reported. Typical studies that evaluate translation efficiency rely on soluble extracts obtained after disruption of cells and ribosome profiling. Yet cellular mRNAs in condensates can be actively translated and may not be present in such extracts.

ResultsIn this work, by analyzing soluble and insoluble mRNA decay intermediates in yeast, we determine that insoluble mRNAs are enriched for ribosomes dwelling at non-optimal codons compared to soluble mRNAs. mRNA decay is higher for soluble RNAs, but the proportion of co-translational degradation relative to the overall mRNA decay is higher for insoluble mRNAs. We show that depletion of Not1 and Not4 inversely impact mRNA solubilities and, for soluble mRNAs, ribosome dwelling according to codon optimality. Depletion of Not4 solubilizes mRNAs with lower non-optimal codon content and higher expression that are rendered insoluble by Not1 depletion. By contrast, depletion of Not1 solubilizes mitochondrial mRNAs, which are rendered insoluble upon Not4 depletion.

ConclusionOur results reveal that mRNA solubility defines dynamics of co-translation events and is oppositely regulated by Not1 and Not4, a mechanism that we additionally determine may already be set by Not1 promoter association in the nucleus.


title: Metabolic reprogramming underlies cavefish muscular endurance despite loss of muscle mass and contractility

abstract:
Physical inactivity - specifically the lack of moderate-to-vigorous activity - is a scourge to human health, promoting metabolic disease and muscle wasting. Interestingly, multiple ecological niches have relaxed investment into physical activity, providing unique evolutionary insight into adaptive physical inactivity. The Mexican cavefish Astyanax mexicanus lost moderate-to-vigorous activity following cave colonization, reaching basal swim speeds ~3-fold slower than their river-dwelling counterpart. We found that this was accompanied by a marked shift in body composition, decreasing muscle mass by 30% and increasing fat mass by 40%. This shift persisted at the single muscle fiber level via increased lipid and sugar accumulation at the expense of myofibrillar volume. Transcriptomic analysis of laboratory-reared and wild-caught cavefish indicated this shift in investment is driven by increased expression of ppar{gamma} - the master regulator of adipogenesis - with a simultaneous decrease in fast myosin heavy chain expression. Ex vivo and in vivo analysis confirmed these investment strategies come with a functional trade-off, decreasing cavefish muscle fiber shortening velocity, time to maximal force, and ultimately maximal swimming velocity. Despite this, cavefish displayed a striking degree of muscular endurance, reaching maximal swim speeds ~3.5-fold faster than their basal swim speeds. Multi-omics analysis indicated metabolic reprogramming, specifically increased phosphoglucomutase-1 abundance, phosphorylation, and activity, as contributing mechanisms enhancing cavefish glycogen utilization under metabolically strenuous conditions. Collectively, we reveal broad skeletal muscle reprogramming following cave colonization, displaying an adaptive skeletal muscle phenotype reminiscent to mammalian disuse and high-fat models while simultaneously maintaining a unique capacity for sustained muscle contraction under fatiguing conditions.

SignificanceThe evolutionary consequence of decreased physical activity upon skeletal muscle physiology remains unexplored. Using the Mexican cavefish, we find loss of moderate-to-vigorous swimming following cave colonization has resulted in broad shifts in skeletal muscle investment - away from muscle mass and instead toward fat and sugar accumulation - ultimately decreasing muscle fiber twitch kinetics. Surprisingly though, cavefish possessed marked muscular endurance, reaching maximal swimming speeds rivaling their river-dwelling counterpart. Multi-omics analysis revealed carbohydrate metabolic reprogramming as a contributing component, most notably elevated abundance and phosphorylation of the glycogenolytic enzyme Phosphoglucomutase-1 - a likely adaptation to cave-specific hypoxia. These findings emphasize the impact multiple selective pressures have on skeletal muscle physiology, providing the first evolutionary insight into skeletal muscle adaptation following decreased activity.


title: Shared and distinct genetic etiologies for different types of clonal hematopoiesis

abstract: Clonal hematopoiesis (CH) - age-related expansion of mutated hematopoietic clones - can differ in frequency and cellular fitness. Descriptive studies have identified a spectrum of events (coding mutations in driver genes (CHIP), gains/losses and copy-neutral loss of chromosomal segments (mCAs) and loss of sex chromosomes), some of which have been associated with disease risk. Co-existence of different CH events raises key questions as to their origin, selection, and impact. Analyses of sequence and genotype array data in up to 482,378 individuals from UK Biobank revealed shared genetic architecture across different types of CH. We observed co-occurrence of CHIP and mCAs with co-localization at TET2, DNMT3A and JAK2, in which CHIP precedes mCA acquisition. CH types are associated with cellular differentiation, DNA repair, and cell cycle regulation pathways, which can drive clonal expansion and reduce telomere length. Insights into the shared architecture of CH could improve detection and prevention of CH-related outcomes.

category: genetics


title: A Microengineered Brain-Chip to Model Neuroinflammation in Humans

abstract: Species differences in the brain and the blood-brain barrier (BBB) biology hamper the translation from animal models to humans and impede the development of specific therapeutics for brain diseases. Here we present a human Brain-Chip engineered to recapitulate critical aspects of the complex brain cell-cell interactions that mediate neuroinflammation development. Our human organotypic microphysiological system (MPS) includes endothelial-like cells, pericytes, glia, and cortical neurons and maintains BBB permeability at in vivo relevant levels, providing a significant improvement in complexity and clinical mimicry compared to previous MPS models. This is the first report of a Brain-Chip with an RNA expression profile close to that of the adult human cortex and that demonstrates advantages over Transwell culture. Through perfusion of TNF-, we recreated key inflammatory features, such as glia activation, the release of proinflammatory cytokines, and increased barrier permeability. Our model may provide a reliable tool for mechanistic studies in neuron-glial interactions and dysregulation of BBB function during neuroinflammation.

category: bioengineering


title: High axial-resolution optical stimulation of neurons in vivo via two-photon optogenetics with speckle-free beaded-ring pattern

abstract: Two-photon optogenetics has become an indispensable technology in neuroscience, due to its capability in precise and specific manipulation of neural activities. Scanless holographic approach is generally adopted to meet the requirement of stimulating neural emsembles simultaneously. However, the commonly used disk patterns fail in achieving single-neuron resolution, especially in axial dimension, and its inherent speckles decrease the stimulation efficiency. Here, we propose a novel speckle-free, beaded-ring pattern for high axial-resolution optical stimulation of neurons in vivo. Using a dye pool and a fluorescent thin-film as samples, we verify that, compared to those with disk patterns, higher axial resolution and better localization ability can be achieved with beaded-ring patterns. Furthermore, we perform two-photon based all-optical physiology with neurons in mouse S1 cortex in vivo, and demonstrate that the axial resolution obtained by beaded-ring patterns can be improved by 24% when stimulating multiple neurons, compared with that of disk patterns.


