title: The trypanosome UDP-glucose pyrophosphorylase is imported by piggybacking into glycosomes where unconventional sugar nucleotide synthesis takes place

abstract:
Glycosomes are peroxisome-related organelles of trypanosomatid parasites containing metabolic pathways usually present in the cytosol of other eukaryotes, such as glycolysis and biosynthesis of sugar nucleotides. UDP-glucose pyrophosphorylase (UGP), the enzyme responsible for the synthesis of the sugar nucleotide UDP-glucose, is localised in the cytosol and glycosomes of the bloodstream and procyclic trypanosomes, despite the absence of any known peroxisomal targeting signal (PTS1 and PTS2). The questions we addressed here are (i) is the unusual glycosomal biosynthetic pathway of sugar nucleotide functional and (ii) how the PTS-free UGP is imported into glycosomes? We showed that UGP is imported into glycosomes by piggybacking on the glycosomal PTS1-containing phosphoenolpyruvate carboxykinase (PEPCK) and identified the domains involved in the UGP/PEPCK interaction. Proximity ligation assays revealed that this interaction occurs in 3-10% of glycosomes, suggesting that these correspond to organelles competent for protein import. We also showed that UGP is essential for growth of trypanosomes and that both the glycosomal and cytosolic metabolic pathways involving UGP are functional, since the lethality of the knock-down UGP mutant cell line (RNAiUGP) was rescued by expressing a recoded UGP in the organelle (RNAiUGP/EXPrUGP-GPDH). Our conclusion was supported by targeted metabolomic analyses (IC-HRMS) showing that UDP-glucose is no longer detectable in the RNAiUGP mutant, while it is still produced in cells expressing UGP exclusively in the cytosol (PEPCK null mutant) or glycosomes (RNAiUGP/EXPrUGP-GPDH). Trypanosomatids are the only known organisms to have selected functional peroxisomal (glycosomal) sugar nucleotide biosynthetic pathways in addition to the canonical cytosolic ones.

ImportanceUnusual compartmentalization of metabolic pathways within organelles is one of the most enigmatic features of trypanosomatids. These unicellular eukaryotes are the only organisms that sequestered glycolysis inside peroxisomes (glycosomes), although the selective advantage of this compartmentalization is still not clear. Trypanosomatids are also unique for the glycosomal localisation of enzymes of the sugar nucleotide biosynthetic pathways, which are also present in the cytosol. Here we showed that the cytosolic and glycosomal pathways are functional. Like in all other eukaryotes, the cytosolic pathways feed glycosylation reactions, however the role of the duplicated glycosomal pathways is currently unknown. We also showed that one of these enzymes (UGP) is imported into glycosomes by piggybacking on another glycosomal enzyme (PEPCK), which are not functionally related. The UGP/PEPCK association is unique since all piggybacking examples reported to date involve functionally related interacting partners, which broadens the possible combinations of carrier-cargo proteins being imported as hetero-oligomers.

category: microbiology


title: Host-virus chimeric events in SARS-CoV2 infected cells are infrequent and artifactual

abstract: Pathogenic mechanisms underlying severe SARS-CoV2 infection remain largely unelucidated. High throughput sequencing technologies that capture genome and transcriptome information are key approaches to gain detailed mechanistic insights from infected cells. These techniques readily detect both pathogen and host-derived sequences, providing a means of studying host-pathogen interactions. Recent studies have reported the presence of host-virus chimeric (HVC) RNA in RNA-seq data from SARS-CoV2 infected cells and interpreted these findings as evidence of viral integration in the human genome as a potential pathogenic mechanism. Since SARS-CoV2 is a positive sense RNA virus that replicates in the cytoplasm it does not have a nuclear phase in its life cycle, it is biologically unlikely to be in a location where splicing events could result in genome integration. Here, we investigated the biological authenticity of HVC events. In contrast to true biological events such as mRNA splicing and genome rearrangement events, which generate reproducible chimeric sequencing fragments across different biological isolates, we found that HVC events across >100 RNA-seq libraries from patients with COVID-19 and infected cell lines, were highly irreproducible. RNA-seq library preparation is inherently error-prone due to random template switching during reverse transcription of RNA to cDNA. By counting chimeric events observed when constructing an RNA-seq library from human RNA and spike-in RNA from an unrelated species, such as fruit-fly, we estimated that ~1% of RNA-seq reads are artifactually chimeric. In SARS-CoV2 RNA-seq we found that the frequency of HVC events was, in fact, not greater than this background "noise". Finally, we developed a novel experimental approach to enrich SARS-CoV2 sequences from bulk RNA of infected cells. This method enriched viral sequences but did not enrich for HVC events, suggesting that the majority of HVC events are, in all likelihood, artifacts of library construction. In conclusion, our findings indicate that HVC events observed in RNA-sequencing libraries from SARS-CoV2 infected cells are extremely rare and are likely artifacts arising from either random template switching of reverse-transcriptase and/or sequence alignment errors. Therefore, the observed HVC events do not support SARS-CoV2 fusion to cellular genes and/or integration into human genomes.


title: CK2 phosphorylation of human papillomavirus 16 E2 on serine 23 promotes interaction with TopBP1 and is critical for E2 plasmid retention function

abstract:
During the human papillomavirus 16 (HPV16) life cycle, the E2 protein interacts with host factors to regulate viral transcription, replication and genome segregation/retention. Our understanding of host partner proteins and their roles in E2 functions remains incomplete. Here, we demonstrate that CK2 phosphorylation of E2 on serine 23 promotes interaction with TopBP1 in vitro and in vivo, and that E2 is phosphorylated on this residue during the HPV16 life cycle. We investigated the consequences of mutating serine 23 on E2 functions. E2-S23A activates and represses transcription identically to E2-WT (wild-type), and E2-S23A is as efficient as E2-WT in transient replication assays. However, E2-S23A has compromised interaction with mitotic chromatin when compared with E2-WT. In E2-WT cells, both E2 and TopBP1 levels increase during mitosis when compared with vector control cells. In E2-S23A cells, neither E2 nor TopBP1 levels increase during mitosis. We next tested whether this difference in E2-S23A levels during mitosis disrupts E2 plasmid retention function. We developed a novel plasmid retention assay and demonstrate that E2-S23A is deficient in plasmid retention when compared with E2-WT. siRNA targeted knockdown of TopBP1 abrogates E2-WT plasmid retention function. Introduction of the S23A mutation into the HPV16 genome resulted in delayed immortalization of human foreskin keratinocytes (HFK) and higher episomal viral genome copy number in resulting established HFK. Overall, our results demonstrate that CK2 phosphorylation of E2 on serine 23 promotes interaction with TopBP1, which is critical for E2 plasmid retention function and in HPV16 immortalization of keratinocytes.

ImportanceHuman papillomaviruses are causative agents in around 5% of all cancers, with no specific anti-viral therapeutics available for treating infections or resultant cancers. In this report, we demonstrate that phosphorylation of HPV16 E2 by CK2 promotes formation of a complex formation with the cellular protein TopBP1 in vitro and in vivo. This complex results in stabilization of E2 during mitosis and mediates plasmid retention by E2. This function promotes the partitioning of viral genomes into the nuclei of daughter cells following mitosis. We demonstrate that CK2 phosphorylates E2 on serine 23 in vivo, and that CK2 inhibitors disrupt the E2-TopBP1 complex. Mutation of E2 serine 23 to alanine disrupts the HPV16 life cycle, demonstrating a critical function for this residue. Together, our results suggest that CK2 inhibitors may disrupt the E2-TopBP1 dependent HPV16 life cycle and potentially kill HPV16 positive cancers, which lays a molecular foundation to develop novel therapeutic approaches for combating HPV16 disease.

category: molecular biology


title: PEAK3 pseudokinase represents a pro-migratory and -invasive signalling scaffold

abstract: The PEAK family of pseudokinases comprises PEAK1 and PEAK2 as well as the recently-identified PEAK3. PEAK1/2 play fundamental roles in regulating tyrosine kinase signal output and oncogenesis, while PEAK3 remains poorly-characterized. Here, we demonstrate that PEAK3 undergoes homotypic association as well as heterotypic interaction with PEAK1/2. PEAK3 also recruits ASAP1/2, Cbl and PYK2 and the adaptors Grb2 and CrkII, with binding dependent on PEAK3 dimerization. PEAK3 tyrosine phosphorylation on Y24 is also dependent on dimerization as well as Src family kinase activity, and interestingly, is decreased via PTPN12 in response to EGF treatment. Y24 phosphorylation is required for binding of Grb2 and ASAP1. Overexpression of PEAK3 in MDA-MB-231 breast cancer cells enhanced cell elongation and cell motility, while knockdown of endogenous PEAK3 decreased cell migration. In addition, overexpression of PEAK3 in PEAK1/2 compound knock-out MCF-10A breast epithelial cells enhanced acinar growth and invasion in 3D culture, with the latter phenotype dependent on PEAK3 tyrosine phosphorylation and binding of Grb2 and ASAP1. These findings characterize PEAK3 as an integral member of the PEAK family with scaffolding roles that promote cell proliferation, migration and invasion.

