title: Improving protein tertiary structure prediction by deep learning and distance prediction in CASP14

abstract: Substantial progresses in protein structure prediction have been made by utilizing deep-learning and residue-residue distance prediction since CASP13. Inspired by the advances, we improve our CASP14 MULTICOM protein structure prediction system in the three main aspects: (1) a new deep-learning based protein inter-residue distance predictor (DeepDist) to improve template-free (ab initio) tertiary structure prediction, (2) an enhanced template-based tertiary structure prediction method, and (3) distance-based model quality assessment methods empowered by deep learning. In the 2020 CASP14 experiment, MULTICOM predictor was ranked 7th out of 146 predictors in protein tertiary structure prediction and ranked 3rd out of 136 predictors in inter-domain structure prediction. The results of MULTICOM demonstrate that the template-free modeling based on deep learning and residue-residue distance prediction can predict the correct topology for almost all template-based modeling targets and a majority of hard targets (template-free targets or targets whose templates cannot be recognized), which is a significant improvement over the CASP13 MULTICOM predictor. The performance of template-free tertiary structure prediction largely depends on the accuracy of distance predictions that is closely related to the quality of multiple sequence alignments. The structural model quality assessment works reasonably well on targets for which a sufficient number of good models can be predicted, but may perform poorly when only a few good models are predicted for a hard target and the distribution of model quality scores is highly skewed.


title: How certain are we? Development of an ensemble based framework for assessing astronaut cancer risks from space radiation

abstract: I.A new approach to NASA space radiation risk modeling has successfully extended the current NASA probabilistic cancer risk model to an ensemble framework able to consider sub-model parameter uncertainty as well as model-form uncertainty associated with differing theoretical or empirical formalisms. Ensemble methodologies are already widely used in weather prediction, modeling of infectious disease outbreaks, and certain terrestrial radiation protection applications to better understand how uncertainty may influence risk decision-making. Applying ensemble methodologies to space radiation risk projections offers the potential to efficiently incorporate emerging research results, allow for the incorporation of future models, improve uncertainty quantification for underlying sub-models, and reduce the impact of subjective bias on risk projections. Moreover, risk forecasting across an ensemble of multiple predictive models can provide stakeholders additional information on risk acceptance if current health/medical standards cannot be met for future space exploration missions, such as human missions to Mars. In this work, ensemble risk projections implementing multiple sub-models of radiation quality, dose and dose-rate effectiveness factors, excess risk, and latency as ensemble members are presented. Initial consensus methods for ensemble model weights and correlations to account for individual model bias are discussed. In these analyses, the ensemble forecast compares well to results from NASAs current operational cancer risk projection model used to assess permissible mission durations for astronauts. However, a large range of projected risk values are obtained at the upper 95th confidence level where models must extrapolate beyond available biological data sets. Closer agreement is seen at the median + one sigma due to the inherent similarities in available models. Identification of potential new models, epidemiological data, and methods for statistical correlation between predictive ensemble members are discussed. Alternate ways of communicating risk and acceptable uncertainty with respect to NASAs current permissible exposure limits are explored.

category: biophysics


title: REFINING THE IDENTITY AND ROLE OF KV4 CHANNELS IN MOUSE SUBSTANTIA NIGRA DOPAMINERGIC NEURONS

abstract:
Substantia nigra pars compacta (SNc) dopaminergic (DA) neurons display a peculiar electrical phenotype characterized in vitro by a spontaneous tonic regular activity (pacemaking activity), a broad action potential and a biphasic post-inhibitory response. Several studies in rodents have underlined the central role played by the transient A-type current (IA) in the control of pacemaking activity and post-inhibitory rebound properties, thereby influencing both DA release and the physiological response of SNc neurons to incoming inhibitory inputs. Kv4.3 potassium channels were considered to be fully responsible for IA in these neurons, their density being tightly related to pacemaking frequency. In spite of this crucial electrophysiological role, we show that Kv4.3-/- transgenic mice exhibit minor alterations in locomotion and motor learning, although no compensation by functionally overlapping ion channels is observed in Kv4.3-/- SNc DA neurons. Using antigen retrieval immunohistochemistry, we further demonstrate that Kv4.2 potassium channels are also expressed in SNc DA neurons, even though their contribution to IA appears significant only in a minority of neurons (~5-10%). Using correlative analysis on recorded electrophysiological parameters and multi-compartment modeling, we then demonstrate that, rather than its conductance level, IA gating kinetics (inactivation time constant) appear as the main biophysical property defining post-inhibitory rebound delay and pacemaking frequency. Moreover, we show that the hyperpolarization-activated current (IH) has an opposing and complementary influence on the same firing features, and that the biophysical properties of IA and IH are likely coregulated in mouse SNc DA neurons.

SIGNIFICANCE STATEMENTSubstantia nigra pars compacta (SNc) dopaminergic (DA) neurons are characterized by pacemaking activity, a broad action potential and biphasic post-inhibitory response. The A-type transient potassium current (IA) plays a central role in both pacemaking activity and post-inhibitory response. While it was thought so far that Kv4.3 ion channels were fully responsible for IA, using a Kv4.3-/- transgenic mouse and antigen retrieval immunohistochemistry we demonstrate that Kv4.2 channels are also expressed in SNc DA neurons, although their contribution is significant in a minority of neurons only. Using electrophysiological recordings and computational modeling, we then demonstrate that IA gating kinetics and its functional complementarity with the hyperpolarization-activated current are major determinants of both pacemaking activity and post-inhibitory response in SNc DA neurons.

category: neuroscience


title: Production of SARS-CoV-2 virus-like particles in insect cells

abstract: Coronavirus disease (COVID-19) causes a serious threat to human health. To production of SARS-COV-2 virus-like particles (VLPs) in insect cells for vaccine development and scientific research. The E, M and S genes were cloned into multiple cloning sites of the new triple expression plasmid with one p10 promoter, two pPH promoters and three multiple cloning sites. The plasmid was transformed into DH10 BacTM Escherichia coli competent cells to obtain recombinant bacmid. Then the recombinant bacmid was transfected in ExpiSf9 insect cells to generate recombinant baculovirus. After ExpiSf9 infected with the recombinant baculovirus, the E, M, and S protein co-expressed in insect cells. Finally, SARS-CoV-2 VLPs were self-assembled in insect cells after infection. The morphology and the size of SARS-CoV-2 VLPs are similar to the native virions.

category: bioengineering


title: Identification of anti-severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) oxysterol derivatives in vitro

abstract: Development of effective antiviral drugs targeting the severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) are urgently needed to combat the coronavirus disease 2019 (COVID-19). Oxysterols, defined as oxidized derivatives of cholesterol, include endogenous (naturally occurring) cholesterol metabolites as well as semi-synthetic oxysterol derivatives. We have previously studied the use of semi-synthetic oxysterol derivatives as drug candidates for inhibition of cancer, fibrosis, and bone regeneration. In this study, we have screened a panel of naturally occurring and semi-synthetic oxysterol derivatives for anti-SARS-CoV-2 activity, using a cell culture infection assay. We show that the natural oxysterols, 7-ketocholesterol, 22(R)-hydroxycholesterol, 24(S)-hydroxycholesterol, and 27-hydroxycholesterol, substantially inhibited SARS-CoV-2 propagation in cultured cells. Among semi-synthetic oxysterols, Oxy186 displayed antiviral activity comparable to natural oxysterols. In addition, related oxysterol analogues Oxy210 and Oxy232 displayed more robust anti-SARS-CoV-2 activities, reducing viral replication more than 90% at 10 M and 99% at 15 M, respectively. When orally administered in mice, peak plasma concentrations of Oxy210 fall into a therapeutically relevant range (19 M), based on the dose-dependent curve for antiviral activity in our cell culture infection assay. Mechanistic studies suggest that Oxy210 reduced replication of SARS-CoV-2 with disrupting the formation of double membrane vesicles (DMVs), intracellular membrane compartments associated with viral replication. Oxy210 also inhibited the replication of hepatitis C virus, another RNA virus whose replication is associated with DMVs, but not the replication of the DMV-independent hepatitis D virus. Our study warrants further evaluation of Oxy210 and Oxy232 as a safe and reliable oral medication, which could help protect vulnerable populations with increased risk developing COVID-19.

category: microbiology


title: Isolating and Cryo-Preserving Pig Skin Cells for Single Cell RNA Sequencing Study

abstract: The Pigskin architecture and physiology are similar to these of humans. Thus, the pig model is valuable for studying skin biology and testing therapeutics for skin diseases. The single-cell RNA sequencing technology allows quantitatively analyzing cell types, cell states, signaling, and receptor-ligand interactome at single-cell resolution and at high throughput. scRNA-Seq has been used to study mouse and human skins. However, studying pigskin with scRNA-Seq is still rare. Here we described a robust method for isolating and cryo-preserving pig single cells for scRNA-Seq. We showed that pigskin could be efficiently dissociated into single cells with high cell viability using the Miltenyi Human Whole Skin Dissociation kit and the Miltenyi gentleMACS Dissociator. Also, we showed that the subsequent single cells could be cryopreserved using DMSO without causing additional cell death, cell aggregation, or changes in gene expression profiles. Using the developed protocol, we were able to identify all the major skin cell types. The protocol and results from this study will be very valuable for the skin research scientific community.

category: cell biology


title: Terpenoid components, antioxidant and antibacterial activities of essential oils from fresh immature and mature leaves of Blumea balsamifera, extracted with different hydrodistillation periods

abstract: Volatiles and antioxidant capacities in essential oils (EOs) from fresh immature and mature leaves of Blumea balsamifera, extracted with different extraction periods of hydrodistillation, were investigated. There were seven major terpenoid compounds in the leaf extracts, including 2 monoterpenes of camphor and L-borneol, and 5 sesquiterpenes of silphiperfol-5-ene, 7-epi-silphiperfol-5-ene, {beta}-caryophyllene, {ramshorn}-eudesmol, and -eudesmol. Different hydrodistillation periods resulted in different quantitates and compositions of the terpenoids in EOs. The yield of EOs from the immature leaves was 1.4 times higher than the mature ones, whereas 73% of the yield was collected from the first 6 h of hydrodistillation. Camphor and L-borneol were almost collected in the first 6 h, while {beta}-caryophyllene, silphiperfolene, and 7-epi-silphiperfolene were above 80%, but {ramshorn}-eudesmol and -eudesmol were only 32 and 54% released. {beta}-Caryophyllene, {ramshorn}-eudesmol, and -eudesmol were found higher in the mature leaf EOs. Antioxidant capacities in EOs were positively related to terpenoid contents. Antibacterial activity of EOs from the immature leaves was subsequently tested. Although EOs from the hydrodistillation period of 12-18 h contained fewer terpenoid compositions, it showed the same minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) on Escherichia coli and Pseudomonas aeruginosa, compared to 0-6 h EOs.