title: Deep brain stimulation pulse sequences to optimally modulate frequency-specific neural activity

abstract:
Precise neuromodulation systems are needed to identify the role of neural oscillatory dynamics in brain function, and to advance the development of electrical stimulation therapies tailored to each patients signature of brain dysfunction. Low-frequency, local field potentials (LFPs) are of increasing interest for the development of these systems because they reflect the synaptic inputs to a recorded neuronal population and can be chronically recorded in humans. Here, we identified stimulation pulse sequences to optimally minimize or maximize the 2-norm of frequency-specific LFP oscillations using a generalized mathematical model of spontaneous and stimulation-evoked LFP activity, and a subject-specific model of neural dynamics in the pallidum of a Parkinsons disease patient. We leveraged convex and mixed-integer optimization tools to identify the pulse patterns, and employed constraints on the pulse frequency and amplitude that are required to keep electrical stimulation within its safety envelope. Our analysis revealed that a combination of phase, amplitude, and frequency pulse modulation is needed to attain optimal suppression or amplification of the targeted oscillations. Phase modulation is sufficient to modulate oscillations with a constant amplitude envelope. To attain optimal modulation for oscillations with a time-varying envelope, a trade-off between frequency and amplitude pulse modulation is needed. The optimized pulse sequences identified here were invariant to changes in the dynamics of stimulation-evoked neural activity, including the damping and natural frequency or complexity (i.e., generalized vs. patient-specific model). Our results reveal the structure of pulse sequences that can be used in closed-loop brain stimulation devices to control neural activity in real-time.

Significance StatementThis computational study reveals the structure of electrical pulse sequences that optimally modulate spontaneous, synaptic-related neural oscillations measured using local field potentials (LFPs). We considered constraints on the pulse amplitude and frequency, relevant to keep stimulation pulses within the safety envelope. Our mathematical analysis indicate that these optimized pulse sequences are invariant to changes in the studied neural dynamics, and a trade-off between amplitude and frequency pulse modulation is critical when the pulse amplitude is constrained. The pulse sequences identified here provide the rationale for the development of closed-loop neuromodulation systems that employ stimulation-evoked responses to control neural activity. These closed-loop systems will be key to characterize the role of neural activity in brain function and ultimately advance personalized neuromodulation devices.


title: Real-time denoising of fluorescence time-lapse imaging enables high-sensitivity observations of biological dynamics beyond the shot-noise limit

abstract: A fundamental challenge in fluorescence microscopy is the inherent photon shot noise caused by the inevitable stochasticity of photon detection. Noise increases measurement uncertainty, degrades image quality, and limits imaging resolution, speed, and sensitivity. To achieve high-sensitivity imaging beyond the shot-noise limit, we provide DeepCAD-RT, a versatile self-supervised method for effective noise suppression of fluorescence time-lapse imaging. We made comprehensive optimizations to reduce its data dependency, processing time, and memory consumption, finally allowing real-time processing on a two-photon microscope. High imaging signal-to-noise ratio (SNR) can be acquired with 10-fold fewer fluorescence photons. Meanwhile, the self-supervised superiority makes it a practical tool in fluorescence microscopy where ground-truth images for training are hard to obtain. We demonstrated the utility of DeepCAD-RT in extensive experiments, including in vivo calcium imaging of various model organisms (mouse, zebrafish larva, fruit fly), 3D migration of neutrophils after acute brain injury, and 3D dynamics of cortical ATP (adenosine 5-triphosphate) release. DeepCAD-RT will facilitate the morphological and functional interrogation of biological dynamics with minimal photon budget.


title: LIPA-driven hydrolysis of cholesteryl arachidonate promotes cancer metastasis via NF-κB

abstract: Cholesteryl ester (CE) is an established marker in many types of aggressive cancers. Yet, the function of CE homeostasis during cancer progression is largely unknown. Here, enabled by Raman spectromicroscopy, pan-cancer bioinformatic analysis, and biocompatible Raman probe of cholesterol, LIPA was identified as the key regulator of CE hydrolysis in cancer cells. LIPA inhibition induced aberrant accumulation of CE-rich lipid droplet at single cell level. LIPA-driven CE hydrolysis was directly visualized by stimulated Raman scattering imaging of alkyne-tagged cholesterol. Cholesteryl arachidonate was identified as a dominant substrate that is rapidly hydrolyzed by LIPA. Inhibition of LIPA effectively suppressed cancer metastasis both in vitro and in vivo. Mechanistically, LIPA inhibition suppresses NF-{kappa}B signaling, while the NF-{kappa}B members positively regulate the expression level of LIPA, indicating regulation of CE homeostasis by a LIPA-CE-NF{kappa}B feedback loop. Collectively, our findings reveal that LIPA drives CE hydrolysis during cancer progression and is an important metabolic target for cancer therapy.

category: cancer biology


title: Invasiveness of Cancer Populations in a Two-dimensional Percolation cluster: a Stochastic Mathematical Approach

abstract: A framework for the software Unstructured Reaction-Diffusion Master Equation (URDME) was developed. A mitogenic paracrine signaling pathway was introduced phenomenologically to show how cells cooperate with one another. We modeled the emerging Allee effect using low seeding density culture (LSDC) assays to fit the model parameters. Finite time scaling (FTS) was found to be a useful tool for quantifying invasiveness in cancer populations. Through simulation, we analyzed the growth-migration dynamics of BT474 cancer cell populations in-vitro in a 2D percolation cluster and calculated the SPR (successful penetration rate). By analyzing the temporal trajectories of the SPR, we could determine the critical exponents of the critical SPR scaling relation [Formula]. Moreover, the SPR transition point defined according to the FTS theory, Pc, is negatively correlated with the invasiveness of cancer cell populations. The Pc of the three virtual cancer populations distinctly designated by varying the parameter set of the same model are 0.3408, 0.3675, and 0.4454, respectively. Therefore, the FTS algorithm may be useful in determining invasiveness. Through the simplistic phenomenological paracrine model, inter-cell cooperation and mutual mitogenic boosting are enabled, causing the Allee effect to occur. Such a method could be applied to other circumstances as an example of the quantitatively falsifiable emerging theory.


title: Effects of sub-chronic, in vivo administration of sigma-1 receptor ligands on platelet and aortic arachidonate cascade in streptozotocin-induced diabetic rats

abstract:
Diabetes mellitus is a chronic metabolic disorder which induces endothelial dysfunction and platelet activation. Eicosanoids produced from arachidonic acid regulate cellular and vascular functions. Sigma-1 receptor expressed in platelets and endothelial cells can regulate intracellular signalization. Our aim was to examine the influence of sub-chronic, in vivo administered sigma-1 receptor ligands (2-(4-morpholino)ethyl-1-phenylcyclohexane-1-carboxylate, PRE-084; S-N-Benzyl-6,7-dimethoxy-1,2,3,4-tetrahydro-1-isoquinolineethanamine, a new compound (S)-L1; and N,N-dipropyl-2-[4-methoxy-3-(2-phenylethoxy)-phenyl]-ethylamine monohydrochloride, NE-100) on the ex vivo arachidonic acid metabolism of platelets and aorta in streptozotocin-induced diabetic rats. The serum level of sigma-1 receptor ligands was detected by liquid chromatography-mass spectrometry before the ex vivo analysis. Sigma-1 receptor and cyclooxygenase gene expression in platelets were determined by reverse transcription coupled quantitative polymerase chain reaction. The eicosanoid synthesis was examined by using of radiolabeled arachidonic acid substrate and enzyme-linked immunosorbent assay.