category: cancer biology


title: CO2 supply modulates lipid remodelling, photosynthetic and respiratory activities in Chlorella species

abstract:
Microalgae represent potential solutions to reduce the atmospheric CO2 level through photosynthesis. To boost CO2 fixation by microalgae it is essential to understand physiologic and metabolic responses at the base of CO2 assimilation and carbon flow. In this work two Trebouxiophyceae species, Chlorella sorokiniana and Chlorella vulgaris, were investigated for their metabolic responses to high and low CO2 (air level) availability. High CO2 availability resulted in an increase in biomass accumulation in both species but with a different chloroplast and mitochondrial responses. In C. sorokiniana we observed increased polar lipids and protein amount and a balanced NADPH redox state and a similar total respiration in the two conditions analysed. In contrast, in C. vulgaris high CO2 level caused an increase in TAG accumulation and a higher NADPH consumption suggesting a CO2 dependent increase of reducing power consumption in the chloroplast, which in turn influences the redox state of the mitochondria by lowering total dark respiration. Several rearrangements of the photosynthetic machinery were observed in both species, which differ from those described for the model organism Chlamydomonas reinhardtii. In the case of C. reinhardtii, adaptation of the photosynthetic apparatus to different CO2 availability relies on the translational repressor NAB1. NAB1 homologous protein could be identified only in C. vulgaris but lacked the regulation mechanisms previously described in C. reinhardtii. These findings highlight that the acclimation strategies to cope with a fluctuating inorganic carbon supply are diverse among green microalgae and point to new biotechnological strategies to boost CO2 fixation.

One sentence summaryHigh/low CO2 availability induces cell responses as lipids remodelling, adaptations of the photosynthetic apparatus and modulation of mitochondrial respiration not conserved among green algae

category: plant biology


title: BREVIPEDICELLUS and ERECTA mediate expression of AtPRX17 in preventing Arabidopsis callus retardation and browning

abstract:
Efficient in vitro callus generation is fundamental to tissue culture propagation, a process required for plant regeneration and transgenic breeding for desired phenotypes. Identifying genes and regulatory elements that prevent callus retardation and browning is essential to facilitate the development of vitro callus systems. Here we show that BREVIPEDICELLUS (BP) and ERECTA (ER) pathways in Arabidopsis callus are converged to prevent callus browning and positively regulate an isoperoxidase gene AtPRX17 expression in the rapid growth callus. Loss of functions in both BP and ER resulted in markedly increasing callus browning. Transgenic lines with pro35S::AtPRX17 in the bp-5 er105 double mutant background fully rescued this phenotypic abnormality. Using plant in vitro DNA-binding assays, we observed that BP protein bound directly to the upstream sequence of AtPRX17 to promote its transcription during callus growth. ER is a universally presenting factor required for cell proliferation and growth, we show that ER positively regulates expression of a transcription factor WRKY6, which also directly binds to an additional site of the AtPRX17 promoter for its high expression. Our data reveals an important molecular mechanism in regulating expression of peroxidase isozyme to reduce Arabidopsis callus browning.

HighlightBREVIPEDICELLUS and ERECTA are involved in regulating Arabidopsis callus browning by controlling expression of AtPRX17.


title: Grasp aperture corrections in reach-to-grasp movements do not alter size perception

abstract: When grasping an object, the opening between the fingertips (grip aperture) scales with the size of the object. If an object changes in size, the grip aperture has to be corrected. In this study, it was investigated whether such corrections would influence the perceived size of objects. The grasping plan was manipulated with a preview of the object, after which participants initiated their reaching movement without vision. In a minority of the grasps, the object changed in size after the preview and participants had to adjust their grasping movement. Visual feedback was manipulated in two experiments. In experiment 1, vision was restored during reach and both visual and haptic information was available to correct the grasp and lift the object. In experiment 2, no visual information was provided during the movement and grasps could only be corrected using haptic information. Participants made reach-to-grasp movements towards two objects and compared these in size. Results showed that participants adjusted their grasp to a change in object size from preview to grasped object in both experiments. However, a change in object size did not bias the perception of object size or alter discrimination performance. In experiment 2, a small perceptual bias was found when objects changed from large to small. However, this bias was much smaller than the difference that could be discriminated and could not be considered meaningful. Therefore, it can be concluded that the planning and execution of reach-to-grasp movements do not affect the perception of object size.

category: neuroscience


title: Development and validation of a miniaturized host range screening assay for bacteriophages

abstract: Antimicrobial resistance is a global health crisis, partly contributed by inappropriate use of antibiotics. The increasing emergence of multidrug resistant infections has led to the resurgent interest in bacteriophages as an alternative treatment. Current procedures assessing susceptibility and breadth of host range to bacteriophage are conducted using large-scale manual processes that are labor-intensive. The aim here was to establish and validate a scaled down methodology for high-throughput screening in order to reduce procedural footprint. Bacteriophages were isolated from wastewater samples and screened for specificity against 29 clinical Pseudomonas aeruginosa isolates and PA01 using a spot test (2 L/ drop). Host range assessment was performed on four representative P. aeruginosa isolates using both double agar overlay assay on petri dishes and 24-well culture plates. The breadth of host range of bacteriophages that exhibited lytic activity on P. aeruginosa isolates were corroborated between the current standard practice of whole plate phage assay and 24-well phage assay. The high correlation achieved in this study confirms miniaturization as the first step in future automation that could test phage diversity and efficacy as antimicrobials.


title: Analysis of the blood microbiome in a porcine model of fecal-induced peritonitis

abstract:
BackgroundRecent studies have proposed the existence of a blood microbiome, even in the healthy host. However, we do not know how the blood microbiome changes when a bloodstream infection (BSI) occurs. Here, we analyzed the dynamics of the blood microbiome in a porcine model of polymicrobial bacteremia induced by fecal peritonitis. Serial blood samples were taken over 12 hours post-induction of fecal peritonitis, and BSI was validated by conventional blood culture and assessment of clinical symptoms.

ResultsThe bacterial populations in the blood microbiome were retained throughout the experimental period. However, there were significant taxonomic differences between the profile in the fecal and blood microbiomes, reflecting tropism for the blood environment. We also confirmed that the microbiota we detected was not contaminated by low mass bacteria in the bloodstream. However, at the same time, we noted a slight increase in Bacteroidetes, which is a major component of the gut microbiome, as sepsis developed. Comparison of the functional pathways in the blood and fecal microbiomes revealed upregulation of pathways involved in environmental interactions, and downregulation of those related to cell proliferation, in the former. Based on the enriched biological pathways, we concluded that communication and stress management pathways are essential for the survival of the blood microbiome under harsh conditions.

ConclusionThis study suggests that the microbiota can be stably retained in the bloodstream over time. Although further investigation in humans is required, we suggest that the blood microbiome may be another factor to be considered in the context of BSI and subsequent sepsis.


title: West Nile virus in crocodiles and mosquitoes in Zimbabwe

abstract: We detected, for the first time, West Nile virus lineages 1 and 2 in Zimbabwe in mosquitoes and crocodile tissue samples, including fluid from egg waste. Our results provide evidence of WNV circulation in Zimbabwe, suggesting that an evaluation of the risk to humans and susceptible animals should be considered.


title: Inferring Ecosystem Networks as Information Flows

abstract: The detection of causal interactions is of great importance when inferring complex ecosystem functional and structural networks for basic and applied research. Convergent cross mapping (CCM) based on nonlinear state-space reconstruction made substantial progress about network inference by measuring how well historical values of one variable can reliably estimate states of other variables. Here we investigate the ability of a developed Optimal Information Flow (OIF) ecosystem model to infer bidirectional causality and compare that to CCM. Results from synthetic datasets generated by a simple predator-prey model, data of a real-world sardine-anchovy-temperature system and of a multispecies fish ecosystem highlight that the proposed OIF performs better than CCM to predict population and community patterns. Specifically, OIF provides a larger gradient of inferred interactions, higher point-value accuracy and smaller fluctuations of interactions and -diversity including their characteristic time delays. We propose an optimal threshold on inferred interactions that maximize accuracy in predicting fluctuations of effective -diversity, defined as the count of model-inferred interacting species. Overall OIF outperforms all other models in assessing predictive causality (also in terms of computational complexity) due to the explicit consideration of synchronization, divergence and diversity of events that define model sensitivity, uncertainty and complexity. Thus, OIF offers a broad ecological information by extracting predictive causal networks of complex ecosystems from time-series data in the space-time continuum. The accurate inference of species interactions at any biological scale of organization is highly valuable because it allows to predict biodiversity changes, for instance as a function of climate and other anthropogenic stressors. This has practical implications for defining optimal ecosystem management and design, such as fish stock prioritization and delineation of marine protected areas based on derived collective multispecies assembly. OIF can be applied to any complex system and used for model evaluation and design where causality should be considered as non-linear predictability of diverse events of populations or communities.