category: plant biology


title: Synthetic Antigen-Presenting Cells for Adoptive T Cell Therapy

abstract: Adoptive T cell therapies are transforming the treatment of solid and liquid tumors, yet their widespread adoption is limited in part by the challenge of generating functional cells. T cell activation and expansion using conventional antigen-presenting cells (APCs) is unreliable due to the variable quality of donor-derived APCs. As a result, engineered approaches using nanomaterials presenting T cell activation signals are a promising alternative due to their ability to be robustly manufactured with precise control over stimulation cues. In this work, we design synthetic APCs that consist of liposomes surface-functionalized with peptide-major histocompatibility complexes (pMHC). Synthetic APCs selectively target and activate antigen-specific T cell populations to levels similar to conventional protocols using non-specific CD3 and CD28 antibodies without the need for costimulation signals. T cells treated with synthetic APCs produce effector cytokines and demonstrate cytotoxic activity when co-cultured with tumor cells presenting target antigen in vitro. Following adoptive transfer into tumor-bearing mice, activated cells control tumor growth and improve overall survival compared to untreated mice. Synthetic APCs could potentially be used in the future to improve the accessibility of adoptive T cell therapies by removing the need for conventional APCs during manufacturing.


title: A deep network-based model of hippocampal memory functions under normal and Alzheimer's disease conditions

abstract: We present a deep network-based model of the associative memory functions of the hippocampus. The proposed network architecture has two key modules: 1) an autoencoder module which represents the forward and backward projections of the cortico-hippocampal projections and 2) a module that computes familiarity of the stimulus and implements hill-climbing over the familiarity which represents the dynamics of the loops within the hippocampus. The proposed network is used in two simulation studies. In the first part of the study, the network is used to simulate image pattern completion by autoassociation under normal conditions. In the second part of the study, the proposed network is extended to a heteroassociative memory and is used to simulate picture naming task in normal and Alzheimers disease (AD) conditions. The network is trained on pictures and names of digits from 0 - 9. The encoder layer of the network is partly damaged to simulate AD conditions. As in case of AD patients, under moderate damage condition, the network recalls superordinate words ("odd" instead of "nine"). Under severe damage conditions, the network shows a null response ("I dont know"). Neurobiological plausibility of the model is extensively discussed.


title: Selfish migrants: How a meiotic driver is selected to increase dispersal

abstract: Meiotic drivers are selfish genetic elements that manipulate meiosis to increase their transmission to the next generation to the detriment of the rest of the genome. One example is the t haplotype in house mice, which is a naturally occurring meiotic driver with deleterious traits--poor fitness in polyandrous matings and homozygote inviability or infertility--that prevent its fixation. Recently, we discovered and validated a novel effect of t in a long-term field study on free-living wild house mice and with experiments: t-carriers are more likely to disperse. Here, we ask what known traits of the t haplotype can select for a difference in dispersal between t-carriers and wildtype mice. To that end, we built individual-based models with dispersal loci on the t and the homologous wildtype chromosomes. We also allow for density-dependent expression of these loci. The t haplotype consistently evolves to increase the dispersal propensity of its carriers, particularly at high densities. By examining variants of the model that modify different costs caused by t, we show that the increase in dispersal is driven by the deleterious traits of t, disadvantage in polyandrous matings and lethal homozygosity or male sterility. Finally, we show that an increase in driver-carrier dispersal can evolve across a range of values in driver strength and disadvantages.

category: evolutionary biology


title: Comparative genomics of Chinese and international isolates of Escherichia albertii: population structure and evolution of virulence and antimicrobial resistance

abstract:
Escherichia albertii is a newly recognized species in the genus Escherichia that causes diarrhea. The population structure, genetic diversity and genomic features has not been fully examined. Here, 169 E. albertii isolates from different sources and regions in China were sequenced and combined with 312 publicly available genomes for phylogenetic and genomic analyses. The E. albertii population was divided into 2 clades and 8 lineages, with lineage 3 (L3), L5 and L8 more common in China. Clinical isolates were observed in all clades/lineages. Virulence genes were found to be distributed differently among lineages: subtypes of the intimin encoding gene eae and the cytolethal distending toxin (Cdt) gene cdtB were lineage associated, the second type three secretion system (ETT2) island was truncated in L3 and L6. Seven new eae subtypes and 1 new cdtB subtype (cdtB-VI) were found. Alarmingly, 85.9% of the Chinese E. albertii isolates were predicted to be multidrug resistant (MDR) with 35.9% harboured genes capable of conferring resistance to 10 to 14 different drug classes. By in silico multi-locus sequence typing, majority of the MDR isolates belonged to 4 STs (ST4638, ST4479, ST4633 and ST4488). Thirty-four intact plasmids carrying MDR and virulence genes, and 130 intact prophages were identified from 17 complete E. albertii genomes. Ten plasmid replicon types were found to be significantly associated with MDR. The 130 intact prophages were clustered into 5 groups, with group 5 prophages harbouring more virulence genes. Our findings provided fundamental insights into the population structure, virulence variation and MDR of E. albertii.

Impact statementE. albertii is newly recognized foodborne pathogen causing diarrhea. Elucidation of its genomic features is important for surveillance and control of E. albertii infections. In this work, 169 E. albertii genomes from difference sources and regions in China were collected and sequenced, which contributed to the currently limited genomic data pool of E. albertii. In combination with 312 publicly available genomes from 14 additional countries, the population structure of E. albertii was defined. The presence and subtypes of virulence genes in different lineages were significantly different, indicating potential pathogenicity variation. Additionally, the presence of multidrug resistance (MDR) genes was alarmingly high in the Chinese dominated lineages. MDR associated STs and plasmid subtypes were identified, which could be used as sentinels for MDR surveillance. Moreover, the subtypes of plasmids and prophages were distributed differently across lineages, and were found to contribute to the acquisition of virulence and MDR genes of E. albertii. Altogether, this work reveals the diversity of E. albertii and characterized its genomic features in unprecedented detail.

Data SummaryAll newly sequenced data in this work were deposited in National Center for Biotechnology Information (NCBI) under the BioProject of PRJNA693666, including 6 complete genomes and raw reads of 164 E. albertii isolates.

category: genomics


title: A Reproducibility Analysis-based Statistical Framework for Residue-Residue Evolutionary Coupling Detection

abstract: Direct coupling analysis (DCA) has been widely used to infer evolutionary coupled residue pairs from the multiple sequence alignment (MSA) of homologous sequences. However, effectively selecting residue pairs with significant evolutionary couplings according to the result of DCA is a non-trivial task. In this study, we developed a general statistical framework for significant evolutionary coupling detection, referred to as IDR-DCA, which is based on reproducibility analysis of the coupling scores obtained from DCA on manually created MSA replicates. IDR-DCA was applied to select residue pairs for contact prediction for monomeric proteins, protein-protein interactions and monomeric RNAs, in which three different versions of DCA were applied. We demonstrated that with the application of IDR-DCA, the residue pairs selected using a universal threshold always yielded stable performance for contact prediction. Comparing with the application of carefully tuned coupling score cutoffs, IDR-DCA always showed better performance. The robustness of IDR-DCA was also supported through the MSA down-sampling analysis. We further demonstrated the effectiveness of applying constraints obtained from residue pairs selected by IDR-DCA to assist RNA secondary structure prediction.

category: bioinformatics


title: The cyclic di-GMP network is a global regulator of phase-transition and attachment-dependent host colonization in Erwinia amylovora

abstract:
Cyclic-di-GMP (c-di-GMP) is an essential bacterial second messenger that regulates the transition to biofilm formation in the phytopathogen Erwinia amylovora. The c-di-GMP system in E. amylovora is comprised of 12 diguanylate cyclase/Edc (dimerize cyclic-di-GMP) and phosphodiesterase/Pde (hydrolyze cyclic-di-GMP) proteins that are characterized by the presence of GGDEF and/or EAL motifs in their domain architecture. In order to study the global regulatory effect (without the inclusion of systemic regulatory impedance) of the c-di-GMP system in E. amylovora, we eliminated all 12 edc and pde genes in E. amylovora Ea1189{Delta}12. Comparisons between the representative transcriptomic profiles of Ea1189{Delta}12 and the combinatorial edc gene knockout mutant (Ea1189{Delta}5) revealed marked overall distinctions in expression levels for targets in a wide range of regulatory categories, including metabolic pathways involved in the utilization of methionine, isoleucine, histidine, etc. as well as critical signal transduction pathways including the Rcs phosphorelay and PhoPQ system. A complete loss of the cyclic-di-GMP signaling components resulted in the inability of Ea1189{Delta}12 cells to attach to and form biofilms in vitro and within the xylem vasculature in apple shoots. Using a flow-based in vitro biofilm system, we found that initial surface sensing was primarily dependent on the flagellar filament (FliC), following which the type IV pilus (HofC) was required to anchor cells to the surface to initialize biofilm development. A transcriptomic analysis of WT E. amylovora Ea1189 and Ea1189{Delta}12 cells in various stages of biofilm development revealed that cyclic-di-GMP based regulation had widespread effects on purine and pyrimidine biosynthesis pathways, amylovoran biosynthesis genes and the EnvZ/OmpR signal transduction system. Additionally, complementing individual eliminated genes back into Ea1189{Delta}12, and the collective evaluation of several virulence factors, enabled the correlative clustering of the functional effect rendered by each Edc and Pde enzyme in the system.