In diabetic rats, the sub-chronic, in vivo administration of the sigma-1 receptor ligands modified the transcript levels of sigma-1 receptor and cyclooxygenase-1, the concentration of cyclooxygenase in platelets and the eicosanoid synthesis in both platelets and aorta. Sigma-1 receptor ligands, by changing platelet and blood vessel eicosanoid synthesis, may play a role in modulating diabetic complications.


title: Culture media, DMSO and efflux affect the antibacterial activity of cisplatin and oxaliplatin

abstract:
Cisplatin was originally discovered through its antibacterial action, and subsequently has found use as a potent broad spectrum anticancer agent. This study determines the effect of growth media and solvent on the antibacterial activity of cisplatin and its analogue, oxaliplatin. E. coli MG1655 or MG1655{Delta} tolC were treated with the platinum compounds under different conditions and susceptibility was determined. Our results showed that DMSO reduced the activity of cisplatin by 4-fold (MIC 12.5 mg/L) compared with 0.9% NaCl-solubilized cisplatin (MIC 3.12 mg/L) when tested in MOPS. Surprisingly, complete loss of activity was observed in Mueller Hinton Broth II (MHB II). By supplementing MOPS with individual components of MHB II such as the sulphur containing amino acids, L-cysteine and L-methionine, individually or in combination reduced activity by [≥]8-fold (MIC [≥]25 mg/L). Oxaliplatin was less active against E. coli (MIC 100 mg/L) but exhibited similar inactivation in the presence of DMSO, MHBII or MOPS spiked with L-cysteine and L-methionine (MIC [≥]400 mg/L). Our data suggest that the antibacterial activity of cisplatin and oxaliplatin is modulated by both choice of solvent and composition of growth media. We demonstrate that this is primarily due to sulphur-containing amino acids cysteine and methionine, an essential component of the recommended media for testing antimicrobial susceptibility, MHBII.

Significance and impact of the studyAs well as an anticancer treatment, cisplatin possesses antibacterial activity and is active against AMR resistant persister cells, opening the possibility of renewed use against resistant bacterial strains. Our findings provide evidence on how the composition of growth media and choice of solvent modulate the antibacterial activity of cisplatin and its analogue, oxaliplatin. These observations provide a necessary, consistent standard for assessing the antibacterial activity of platinum-based compounds, as a precursor towards their application against bacterial infection.

Graphical abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY


title: Genome-wide analysis of PTR/POT transporters in Candida species and their functional characterization in the newly emerged pathogen Candida auris

abstract: The PTR or proton-dependent oligopeptide transporter (POT) family exploits the inwardly directed proton motive force to facilitate the cellular uptake of di- and tripeptides. Interestingly, representatives from the family have shown efficacy in delivering peptide-based antifungal derivatives in certain Candida species. Given the increased incidences of fungal infections by Candida species and the associated escalating orders of resistance against frontline antifungals, peptide derivatives are attractive therapeutic options. In that direction, the identification and characterization of PTR transporters serve as an essential first step in the translation of peptide-based antifungals as next-gen therapeutics. Herein, we present a genome-wide inventory of the PTR transporters in five prominent Candida species. Our study identifies 2 PTR transporters each in C. albicans and C. dubliniensis, 1 in C. glabrata, 4 in C. parapsilosis, and 3 in C. auris. Notably, despite all representatives retaining the conserved features seen in the PTR family, there exist two distinct classes of PTR transporters that differ in terms of their sequence identities and membrane topology. Further, we also evaluated the contribution of each PTR protein of the newly emerged multidrug-resistant C. auris in di-/tripeptide uptake. Notably, deletion of the PTR transporters encoded by BNJ08_003830 and BNJ08_005124 led to a marked reduction in the transport capabilities of several tested di-/tripeptides. Besides, BNJ08_005124 deletion also resulted in increased resistance towards the peptide-nucleoside drug Nikkomycin Z, pointing towards its predominant role in the uptake mechanism. Altogether, the study provides an important template for future structure-function investigations of PTR transporters in Candida species.


title: Revisiting Ancient Polyploidy in Leptosporangiate Ferns

abstract: Ferns, and particularly homosporous ferns, have long been assumed to have experienced recurrent whole-genome duplication (WGD) events because of their substantially large genome sizes, surprisingly high chromosome numbers, and high degrees of polyploidy among many extant members. Although, consequently, the number of sequenced fern genomes is very limited, recent studies using transcriptome data to find evidence for WGDs in ferns reached conflicting results concerning the occurrence of ancient polyploidy, for instance, in the lineage of leptosporangiate ferns. Because identifying WGDs in a phylogenetic context is the foremost step in studying the contribution of ancient polyploidy to evolution, we revisited earlier identified WGDs in leptosporangiate ferns, mainly the core leptosporangiate ferns, by building age distributions and applying substitution rate corrections and by conducting statistical gene tree - species tree reconciliation analyses. Our integrative analyses confidently identified four ancient WGDs in the sampled core leptosporangiates and suggest both false positives and false negatives for the WGDs that recent studies have reported earlier. In conclusion, we underscore the significance of substitution rate corrections and uncertainties in gene tree - species tree reconciliations in calling WGD events, and that failing to do so likely leads to incorrect conclusions.


title: Variation in spontaneous mutation rate and spectrum across the genome of Neurospora crassa

abstract: Mutation rate have been extensively studies in eukaryotes. However, much less is known about the variation of mutation rate across the genome. Chromatin modifications may be an important factor in determining mutation rate variation in eukaryotic genomes. We performed a mutation accumulation experiment in the filamentous fungus Neurospora crassa and detected mutations in the MA-lines by genome sequencing. We detected over 1300 mutations, which happened during asexual propagation. This leads to markedly different mutation rate and spectrum than during sexual reproduction as previously investigated. We observed that GC-content, H3K9 methylation, and centromeric regions have large influence on mutation rate, with higher mutation rate in H3K9 and centromeric regions. H3K27 trimethylation had no effect on mutation rate. We also observe that the spectrum of single nucleotide mutations is different in H3K9 and euchromatic domains. We validate our mutation model by comparing the predictions to natural genetic variation and observed that a moderate amount of extant genetic variation can be predicted by our model. Furthermore, we characterize structural variants and complex mutations that happen in Neurospora crassa. Our study highlights that chromatin modifications influence mutation rate and accurate evolutionary inferences must take this variation in mutation rates into account.