category: ecology


title: Heavy-tailed abundance distributions from stochastic Lotka-Volterra models

abstract: Microbial communities found in nature are composed of many rare species and few abundant ones, as reflected by their heavy-tailed abundance distributions. How a large number of species can coexist in those complex communities and why they are dominated by rare species is still not fully understood. We show how heavy-tailed distributions arise as an emergent property from large communities with many interacting species in population-level models. To do so we rely on stochastic logistic and generalized Lotka-Volterra models for which we introduce a global maximal capacity. This maximal capacity accounts for the fact that communities are limited by available resources and space. In a parallel  ad-hoc approach, we obtain heavy-tailed abundance distributions from non-interacting models through specific distributions of the parameters. We expect both mechanisms, interactions between many species and specific parameter distributions, to be relevant to explain the observed heavy tails.


title: Light and noise pollution impacts specialist wildlife species disproportionately

abstract: Global expansion of lighting and noise pollution alters how animals receive and interpret environmental cues. Yet we lack a cross-taxon understanding of how animal traits influence species vulnerability to this growing phenomenon. This knowledge is needed to improve the design and implementation of policies that mitigate or reduce sensory pollutants. We present results from an expert knowledge survey that quantified the relative influence of several ecological, anatomical, and physiological traits on the vulnerability of terrestrial vertebrates to elevated levels of anthropogenic lighting and noise. Our findings, based on 280 responses, highlight the increasing recognition among experts that sensory pollutants are important to consider in management and conservation decisions. Participant responses show mounting threats to species with narrow niches; especially habitat specialists, nocturnal species, and those with the greatest ability to differentiate environmental visual and auditory cues. Our results call attention to the threat specialist species face and provide a generalizable understanding of which species require additional considerations when developing conservation policies and mitigation strategies in a world altered by expanding sensory pollutant footprints. We provide a step-by-step example for translating these results to on-the-ground conservation planning using two species as case studies.


title: Roadkill islands: carnivore extinction shifts seasonal use of roadside carrion by generalist avian scavenger

abstract:
O_LIGlobal road networks facilitate habitat modification and are integral to human expansion. Many animals, particularly scavengers, use roads as they provide a reliable source of food, such as carrion left after vehicle collisions. Tasmania is often cited as the  roadkill capital of Australia, with the isolated offshore islands in the Bass Strait experiencing similar, if not higher, levels of roadkill. However, native mammalian predators on the islands are extirpated, meaning the remaining scavengers are likely to experience lower interference competition.
C_LIO_LIIn this study, we use a naturally occurring experiment to examine how the loss of mammalian carnivores within a community impacts roadside foraging behaviour by avian scavengers.
C_LIO_LIWe monitored the locations of roadkill and forest ravens (Corvus tasmanicus), an abundant scavenger species, on eight road transects across the Tasmanian mainland (high scavenging competition) and the Bass Strait islands (low scavenging competition). We represented raven observations as one-dimensional point patterns, using hierarchical Bayesian models to investigate the dependence of raven spatial intensity on habitat, season, distance to roadkill and route location.
C_LIO_LIWe found that roadkill carcasses were a strong predictor of raven presence along road networks. The effect of roadkill was amplified on roads on the Bass Strait islands, where roadside carrion was a predictor of raven presence across the entire year. In contrast, ravens were more often associated with roadkill on Tasmanian mainland roads in the autumn, when other resources were low. This suggests that in the absence of competing mammalian scavengers, ravens choose to feed on roadside carrion throughout the year, even in seasons when other resources are available. This low interference competition could be disproportionately benefiting forest ravens, leading to augmented raven populations and changes to the vertebrate community structure.
C_LIO_LIOur study provides evidence that scavengers modify their behaviour in response to reduced scavenger species diversity, potentially triggering trophic shifts and highlighting the importance of conserving or reintroducing carnivores within ecosystems.
C_LI


title: A Multiple Regression Assessment of the Biomineral Urease Activity from Urine Drainpipes of California Rest Areas

abstract: Clogging and odor is strongly associated with ureolytic biomineralization in waterless and low-flow urinal drainage systems in high usage settings. These blockages continue to hinder widespread waterless and low-flow urinal adoption due to subsequent high maintenance requirements and hygiene concerns. Through field observations, hypothesis testing, and multiple regression analysis, this study attempts to characterize, for the first time, the ureolytic activity of the biomineralization found in alternative technologies located at 9 State-owned restrooms. Multiple regression analysis (n = 55, df = 4, R2 = 0.665) suggests that intrasystem sampling location [Formula], annual users per rest area [Formula], and the organic/inorganic mass fraction [Formula], are statistically significant influencers of the ureolytic activity of biomineral samples (p < 0.05). Conversely, ureC gene abundance (p = 0.551), urinal type (p = 0.521) and sampling season (p = 0.956) are not significant predictors of biomineral ureolytic activity. We conclude that high concentrations of the urease alpha subunit, ureC, which can be interpreted as proxy measure of a strong, potentially ureolytic community, does not necessarily mean that the gene is being expressed. Future studies should assess ureC transcriptional activity to measure gene expression rather than gene abundance to assess the relationship between environmental conditions, their role in transcription, and urease activities. In sum, this study presents a method to characterize biomineral ureolysis and establishes baseline values for future ureolytic inhibition treatment studies that seek to improve the usability of urine collection and related source separation technologies.


title: ClusterMap: multi-scale clustering analysis of spatial gene expression

abstract: Quantifying RNAs in their spatial context is crucial to understanding gene expression and regulation in complex tissues. In situ transcriptomic methods generate spatially resolved RNA profiles in intact tissues. However, there is a lack of a unified computational framework for integrative analysis of in situ transcriptomic data. Here, we present an unsupervised and annotation-free framework, termed ClusterMap, which incorporates physical proximity and gene identity of RNAs, formulates the task as a point pattern analysis problem, and thus defines biologically meaningful structures and groups. Specifically, ClusterMap precisely clusters RNAs into subcellular structures, cell bodies, and tissue regions in both two- and three-dimensional space, and consistently performs on diverse tissue types, including mouse brain, placenta, gut, and human cardiac organoids. We demonstrate ClusterMap to be broadly applicable to various in situ transcriptomic measurements to uncover gene expression patterns, cell-cell interactions, and tissue organization principles from high-dimensional transcriptomic images.

category: genomics


title: Effects of early geometric confinement on the transcriptomic profile of human cerebral organoids

abstract:
BackgroundBiophysical factors such as shape and mechanical forces are known to play crucial roles in stem cell differentiation, embryogenesis and neurodevelopment. However, the complexity and experimental challenges capturing such early stages of development, and ethical concerns associated with human embryo and fetal research, limit our understanding of how these factors affect human brain organogenesis. Human cerebral organoids (hCO) are attractive models due to their ability to model important brain regions and transcriptomics of early in vivo brain development. Furthermore, they provide three-dimensional environments that better mimic the in vivo environment. To date, they have been used to understand the effects of genetics and soluble factors on neurodevelopment. Establishing links between spatial factors and hCO development will require the development of new approaches.

ResultsHere, we investigated the effects of early geometric confinements on transcriptomic changes during hCO differentiation. Using a custom and tunable agarose microwell platform we generated embryoid bodies (EB) of diverse shapes and then further differentiated those EBs to whole brain hCOs. Our results showed that the microwells did not have negative gross impacts on the ability of the hCOs to differentiate generally towards neural fates, and there were clear shape dependent effects on neural lineage specification. In particular, we observed that non-spherical shapes showed signs of altered neurodevelopmental kinetics and favored the development of medial ganglionic eminence-associated brain regions and cell types over cortical regions.