SignificanceCyclic-di-GMP dependent regulation, in the context of biofilm formation, has been studied in several bacterial systems. However, the comprehensiveness of the studies exploring the role of individual genetic components related to cyclic-di-GMP is affected by the often large number of diguanylate cyclase and phosphodiesterase enzymes present within individual bacterial systems. To explore the evolutionary dependencies related to cyclic-di-GMP in E. amylovora, we used a collective elimination approach, whereby all of the enzymes involved in cyclic-di-GMP metabolism were eliminated from the system. This approach enabled us to highlight the critical importance of cyclic-di-GMP in plant xylem colonization due to its effect on surface attachment. Additionally, we highlight the global transcriptomic effect of cyclic-di-GMP dependent signaling at various stages of biofilm development. Our approach is aimed at exploring the regulatory role of individual cyclic-di-GMP related enzymes in a background that is free from any redundancy-based feedback.


title: Kv1.1 subunits localize to cardiorespiratory brain networks in mice where their absence induces astrogliosis and microgliosis

abstract: Cardiorespiratory collapse following a seizure is a suspected cause of sudden unexpected death in epilepsy (SUDEP), the leading cause of epilepsy-related mortality. In the commonly used Kcna1 gene knockout (Kcna1-/-) mouse model of SUDEP, cardiorespiratory profiling reveals an array of aberrant breathing patterns that could contribute to risk of seizure-related mortality. However, the brain structures mediating these respiratory abnormalities remain unknown. We hypothesize that Kv1.1 deficiency in respiratory control centers of the brain contribute to respiratory dysfunction in Kcna1-/- mice leading to increased SUDEP risk. Thus, in this study, we first used immunohistochemistry to map expression of Kv1.1 protein in cardiorespiratory brain regions of wild-type Kcna1+/+ (WT) mice. Next, GFAP and Iba1 immunostaining was used to test for the presence of astrogliosis and microgliosis, respectively, in the cardiorespiratory centers of Kcna1-/- mice, which could be indicative of seizure-related brain injury that could impair breathing. In WT type mice, we detected Kv1.1 protein in all cardiorespiratory centers examined, including the basolateral amygdala, dorsal respiratory group, dorsal motor nucleus of vagus, nucleus ambiguus, ventral respiratory column, and pontine respiratory group, as well as chemosensory centers including the retrotrapezoid and median raphae nuclei. Extensive gliosis was observed in the same areas in Kcna1-/- mice suggesting that seizure-associated brain injury could contribute to respiratory abnormalities.


title: Molecular mechanism underlying the non-essentiality of Bub1 for the fidelity of chromosome segregation in human cells

abstract: The multi-task protein kinase Bub1 has long been considered important for chromosome alignment and spindle assembly checkpoint signaling during mitosis. However, recent studies provide surprising evidence that Bub1 may not be essential in human cells, with the underlying mechanism unknown. Here we show that Bub1 plays a redundant role with the non-essential CENP-U complex in recruiting Polo-like kinase 1 (Plk1) to the kinetochore. While disrupting either pathway of Plk1 recruitment does not affect the accuracy of whole chromosome segregation, loss of both pathways leads to a strong reduction in the kinetochore accumulation of Plk1 under a threshold level required for proper chromosome alignment and segregation. Thus, parallel recruitment of Plk1 to kinetochores by Bub1 and the CENP-U complex ensures high fidelity of mitotic chromosome segregation. This study may have implications for targeted treatment of cancer cells harboring mutations in either Bub1 or the CENP-U complex.


title: Distinct neurophysiological correlates of the fMRI BOLD signal in the hippocampus and neocortex

abstract:
Functional magnetic resonance imaging (fMRI) is among the foremost methods for mapping human brain function but provides only an indirect measure of underlying neural activity. Recent findings suggest that the neurophysiological correlates of the fMRI blood-oxygen-level-dependent (BOLD) signal might be regionally specific. We examined the neurophysiological correlates of the fMRI BOLD signal in the hippocampus and neocortex, where differences in neural architecture might result in a different relationship between the respective signals. Fifteen human neurosurgical patients (10 female, 5 male) implanted with depth electrodes performed a verbal free recall task while electrophysiological activity was recorded simultaneously from hippocampal and neocortical sites. The same patients subsequently performed a similar version of the task during a later fMRI session. Subsequent memory effects (SMEs) were computed for both imaging modalities as patterns of encoding-related brain activity predictive of later free recall. Linear mixed-effects modelling revealed that the relationship between BOLD and gamma-band SMEs was moderated by the lobar location of the recording site. BOLD and high gamma (70-150 Hz) SMEs positively covaried across much of the neocortex. This relationship was reversed in the hippocampus, where a negative correlation between BOLD and high gamma SMEs was evident. We also observed a negative relationship between BOLD and low gamma (30-70 Hz) SMEs in the medial temporal lobe more broadly. These results suggest that the neurophysiological correlates of the BOLD signal in the hippocampus differ from those observed in the neocortex.

Significance StatementThe blood-oxygen-level-dependent (BOLD) signal forms the basis of fMRI but provides only an indirect measure of neural activity. Task-related modulation of BOLD signals are typically equated with changes in gamma-band activity; however, relevant empirical evidence comes largely from the neocortex. We examined neurophysiological correlates of the BOLD signal in the hippocampus, where the differing neural architecture might result in a different relationship between the respective signals. We identified a positive relationship between encoding-related changes in BOLD and gamma-band activity in frontal, temporal, and parietal cortex. This effect was reversed in the hippocampus, where BOLD and gamma-band effects negatively covaried. These results suggest regional variability in the transfer function between neural activity and the BOLD signal in the hippocampus and neocortex.


title: Therapeutic antibodies, targeting the SARS-CoV-2 spike N-terminal domain, protect lethally infected K18-hACE2 mice

abstract: Since the onset of the current COVID-19 pandemic, high priority is given to the development of neutralizing antibodies, as a key approach for the design of therapeutic strategies to countermeasure and eradicate the disease. Previously, we reported the development of human therapeutic monoclonal antibodies (mAbs) exhibiting very high protective ability. These mAbs recognize epitopes on the spike receptor binding domain (RBD) of SARS-CoV-2 that is considered to represent the main rout of receptor engagement by the SARS-CoV-2 virus. The recent emergence of viral variants emphasizes the notion that efficient antibody treatments need to rely on mAbs against several distinct key epitopes in order to circumvent the occurrence of therapy escape-mutants. Here we report the isolation and characterization of 12 neutralizing mAbs, identified by screening a phage-display library constructed from lymphatic cells collected from severe COVID-19 patients. The antibodies target three distinct epitopes on the spike N-terminal domain (NTD) of SARS-CoV-2, one of them defining a major site of vulnerability of the virus. Extensive characterization of these mAbs suggests a neutralization mechanism which relies both on amino-acid and N-glycan recognition on the virus, and involvement of receptors other than the hACE2 on the target cell. Two of the selected mAbs, which demonstrated superior neutralization potency in vitro, were further evaluated in vivo, demonstrating their ability to fully protect K18-hACE2 transgenic mice even when administered at low doses and late after infection. The study demonstrates the high potential of the mAbs for therapy of SARS-CoV-2 infection and underlines the possible role of the NTD in mediating infection of host cells via alternative cellular portals other than the canonical ACE2 receptor.

category: immunology


title: Paradoxical hyperexcitability from NaV1.2 sodium channel loss in neocortical pyramidal cells

abstract: Loss-of-function variants in the gene SCN2A, which encodes the sodium channel NaV1.2, are strongly associated with autism spectrum disorder and intellectual disability. An estimated 20-30% of children with these variants are co-morbid for epilepsy, with altered neuronal activity originating in neocortex, a region where NaV1.2 channels are expressed predominantly in excitatory pyramidal cells. This is paradoxical, as sodium channel loss in excitatory cells would be expected to dampen neocortical activity rather than promote seizure. Here, we examined pyramidal neurons lacking NaV1.2 channels and found that they were intrinsically hyperexcitable, firing high-frequency bursts of action potentials (APs) despite decrements in AP size and speed. Compartmental modeling and dynamic clamp recordings revealed that NaV1.2 loss prevented potassium channels from properly repolarizing neurons between APs, increasing overall excitability by allowing neurons to reach threshold for subsequent APs more rapidly. This cell-intrinsic mechanism may therefore account for why SCN2A loss-of-function can paradoxically promote seizure.


title: Accurate and robust inference of microbial growth dynamics from metagenomic sequencing

abstract:
Patterns of sequencing coverage along a bacterial genome--summarized by a peak-to-trough ratio (PTR)--have been shown to accurately reflect microbial growth rates, revealing a new facet of microbial dynamics and host-microbe interactions. Here, we introduce CoPTR (Compute PTR): a tool for computing PTRs from complete reference genomes and assemblies. We show that CoPTR is more accurate than the current state-of-the-art, while also providing more PTR estimates overall. We further develop theory formalizing a biological interpretation for PTRs. Using a reference database of 2935 species, we applied CoPTR to a case-control study of 1304 metagenomic samples from 106 individuals with irritable bowel disease. We show that PTRs have high inter-individual variation, are only loosely correlated with relative abundances, and are associated with disease status. We conclude by demonstrating how PTRs can be combined with relative abundances and metabolomics to investigate their effect on the microbiome.