title: LANTSA: Landmark-based transferable subspace analysis for single-cell and spatial transcriptomics

abstract: Single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) technologies provide new insights to understand tissue organization and biological function. Accurately capturing the relationships of samples (e.g., sequenced cells, spatial locations) will result in reliable and consistent outcomes in downstream analyses. However, this undertaking remains a challenge for large-volume or cross-platform datasets due to transcriptional heterogeneity and high computational demands. Here, we introduce landmark-based transferable subspace analysis (LANTSA) to solve such challenges for scRNA-seq and ST datasets. Specifically, LANTSA constructs a representation graph of samples for clustering and visualization based on a novel subspace model, which can learn a more accurate representation and is theoretically proven to be linearly proportional to data size in terms of the time consumption. Furthermore, LANTSA uses a dimensionality reduction technique as an integrative method to extract the discriminants underlying the representation structure, which enables label transfer from one (learning) dataset (i.e., scRNA-seq profiles) to the other (prediction) datasets (e.g., scRNA-seq or ST profiles), thus solving the massive-volume or cross-platform problem. We demonstrated the superiority of LANTSA to identify accurate data structures via clustering evaluation on benchmark datasets of various scRNA-seq protocols, 10x Visium, and Slide-seq ST platforms. Moreover, we confirmed the integration capability of LANTSA to transfer cell annotation on large-scale and cross-platform scRNA-seq datasets. Finally, we validated the effectiveness of LANTSA for the identification of multiple mouse brain areas as well as the spatial mapping of cell types within cortical layers by integrating scRNA-seq and ST data.


title: High-throughput Production of Diverse Xenobiotic Metabolites with P450-transduced Huh7 Hepatoma Cell Lines

abstract:
Precision medicine requires methods to assess drug metabolism and distribution, including the identification of known and undocumented drug and chemical exposures as well as their metabolites. Recent work demonstrated high-throughput generation of xenobiotic metabolites with human liver S-9 fractions and detection in human plasma and urine. Here, we developed a panel of lentivirally transduced human hepatoma cell lines (Huh7) that stably express individual cytochrome P450 (P450) enzymes and generate P450-specific xenobiotic metabolites. We verified protein expression by immunoblotting and demonstrated that the cell lines generate P450-specific metabolites from probe substrates. To increase analytical throughput, we used a pooling strategy where 36 chemicals were grouped into 12 unique mixtures, each mixture containing 6 randomly selected compounds, and each compound being present in two separate mixtures. Each mixture of compounds was incubated with 8 different P450 cell lines with cell extracts analyzed at 0 and 2 h. Extracts were analyzed using liquid chromatography-high resolution mass spectrometry. Cell lines selectively metabolized test substrates, with pazopanib metabolized by CYP3A4 and CYP2C8 cells, bupropion by CYP2B6, and {beta}-naphthoflavone by CYP1A2 for example, showing substrate-enzyme specificity. Predicted metabolites from the remaining 33 compounds as well as many unidentified m/z features were detected. We also show that a specific metabolite generated by CYP2B6 cells, but not detected in the S9 system, was identified in human samples. Our data show that incubating these cell lines with chemical mixtures accelerated characterization of xenobiotic chemical space, while simultaneously allowing for the contributions of specific P450 enzymes to be identified.

Significance statementHigh resolution mass spectrometry enables the identification of exposures to drugs and other xenobiotics in human samples. This paper demonstrates a workflow for high throughput production of xenobiotic metabolites using a panel of engineered cytochrome P450-expressing hepatoma cells. Active substrate-enzyme pairs can be identified using this workflow and generated metabolites can be used as surrogate standards to validate xenobiotic detection in humans.


title: Boosting transformation in wheat by BBM-WUS

abstract: Agrobacterium-mediated transformation is a cost-effective and convenient way to introduce foreign genetic elements to plants. However, only limited protocols successfully generates transgenic plants with fielder, a spring wheat variety. Wheat transformation method with higher efficiency and without genotype restriction is heavily demanded. Here, a heat-shock protocol, independent of Japan Tobacco had been established. Transgenic plants can be obtained from immature embryo within only 60 days by this protocol. Morphogenic regulators Baby boom and Wuschel (BBM-WUS) was proved to promote transformation efficiency for five to six times in wheat when co-infiltrated with agrobacterium containing target construct. Notably, half of the transformants are BBM-WUS free and moreover, the BBM-WUS containing plants could be picked by florescent marker that was co-expressed with BBM-WUS. In conclusion, we managed to establish a new wheat transformation protocol with shorter duration than published protocol.


title: Direct and indirect neurogenesis generate a mosaic of distinct glutamatergic projection neuron types and cortical subnetworks

abstract: Variations in size and complexity of the cerebral cortex result from differences in neuron number and composition, which are rooted in evolutionary changes in direct and indirect neurogenesis (dNG and iNG) mediated by radial glial progenitors and intermediate progenitors, respectively. How dNG and iNG differentially contribute to cortical neuronal number, diversity, and connectivity are unknown. Establishing a genetic fate-mapping method to differentially visualize dNG and iNG in mice, we found that while both dNG and iNG contribute to all cortical structures, iNG contributes the largest relative proportions to the hippocampus and neocortex compared to insular and piriform cortex, claustrum, and the pallial amygdala. Within the neocortex, whereas dNG generates all major glutamatergic projection neuron (PN) classes, iNG differentially amplifies and diversifies PNs within each class; the two neurogenic pathways generate distinct PN types and assemble fine mosaics of lineage-based cortical subnetworks. Our results establish a ground-level lineage framework for understanding cortical development and evolution by linking foundational progenitor types and neurogenic pathways to PN types.


title: N-Terminomic Changes of Neurons During Excitotoxicity Reveals Proteolytic Events Associated with Synaptic Dysfunctions and Potential Targets for Neuroprotection

abstract:
Excitotoxicity is a neuronal death process initiated by over-stimulation of ionotropic glutamate receptors. Although dysregulation of proteolysis and protein phosphorylation signaling networks is critical for excitotoxicity, the identity of affected proteins and mechanisms by which they induce neuronal cell death remains unclear. To address this, we used quantitative N-terminomics to identify proteins modified by proteolysis in neurons undergoing excitotoxic cell death. Our investigation led to the discovery of proteins that, upon proteolysis by calpains, perturb synaptic organization and function. These included key synaptic regulatory proteins including CRMP2, doublecortin-like kinase I, Src tyrosine kinase and calmodulin-dependent protein kinase II{beta} (CaMKII{beta}), which we found to undergo calpain-catalyzed proteolytic processing to generate stable truncated fragments with altered activities. We further show that blockade of proteolysis of Src by calpains could protect against neuronal loss in a rat model of neurotoxicity, and that CaMKII{beta} and its isoform CaMKII undergo differential processing by calpains in mouse brains under physiological conditions and during ischemic stroke. Our findings thus reveal new insights into excitotoxic neuronal death mechanisms and suggest potential therapeutic targets for neurological disorders.