ConclusionsThe findings presented here suggest a role for spatial factors in brain region specification during hCO development. Understanding these spatial patterning factors will not only improve understanding of in vivo development and differentiation, but also provide important handles with which to advance and improve control over human model systems for in vitro applications.

category: bioengineering


title: Deep Learning-Based Approaches for Decoding Motor Intent from Peripheral Nerve Signals

abstract: The ultimate goal of an upper-limb neuroprosthesis is to achieve dexterous and intuitive control of individual fingers. Previous literature shows that deep learning (DL) is an effective tool to decode the motor intent from neural signals obtained from different parts of the nervous system. However, it still requires complicated deep neural networks that are inefficient and not feasible to work in real-time. Here we investigate different approaches to enhance the efficiency of the DL-based motor decoding paradigm. First, a comprehensive collection of feature extraction techniques is applied to reduce the input data dimensionality. Next, we investigate two different strategies for deploying DL models: a one-step (1S) approach when big input data are available and a two-step (2S) when input data are limited. With the 1S approach, a single regression stage predicts the trajectories of all fingers. With the 2S approach, a classification stage identifies the fingers in motion, followed by a regression stage that predicts those active digits trajectories. The addition of feature extraction substantially lowers the motor decoders complexity, making it feasible for translation to a real-time paradigm. The 1S approach using a recurrent neural network (RNN) generally gives better prediction results than all the ML algorithms with mean squared error (MSE) ranges from 10-3 to 10-4 for all finger while variance accounted for (VAF) scores are above 0.8 for the most degree of freedom (DOF). This result reaffirms that DL is more advantageous than classic ML methods for handling a large dataset. However, when training on a smaller input data set as in the 2S approach, ML techniques offers a simpler implementation while ensuring comparably good decoding outcome to the DL ones. In the classification step, either machine-learning (ML) or DL models achieve the accuracy and F1 score of 0.99. Thanks to the classification step, in the regression step, both types of models result in comparable MSE and VAF scores as those of the 1S approach. Our study outlines the trade-offs to inform the implementation of real-time, low-latency, and high accuracy DL-based motor decoder for clinical applications.


title: scMM: Mixture-of-experts multimodal deep generative model for single-cell multiomics data analysis.

abstract: AO_SCPLOWBSTRACTC_SCPLOWThe recent development in single-cell multiomics analysis has enabled simultaneous detection of multiple traits at the single-cell level, thus providing deeper insights into the cellular phenotypes and functions in diverse tissues. However, currently, it is challenging to infer the joint representations and learn relationships among multiple modalities from complex multimodal single-cell data. Herein, we present scMM, a novel deep generative model-based framework for the extraction of interpretable joint representations and cross-modal generation. scMM addresses the complexity of data by leveraging a mixture-of-experts multimodal variational autoencoder. The pseudocell generation strategy of scMM compensates for the limited interpretability of deep learning models and discovered multimodal regulatory programs associated with latent dimensions. Analysis of recently produced datasets validated that scMM facilitates high-resolution clustering with rich interpretability. Furthermore, we show that cross-modal generation by scMM leads to more precise prediction and data integration compared with the state-of-the-art and conventional approaches.

category: bioinformatics


title: Somatic hypomethylation of pericentromeric SST1 repeats and tetraploidization in human colorectal cancer cells

abstract: Somatic DNA hypomethylation and aneuploidy are hallmarks of cancer, and there is evidence for a causal relationship between them in knockout mice, but not in human cancer. The non-mobile pericentromeric repetitive elements SST1 are hypomethylated in about 17% of human colorectal cancers (CRC) with some 5-7% exhibiting a more severe age-independent demethylation. Tetraploidy is a common and early event in solid tumors generating subsequent aneuploidy. We compared the relative frequency of chromosomal variations during culture of randomly selected single cell clones of diploid LS174T human CRC cells differing in their levels of SST1 demethylation. Diploid cells underwent frequent genome reduplication events generating tetraploid clones that correlated with SST1 demethylation. In primary CRC, severe SST1 hypomethylation was significantly associated with global genomic hypomethylation and mutations in TP53. This work uncovers the association of the naturally occurring demethylation of the SST1 pericentromeric repeat with the onset of spontaneous tetraploidization in human CRC cells in culture, and with TP53 mutations in primary CRCs. Altogether, our findings provide further support for an oncogenic pathway linking somatic epigenetic and genetic alterations in a subset of human CRC.


title: Analysis of motor unit spike trains estimated from high-density surface electromyography is highly reliable across operators

abstract: There is a growing interest in decomposing high-density surface electromyography (HDsEMG) into motor unit spike trains to improve knowledge on the neural control of muscle contraction. However, the reliability of decomposition approaches is sometimes questioned, especially because they require manual editing of the outputs. We aimed to assess the inter-operator reliability of the identification of motor unit spike trains. Eight operators with varying experience in HDsEMG decomposition were provided with the same data extracted using the convolutive kernel compensation method. They were asked to manually edit them following established procedures. Data included signals from three lower leg muscles and different submaximal intensities. After manual analysis, 126 {+/-} 5 motor units were retained (range across operators: 119-134). A total of 3380 rate of agreement values were calculated (28 pairwise comparisons x 11 contractions/muscles x 4-28 motor units). The median rate of agreement value was 99.6%. Inter-operator reliability was excellent for both mean discharge rate and time at recruitment (intraclass correlation coefficient > 0.99). These results show that when provided with the same decomposed data and the same basic instructions, operators converge toward almost identical results. Our data have been made available so that they can be used for training new operators.


title: Constructing An Adult Orofacial Premotor Atlas In Allen Mouse CCF

abstract: Premotor circuits in the brainstem control pools of orofacial motoneurons to execute essential functions such as drinking, eating, breathing, and in rodent, whisking. Previous transsynaptic tracing studies only mapped orofacial premotor circuits in neonatal mice but the adult circuits remain unknown due to technical difficulties. Here we developed a three-step monosynaptic transsynaptic tracing strategy to identify premotor neurons controlling whisker, tongue protrusion, and jaw-closing muscles in the adult. We registered these different groups of premotor neurons onto the Allen mouse brain common coordinate framework (CCF) and consequently generated a combined 3D orofacial premotor atlas, revealing unique spatial organizations of distinct premotor circuits. We also uncovered premotor neurons simultaneously innervating multiple motor nuclei and, thus, likely coordinating different muscles involved in the same orofacial behaviors. Our method for tracing adult premotor circuits and registering to Allen CCF is generally applicable and should facilitate the investigations of motor controls of diverse behaviors.


title: Transcriptomic and metabolomic responses to carbon and nitrogen sources in Methylomicrobium album BG8

abstract:
Methanotrophs use methane as their sole carbon and energy source and represent an attractive platform for converting single-carbon feedstocks into value-added compounds. Optimizing these species for biotechnological applications involves choosing an optimal growth substrate based on an understanding of cellular responses to different nutrients. Although many studies of methanotrophs have examined growth rate, yield, and central carbon flux in cultures grown with different carbon and nitrogen sources, few studies have examined more global cellular responses to different media. Here, we evaluated global transcriptomic and metabolomic profiles of Methylomicrobium album BG8 when grown with methane or methanol as the carbon source and nitrate or ammonium as the nitrogen source. We identified five key physiological changes during growth on methanol: M. album BG8 cultures upregulated transcripts for the Entner-Doudoroff and pentose phosphate pathways for sugar catabolism, produced more ribosomes, remodeled its phospholipid membrane, activated various stress response systems, and upregulated glutathione-dependent formaldehyde detoxification. When using ammonium, M. album BG8 upregulated haoAB hydroxylamine dehydrogenase and the overall central metabolic activity; whereas when using nitrate, cultures upregulated genes for nitrate assimilation and conversion. Overall, we identified several nutrient source-specific responses that could provide a valuable basis for future research on the biotechnological optimization of these species.

IMPORTANCEMethanotrophs are gaining increasing interest for their biotechnological potential to convert single-carbon compounds into value-added products such as industrial chemicals, fuels, and bioplastics. Optimizing these species for biotechnological applications requires a detailed understanding of how cellular activity and metabolism varies across different growth substrates. Although each of the two most commonly used carbon sources (methane or methanol) and nitrogen sources (ammonium or nitrate) in methanotroph growth media have well-described advantages and disadvantages in an industrial context, their effects on global cellular activity remain poorly characterized. Here, we comprehensively describe the transcriptomic and metabolomic changes that characterize the growth of an industrially promising methanotroph strain on multiple combinations of carbon and nitrogen sources. Our results represent a more holistic evaluation of cellular activity than previous studies of core metabolic pathways and provide a valuable basis for the future biotechnological optimization of these species.


title: An Exhaustive Multiple Knockout Approach to Understanding Cell Wall Hydrolase Function in Bacillus subtilis

abstract:
Most bacteria are surrounded by their cell wall, a highly crosslinked protective envelope of peptidoglycan. To grow, bacteria must continuously remodel their wall, inserting new material and breaking old bonds. Bond cleavage is performed by cell wall hydrolases, allowing the wall to expand. Understanding the functions of individual hydrolases has been impeded by their redundancy: single knockouts usually present no phenotype. We used an exhaustive multiple-knockout approach to determine the minimal set of hydrolases required for growth in Bacillus subtilis. We identified 42 candidate cell wall hydrolases. Strikingly, we were able to remove all but two of these genes in a single strain; this "{Delta}40" strain shows a normal growth rate, indicating that none of the 40 hydrolases are necessary for cell growth. The {Delta}40 strain does not shed old cell wall, demonstrating that turnover is not essential for growth.

The remaining two hydrolases in the {Delta}40 strain are LytE and CwlO, previously shown to be synthetically lethal. Either can be knocked out in {Delta}40, indicating that either hydrolase alone is sufficient for cell growth. Environmental screening and zymography revealed that LytE activity is inhibited by Mg2+ and that RlpA-like proteins may stimulate LytE activity. Together, these results demonstrate that the only essential function of cell wall hydrolases in B. subtilis is to enable cell growth by expanding the wall and that LytE or CwlO alone is sufficient for this function. These experiments introduce the {Delta}40 strain as a tool to study hydrolase activity and regulation in B. subtilis.