AvailabilityCoPTR is available from https://github.com/tyjo/coptr, with documentation on https://coptr.readthedocs.io.


title: Establishing regulated unconventional secretion for production of heterologous proteins

abstract: Heterologous protein production is a highly demanded biotechnological process. Secretion of the product to the culture broth is advantageous because it drastically reduces downstream pro-cessing costs. We exploit unconventional secretion for heterologous protein expression in the fungal model microorganism Ustilago maydis. Proteins of interest are fused to carrier chitinase Cts1 for export via the fragmentation zone of dividing yeast cells in a lock-type mechanism. Here, we are first to develop regulatory systems for unconventional protein secretion. This enables uncoupling the accumulation of biomass and protein synthesis of a product of choice from its export. Regulation was successfully established at two different levels using transcriptional and post-translational induction strategies. As a proof-of-principle, we applied autoinduction based on transcriptional regulation for the production and secretion of functional anti-Gfp nanobodies. The presented developments comprise tailored solutions for differentially prized products and thus constitute another important step towards a competitive protein production platform.

category: molecular biology


title: Synergistic Therapy of Doxorubicin with Cationic Anticancer Peptide L-K6 Reverses Multidrug Resistance in Cancer Cells in vitro via P-glycoprotein Inhibition

abstract: Multidrug resistance (MDR) is one of the major obstacles to efficient chemotherapy against cancers, resulting from the overexpression of drug efflux transporters such as P-glycoprotein (P-gP). In the present study, we aimed to evaluate the MDR reversal activity and synergistic therapeutic potential of cationic anticancer peptide L-K6 with doxorubicin (DOX) on P-gP-overexpressing and DOX-resistant MCF-7/Adr human breast cancer cells. Flow cytometry and confocal laser scanning microscopy were used to determine the intracellular accumulation of DOX and another P-gP substrate, Rho123. P-gP-Glo assay, Western blot and Biacore analysis were further performed to evaluate the P-gP function and expression. The cytotoxicity in MCF-7 or MCF-7/Adr cells was measured by MTT assay. Flow cytometry assay and confocal laser scanning microscopy observation clearly revealed an increased intracellular accumulation of DOX and Rho123 in MCF-7/Adr cells treated with L-K6, suggesting a P-gP inhibiting potential. Biacore analysis, P-gP-Glo assay and Western blot further confirmed that L-K6 could directly interact with P-gP, inhibit P-gP function and decrease P-gP expression in MCF-7/Adr cells. In addition, as expected, the data from MTT assay indicated that L-K6 restored the sensitivity of MCF-7/Adr cells to DOX, indicating a MDR reversal potential and a promising synergistic anticancer activity. All these findings may provide experimental evidence to support the promising applications and synergistic therapeutic potential of peptidic P-gP inhibitors against MDR cancer.

category: pharmacology and toxicology


title: Progressive domain segregation in early embryonic development and underlying correlation to genetic and epigenetic changes

abstract: The author has withdrawn this manuscript due to a duplicate posting of manuscript number BIORXIV/2019/521401. Therefore, the author does not wish this work to be cited as a reference for the project. Please cite and refer to the preprint BIORXIV/2019/521401 if necessary. If you have any questions, please contact the corresponding author (gaoyq@pku.edu.cn).

category: developmental biology


title: PolyQ expansion does not alter the Huntingtin-HAP40 complex

abstract: The abnormal amplification of a CAG repeat in the gene coding for huntingtin (HTT) leads to Huntington disease (HD). At the protein level, this translates into the expansion of a poly-glutamine (polyQ) stretch located at the HTT N-terminus, which renders it aggregation-prone by unknown mechanisms. Here we investigated the effects of polyQ expansion on HTT in a complex with its stabilizing interaction partner huntingtin-associated protein 40 (HAP40). Surprisingly, our comprehensive biophysical, crosslinking mass spectrometry and cryo-EM experiments revealed no major differences in the conformation of HTT-HAP40 complexes of various polyQ length, including 17QHTT-HAP40 (wild type), 46QHTT-HAP40 (typical polyQ length in HD patients) and 128QHTT-HAP40 (extreme polyQ length). Thus, HTT polyQ expansion does not alter the global structure of HTT when associated with HAP40.


title: Genetic autonomy and low singlet oxygen yield support kleptoplast functionality in photosynthetic sea slugs

abstract:
Elysia chlorotica is a kleptoplastic sea slug that preys on Vaucheria litorea, stealing its plastids which then continue to photosynthesize for months inside the animal cells. We investigated the native properties of V. litorea plastids to understand how they withstand the rigors of photosynthesis in isolation. Transcription of specific genes in laboratory-isolated V. litorea plastids was monitored up to seven days. The involvement of plastid-encoded FtsH, a key plastid maintenance protease, in recovery from photoinhibition in V. litorea was estimated in cycloheximide-treated cells. In vitro comparison of V. litorea and spinach thylakoids was applied to investigate ROS formation in V. litorea. Isolating V. litorea plastids triggered upregulation of ftsH and translation elongation factor EF-Tu (tufA). Upregulation of FtsH was also evident in cycloheximide-treated cells during recovery from photoinhibition. Charge recombination in PSII of V. litorea was found to be fine-tuned to produce only small quantities of singlet oxygen (1O2). Our results support the view that the genetic characteristics of the plastids themselves are crucial in creating a photosynthetic sea slug. The plastids autonomous repair machinery is likely enhanced by low 1O2 production and by upregulation of FtsH in the plastids.

HighlightIsolated Vaucheria litorea plastids exhibit upregulation of tufA and ftsH, key plastid maintenance genes, and produce only little singlet oxygen. These factors likely contribute to plastid longevity in kleptoplastic slugs.


title: Analysis of gastric cancer transcriptome allows the identification of histotype specific molecular signatures with prognostic potential

abstract:
Gastric cancer is the fifth most common malignancy but the third leading cause of cancer-associated mortality worldwide. Therapy for gastric cancer remain largely suboptimal making the identification of novel therapeutic targets an urgent medical need. In the present study we have carried out a high-throughput sequencing of transcriptome expression in patients with gastric cancers. Twenty-four patients, among a series of 53, who underwent an attempt of curative surgery for gastric cancers in a single center, were enrolled. Patients were sub-grouped according to their histopathology into diffuse and intestinal types, and the transcriptome of the two subgroups assessed by RNAseq analysis and compared to the normal gastric mucosa. The results of this investigation demonstrated that the two histopathology phenotypes express two different patterns of gene expression. A total of 2064 transcripts were differentially expressed between neoplastic and non neoplastic tissues: 772 were specific for the intestinal type and 407 for the diffuse type. Only 885 transcripts were simultaneously differentially expressed by both tumors. The per pathway analysis demonstrated an enrichment of extracellular matrix and immune dysfunction in the intestinal type including CXCR2, CXCR1, FPR2, CARD14, EFNA2, AQ9, TRIP13, KLK11 and GHRL. At the univariate analysis reduced levels AQP9 was found to be a negative predictor of 4 years survival. In the diffuse type low levels CXCR2 and high levels of CARD14 mRNA were negative predictors of 4 years survival. In summary, we have identified a group of genes differentially regulated in the intestinal and diffuse histo-types of gastric cancers with AQP9, CARD14 and CXCR2 impacting on patients prognosis, although CXCR2 is the only factor independently impacting overall survival.

Simple summaryGastric cancer is the fifth most common malignancy and the third leading cause of cancer-associated mortality worldwide. Although several new pharmacological approaches are currently developed, surgery remains the unique valid option of treatment but survival remains very poor over the last decades. Therefore, understanding the underlying molecular mechanisms of the gastric carcinogenesis and identifying sensitive biomarkers could be helpful for the prevention and treatment of the disease. Currently, the high-throughput sequencing techniques, in particular the transcriptomic analysis (RNA-seq) represents a validated technique to obtain a molecular characterization of human cancers. Moreover, it has been established that genetic susceptibility and environmental factors, such as microbial infections may contribute to carcinogenesis. We have characterized the different patterns of gene expression, using RNA-seq analysis and correlated these findings with gastric cancer histological subtypes.

category: cancer biology


title: Angiotensin-II modulates GABAergic neurotransmission in the mouse substantia nigra.

abstract:
GABAergic projections neurons of the substantia nigra reticulata (SNr), through an extensive network of dendritic arbors and axon collaterals, provide robust inhibitory input to neighboring dopaminergic neurons in the substantia nigra compacta (SNc). Angiotensin-II (Ang-II) receptor signaling increases SNc dopaminergic neuronal sensitivity to insult, thus rendering these cells susceptible to dysfunction and destruction. However, the mechanisms by which Ang-II regulates SNc dopaminergic neuronal activity are unclear. Given the complex relationship between SN dopaminergic and GABAergic neurons, we hypothesized that Ang-II could regulate SNc dopaminergic neuronal activity directly and indirectly by modulating SNr GABAergic neurotransmission. Herein, using transgenic mice, slice electrophysiology, and optogenetics, we provide evidence of an AT1 receptor-mediated signaling mechanism in SNr GABAergic neurons where Ang-II suppresses electrically-evoked neuronal output by facilitating postsynaptic GABAA receptors and prolonging the action potential duration. Unexpectedly, Ang-II had no discernable effects on the electrical properties of SNc dopaminergic neurons. Also, and indicating a nonlinear relationship between electrical activity and neuronal output, following phasic photoactivation of SNr GABAergic neurons, Ang-II paradoxically enhanced the feedforward inhibitory input to SNc dopaminergic neurons. In sum, our observations describe an increasingly complex and heterogeneous response of the SN to Ang-II by revealing cell-specific responses and nonlinear effects on intranigral GABAergic neurotransmission. Our data further implicate the renin-angiotensin-system as a functionally relevant neuromodulator in the basal ganglia, thus underscoring a need for additional inquiry.

SIGNIFICANCE STATEMENTAngiotensin II (Ang-II) promotes dopamine release in the striatum and, in the substantia nigra compacta (SNc), exacerbates dopaminergic cell loss in animal models of Parkinsons disease. Despite a potential association with Parkinsons disease, the effects of Ang-II on neuronal activity in the basal ganglia is unknown. Here we describe a novel AT1 receptor-dependent signaling mechanism in GABAergic projection neurons of the SN reticulata (SNr), a major inhibitory regulator of SNc dopaminergic neurons. Specifically, Ang-II suppresses SNr GABAergic neuronal activity, subsequently altering GABAergic modulation of SNc dopaminergic neurons in a nonlinear fashion. Altogether, our data provide the first indication of Ang-II-dependent modulation of GABAergic neurotransmission in the SN, which could impact output from the basal ganglia in health and disease.


title: The structural and electrophysiological properties of progesterone receptor expressing neurons vary along the anterior-posterior axis of the ventromedial hypothalamus and undergo local changes across the reproductive cycle

abstract: Sex hormone levels continuously fluctuate across the reproductive cycle, changing the activity of neuronal circuits to coordinate female behavior and reproductive capacity. The ventrolateral division of the ventromedial hypothalamus (VMHvl) contains neurons expressing receptors for sex hormones and its function is intimately linked to female sexual receptivity. However, recent findings suggest that the VMHvl is functionally heterogeneous. Here, we used whole cell recordings and intracellular labeling to characterize the electrophysiological and morphological properties of individual VMHvl neurons in naturally cycling females. We found that the properties of progesterone receptor expressing (PR+) neurons, but not PR- neurons, depended systematically on the neurons location along the anterior-posterior axis of the VMHvl and the phase within the reproductive cycle. Prominent amongst this, the resting membrane potential of anterior PR+ neurons decreased during the receptive phase, while the excitability of medial PR+ neurons increased during the non-receptive phase. During the receptive phase of the cycle, posterior PR+ neurons simultaneously showed an increase in dendritic complexity and a decrease in spine density. These findings reveal an extensive diversity of local rules driving structural and physiological changes in response to fluctuating levels of sex hormones, supporting the anatomical and functional subdivision of the VMHvl and its possible role in the orchestration of different aspects of female socio-sexual behavior.


title: Semi-quantitative detection for L-asparaginase producing fungi and the impact of carbon and nitrogen sources on enzyme activity

abstract:
ObjectiveTo semi-quantitively screen filamentous fungi isolated from different habitats for L-asparaginase production by three indicators; phenol red, cresol red and bromothymol blue and to examine the impact of different carbon and nitrogen sources on the enzyme production using different fungal isolates.