One Sentence SummaryProteolytic events important for excitotoxic neuronal death as potential novel therapeutic targets.

Graphical Abstract

O_FIG O_LINKSMALLFIG WIDTH=192 HEIGHT=200 SRC="FIGDIR/small/484119v1_ufig1.gif" ALT="Figure 1">
View larger version (39K):
org.highwire.dtl.DTLVardef@1478fe7org.highwire.dtl.DTLVardef@1389ad6org.highwire.dtl.DTLVardef@13d7e2eorg.highwire.dtl.DTLVardef@273816_HPS_FORMAT_FIGEXP  M_FIG C_FIG In BriefAmeen, et al. used an N-terminomic method to identify neuronal proteins and the exact cleavage sites proteolyzed by calpains during excitotoxicity. Upon proteolysis, these proteins generate stable truncated fragments, which potentially induce synaptic dysfunction and loss, eventually leading to neuronal death. As such, some of these proteins such as protein kinases Src and CaMKII are potential targets for neuroprotection.

HighlightsO_LIOver 300 neuronal proteins are cleaved by calpains to form stable truncated fragments during excitotoxicity.
C_LIO_LIThe calpain cleavage sites of these proteins unveil for the first time the preferred cleavage sequences of calpains in neurons.
C_LIO_LIThese pathological proteolytic events potentially induce synaptic dysfunction and loss, which leads to excitotoxic neuronal death.
C_LIO_LISome of the neuronal proteins proteolyzed by calpains are potential targets of neuroprotection.
C_LI


title: A consensus protocol for the recovery of mercury methylation genes from metagenomes

abstract: Mercury methylation genes (hgcAB) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal-ash amended sediments, chlor-alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg-MATE (Hg-cycling Microorganisms in Aquatic and Terrestrial Ecosystems) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in the environment. Furthermore, we introduce "marky-coco", a ready-to-use bioinformatic pipeline based on de novo single-metagenome assembly, for easy and accurate characterization of hgc genes from environmental samples. We compared the recovery of hgc genes from environmental metagenomes using the marky-coco pipeline with an approach based on co-assembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high diversity (i.e., paddy soils) for which a co-assembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes.


title: A surface pocket in the cytoplasmic domain of the herpes simplex virus fusogen gB controls membrane fusion

abstract:
Membrane fusion during the entry of herpesviruses is carried out by the viral fusogen gB that is activated by its partner protein gH. Unusually, the fusogenic activity of gB is controlled by its cytoplasmic (or intraviral) domain (gBCTD) and, according to the current model, the gBCTD is a trimeric, inhibitory clamp that restrains gB in the prefusion conformation. But how the gBCTD clamp is released by gH is unclear. Here, we identified two new regulatory elements within gB and gH from the prototypical herpes simplex virus 1: a surface pocket within the gBCTD and residue V831 within the gH cytoplasmic tail. Mutagenesis and structural modeling suggest that gH V831 interacts with the gB pocket. The gB pocket is located above the "fault line" between adjacent protomers, and we hypothesize that insertion of the gH V831 wedge into the pocket serves to push the protomers apart. This releases the inhibitory clamp on the gB prefusion conformation and activates gB fusogenic activity. Both gB and gH are conserved across all herpesviruses, and this activation mechanism could be used by other gB homologs. Our proposed mechanism emphasizes a central role for the cytoplasmic regions in regulating the activity of a viral fusogen.

AUTHOR SUMMARYHerpes simplex virus 1 (HSV-1) establishes lifelong infections in over a half of people and causes diseases ranging from oral or genital sores to blindness and brain inflammation. No vaccines or curative treatments are currently available. To infect cells, HSV-1 must first penetrate them by merging its lipid envelope with the membrane of the target cell. This process requires the collective actions of several viral and cellular proteins, notably, viral glycoproteins B and H (gB and gH). gH is thought to activate the fusogenic function of gB, but how the two proteins interact is unclear. Here, using mutational analysis, we have identified two new functional elements within the cytoplasmic regions of gB and gH: a surface pocket in gB and a single residue in gH, both of which are important for membrane fusion. Based on structural modeling, we propose that the gB pocket is the binding site for the gH residue, and that their interaction activates gB to cause membrane fusion. These findings extend our knowledge of the HSV-1 membrane fusion mechanism. Mechanistic understanding of HSV-1 entry is essential for understanding its pathogenesis and developing new strategies to prevent infections.


title: A new insight into RecA filament regulation by RecX from the analysis of conformation-specific interactions

abstract: RecA protein mediates homologous recombination repair in bacteria through assembly of long helical filaments on single-stranded DNA (ssDNA) in an ATP dependent manner. RecX, an important negative regulator of RecA, is known to inhibit RecA activity by stimulating the disassembly of RecA nucleoprotein filaments. Here we use a single-molecule approach to address the regulation of (E. coli) RecA-ssDNA filaments by RecX (E. coli) within the framework of distinct conformational states of RecA-ssDNA filament. Our findings revealed that RecX effectively binds the inactive conformation of RecA-ssDNA filaments and slows down the transition to the active state. Results of this work provide new mechanistic insights into the RecX-RecA interactions and highlight the importance of conformational transitions of RecA filaments as an additional level of regulation of its biological activity.


title: Prior selection affects phenotypic and transcriptional response to hypoxia

abstract: Hypoxia has profound and diverse effects on aerobic organisms, disrupting oxidative phosphorylation and activating several protective pathways. Predictions have been made that exposure to mild intermittent hypoxia may be protective against more severe exposure and may extend lifespan. Both effects are likely to depend on prior selection on phenotypic and transcriptional plasticity in response to hypoxia, and may therefore show signs of local adaptation. Here we report the lifespan effects of chronic, mild, intermittent hypoxia (CMIH) and short-term survival in acute severe hypoxia (ASH) in four clones of Daphnia magna originating from either permanent or intermittent habitats, the latter regularly drying up with frequent hypoxic conditions. We show that CMIH extended the lifespan in the two clones originating from intermittent habitats but had the opposite effect in the two clones from permanent habitats, which also showed lower tolerance to ASH. Exposure to CMIH did not protect against ASH; to the contrary, Daphnia from the CMIH treatment had lower ASH tolerance than normoxic controls. Few transcripts changed their abundance in response to the CMIH treatment in any of the clones. After 12 hours of ASH treatment, the transcriptional response was more pronounced, with numerous protein-coding genes with functionality in mitochondrial and respiratory metabolism, oxygen transport, and gluconeogenesis showing up-regulation. While clones from intermittent habitats showed somewhat stronger differential expression in response to ASH than those from permanent habitats, there were no significant hypoxia-by-habitat of origin or CMIH-by-ASH interactions. GO enrichment analysis revealed a possible hypoxia tolerance role by accelerating the molting cycle and regulating neuron survival through up-regulation of cuticular proteins and neurotrophins, respectively.


title: Landing manoeuvres predict roost-site preferences in bats

abstract:
Roosts are vital for the survival of many species, and how individuals choose one site over another is affected by various ecological factors. Biomechanical constraints could also affect roost selection, particularly in volant taxa that require sites with easy access, thereby reducing costs (i.e., predation, accidents). To date, no studies have established an association between landing performance and roost-site selection, as predicted by biomechanical constraints associated with flight. We aim to determine roost-site selection in disc-winged bats (Thyroptera tricolor), a species known to roost within developing tubular leaves. This study is coupled with various experiments that measure how a conspicuous apex affects landing tactics and performance. We show that T. tricolor prefers leaves with a longer apex, the space typically used for landing. Bats also approach and enter these leaves more consistently, increasing task performance while reducing the risk of injuries.