IMPORTANCEIn order to grow, bacterial cells must both create and break down their cell wall. The enzymes that are responsible for these processes are the target of some of our best antibiotics. Our understanding of the proteins that break down the wall - cell wall hydrolases - has been limited by redundancy among the large number of hydrolases many bacteria contain. To solve this problem, we identified 42 cell wall hydrolases in Bacillus subtilis and created a strain lacking 40 of them. We show that cells can survive using only a single cell wall hydrolase; this means that to understand the growth of B. subtilis in standard laboratory conditions, it is only necessary to study a very limited number of proteins, simplifying the problem substantially. We additionally show that the {Delta}40 strain is a research tool to characterize hydrolases, using it to identify 3  helper hydrolases that act in certain stress conditions.


title: Concentration and dosage sensitivity of proteins driving liquid-liquid phase separation

abstract: Liquid-liquid phase separation (LLPS) is a molecular process that leads to the formation of membraneless organelles (MLOs), i.e. functionally specialized liquid-like cellular condensates formed by proteins and nucleic acids. Integration of data on LLPS-associated proteins from dedicated databases revealed only modest overlap between them and resulted in a confident set of 89 human LLPS driver proteins. Since LLPS is highly concentration-sensitive, the underlying experiments are often criticized for applying higher-than-physiological protein concentrations. To clarify this issue, we performed a naive comparison of in vitro applied and quantitative proteomics-derived protein concentrations and discuss a number of considerations that rationalize the choice of apparently high in vitro concentrations in most LLPS studies. The validity of in vitro LLPS experiments is further supported by in vivo phase-separation experiments and by the observation that the corresponding genes show a strong propensity for dosage sensitivity. This observation implies that the availability of the respective proteins is tightly regulated in cells to avoid erroneous condensate formation. In all, we propose that although local protein concentrations are practically impossible to determine in cells, proteomics-derived cellular concentrations should rather be considered as lower limits of protein concentrations, than strict upper bounds, to be respected by in vitro experiments.


title: ESC - a comprehensive resource for SARS-CoV-2 immune escape variants

abstract:
Ever since the breakout of COVID-19 disease, ceaseless genomic research to inspect the epidemiology and evolution of the pathogen has been undertaken globally. Large scale viral genome sequencing and analysis have uncovered the functional impact of numerous genetic variants in disease pathogenesis and transmission. Emerging evidence of mutations in spike protein domains escaping antibody neutralization is reported. We have built a database with precise collation of manually curated variants in SARS-CoV-2 from literature with potential escape mechanisms from a range of neutralizing antibodies. This comprehensive repository encompasses a total of 5258 variants accounting for 2068 unique variants tested against 230 antibodies, patient convalescent plasma and vaccine breakthrough events. This resource enables the user to gain access to an extensive annotation of SARS-CoV-2 escape variants which would contribute to exploring and understanding the underlying mechanisms of immune response against the pathogen. The resource is available at http://clingen.igib.res.in/esc/

GRAPHICAL ABSTRACT

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title: Decreased neutralization of SARS-CoV-2 global variants by therapeutic anti-spike protein monoclonal antibodies

abstract: Monoclonal antibodies against the SARS-CoV-2 spike protein, notably, those developed by Regeneron Pharmaceuticals and Eli Lilly and Company have proven to provide protection against severe COVID-19. The emergence of SARS-CoV-2 variants with heavily mutated spike proteins raises the concern that the therapy could become less effective if any of the mutations disrupt epitopes engaged by the antibodies. In this study, we tested monoclonal antibodies REGN10933 and REGN10987 that are used in combination, for their ability to neutralize SARS-CoV-2 variants B.1.1.7, B.1.351, mink cluster 5 and COH.20G/677H. We report that REGN10987 maintains most of its neutralization activity against viruses with B.1.1.7, B.1.351 and mink cluster 5 spike proteins but that REGN10933 has lost activity against B.1.351 and mink cluster 5. The failure of REGN10933 to neutralize B.1.351 is caused by the K417N and E484K mutations in the receptor binding domain; the failure to neutralize the mink cluster 5 spike protein is caused by the Y453F mutation. The REGN10933 and REGN10987 combination was 9.1-fold less potent on B.1.351 and 16.2-fold less potent on mink cluster 5, raising concerns of reduced efficacy in the treatment of patients infected with variant viruses. The results suggest that there is a need to develop additional monoclonal antibodies that are not affected by the current spike protein mutations.

category: immunology


title: Predicting the zoonotic capacity of mammal species for SARS-CoV-2

abstract: Back and forth transmission of SARS-CoV-2 between humans and animals may lead to wild reservoirs of virus that can endanger efforts toward long-term control of COVID-19 in people, and protecting vulnerable animal populations that are particularly susceptible to lethal disease. Predicting high risk host species is key to targeting field surveillance and lab experiments that validate host zoonotic potential. A major bottleneck to predicting animal hosts is the small number of species with available molecular information about the structure of ACE2, a key cellular receptor required for viral cell entry. We overcome this bottleneck by combining species ecological and biological traits with 3D modeling of virus and host cell protein interactions using machine learning methods. This approach enables predictions about the zoonotic capacity of SARS-CoV-2 for over 5,000 mammals -- an order of magnitude more species than previously possible. The high accuracy predictions achieved by this approach are strongly corroborated by in vivo empirical studies. We identify numerous common mammal species whose predicted zoonotic capacity and close proximity to humans may further enhance the risk of spillover and spillback transmission of SARS-CoV-2. Our results reveal high priority areas of geographic overlap between global COVID-19 hotspots and potential new mammal hosts of SARS-CoV-2. With molecular sequence data available for only a small fraction of potential host species, predictive modeling integrating data across multiple biological scales offers a conceptual advance that may expand our predictive capacity for zoonotic viruses with similarly unknown and potentially broad host ranges.


title: Predicting the zoonotic capacity of mammals to transmit SARS-CoV-2


title: Combined Metabolic Activators decrease liver steatosis by activating mitochondrial metabolism in a Golden Syrian hamster study

abstract: The prevalence of non-alcohol fatty liver disease (NAFLD), defined as the livers excessive fat accumulation, continues to increase dramatically. We have recently revealed the molecular mechanism underlying NAFLD using in-depth multi-omics profiling and identified that combined metabolic activators (CMA) could be administered to decrease the amount of hepatic steatosis (HS) in mouse model and NAFLD patients based on systems analysis. Here, we investigated the effects of a CMA including L-carnitine, N-acetyl-l-cysteine, nicotinamide riboside and betaine on a Golden Syrian hamster NAFLD model fed with HFD, and found that HS was decreased with the administration of CMA. To explore the mechanisms involved in the clearance HS, we generated liver transcriptomics data before and after CMA administration, and integrated these data using liver-specific genome-scale metabolic model of liver tissue. We systemically determined the molecular changes after the supplementation of CMAs and found that it activates mitochondria in the liver tissue by modulating the global fatty acid, amino acids, antioxidant and folate metabolism.

category: systems biology


title: Cryo-TEM simulations of amorphous radiation-sensitive samples using multislice wave propagation.

abstract: Image simulation plays a central role in the development and practice of high-resolution electron microscopy, including transmission electron microscopy of frozen-hydrated specimens (cryo-EM). Simulating images with contrast that matches the contrast observed in experimental images remains challenging, especially for amorphous samples. Current state-of-the-art simulators apply post hoc scaling to approximate empirical solvent contrast, attenuated image intensity due to specimen thickness, and amplitude contrast. This practice fails for images that require spatially variable scaling, e.g., simulations of a crowded or cellular environment. Modeling both the signal and the noise accurately is necessary to simulate images of biological specimens with contrast that is correct on an absolute scale. The "Frozen-Plasmon" method is introduced which explicitly models spatially variable inelastic scattering processes in cryo-EM specimens. This approach produces amplitude contrast that depends on the atomic composition of the specimen, reproduces the total inelastic mean free path as observed experimentally, and allows for the incorporation of radiation damage in the simulation. These improvements are quantified using the matched-filter concept to compare simulation and experiment. The Frozen-Plasmon method, in combination with a new mathematical formulation for accurately sampling the tabulated atomic scattering potentials onto a Cartesian grid, is implemented in the open-source software package cisTEM.

category: biophysics


title: Rapid neural categorization of facelike objects predicts the perceptual awareness of a face (face pareidolia)

abstract:
The human brain rapidly and automatically categorizes faces vs. other visual objects. However, whether face-selective neural activity predicts the subjective experience of a face - perceptual awareness - is debated. To clarify this issue, here we use face pareidolia, i.e., the illusory perception of a face, as a proxy to relate the neural categorization of a variety of facelike objects to conscious face perception. In Experiment 1, scalp electroencephalogram (EEG) is recorded while pictures of human faces or facelike objects - in different stimulation sequences - are interleaved every second (i.e., at 1 Hz) in a rapid 6-Hz train of natural images of nonface objects. Participants do not perform any explicit face categorization task during stimulation, and report whether they perceived illusory faces post-stimulation. A robust categorization response to facelike objects is identified at 1 Hz and harmonics in the EEG frequency spectrum with a facelike occipito-temporal topography. Across all individuals, the facelike categorization response is of about 20% of the response to human faces, but more strongly right-lateralized. Critically, its amplitude is much larger in participants who report having perceived illusory faces. In Experiment 2, facelike or matched nonface objects from the same categories appear at 1 Hz in sequences of nonface objects presented at variable stimulation rates (60 Hz to 12 Hz) and participants explicitly report after each sequence whether they perceived illusory faces. The facelike categorization response already emerges at the shortest stimulus duration (i.e., 17 ms at 60 Hz) and predicts the behavioral report of conscious perception. Strikingly, neural facelike-selectivity emerges exclusively when participants report illusory faces. Collectively, these experiments characterize a neural signature of face pareidolia in the context of rapid categorization, supporting the view that face-selective brain activity reliably predicts the subjective experience of a face from a single glance at a variety of stimuli.