Materials and methodsFifty-five fungal isolates were tested for L-asparaginase production by plate assay using Modified Czapek-Dox (MCD) medium. The enzyme activity was estimated using the Nessler method which measures the concentration of ammonia formed owing to the enzyme action on the substrate. The impact of nitrogen and carbon sources on the enzyme production was done by using the best three L-asparaginase producers from the semi-quantitative screening.

Results and conclusionsA total of 53/55 (96.36%) fungal isolates were L-asparaginase producing strains, of them, Cladosporium tenuissimum, Penicillium camembertii and Aspergillus carneus showed high enzyme production. Production of L-asparaginase was higher with the glucose and urea as carbon and nitrogen sources, respectively. The highest enzyme level (5,558 U/ml) was produced by C. tenuissimum in a glucose-containing medium. This study shows that P. camemberti, A. carneus, and C. tenuissimum are good L-asparaginase producers and thus could be used for L-asparaginase production


title: Adaptive stimulation of macropinocytosis overcomes aspartate limitation in cancer cells under hypoxia

abstract: Stress-adaptive mechanisms enable tumor cells to overcome metabolic constraints in nutrient and oxygen poor tumors. Aspartate is an endogenous metabolic limitation under hypoxic conditions, but the nature of the adaptive mechanisms that contribute to aspartate availability and hypoxic tumor growth are poorly understood. Here, using a combination of metabolomics and CRISPR-based genetic screens, we identify GOT2-catalyzed mitochondrial aspartate synthesis as an essential metabolic dependency for the proliferation of pancreatic tumor cells under hypoxic culture conditions. In contrast, GOT2-catalyzed aspartate synthesis is dispensable for pancreatic tumor formation in vivo. The dependence of pancreatic tumor cells on aspartate synthesis is bypassed in part by a hypoxia-induced potentiation of extracellular protein scavenging via macropinocytosis. This effect is mutant KRas-dependent, and is mediated by hypoxia inducible factor 1 (HIF1A) and its canonical target carbonic anhydrase-9 (CA9) through the cooption of the bicarbonate-macropinocytosis signaling axis. Our findings reveal high plasticity of aspartate metabolism and define an adaptive regulatory role for macropinocytosis by which mutant KRas tumors can overcome nutrient deprivation under hypoxic conditions.


title: Extracellular membrane tubules involved in suberin deposition in plant cell walls

abstract:
Suberin is a fundamental plant biopolymer, found in protective tissues, such as seed coats, exodermis and endodermis of roots, the outer layers of stems and roots with secondary growth, as well as in wound-induced tissues. Its presence allows organs to resist various environmental stresses, such as pathogen attack, drought or excessive salt concentrations. Suberin is a mostly aliphatic polyester of long-chain fatty acids and alcohols, often co-occurring with lignin-like polymers in the same cells. Most suberizing cells appear to deposit suberin in the form of lamellae just outside of the plasma membrane, below the primary cell wall. The monomeric precursors of suberin are thought to be glycerated fatty acids, synthesized at the endoplasmic reticulum. However, it has remained obscure how these monomers are transported outside of the cell, where they will be polymerized to form suberin lamellae. Here, we demonstrate that extracellular vesicular-tubular structures accumulate specifically in suberizing cells. By employing various, independent mutational and hormonal challenges, known to affect suberization in distinct ways, we demonstrate that their presence correlates perfectly with root suberization. Surprisingly, no endosomal compartment marker showed any conspicuous changes upon induction of suberization, suggesting that this compartment might not derive from endosomal multi-vesicular bodies, but possibly form directly from endoplasmic reticulum subdomains. Consistent with this, we could block formation of both, suberin deposition and vesicle accumulation by a pharmacogenetic manipulation affecting early steps in the secretory pathway. Whereas many previous reports have described extracellular vesicle occurrence in the context of biotic interactions, our results suggest a developmental role for extracellular vesicles in suberin formation.

One Sentence SummarySuberin lamellae formation is associated with extracellular membrane tubules.


title: Hoplonemertean larvae are planktonic predators that capture and devour active animal prey

abstract: The superficially-simple ciliated planktonic larvae of hoplonemerteans have been assumed to be lecithotrophic direct developers, even though many develop from such small eggs that it is hard to imagine how they could give rise to a viable juvenile without some phase of larval feeding. Indeed, attempts to raise such larvae to settlement without food invariably fail. Observations that some hoplonemertean larvae are found in plankton samples at a range of sizes, and much larger than hatchlings, suggests they must indeed feed somehow. Since these "planuliform" larvae lack apparent means to concentrate suspended algae or other unicellular food, one alternative hypothesis is that they are planktonic predators that hunt large prey. Here we provide direct evidence that this is indeed the case for six distinct species of hoplonemerteans. We recorded wild-caught larvae of Paranemertes californica, Paranemertes sp., Gurjanovella littoralis, Emplectonema viride, Carcinonemertes epialti, and Ototyphlonemertes sp. attacking, subduing, and devouring pelagic crustaceans, including barnacle nauplii, cyprids, copepods and their nauplii, and others. While there is no doubt that some hoplonemerteans are genuine lecithotrophs, our evidence suggests that many species in this group both feed and grow during an extended planktonic larval period. This conclusion has important consequences for biogeographic and life-history studies in this group, because it implies enhanced potential for long-distance dispersal. More broadly, the possibility that many animal larvae are actually carnivores invites reconsideration of prevailing stereotypes about metazoan developmental modes and the trade-offs between them.

category: zoology


title: Pathogenic bacteria grown in iron and zinc milieu exhibit magnetotaxis

abstract: The growing number of multiple drug resistant (MDR) bacteria and the dwindling pipeline of new antibiotics are driving us towards a  post-antibiotic era in which even common infections would become difficult to treat. To address this, an antibiotic-free strategy that can combat multiple bacteria is recommended. Most of the proposed approaches nevertheless have several limitations, including bacterial targeting. To overcome such limitations, the proposed strategy employs the bacterial machinery to self-destruct. Herein, the biosynthesis of magnetic nanoparticle (MNP) is reported for the first time in multiple pathogenic bacteria, including MDR bacteria. The intracellular MNPs composed of superparamagnetic zinc ferrites were formed in presence of iron and zinc precursors. Exposure of the treated bacteria/biofilms to an alternating magnetic field (AMF) exhibited hyperthermia (5-6{degrees}C) and a dramatic decrease in bacterial viability, suggesting the MNPs therapeutic potential. Likewise, the bacteria existing in vivo biosynthesize the MNPs by mining these elements from the host. To determine its therapeutic efficacy, the infected tissues were exposed directly to AMF. A 3-4 log reduction in bacterial burden, as compared to antibiotics treatment, confirmed the significance of using naturally existing MNPs to combat bacterial infections. The proposed broad-spectrum approach can therefore aid in overcoming the challenges facing anti-bacterial therapies.


title: Revealing the inherent susceptibility of pathogenic bacteria to magnetic hyperthermia


title: A Drug-free, Self-destruction Strategy to Combat Bacterial Infections by Using the Intrinsically formed Magnetic Nanoparticles in Bacterial Pathogens


title: Large portion of essential genes is missed by screening either fly or beetle indicating unexpected diversity of insect gene function

abstract:
Most gene functions were detected by screens in very few model organisms but it has remained unclear how comprehensive these data are. Here, we expanded our RNAi screen in the red flour beetle Tribolium castaneum to cover more than half of the protein-coding genes and we compared the gene sets involved in several processes between beetle and fly.

We find that around 50 % of the gene functions are detected in both species while the rest was found only in fly (~10%) or beetle (~40%) reflecting both technical and biological differences. We conclude that work in complementary model systems is required to gain a comprehensive picture on gene functions documented by the annotation of novel GO terms for 96 genes studied here. The RNAi screening resources developed in this project, the expanding transgenic tool-kit and our large-scale functional data make T. castaneum an excellent model system in that endeavor.

category: genetics


title: Assessment of immunogenicity and protective efficacy of ZyCoV-D DNA vaccine candidates in Rhesus macaques against SARS-CoV-2 infection

abstract: Vaccines remain the key protective measure to achieve herd immunity to control the disease burden and stop COVID-19 pandemic. We have developed and assessed the immunogenicity and protective efficacy of two formulations (1mg and 2mg) of ZyCoV-D (a plasmid DNA based vaccine candidates) administered through Needle Free Injection System (NFIS) and syringe-needle (intradermal) in rhesus macaques with three dose vaccine regimens. The vaccine candidate 2mg dose administered using Needle Free Injection System (NFIS) elicited a significant immune response with development of SARS-CoV-2 S1 spike region specific IgG and neutralizing antibody (NAb) titers during the immunization phase and significant enhancement in the levels after the virus challenge. In 2 mg NFIS group the IgG and NAb titers were maintained and showed gradual rise during the immunization period (15 weeks) and till 2 weeks after the virus challenge. It also conferred better protection to macaques evident by the viral clearance from nasal swab, throat swab and bronchoalveolar lavage fluid specimens in comparison with macaques from other immunized groups. In contrast, the animals from placebo group developed high levels of viremia and lung disease following the virus challenge. Besides this, the vaccine candidate also induced increase lymphocyte proliferation and cytokines response (IL-6, IL-5).The administration of the vaccine candidate with NFIS generated a better immunogenicity response in comparison to syringe-needle (intradermal route). The study demonstrated immunogenicity and protective efficacy of the vaccine candidate, ZyCoV-D in rhesus macaques.