Summary statementSpixs disc-winged bats prefer to roost in some types of leaves, which we show may be related to costly maneuvers during the approach and landing phases.


title: Asymmetrical lineage introgression and recombination in populations of Aspergillus flavus: implications for biological control

abstract: Aspergillus flavus is an agriculturally important fungus that causes ear rot of maize and produces aflatoxins (AFs), of which B1 is the most potent carcinogen known. In the US, the management of AFs includes the deployment of biological control agents that comprise two nonaflatoxigenic A. flavus strains, either Afla-Guard(R) (member of lineage IB) or AF36 (lineage IC). We used genotyping-by-sequencing to examine the influence of both biocontrol agents on native populations of A. flavus in cornfields in Texas, North Carolina, Arkansas, and Indiana. This study examined up to 27,529 single-nucleotide polymorphisms (SNPs) in a total of 815 A. flavus isolates, and 353 genome-wide haplotypes sampled before biocontrol application, three months after biocontrol application, and up to three years after initial application. Here, we report that the two distinct A. flavus evolutionary lineages IB and IC differ significantly in their frequency distributions across states. We provide evidence of increased unidirectional gene flow from lineage IB into IC, inferred to be due to the applied Afla-Guard biocontrol strain. Genetic exchange and recombination of biocontrol strains with native strains was detected in as little as three months after biocontrol application and up to one and three years later. There was limited inter-lineage migration in the untreated fields. These findings suggest that biocontrol products that include strains from lineage IB offer the greatest potential for sustained reductions in aflatoxin levels over several years. This knowledge has important implications for developing new biocontrol strategies.


title: Graph-based algorithms for phase-type distributions

abstract: Phase-type distributions model the time until absorption in continuous or discrete-time Markov chains on a finite state space. The multivariate phase-type distributions have diverse and important applications by modeling rewards accumulated at visited states. However, even moderately-sized state spaces make the traditional matrix-based equations computationally infeasible. State spaces of phase-type distributions are often very large but sparse, with only a few transitions from a state. This sparseness makes a graph-based representation of the phase-type distribution more natural and efficient than the traditional matrix-based representation. In this paper, we develop graph-based algorithms for analyses of phase-type distributions. In addition to algorithms for state-space construction, reward transformation, and moments calculation, we give algorithms for the marginal distribution functions of multivariate phase-type distributions and for the state probability vector of the underlying Markov chains of both time-homogeneous and time-inhomogeneous phase-type distributions. The algorithms are available as a numerically stable and memory-efficient open-source software package written in C named ptdalgorithms. This library exposes all methods in the programming languages C and R. We demonstrate with a classic problem from population genetics how ptdalgorithms serves as a much faster, much simpler, and completely general modeling alternative.


title: Organellar transcripts dominate the cellular mRNA pool across plants of varying ploidy levels

abstract: Mitochondrial and plastid functions depend on coordinated expression of proteins encoded by genomic compartments that have radical differences in copy number of organellar and nuclear genomes. In polyploids, doubling of the nuclear genome may add challenges to maintaining balanced expression of proteins involved in cytonuclear interactions. Here, we use ribo-depleted RNA-seq to analyze transcript abundance for nuclear and organellar genomes in leaf tissue from four different polyploid angiosperms and their close diploid relatives. We find that, even though plastid genomes contain <1% of the number of genes in the nuclear genome, they generate the majority (69.9-82.3%) of mRNA transcripts in the cell. Mitochondrial genes are responsible for a much smaller percentage (1.3-3.7%) of the leaf mRNA pool but still produce much higher transcript abundances per gene compared to nuclear genome. Nuclear genes encoding proteins that functionally interact with mitochondrial or plastid gene products exhibit mRNA expression levels that are consistently more than ten-fold lower than their organellar counterparts, indicating an extreme cytonuclear imbalance at the RNA level despite the predominance of equimolar interactions at the protein level. Nevertheless, interacting nuclear and organellar genes show strongly correlated transcript abundances across functional categories, suggesting that the observed mRNA stoichiometric imbalance does not preclude coordination of cytonuclear expression. Finally, we show that nuclear genome doubling does not alter the cytonuclear expression ratios observed in diploid relatives in consistent or systematic ways, indicating that successful polyploid plants are able to compensate for cytonuclear perturbations associated with nuclear genome doubling.


title: Accelerating PERx Reaction Enables Covalent Nanobodies for Potent Neutralization of SARS-Cov-2 and Variants

abstract: The long-lasting COVID-19 pandemic and increasing SARS-CoV-2 variants demand effective drugs for prophylactics and treatment. Protein-based biologics offer high specificity yet their noncovalent interactions often lead to drug dissociation and incomplete inhibition. Here we developed covalent nanobodies capable of binding with SARS-CoV-2 spike protein irreversibly via proximity-enabled reactive therapeutic (PERx) mechanism. A novel latent bioreactive amino acid FFY was designed and genetically encoded into nanobodies to accelerate PERx reaction rate. After covalent engineering, nanobodies binding with the Spike in the down state, but not in the up state, were discovered to possess striking enhancement in inhibiting viral infection. In comparison with the noncovalent wildtype nanobody, the FFY-incorporated covalent nanobody neutralized both authentic SARS-CoV-2 and its Alpha and Delta variants with potency drastically increased over tens of folds. This PERx-enabled covalent nanobody strategy and uncovered insights on potency increase can be valuable to developing effective therapeutics for various viral infections.