Highlights- EEG frequency-tagging measures the rapid categorization of facelike objects
- Facelike objects elicit a facelike neural categorization response
- Neural face categorization predicts conscious face perception across variable inputs


title: Aedes albopictus bionomics in Procida Island, a promising Mediterranean site for the assessment of innovative and community-based integrated pest management methods.

abstract: The colonization of Mediterranean Europe and of other temperate regions by Aedes albopictus created in the last decades an unprecedented nuisance problem in highly infested areas, as well as a new public health threat due to the species competence to transmit exotic arboviruses, such as dengue, chikungunya and zika. The Sterile Insect Technique (SIT) and the Incompatible Insect Technique (IIT) are insecticide-free mosquito-control methods relying on mass release of irradiated/manipulated males which are believed to have a potential in complementing existing and only partially effective control tools. Testing and implementing these approaches are challenging and selection of study sites is an instrumental and crucial step. We carried out a 4-year study in Procida Island (Gulf of Naples, Italy) in strict collaboration with local administrators and citizens to estimate: i) the temporal dynamics, spatial distribution, and population size of Ae. albopictus; and ii) the dispersal and survival of irradiated males. Overall, results provide insights on the bionomics of the mosquito in Southern Europe and draw attention to Procida Island as an ideal site to test innovative control programs against Ae. albopictus which may be used in other Mediterranean and temperate areas."


title: Relative and quantitative rhizosphere microbiome profiling result in distinct abundance patterns

abstract: Next-generation sequencing is recognized as one of the most popular and cost-effective way of characterizing microbiome in multiple samples. However, most of the currently available amplicon sequencing approaches are inherently limited, as they are often presented based on the relative abundance of microbial taxa, which may not fully represent actual microbiome profiles. Here, we combined amplicon sequencing (16S rRNA gene for bacteria and ITS region for fungi) with real-time quantitative PCR (qPCR) to characterize the rhizosphere microbiome of wheat. We show that the increase in relative abundance of major microbial phyla does not necessarily result in an increase in abundance. One striking observation when comparing relative and quantitative abundances was a substantial increase in the abundance of almost all phyla associated with the rhizosphere of plants grown in soil with no history of water stress as compared with the rhizosphere of plants growing in soil with a history of water stress, which was in contradiction with the trends observed in the relative abundance data. Our results suggest that the estimated absolute abundance approach gives a different perspective than the relative abundance approach, providing complementary information that helps to better understand the rhizosphere microbiome.


title: Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-Path Neolithic expansion to Western Europe

abstract:
Uniparentally-inherited markers on mitochondrial DNA (mtDNA) and the non-recombining regions of the Y chromosome (NRY), have been used for the past 30 years to investigate the history of humans from a maternal and paternal perspective.

Researchers have preferred mtDNA due to its abundance in the cells, and comparatively high substitution rate. Conversely, the NRY is less susceptible to back mutations and saturation, and is potentially more informative than mtDNA owing to its longer sequence length. However, due to comparatively poor NRY coverage via shotgun sequencing, and the relatively low and biased representation of Y-chromosome variants on capture arrays such as the 1240K, ancient DNA studies often fail to utilize the unique perspective that the NRY can yield.

Here we introduce a new DNA enrichment assay, coined YMCA (Y-mappable capture assay), that targets the "mappable" regions of the NRY. We show that compared to low-coverage shotgun sequencing and 1240K capture, YMCA significantly improves the coverage and number of sites hit on the NRY, increasing the number of Y-haplogroup informative SNPs, and allowing for the identification of previously undiscovered variants.

To illustrate the power of YMCA, we show that the analysis of ancient Y-chromosome lineages can help to resolve Y-chromosomal haplogroups. As a case study, we focus on H2, a haplogroup associated with a critical event in European human history: the Neolithic transition. By disentangling the evolutionary history of this haplogroup, we further elucidate the two separate paths by which early farmers expanded from Anatolia and the Near East to western Europe.

category: genetics


title: Genetic diversification of persistent Mycobacterium abscessus within Cystic Fibrosis patients

abstract: Mycobacterium (M.) abscessus infections in Cystic Fibrosis (CF) patients cause a deterioration of lung function. Treatment of these multidrug-resistant pathogens is associated with severe side-effects, while frequently unsuccessful. Insight on M. abscessus genomic evolvement during chronic lung infection would be beneficial for improving treatment strategies. A longitudinal study enrolling 42 CF patients was performed at a CF center in Berlin, Germany, to elaborate phylogeny and genomic diversification of in-patient M. abscessus. Eleven of the 42 CF patients were infected with M. abscessus. Global human-transmissible M. abscessus cluster strains were isolated from five of these 11 patients. Phylogenetic analysis of 88 genomes from isolates of the 11 patients excluded occurrence of M. abscessus transmission among members of the study group. Genome sequencing and variant analysis of 30 isolates from 11 serial respiratory samples collected over four years from a chronically infected patient demonstrated accumulation of gene mutations. In total, 53 genes exhibiting non-synonymous variations were identified. Enrichment analysis emphasized genes involved in synthesis of glycopeptidolipids, genes from the embABC (arabinosyltransferase) operon, betA (glucose-methanol-choline oxidoreductase) and choD (cholesterol oxidase). Genetic diversity evolved in a variety of virulence- and resistance-associated genes. The strategy of M. abscessus populations in chronic lung infection is not clonal expansion of dominant variants, but to sustain simultaneously a wide range of genetic variants facilitating adaptation of the population to changing living conditions in the lung. Genomic diversification during chronic infection requires increased attention when new control strategies against M. abscessus infections are explored.


title: Establishment of a human three-dimensional chip-based chondro-synovial co-culture joint model for reciprocal cross-talk studies in arthritis research

abstract: Rheumatoid arthritis is characterised by a progressive, intermittent inflammation at the synovial membrane, which ultimately leads to the destruction of the synovial joint. The synovial membrane, which is the joint capsules inner layer, is lined with fibroblast-like synoviocytes that are the key player supporting persistent arthritis leading to bone erosion and cartilage destruction. While microfluidic models that model molecular aspects of bone erosion between bone-derived cells and synoviocytes have been established, RAs synovial-chondral axis has yet not been realised using a microfluidic 3D model based on human patient in vitro cultures. Consequently, we established a chip-based three-dimensional tissue co-culture model that simulates the reciprocal cross-talk between individual synovial and chondral organoids. We now demonstrate that chondral organoids, when co-cultivated with synovial organoids, induce a higher degree of cartilage physiology and architecture and show differential cytokine response compared to their respective monocultures highlighting the importance of reciprocal tissue-level cross-talk in the modelling of arthritic diseases.


title: An Interpretable Deep Learning Approach for Biomarker Detection in LC-MS Proteomics Data

abstract:
Analyzing mass spectrometry-based proteomics data with deep learning (DL) approaches poses several challenges due to the high dimensionality, low sample size, and high level of noise. Additionally, DL-based workflows are often hindered to be integrated into medical settings due to the lack of interpretable explanation. We present DLearnMS, a DL biomarker detection framework, to address these challenges on proteomics instances of liquid chromatography-mass spectrometry (LC-MS) - a well-established tool for quantifying complex protein mixtures. Our DLearnMS framework learns the clinical state of LC-MS data instances using convolutional neural networks. Based on the trained neural networks, we show how biomarkers can be identified using layer-wise relevance propagation. This enables detecting discriminating regions of the data and the design of more robust networks. One of the main advantages over other established methods is that no explicit preprocessing step is needed in our DLearnMS framework.

Our evaluation shows that DLearnMS outperforms conventional LC-MS biomarker detection approaches in identifying fewer false positive peaks while maintaining a comparable amount of true positives peaks.