title: In silico, in vitro and in cellulo models for monitoring SARS-CoV-2 spike/human ACE2 complex, viral entry and cell fusion

abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent responsible for the recent coronavirus disease 2019 (COVID-19) pandemic. Productive SARS-CoV-2 infection relies on viral entry into cells expressing angiotensin-converting enzyme 2 (ACE2). Indeed, viral entry into cells is mostly mediated by the early interaction between the viral spike protein S and its ACE2 receptor. The S/ACE2 complex is, thus, the first contact point between the incoming virus and its cellular target; consequently, it has been considered an attractive therapeutic target. To further characterize this interaction and the cellular processes engaged in the entry step of the virus, we set up various in silico, in vitro and in cellulo approaches that allowed us to specifically monitor the S/ACE2 association. We report here a novel computational model of the SARS-CoV-2 S/ACE2 complex as well as its biochemical and biophysical monitoring using pulldown, AlphaLISA and biolayer interferometry (BLI) binding assays. This led us to determine the kinetic parameters of the S/ACE2 association and dissociation steps. In parallel to these in vitro approaches, we developed in cellulo transduction assays using SARS-CoV-2 pseudotyped lentiviral vectors and HEK293T-ACE2 cell lines generated in-house. This allowed us to recapitulate the early replication stage of the infection mediated by the S/ACE2 interaction and to detect cell fusion induced by the interaction. Finally, a cell imaging system was set up to directly monitor the S/ACE2 interaction in a cellular context, and a flow cytometry assay was developed to quantify this association at the cell surface. Together, these different approaches are available for both basic and clinical research aiming to characterize the entry step of the original SARS-CoV-2 strain and its variants as well as to investigate the possible chemical modulation of this interaction. All these models will help in identifying new antiviral agents and new chemical tools for dissecting the virus entry step.


title: Potential global impact of the N501Y mutation on MHC-II presentation and immune escape

abstract: The B.1.1.7 SARS-CoV-2 variant, characterized by the N501Y mutation, is rapidly emerging, raising concerns about its effectiveness on natural as well as vaccine-induced adaptive viral immunity at the population level. Since CD4 T cell responses are of critical importance to the antibody response, we examined the global effects of N501Y mutation on MHC-II presentation compared to the N501 wildtype and found poorer presentation across the majority of MHC-II alleles. This suggests that the N501Y mutation may not only diminish binding of antibodies to the RBD but also interfere with their production by weakening the cooperation between T and B cells, facilitating immune escape.


title: Allogeneic CAR-invariant Natural Killer T Cells Exert Potent Antitumor Effects Through Host CD8 T cell Cross-Priming

abstract: The development of allogeneic chimeric antigen receptor (CAR) T cell therapies for off-the-shelf use is a major goal yet faces two main immunological challenges, namely the risk of graft-versus-host-disease (GvHD) induction by the transferred cells and the rejection by the host immune system limiting their persistence. We demonstrate that allogeneic CAR-engineered invariant natural killer T (iNKT) cells, a cell population without GvHD-induction potential that displays immunomodulatory properties, exerted potent direct and indirect antitumor activity in murine models of B-cell lymphoma when administered across major MHC-barriers. In addition to their known direct cytotoxic effect, allogeneic CAR iNKT cells induced tumor-specific antitumor immunity through host CD8 T cell cross-priming, resulting in a potent antitumor effect lasting longer than the physical persistence of the allogeneic cells. The utilization of off-the-shelf allogeneic CAR iNKT cells could meet significant unmet needs in the clinic.


title: Microbial population dynamics are dominated by stochastic forces in a low biomass subseafloor habitat

abstract:
The subseafloor is a vast habitat that supports microorganisms that have a global scale impact on geochemical cycles. Many of the endemic microbial communities inhabiting the subseafloor consist of small populations under growth-limited conditions. For small populations, stochastic evolutionary events can have large impacts on intraspecific population dynamics and allele frequencies. These conditions are fundamentally different from those experienced by most microorganisms in surface environments, and it is unknown how small population sizes and growth-limiting conditions influence evolution and population structure in the subsurface. Using a two-year, high-resolution environmental time-series, we examine the dynamics of microbial populations from cold, oxic crustal fluids collected from the subseafloor site North Pond, located near the mid-Atlantic ridge. Our results reveal rapid shifts in overall abundance, allele frequency, and strain abundance across the time points observed, with evidence for homologous recombination between coexisting lineages. We show that the subseafloor aquifer is a dynamic habitat that hosts microbial metapopulations that disperse frequently through the crustal fluids, enabling gene flow and recombination between microbial populations. The dynamism and stochasticity of microbial population dynamics in North Pond suggests that these forces are important drivers in the evolution of microbial populations in the vast subseafloor habitat.

Significance StatementThe cold, oxic subseafloor is an understudied habitat that is difficult to access, yet important to global biogeochemical cycles and starkly different compared to microbial habitats on the surface of the Earth. Our understanding of microbial evolution and population dynamics is largely molded by studies of microbes living in surface habitats that can host 10-1,000 times more microbial biomass than is frequently observed in the subsurface. This study provides an opportunity to observe population dynamics within a low biomass, growth-limited environment and reveals that microbial populations in the subseafloor are influenced by changes in selection pressure and gene sweeps. In addition, recombination between strains that have dispersed from elsewhere within the aquifer has an important impact on the evolution of microbial populations. Much of the microbial life on the planet exists under growth-limited conditions and the subseafloor provides a natural laboratory to explore how life evolves in such environments.


title: Microbial populations are shaped by dispersal and recombination in a low biomass subseafloor habitat


title: Nonsense-mediated decay is highly stable across individuals and tissues.

abstract: Precise interpretation of the effects of protein-truncating variants (PTVs) is important for accurate determination of variant impact. Current methods for assessing the ability of PTVs to induce nonsense-mediated decay (NMD) focus primarily on the position of the variant in the transcript. We used RNA-sequencing of the Genotype Tissue Expression v8 cohort to compute the efficiency of NMD using allelic imbalance for 2,320 rare (genome aggregation database minor allele frequency <=1%) PTVs across 809 individuals in 49 tissues. We created an interpretable predictive model using penalized logistic regression in order to evaluate the comprehensive influence of variant annotation, tissue, and inter-individual variation on NMD. We found that variant position, allele frequency, including ultra-rare and singleton variants, and conservation were predictive of allelic imbalance. Furthermore, we found that NMD effects were highly concordant across tissues and individuals. Due to this high consistency, we demonstrate in silico that utilizing peripheral tissues or cell lines provides accurate prediction of NMD for PTVs.


title: Pre-mutagenic and mutagenic changes imprinted on the genomes of mammalian cells after irradiation with a nail polish dryer

abstract: Ultraviolet A light (UVA) is commonly emitted by nail polish dryers with recent reports suggesting that long-term use of UV-nail polish dryers may increase the risk for developing skin cancer. However, no experimental evaluation has been conducted to reveal the effect of radiation emitted by UV-nail polish dryers on mammalian cells. Here, we examine the pre-mutagenic and mutagenic changes imprinted on the genomes of human and murine primary cell models due to irradiation by a UV-nail dryer. Our findings demonstrate that radiation from UV-nail devices is cytotoxic and genotoxic. Importantly, high levels of reactive oxygen species were observed in all irradiated samples. Analysis of somatic mutations revealed a dose-dependent increase of C:G>A:T substitutions in irradiated samples with a pattern consistent to the one of COSMIC signature 18, a mutational signature attributed to reactive oxygen species. Examination of previously generated skin cancer genomics data revealed that signature 18 is ubiquitously present in melanoma and that it accounts for ~12% of the observed driver mutations. In summary, this study demonstrates that radiation emitted by UV-nail polish dryers can both damage DNA and can permanently imprint somatic mutations on the genomes of mammalian cells. These results have far reaching implications in regard to public health and to preventing skin cancer due to occupational- or consumer-based exposure to ultraviolet light from artificial sources.


title: Albendazole reduces endoplasmic reticulum stress induced by Echinococcus multilocularis in mice

abstract:
BackgroundEchinococcus multilocularis causes alveolar echinococcosis (AE), a rising zoonotic disease in the northern hemisphere. Treatment of this fatal disease is limited to chemotherapy using benzimidazoles and surgical intervention, with relatively frequent disease recurrence in cases without radical surgery. Elucidating the molecular mechanisms underlying E. multilocularis infections and host-parasite interactions aids developing novel therapeutic options. This study explored an involvement of unfolded protein response (UPR) and endoplasmic reticulum-stress (ERS) during E. multilocularis infection in mice.

MethodsE. multilocularis- and mock-infected C57BL/6 mice were subdivided six weeks after infection into vehicle and albendazole (ABZ) treated groups. Eight weeks later, liver tissue was collected to examine mRNA, microRNA (miR) and protein expression of UPR- and ERS-related genes.

ResultsE. multilocularis infection upregulated UPR- and ERS-related proteins, including ATF6, CHOP, GRP78, ERP72, H6PD and calreticulin, whilst PERK and its target eIF2 were not affected, and IRE1 and ATF4 were downregulated. ABZ treatment in E. multilocularis infected mice reversed the increased ATF6 and calreticulin protein expression, tended to reverse increased CHOP, GRP78, ERP72 and H6PD expression, and decreased ATF4 and IRE1 expression to levels seen in mock-infected mice. The expression of miR-146a-5p (downregulated by IRE1) and miR-1839-5p (exhibiting a unique target site in the IRE1 3UTR) were significantly increased in E. multilocularis infected mice, an effect reversed by ABZ treatment. Other miRs analyzed were not altered in E. multilocularis infected mice.

Conclusions and SignificanceAE causes UPR activation and ERS in mice. The E. multilocularis-induced ERS was ameliorated by ABZ treatment, indicating its effectiveness to inhibit parasite proliferation and downregulate its activity status. ABZ itself did not affect UPR in control mice. Identified miR-146a-5p and miR-1839-5p might represent biomarkers of E. multilocularis infection. Modulation of UPR and ERS, in addition to ABZ administration, could be exploited to treat E. multilocularis infection.