category: synthetic biology


title: Development of a ferritin-based nanoparticle vaccine against the SARS-CoV-2 Omicron variant

abstract: A new SARS-CoV-2 variant named Omicron (B.1.1.529) discovered initially in South Africa has recently been proposed as a variant of concern (VOC) by the World Health Organization, because of its high transmissibility and resistance to current vaccines and therapeutic antibodies. Therefore, rapid development of vaccines against prevalent variants including Omicron is urgently needed for COVID-19 prevention. Here, we designed a self-assembling ferritin-based nanoparticle (FNP) vaccine against the SARS-CoV-2 Omicron variant. The purified Fc-RBDOmicron automatically formed a dimer depending on the nature of the Fc tag, thus assembling onto the nanoparticles by the Fc-protein A tag interaction (FNP-Fc-RBDOmicron). The results of hACE2-transgenic mice immunization showed that SARS-CoV-2 Omicron RBD-specific IgG titer induced by FNP-Fc-RBDOmicron was much higher than that by Fc-RBDOmicron. Consistently, the sera showed a higher neutralizing activity against SARS-CoV-2 Omicron BA.1 and BA.2 in the FNP-Fc-RBDOmicron immunized mice, indicating that immunization of a self-assembling ferritin-based nanoparticle vaccine offers a robust humoral immune response against Omicron variants. This study offers a great potential for the quick response of the emerging SARS-CoV-2 variants and affords versatility to develop universal vaccines against other emerging and reemerging coronaviruses in the future.


title: The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes

abstract: Exposure histories to SARS-CoV-2 variants and vaccinations will shape the specificity of antibody responses. To understand the specificity of Delta-elicited antibody immunity, we characterize the polyclonal antibody response elicited by primary or mRNA vaccine-breakthrough Delta infections. Both types of infection elicit a neutralizing antibody response focused heavily on the receptor-binding domain (RBD). We use deep mutational scanning to show that mutations to the RBDs class 1 and class 2 epitopes, including sites 417, 478, and 484-486 often reduce binding of these Delta-elicited antibodies. The anti-Delta antibody response is more similar to that elicited by early 2020 viruses than the Beta variant, with mutations to the class 1 and 2, but not class 3 epitopes, having the largest effects on polyclonal antibody binding. In addition, mutations to the class 1 epitope (e.g., K417N) tend to have larger effects on antibody binding and neutralization in the Delta spike than in the D614G spike, both for vaccine- and Delta-infection-elicited antibodies. These results help elucidate how the antigenic impacts of SARS-CoV-2 mutations depend on exposure history.


title: Tracking SARS-CoV-2 Omicron diverse spike gene mutations identifies multiple inter-variant recombination events

abstract: The current pandemic of COVID-19 is fueled by more infectious emergent Omicron variants. Ongoing concerns of emergent variants include possible recombinants, as genome recombination is an important evolutionary mechanism for the emergence and re-emergence of human viral pathogens. Although recombination events among SARS-CoV-1 and MERS-CoV were well-documented, it has been difficult to detect the recombination signatures in SARS-CoV-2 variants due to their high degree of sequence similarity. In this study, we identified diverse recombination events between two Omicron major subvariants (BA.1 and BA.2) and other variants of concern (VOCs) and variants of interest (VOIs), suggesting that co-infection and subsequent genome recombination play important roles in the ongoing evolution of SARS-CoV-2. Through scanning high-quality completed Omicron spike gene sequences, eighteen core mutations of BA.1 variants (frequency >99%) were identified (eight in NTD, five near the S1/S2 cleavage site, and five in S2). BA.2 variants share three additional amino acid deletions with the Alpha variants. BA.1 subvariants share nine common amino acid mutations (three more than BA.2) in the spike protein with most VOCs, suggesting a possible recombination origin of Omicron from these VOCs. There are three more Alpha-related mutations (del69-70, del144) in BA.1 than BA.2, and therefore BA.1 may be phylogenetically closer to the Alpha variant. Revertant mutations are found in some dominant mutations (frequency >95%) in the BA.1 subvariant. Most notably, multiple additional amino acid mutations in the Delta spike protein were also identified in the recently emerged Omicron isolates, which implied possible recombination events occurred between the Omicron and Delta variants during the on-going pandemic. Monitoring the evolving SARS-CoV-2 genomes especially for recombination is critically important for recognition of abrupt changes to viral attributes including its epitopes which may call for vaccine modifications.


title: A broad and potent neutralization epitope in SARS-related coronaviruses

abstract: Many neutralizing antibodies (nAbs) elicited to ancestral SARS-CoV-2 through natural infection and vaccination generally have reduced effectiveness to SARS-CoV-2 variants. Here we show therapeutic antibody ADG20 is able to neutralize all SARS-CoV-2 variants of concern (VOCs) including Omicron (B.1.1.529) as well as other SARS-related coronaviruses. We delineate the structural basis of this relatively escape-resistant epitope that extends from one end of the receptor binding site (RBS) into the highly conserved CR3022 site. ADG20 can then benefit from high potency through direct competition with ACE2 in the more variable RBS and interaction with the more highly conserved CR3022 site. Importantly, antibodies that are able to target this site generally neutralize all VOCs, albeit with reduced potency against Omicron. Thus, this highly conserved and vulnerable site can be exploited for design of universal vaccines and therapeutic antibodies.


title: Discovery of anti-SARS-CoV-2 molecules using structure-assisted repurposing approach targeting N-protein

abstract: SARS-CoV-2 nucleocapsid protein (N-protein) is a virus specific multitasking protein, responsible for recognition and encapsidation of the viral genome. The N-terminal domain (NTD) of N-protein has a major role of packaging viral RNA genome into a long helical nucleocapsid structure. In this study, using structure-based drug repurposing strategy, small molecules from a FDA approved, natural product, and LOPAC1280 libraries have been virtually screened against the RNA binding pocket of SARS-CoV-2 NTD and twelve candidate molecules with high binding affinity were identified. Highly sensitive isothermal titration calorimetry (ITC) method was utilized to confirm binding of these molecules to purified NTD protein. In vitro cell-based SARS-CoV-2 antiviral assays demonstrate that nine of these identified molecules are highly efficacious in inhibiting virus replication with half maximal effective concentration (EC50) ranging from 0.98 M-10 M. FDA approved drugs: Telmisartan, an angiotensin II type 1 (AT1) receptor antagonist used in the management of hypertension and Bictegravir, an HIV-1 integrase inhibitor showed significant inhibitory activity against SARS-CoV-2 with a EC50 values of 1.02 M and 8.11 M respectively. Additionally, Bisdemethoxycurcumin, a natural analogue of curcumin and MCC-555, an anti-diabetic drug exerted antiviral activity with EC50 values of 1.64 M and 4.26 M, respectively. Taken together, this is the first report of drug molecules targeting the NTD of SARS-CoV-2 N-protein and the data presented in this study exhibit high potential for development of COVID-19 therapy based on drug repurposing.