Code availabilityThe code is available from the following GIT repository: https://github.com/SaharIravani/DlearnMS


title: Selective MAP1LC3C (LC3C) autophagy requires noncanonical initiation regulators and the paralog-specific C-terminal peptide

abstract: LC3s are canonical proteins necessary for the formation of autophagosomes. We have previously established that two paralogs, LC3B and LC3C, have opposite activities in renal cancer, with LC3B playing oncogenic role and LC3C tumor suppressing role. LC3C is an evolutionary late gene, present only in higher primates and humans. Its most distinct feature is a C-terminal 20 amino acid peptide cleaved in the process of glycine 126 lipidation. Here we investigated mechanisms of LC3C selective autophagy. LC3C autophagy requires noncanonical upstream regulatory complexes that include ULK3, UVRAG, RUBCN, PIK3C2A, and a member of ESCRT, TSG101. We established that Postdivision Midbody Rings (PDMBs) implicated in cancer stem cell regulation are direct targets of LC3C autophagy. LC3C C-terminal peptide is necessary and sufficient to mediate LC3C-dependent selective degradation of PDMBs. This work establishes a new noncanonical human-specific selective autophagic program relevant to cancer stem cells.


title: Messages From the Small Intestine Carried by Extracellular Vesicles in Prediabetes: a Proteomic Portrait

abstract: Extracellular vesicles (EVs) mediate communication in physiological and pathological conditions. In the pathogenesis of type 2 diabetes, inter-organ communication plays an important role in its progress and metabolic surgery leads to its remission. Moreover, gut dysbiosis is emerging as a diabetogenic factor. However, it remains unclear how gut senses metabolic alterations and whether this is transmitted to other tissues via EVs. Using a diet induced-prediabetic mouse model, we observed that protein packaging in gut derived EVs (GDE), specifically small intestine, is increased in prediabetes. Proteins related to lipid metabolism and to oxidative stress management were more abundant in prediabetic GDE compared to healthy controls. On the other hand, proteins related to glycolytic activity, as well as those responsible for the degradation of polyubiquitinated composites, were depleted in prediabetic GDE. Together, our findings show that protein packaging in GDE is markedly modified during prediabetes pathogenesis. Thus, suggesting that prediabetic alterations in small intestine are translated into modified GDE proteome, which are dispersed into the circulation where they can interact with and influence the metabolic status of other tissues. This study highlights the importance of the small intestine as a tissue that propagates prediabetic metabolic dysfunction throughout the body and the importance of GDE as the messenger.

category: pathology


title: The biosynthesis of phospholipids is linked to the cell cycle in a model eukaryote

abstract: The structural challenges faced by eukaryotic cells through the cell cycle are key for understanding cell viability and proliferation. In this study, we tested the hypothesis that the biosynthesis of structural lipids is linked to the cell cycle. If true, this would suggest that the cells structure would form part the control of the cell cycle. Lipidomics (31P NMR and MS), proteomics (Western immunoblotting) and transcriptomics (RT-qPCR) techniques were used to profile the lipid fraction and characterise aspects of its metabolism at seven stages of the cell cycle of the model eukaryote, Desmodesmus quadricauda. We found considerable, transient increases in the abundance of phosphatidylethanolamine during the G1 phase (+35%, ethanolamine phosphate cytidylyltransferase increased 2{middle dot}5x) and phosphatidylglycerol over the G1/pre-replication phase boundary (+100%, phosphatidylglycerol synthase increased 22x). The relative abundance of phosphatidylcholine fell by ~35% during the G1. N-Methyl transferases for the conversion of phosphatidylethanolamine into phosphatidylcholine were not found in the de novo transcriptome profile, though a choline phosphate transferase was found, suggesting that the Kennedy pathway is the principal route for the synthesis of PC. The fatty acid profiles of the four most abundant lipids suggested that these lipids were not generally converted between one another. The relative abundance of both phosphatidylinositol and its synthase remained constant despite an eightfold increase in cell volume. We conclude that the biosynthesis of the three most abundant structural phospholipids is linked to the cell cycle in D. quadricauda.


title: MVPA does not reveal neural representations of hierarchical linguistic structure in MEG

abstract: During comprehension, the meaning extracted from serial language input can be described by hierarchical phrase structure. Whether our brains explicitly encode hierarchical structure during processing is, however, debated. In this study we recorded Magnetoencephalography (MEG) during reading of structurally ambiguous sentences to probe neural activity for representations of underlying phrase structure. 10 human subjects were presented with simple sentences, each containing a prepositional phrase that was ambiguous with respect to its attachment site. Disambiguation was possible based on semantic information. We applied multivariate pattern analyses (MVPA) to the MEG data using linear classifiers as well as representational similarity analysis to probe various effects of phrase structure building on the neural signal. Using MVPA techniques we successfully decoded both syntactic (part-of-speech) as well as semantic information from the brain signal. Importantly, however, we did not find any patterns in the neural signal that differentiate between different hierarchical structures. Nor did we find neural traces of syntactic or semantic reactivation following disambiguating sentence material. These null findings suggest that subjects may not have processed the sentences with respect to their underlying phrase structure. We discuss methodological limits of our analysis as well as cognitive theories of "shallow processing", i.e. in how far rich semantic information can prevent thorough syntactic analysis during processing.


title: The effect of hydrophobic gases on the nervous system of Daphnia magna

abstract: Hundreds of hydrophobic substances: alkanes, alcohols, benzodiacepines, barbiturates, ethers and even gases, can induce General Anaesthesia (GA) in mammal animals. Moreover, it has been suggested that the primary site of action of such agents is on the spinal cord. Here, we investigate a scenario that is in double measure important to understand the mechanisms behind GA: its induction under water in invertebrate animals. We evaluate the capacity of xenon, nitrous oxide and krypton to suppress harmful sensations, provoked by intense light, in the crustacean D. magna. Due to the hydrophobic characteristics of those gases, we designed a special chamber to force them to dissolve in water at pressures up to to 50 atmospheres, whereas at the same time measure in real time the motility of the animals. Surprisingly, the aquatic animals are immobilized with xenon and nitrous oxide. Under this condition, they dont respond to a noxious stimulus. Our results are crucial to understand the action of inert gases in GA and the role of the spinal cord.


title: Stable behavioral state-specific large scale activity patterns in the developing cortex of neonates

abstract: Endogenous neuronal activity is a hallmark of the developing brain. In rodents, a handful of such activities were described in different cortical areas but the unifying macroscopic perspective is still lacking. Here we combined large-scale in vivo Ca2+ imaging of the dorsal cortex in non-anesthetized neonatal mice with advanced mathematical analyses to reveal unique behavioral state-specific maps of endogenous activity. These maps were remarkably stable over time within and across experiments and used patches of correlated activity with little hemispheric symmetry as well as stationary and propagating waves as building blocks. Importantly, the maps recorded during motion and rest were almost inverse, with sensory-motor areas active during motion and posterior-lateral areas active at rest. The retrosplenial cortex engaged in both resting- and motion-related activities, building functional long-range connections with respective cortical areas. The data obtained bind different region-specific activity patterns described so far into a single consistent picture and set the stage for future inactivation studies, probing the exact function of this complex activity pattern for cortical wiring in neonates.


title: Whole-genome analysis of antimicrobial-resistant Escherichia coli in human gut microbiota reveals its origin and flexibility in transmitting mcr-1

abstract:
Multidrug resistant (MDR) Escherichia coli strains that carry extended-spectrum {beta}-lactamases (ESBLs) or colistin resistance gene mcr-1 have been identified in the human gut at an increasing incidence worldwide. In this study, we sampled and characterized MDR Enterobacteriaceae from the gut microbiota of healthy Singaporeans and show that the prevalence of ESBL-producing and mcr-positive Enterobacteriaceae is 26.6% and 7.3%, respectively. Whole-genome sequencing of 37 E. coli isolates identified 25 sequence types and assigned them into six different phylogroups, suggesting that the human intestinal MDR E. coli strains are highly diverse. In addition, we found that E. coli isolates belonging to phylogroup D, B2 and F carry a higher number of virulence genes, whereas isolates of phylogroup A, B1 and E carry fewer virulence factor genes but are frequent carriers of florfenicol resistance gene floR and colistin resistance gene mcr-1. Comparison of the seven mcr-1-positive E. coli isolates revealed that mcr-1 is carried by conjugative plasmids or embedded in composite transposons, which could potentially mobilize mcr-1 to other pathogenic Enterobacteriaceae strains or MDR plasmids. Finally, we found that 12 out of the 37 MDR E. coli isolates in this study show high similarity to ESBL-producing E. coli isolates from raw meats from local markets, suggesting a potential transmission of MDR E. coli from meat products to the human gut microbiota. Our findings show diverse antibiotic resistance and virulence profiles of intestinal E. coli and call for better countermeasures to block the transmission of MDR E. coli via the food chain.