Author summaryAlveolar echinococcosis is a zoonotic disease caused by the fox tapeworm Echinococcus multilocularis. Treatment of this fatal disease is limited to surgical intervention, preferably radical curative surgery if possible, and the use of parasitostatic benzimidazoles. It is not yet fully understood how the parasite can remain in the hosts tissue for prolonged periods, complicating the development of therapeutic applications. This work investigated an involvement of the unfolded protein response (UPR) and endoplasmic reticulum-stress (ERS) during E. multilocularis infection and upon treatment with albendazole (ABZ) in mice. The results revealed increased expression levels of the ERS sensor ATF6 and of downstream target genes in liver tissue of E. multilocularis- compared to mock-infected mice. Additionally, H6PD, generating NADPH within the endoplasmic reticulum, and the lectin-chaperone calreticulin were increased in E. multilocularis infected liver tissue while the expression of the ERS associated genes ATF4 and IRE1 were decreased. The miR-1839-5p and miR-146-p, linked to IRE1, were elevated upon E. multilocularis infection, offering potential as novel biomarkers of alveolar echinococcosis. The observed gene expression changes were at least partially reversed by ABZ treatment. Whether modulation of UPR and ERS targets can improve the therapy of alveolar echinococcosis remains to be investigated.

category: pathology


title: In vivo identification and validation of novel potential predictors for human cardiovascular diseases

abstract: Genetics crucially contributes to cardiovascular diseases (CVDs), the global leading cause of death. Since the majority of CVDs can be prevented by early intervention there is a high demand for predictive markers. While genome wide association studies (GWAS) correlate genes and CVDs after diagnosis and provide a valuable resource for such markers, preferentially those with previously known or suspected function are addressed further. To tackle the unaddressed blind spot of understudied genes, we particularly focused on the validation of heart GWAS candidates with little or no apparent connection to cardiac function. Building on the high conservation of basic heart function and underlying genetics from fish to human we combined CRISPR/Cas9 genome editing of the orthologs of human GWAS candidates in isogenic medaka with automated high-throughput heart rate analysis. Our functional analyses of understudied human candidates uncovered a prominent fraction of heart rate associated genes from adult human patients displaying a heart rate effect in embryonic medaka already in the injected generation. Following this pipeline, we identified 16 GWAS candidates with potential diagnostic and predictive power for human CVDs.


title: Knowledge and Awareness of coronavirus disease 2019 (COVID-19) among Chinese dental students----a comparison study.

abstract:
BackgroudThis study aimed to measure the knowledge and awareness of COVID-19 among Chinese dental students during the global outbreak recently.

MethodA descriptive cross-sectional study was performed among dental students and nonmedical college students in China. All the participants were required to anonymously answer a reliable online questionnaire, which covered 3 different fields of COVID-19. Average scores of dental students (D group), including junior (JD group) and senior dental students (SD group), and nonmedical college students (N group) were compared respectively. Chi-square test and independent sample T test were taken for statistical analysis with SPSS.12.

ResultsTotally 497 questionnaires were collected, including 224 from dental students and 273 from non-medical students. The overall average score was 57{+/-}19.2. The average scores of dental students were 64.5{+/-}18. The D group had significantly higher scores on the total score, section scores, and 20 questions respectively than with the N group. No significant differences were found on 5 questions. Compared with the N group, the SD group won on all three sections while JD group failed to win on the diagnose section.

ConclusionAlthough the dental student showed good awareness regarding the clinical aspects of COVID-19 than non-medical students, there are still some weakness in the part of treatment and prevention, which need to be strengthened for better prepare during work. Besides, the low accuracy rate of lower grade dental students is also worth noting.

category: scientific communication and education


title: The SARS-CoV-2 transcriptome and the dynamics of the S gene furin cleavage site in primary human airway epithelia

abstract: The novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) caused the devastating ongoing coronavirus disease-2019 (COVID-19) pandemic which poses a great threat to global public health. The spike (S) polypeptide of SARS-CoV-2 consists of the S1 and S2 subunits and is processed by cellular proteases at the S1/S2 boundary. The inclusion of the 4 amino acids (PRRA) at the S1/S2 boundary forms a furin cleavage site (FCS), 682RRAR{downarrow}S686, distinguishing SARS-CoV-2 from its closest relative, the SARS-CoV. Various deletions surrounding the FCS have been identified in patients. When SARS-CoV-2 propagated in Vero cells, the virus acquired various deletions surrounding the FCS. In the present study, we studied the viral transcriptome in SARS-CoV-2 infected primary human airway epithelia (HAE) cultured at an air-liquid interface (ALI) with an emphasis on the viral genome stability at the S1/S2 boundary using RNA-seq. While we found overall the viral transcriptome is similar to that generated from infected Vero cells, we identified a high percentage of mutated viral genome and transcripts in HAE-ALI. Two highly frequent deletions were found at the S1/S2 boundary of the S gene: one is a deletion of 12 amino acids, 678TNSPRRAR{downarrow}SVAS689, which contains the FCS, another is a deletion of 5 amino acids, 675QTQTN679, which is two amino acids upstream of the FCS. Further studies on the dynamics of the FCS deletions in apically released virions revealed that the selective pressure for the FCS maintains the S gene stability in HAE-ALI but with exceptions, in which the FCS deletions are remained at a high rate. Thus, our study presents evidence for the role of unique properties of human airway epithelia in the dynamics of the FCS region during infection of human airways, which is donor-dependent.


title: Bronchoalveolar lavage affects thorax computed tomography of healthy and SARS-CoV-2 infected rhesus macaques (Macaca mulatta)

abstract: Medical imaging as method to assess the longitudinal process of a SARS-CoV-2 infection in non-human primates is commonly used in research settings. Bronchoalveolar lavage (BAL) is also regularly used to determine the local virus production and immune effects of SARS-CoV-2 in the lower respiratory tract. However, the potential interference of those two diagnostic modalities with each other is unknown in non-human primates. The current study investigated the effect and duration of BAL on computed tomography (CT) in both healthy and experimentally SARS-CoV-2-infected female rhesus macaques (Macaca mulatta). In addition, the effect of subsequent BALs was reviewed. Thorax CTs and BALs were obtained from four healthy animals and 11 experimentally SARS-CoV-2-infected animals. From all animals, CTs were obtained just before BAL, and 24 hours post-BAL. Additionally, from the healthy animals, CTs immediately after and four hours post-BAL were obtained. Thorax CTs were evaluated for alterations in lung density, measured in Hounsfield units, and a visual semi-quantitative scoring system. An increase in the lung density was observed on the immediately post-BAL CT but resolved within 24 hours in the healthy animals. In the infected animals, a significant difference in both the lung density and CT score was still found 24 hours after BAL. Furthermore, the differences between timepoints in CT score were increased for the second BAL. These results indicate that the effect of BAL on infected lungs is not completed within the first 24 hours. Therefore, it is of importance to acknowledge the interference between BAL and CT in rhesus macaques.

category: biophysics


title: Type-I interferon signatures in SARS-CoV-2 infected Huh7 cells

abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes Coronavirus disease 2019 (COVID-19) has caused a global health emergency. A key feature of COVID-19 is dysregulated interferon-response. Type-I interferon (IFN-I) is one of the earliest antiviral innate immune responses following viral infection and plays a significant role in the pathogenesis of SARS-CoV-2. In this study, using a proteomics-based approach, we identified that SARS-CoV-2 infection induces delayed and dysregulated IFN-I signaling in Huh7 cells. We demonstrate that SARS-CoV-2 is able to inhibit RIG-I mediated IFN-{beta} production. Our results also confirm the recent findings that IFN-I pretreatment is able to reduce susceptibility of Huh7 cells to SARS-CoV-2, but not post-treatment. Moreover, senescent Huh7 cells, in spite of showing accentuated IFN-I response were more susceptible to SARS-CoV-2 infection, and the virus effectively inhibited IFIT1 in these cells. Finally, proteomic comparison between SARS-CoV-2, SARS-CoV and MERS-CoV revealed a distinct differential regulatory signature of interferon-related proteins emphasizing that therapeutic strategies based on observations in SARS-CoV and MERS-CoV should be used with caution. Our findings provide a better understanding of SARS-CoV-2 regulation of cellular interferon response and a perspective on its use as a treatment. Investigation of different interferon stimulated genes and their role in inhibition of SARS-CoV-2 pathogenesis may direct novel antiviral strategies.


title: Does Food Insecurity exist among Farm households? Evidence from Ghana

abstract: Household food security exists when households have physical, social and economic access to sufficient, safe and nutritious food at all times that meets their dietary needs and food preferences for an active and healthy life. Food security remains a serious challenge for many households in Ghana and the situation is even more prevalent among smallholder farmers. Using data collected from 2,603 farm households across Ghana and employing an ordered probit model the determinants of food security among farm households were assessed. The food security indicator-Food Consumption Score (FCS) which combines diet diversity, frequency of consumption and relative nutritional importance of different food groups was used for the analysis. Results indicated that farm households (76%) across Ghana were within the acceptable household food consumption groups. Nonetheless, 19% and 6% of farm households respectively were within the borderline and poor food consumption groups respectively. Further analysis revealed the determinants of food security to include experience, gender, improved variety adoption, access to credit and location. The suggestion is that government and private institutions should create an enabling environment to enhancing production capacities, economic and social resilience to improve on food security and nutrition.


title: In-planta Gene Targeting in Barley using Cas9, with and without Geminiviral Replicons

abstract: Advances in the use of RNA-guided Cas9-based genome editing in plants have been rapid over the last few years. A desirable application of genome editing is gene targeting (GT), as it allows a wide range of precise modifications, however this remains inefficient especially in key crop species. Here we describe successful, heritable gene targeting in barley using an in-planta strategy but fail to achieve the same using a wheat dwarf virus replicon to increase copy number of the repair template. Without the replicon, we were able to delete 150bp of the coding sequence of our target gene whilst simultaneously fusing in-frame mCherry in its place. Starting from 14 original transgenic plants, two plants appeared to have the required gene targeting event. From one of these T0 plants, three independent gene targeting events were identified, two of which were heritable. When the replicon was included, 39 T0 plants were produced and shown to have high copy numbers of the repair template. However, none of the 17 lines screened in T1 gave rise to significant or heritable gene targeting events despite screening twice the number of plants in T1 compared to the non-replicon strategy. Investigation indicated that high copy numbers of repair template created by the replicon approach cause false positive PCR results which are indistinguishable at the sequence level to true GT events in junction PCR screens widely used in GT studies. In the successful non-replicon approach, heritable gene targeting events were obtained in T1 and subsequently the T-DNA was found to be linked to the targeted locus. Thus, physical proximity of target and donor sites may be a factor in successful gene targeting.