title: Dual inhibition of vacuolar ATPase and TMPRSS2 is required for complete blockade of SARS-CoV-2 entry into cells

abstract: An essential step in the infection life cycle of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the proteolytic activation of the viral spike (S) protein, which enables membrane fusion and entry into the host cell. Two distinct classes of host proteases have been implicated in the S protein activation step: cell-surface serine proteases, such as the cell-surface transmembrane protease, serine 2 (TMPRSS2), and endosomal cathepsins, leading to entry through either the cell-surface route or the endosomal route, respectively. In cells expressing TMPRSS2, inhibiting endosomal proteases using non-specific cathepsin inhibitors such as E64d or lysosomotropic compounds such as hydroxychloroquine fails to prevent viral entry, suggesting that the endosomal route of entry is unimportant; however, mechanism-based toxicities and poor efficacy of these compounds confound our understanding of the importance of the endosomal route of entry. Here, to identify better pharmacological agents to elucidate the role of the endosomal route of entry, we profiled a panel of molecules identified through a high throughput screen that inhibit endosomal pH and/or maturation through different mechanisms. Among the three distinct classes of inhibitors, we found that inhibiting vacuolar-ATPase using the macrolide bafilomycin A1 was the only agent able to potently block viral entry without associated cellular toxicity. Using both pseudotyped and authentic virus, we showed that bafilomycin A1 inhibits SARS-CoV-2 infection both in the absence and presence of TMPRSS2. Moreover, synergy was observed upon combining bafilomycin A1 with Camostat, a TMPRSS2 inhibitor, in neutralizing SARS-CoV-2 entry into TMPRSS2-expressing cells. Overall, this study highlights the importance of the endosomal route of entry for SARS-CoV-2 and provides a rationale for the generation of successful intervention strategies against this virus that combine inhibitors of both entry pathways.

category: cell biology


title: The triadic structure of personality space in the house mouse resembles that of species with known personality badges; suggesting reciprocal hierarchies are an evolutionary motif with mixed strategies being more common

abstract: Differences in animal personalities are generally hard to measure - even in an animal as common as the house mouse. Yet, in some rare cases, nature has provided us with clear visual cues as to the nature of a specific individual. These so-called badges are the case for the side botched lizard, often referred to as the  rock-paper-scissor lizard. Here, we show that mice have behavioral archetypes that are similar to the triadic social dynamics of the lizards. We find analogs in territoriality, aggressiveness, and pro-social behavior linking ultra-dominant, dominant, and subordinate mice to the lizards orange, blue, and yellow morphs accordingly. Yet, unlike the lizards, most mice in the study displayed mixed strategies rather than fall into clear behavioral archetypes. In such a case, it makes less sense to have distinct visual cues to distinguish between personalities. The result implies that, although visual distinctions are infrequent in nature, having multiple behavioral archetypes might serve as an evolutionary motif. In addition, we find that mammals, like mice, might have circular hierarchies, similar to the lizards, where no single behavioral strategy outweighs others.


title: Parchment Glutamine Index (PQI): A novel method to estimate glutamine deamidation levels in parchment collagen obtained from low-quality MALDI-TOF data

abstract: Parchment was used as a writing material in the Middle Ages and was made using animal skins by liming them with Ca(OH)2. During liming, collagen peptides containing Glutamine (Q) undergo deamidation resulting in a mass shift of 0.984 Da. Assessing the extent of deamidation can inform us about parchment production patterns and quality. In this study, we propose a simple three-step workflow, developed as an R package called MALDIpqi(), to estimate deamidation in parchment derived collagen using low-resolution MALDI spectra. After pre-processing raw spectra, we used weighted least-squares linear regression to estimate Q deamidation levels from the convoluted isotopic envelope for seven collagen-peptide markers. Finally, we employed a linear mixed effect model to predict the overall deamidation level of a parchment sample termed Parchment Glutamine Index (PQI). To test the robustness of the workflow, we applied MALDIpqi() to previously published ZooMS data generated from almost an entire library of the Cistercian monastery at Orval Abbey, Belgium. In addition to reliably predicting PQI, we observed interesting patterns pertaining to parchment production. MALDIpqi() holds excellent potential for biocodicological and other archaeological studies involving collagen, such as bone, but we also foresee its application in the food and biomedical industry.


title: Antiviral State of CD1c+ cDC contributes to Increased Maturation and Activation of Cytotoxic Natural Killer cells in Sjogrens Syndrome

abstract:
ObjectivePrimary Sjogrens syndrome (pSS) is an inflammatory autoimmune disorder characterized by damage of exocrine glands and linked to IFN responses and the induction of autoreactive adaptive immune cells. However, the role of innate immune cells in pSS pathology remains understudied.

MethodsWe studied differential phenotypical characteristics of different NK cell, conventional dendritic cell (cDC) and monocyte subsets in the blood and salivary glands from pSS individuals. Transcriptional patterns of circulating cDC and Mo from pSS and healthy controls were also compared. Finally, in vivo alterations in these cell populations in the salivary gland were investigated in a mouse model.

ResultsHere, we identified CD16+ CD56hi NK cells enriched in pSS patients which associates with higher natural cytotoxic function and increased proportions of circulating CD64+ CD1c+ cDC exhibiting antiviral transcriptional IFN signatures. CD64hi cDC and NK cell were detected infiltrated into the salivary glands from pSS patients and a murine SS model. CD1c+ cDC from patients with pSS expressed high levels of ligands for activating NK receptors and increased ability to activate NK cells ex vivo. Finally, the antiviral RIG-I and DDX60 sensors regulated the expression of NK cell receptor ligands on CD1c+ cDC.

ConclusionsTherefore, the interplay of CD1c+ cDCs and NK cells could contribute to pSS pathology.


title: Immunization with recombinant accessory protein-deficient SARS-CoV-2 protects against lethal challenge and viral transmission

abstract: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has led to a worldwide Coronavirus Disease 2019 (COVID-19) pandemic. Despite high efficacy of the authorized vaccines, protection against the surging variants of concern (VoC) was less robust. Live-attenuated vaccines (LAV) have been shown to elicit robust and long-term protection by induction of host innate and adaptive immune responses. We sought to develop a COVID-19 LAV by generating 3 double open reading frame (ORF)-deficient recombinant (r)SARS-CoV-2 simultaneously lacking two accessory open reading frame (ORF) proteins (ORF3a/ORF6, ORF3a/ORF7a, and ORF3a/ORF7b). Here, we report that these double ORF-deficient rSARS-CoV-2 have slower replication kinetics and reduced fitness in cultured cells as compared to their parental wild-type (WT) counterpart. Importantly, these double ORF-deficient rSARS-CoV-2 showed attenuation in both K18 hACE2 transgenic mice and golden Syrian hamsters. A single intranasal dose vaccination induced high levels of neutralizing antibodies against different SARS-CoV-2 VoC, and also activated viral component-specific T-cell responses. Notably, the double ORF-deficient rSARS-CoV-2 were able to protect, as determined by inhibition of viral replication, shedding, and transmission, against challenge with SARS-CoV-2. Collectively, our results demonstrate the feasibility to implement these double ORF-deficient rSARS-CoV-2 as safe, stable, immunogenic and protective LAV for the prevention of SARS-CoV-2 infection and associated COVID-19 disease.