title: New lessons on TDP-43 from the killifish N. furzeri

abstract: Frontotemporal dementia and amyotrophic lateral sclerosis are fatal and incurable neurodegenerative diseases linked to the pathological aggregation of the TDP-43 protein. This is an essential DNA/RNA binding protein involved in transcription regulation, pre-RNA processing and RNA transport. Having suitable animal models to study the mechanisms of TDP-43 aggregation is crucial to develop treatments against disease. We have previously demonstrated that the killifish Nothobranchius furzeri offers the unique advantage as a model system that it is an organism with compressed lifespan and a conserved ageing phenotype that develops within months, making this organism the available shortest-lived vertebrate with a clear ageing phenotype. Here, we show that the two paralogs of TDP-43 from the killifish N. furzeri share high sequence homology with the human protein and recapitulate its cellular and biophysical behaviour. We prove that, during ageing, N. furzeri TDP-43 spontaneously forms insoluble intracellular TDP-43 aggregates that have amyloid characteristics and colocalize with the stress granule core protein G3BP. Our results propose this organism as a valuable model of TDP-43-related pathologies and show that even minute differences between the human and N. furzeri proteins may help to shed new light onto the role of TDP-43 in RNA recognition and granule formation.

category: neuroscience


title: ASIGNTF: AGNOSTIC SIGNATURE USING NTF: A UNIVERSAL AGNOSTIC STRATEGY TO ESTIMATE CELL-TYPES ABUNDANCE FROM TRANSCRIPTOMIC DATASETS

abstract:
AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSBackgroundC_ST_ABSMolecular signatures for deconvolution of immune cell types have been proposed, based on a methodology that relies on the biological classification of the cell types being studied. When working with less known biological material, a data-driven approach is needed to uncover the underlying classes and construct ad hoc signatures.

ResultsWe introduce a new approach, ASigNTF: Agnostic Signature using Non-negative Tensor Factorization, to perform the deconvolution of cell types from transcriptomics data (RNAseq and microarray). ASigNTF, which is based on two complementary statistical/mathematical tools: non-negative tensor factorization (for dimensionality reduction) and the Herfindahl-Hirschman index (for signature selection), can be applied to any type of tissue as long as transcriptomic data on isolated cells is available. As a direct result of the new method, we propose two new signatures for the deconvolution of immune cell types, one consisting of a relatively small set of 415 genes, which is more compatible with microarray platforms, and a larger set of 915 genes. Using external datasets, our two signatures outperform the CIBERSORT LM22 signature in deconvolution of RNA-seq data. Our signature with 415 genes allows to recognize a larger number of cell types compared to the ABIS microarray signature.

ConclusionsThe paper proposes a new method, ASigNTF; applies the method, and also provides a software implementation that allows to identify molecular signatures for deconvolution of complex tissues and specifically up to 16 immune cell types from micro-array or RNA-seq data.

HO_SCPLOWIGHLIGHTSC_SCPLOWO_LISeveral signatures of immune cell types have been proposed, which follow a methodology deeply rooted in the known biological classification of the investigated cell types.
C_LIO_LIWhen working with less known biological material, a more agnostic, data-driven approach is required to uncover the underlying classes and construct ad hoc signatures.
C_LIO_LIWe present ASigNTF, a new agnostic approach to cell type classification and signature selection supported by an application software.
C_LIO_LIWe discuss the results of benchmarking our proposed signatures, ABIS-seq and CIBERSORT on external datasets.
C_LI


title: JNK activation in TA and EDL muscle is load-dependent in rats receiving identical excitation patterns

abstract:
ABSTACTO_ST_ABSAimC_ST_ABSAs the excitation-contraction coupling is inseparable during voluntary exercise, the relative contribution of the mechanical and neural input is poorly understood. Herein, we use a rat in-vivo strength training setup with an electrically induced standardized excitation pattern previously shown to lead to a load-dependent increase in myonuclear number and hypertrophy, to study acute effects of load per se on molecular signalling.

MethodsAnaesthetized rats were subjected to unliteral identical electrically-paced contractions of the TA and EDL muscles under a high or low load for a duration of 2, 10 or 28-minutes. Muscle soluble proteins were extracted, and abundance and specific phosphorylations of FAK, mTOR, p70S6K and JNK were measured. Effects of exercise, load, muscle and exercise duration were assessed.

ResultsSpecific phosphorylation of S2448-mTOR, T421/S424-p70S6K and T183/Y185-JNK was increased after 28-minutes of exercise under the high- and low-load protocol. Elevated phosphorylation of mTOR and JNK was detectable already after 2 and 10 minutes of exercise, respectively, but greatest after 28-minutes of exercise. T183/Y185-JNK and S2448-mTOR demonstrated a load-dependent increase in phosphorylation in the exercised muscles that for mTOR depended on muscle type. The abundance of all four kinases was higher in TA compared to EDL muscle. FAK and JNK abundance was reduced after 28 minutes of exercise in both the exercised and control muscle.

ConclusionThe current study shows that JNK and mTOR activation is load-driven, and together with muscle-type specific mTOR and p70S6K effects it may drive muscle-type specific exercise and load-responses.

category: physiology


title: Pulsed Focal ultrasound as a non-invasive method to deliver exosomes in the brain/stroke

abstract: Exosomes, a component of extracellular vesicles are shown to carry important small RNAs, mRNAs, protein, and bioactive lipid from parent cells and are found in most biological fluids. Investigators have demonstrated the importance of mesenchymal stem cells (MSCs) derived exosomes in repairing stroke lesions. However, exosomes from endothelial progenitor cells (EPCs) have not been tested in any stroke model nor has there been an evaluation of whether these exosomes target/home to areas of pathology. Targeted delivery of IV administered exosomes has been a great challenge and a targeted delivery system is lacking to deliver naive (unmodified) exosomes from EPCs to the site of interest. Pulsed focused ultrasound (pFUS) is being used for therapeutic and experimental purposes. There has not been any report showing the use of pulsed low-intensity pFUS to deliver exosomes to the site of interest in models of stroke. In this proof of principle study, we have shown different parameters of pFUS to deliver exosomes in the intact and stroke brain with or without IV administration of nanobubbles. The study results showed that administration of nanobubbles is detrimental to the brain structures (micro bleeding and white matter destruction) at peak negative pressure (PNP) of >0.25 MPa, despite enhanced delivery of IV administered exosomes. However, without nanobubbles, pFUS PNP = 1 to 2 MPa enhances the delivery of exosomes in the stroke area without altering the brain structures.


title: Functional traits of carabid beetles reveal seasonal variation in community assembly in annual crops

abstract:
O_LITrait-based community assembly studies have mostly been addressed along spatial gradients, and do not consider explicitly a fundamental dimension governing community assembly, the time. Nevertheless, such consideration seems particularly necessary in systems in which organisms have to face regular disturbances and rapid changes in vegetation phenology, such as in intensively managed farmlands.
C_LIO_LIIn this study, we aimed at understanding how the functional diversity of carabid beetle communities varied across the growing season in response to crop type. We tested three alternative hypotheses on mechanisms underlying the community assembly.
C_LIO_LIWe used data from a long-term monitoring conducted over nine years in an intensively-managed farmland in central western France, in a total of 625 fields. First, we measured morphological traits related to body size, dispersal mode, and resource acquisition on the 13 dominant carabid species (> 85 % of all trapped individuals) and identified three independent dimensions of functional specialization within our species pool along axes of a PCA and highlighted key traits for community assembly. Second, we evaluated the community assembly temporal dynamics and the impact of habitat filtering and niche differentiation in the different crop types with time, using linear mixed-effects models.
C_LIO_LIWe showed that functional species assembly of carabid beetle communities occurring in crop fields varies importantly intra-annually, with strong variations in these dynamics depending on crop type and crop phenology. Each crop acted as a filter on carabid communities for body size and resource-acquisition traits, and functional differentiation between crops increased with time. We did not find any evidence of habitat filtering on traits related to dispersal mode.
C_LIO_LIOur results emphasize the major role of crop phenology but also disturbances involved by agricultural practices such as crop harvesting on changes in community assembly, likely due to seasonal and inter-annual redistributions of species in agricultural landscapes in response to such changes. The temporal dimension cannot be ignored to understand the assembly of local carabid communities in farmlands.
C_LI

category: ecology


title: Nitroxoline as a promising alternative drug for the treatment of Lyme disease based on an in-vitro study

abstract: Lyme disease (LD) is the most common vector-borne disease in USA and Europe and is caused by Borrelia burgdorferi. Despite proper treatment, approximately one fifth of patients will develop post-treatment LD syndrome (PTLDS), a condition which is poorly understood. One of the possible causes is thought to be due to persister forms of B. burgdorferi that are not effectively killed by the current Lyme antibiotics. In this study, we evaluated nitroxoline, an antibiotic used to treat urinary tract infections, for its activity against a stationary-phase culture enriched with persister forms of B. burgdorferi. Nitroxoline was found to be equivalent in activity against B. burgdorferi to cefuroxime (standard Lyme antibiotic) in different experiments. Moreover, we found that the three-drug combination cefuroxime + nitroxoline + clarithromycin eradicated 98.3% of stationary phase bacteria in the drug-exposure experiment and prevented the regrowth in the subculture study after drug exposure, as well as two-drug combinations cefuroxime + nitroxoline and clarithromycin + nitroxoline. These drug combinations should be further evaluated in a LD mouse model to assess if eradication of persister forms of B. burgdorferi in-vivo is possible and if so, whether nitroxoline could be repurposed as an alternative drug for the treatment of LD.

category: microbiology