ImportanceThe human gut can harbor both antibiotic resistant and virulent E. coli which may subsequently cause infections. In this study, the antibiotic resistance and virulence traits of antibiotic-resistant E. coli isolates from human gut microbiota of healthy subjects were investigated. The isolated E. coli strains carry a diverse range of antibiotic resistance mechanisms and virulence factor genes, are highly diverse to each other, and are likely to originate from raw meat products from the local markets. Of particular concern are seven E. coli isolates which carry colistin resistance gene mcr-1. This gene can be mobilized into other pathogens and MDR plasmids, thereby spreading resistance to the last-resort antibiotic colistin. Our findings also suggest that raw meat could serve as important source to transmit MDR bacteria into the human gut microbiota.


title: Dispersal syndromes affect ecosystem functioning in ciliate microcosms

abstract: Dispersal is a key process mediating ecological and evolutionary dynamics. Its effects on metapopulations dynamics, population genetics or species range distribution can depend on phenotypic differences between dispersing and non-dispersing individuals (i.e., dispersal syndromes). However, scaling up to the importance of dispersal syndromes for meta-ecosystems have rarely been considered, despite intraspecific phenotypic variability is now recognised as an important factor mediating ecosystem functioning. In this study, we characterised the intraspecific variability of dispersal syndromes in twenty isolated genotypes of the ciliate Tetrahymena thermophila to test their consequences for biomass productivity in communities composed of five Tetrahymena species. To do so, dispersers and residents of each genotype were introduced, each separately, in ciliate communities composed of four other competing species of the genus Tetrahymena to investigate the effects of dispersal syndromes. We found that introducing dispersers led to a lower biomass compared to introducing residents. This effect was highly consistent across the twenty T. thermophila genotypes despite their marked differences of dispersal syndromes. Finally, we found a strong genotypic effect on biomass production, confirming that intraspecific variability in general affected ecosystem functions in our system. Our study shows that intraspecific variability and the existence of dispersal syndromes can impact the functioning of spatially structured ecosystems in a consistent and therefore predictable way.


title: Strategies to assure optimal trade-offs among competing objectives for genetic improvement of soybean

abstract: Plant breeding is a decision making discipline based on understanding project objectives. Genetic improvement projects can have two competing objectives: maximize rate of genetic improvement and minimize loss of useful genetic variance. For commercial plant breeders competition in the marketplace forces greater emphasis on maximizing immediate genetic improvements. In contrast public plant breeders have an opportunity, perhaps an obligation, to place greater emphasis on minimizing loss of useful genetic variance while realizing genetic improvements. Considerable research indicates that short term genetic gains from Genomic Selection (GS) are much greater than Phenotypic Selection (PS), while PS provides better long term genetic gains because PS retains useful genetic diversity during the early cycles of selection. With limited resources must a soybean breeder choose between the two extreme responses provided by GS or PS? Or is it possible to develop novel breeding strategies that will provide a desirable compromise between the competing objectives? To address these questions, we decomposed breeding strategies into decisions about selection methods, mating designs and whether the breeding population should be organized as family islands. For breeding populations organized into islands decisions about possible migration rules among family islands were included. From among 60 possible strategies, genetic improvement is maximized for the first five to ten cycles using GS, a hub network mating design in breeding populations organized as fully connected family islands and migration rules allowing exchange of two lines among islands every other cycle of selection. If the objectives are to maximize both short-term and long-term gains, then the best compromise strategy is similar except a genomic mating design, instead of a hub networked mating design, is used. This strategy also resulted in realizing the greatest proportion of genetic potential of the founder populations. Weighted genomic selection applied to both non-isolated and island populations also resulted in realization of the greatest proportion of genetic potential of the founders, but required more cycles than the best compromise strategy.


title: Antiviral activity of influenza A virus defective interfering particles against SARS-CoV-2 replication in vitro through stimulation of innate immunity

abstract: SARS-CoV-2 causing COVID-19 emerged in late 2019 and resulted in a devastating pandemic. Although the first approved vaccines were already administered by the end of 2020, worldwide vaccine availability is still limited. Moreover, immune escape variants of the virus are emerging against which the current vaccines may confer only limited protection. Further, existing antivirals and treatment options against COVID-19 only show limited efficacy. Influenza A virus (IAV) defective interfering particles (DIPs) were previously proposed not only for antiviral treatment of the influenza disease but also for pan-specific treatment of interferon (IFN)-sensitive respiratory virus infections. To investigate the applicability of IAV DIPs as an antiviral for the treatment of COVID-19, we conducted in vitro co-infection experiments with cell culture-derived DIPs and the IFN-sensitive SARS-CoV-2 in human lung cells. We show that treatment with IAV DIPs leads to complete abrogation of SARS-CoV-2 replication. Moreover, this inhibitory effect was dependent on janus kinase/signal transducers and activators of transcription (JAK/STAT) signaling. Further, our results suggest boosting of IFN-induced antiviral activity by IAV DIPs as a major contributor in suppressing SARS-CoV-2 replication. Thus, we propose IAV DIPs as an effective antiviral agent for treatment of COVID-19, and potentially also for suppressing the replication of new variants of SARS-CoV-2.


title: SARS-CoV-2 variant evolution in the United States: High accumulation of viral mutations over time likely through serial Founder Events and mutational bursts.

abstract:
Since the first case of COVID-19 in December 2019 in Wuhan, China, SARS-CoV-2 has spread worldwide and within a year has caused 2.29 million deaths globally. With dramatically increasing infection numbers, and the arrival of new variants with increased infectivity, tracking the evolution of its genome is crucial for effectively controlling the pandemic and informing vaccine platform development. Our study explores evolution of SARS-CoV-2 in a representative cohort of sequences covering the entire genome in the United States, through all of 2020 and early 2021. Strikingly, we detected many accumulating Single Nucleotide Variations (SNVs) encoding amino acid changes in the SARS-CoV-2 genome, with a pattern indicative of RNA editing enzymes as major mutators of SARS-CoV-2 genomes. We report three major variants through October of 2020. These revealed 14 key mutations that were found in various combinations among 14 distinct predominant signatures. These signatures likely represent evolutionary lineages of SARS-CoV-2 in the U.S. and reveal clues to its evolution such as a mutational burst in the summer of 2020 likely leading to a homegrown new variant, and a trend towards higher mutational load among viral isolates, but with occasional mutation loss. The last quartile of 2020 revealed a concerning accumulation of mostly novel low frequency replacement mutations in the Spike protein, and a hypermutable glutamine residue near the putative furin cleavage site. Finally, the end of the year data revealed the presence of known variants of concern including B.1.1.7, which has acquired additional Spike mutations. Overall, our results suggest that predominant viral sequences are dynamically evolving over time, with periods of mutational bursts and unabated mutation accumulation. This high level of existing variation, even at low frequencies and especially in the Spike-encoding region may be become problematic when superspreader events, akin to serial Founder Events in evolution, drive these rare mutations to prominence.

AUTHOR SUMMARYThe pandemic of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused the death of more than 2.29 million people and continues to be a severe threat internationally. Although simple measures such as social distancing, periodic lockdowns and hygiene protocols were immediately put into force, the infection rates were only temporarily minimized. When infection rates exploded again new variants of the virus began to emerge. Our study focuses on a representative set of sequences from the United States throughout 2020 and early 2021. We show that the driving force behind the variants of public health concern, is widespread infection and superspreader events. In particular, we show accumulation of mutations over time with little loss from genetic drift, including in the Spike region, which could be problematic for vaccines and therapies. This lurking accumulated genetic variation may be a superspreader event from becoming more common and lead to variants that can escape the immune protection provided by the existing vaccines.


title: Viperin inhibits cholesterol biosynthesis and interacts with enzymes in the cholesterol biosynthetic pathway

abstract: Many enveloped viruses bud from cholesterol-rich lipid rafts on the cell membrane. Depleting cellular cholesterol impedes this process and results in viral particles with reduced viability. Viperin (virus inhibitory protein endoplasmic reticulum-associated, interferon-induced) is an ER membrane-associated enzyme that when expressed in response to viral infections exerts broad-ranging antiviral effects, including inhibiting the budding of some enveloped viruses. Here we have investigated the effect of viperin expression on cholesterol biosynthesis. We found that viperin expression reduces cholesterol levels by 20 - 30 % in HEK293T cells. A proteomic screen of the viperin interactome identified several cholesterol biosynthetic enzymes among the top hits. The two most highly enriched proteins were lanosterol synthase and squalene monooxygenase, enzymes that catalyze key steps establishing the sterol carbon skeleton. Co-immunoprecipitation experiments established that viperin, lanosterol synthase and squalene monooxygenase form a complex at the ER membrane. Co-expression of viperin was found to significantly inhibit the specific activity of lanosterol synthase in HEK293T cell lysates. Co-expression of viperin had no effect on the specific activity of squalene monooxygenase, but reduced its expression levels in the cells by approximately 30 %. Despite these inhibitory effects, co-expression of either LS or SM failed to reverse the viperin-induced depletion of cellular cholesterol levels in HEK293T cells. Our results establish a clear link between the down-regulation of cholesterol biosynthesis and viperin, although at this point the effect cannot be unambiguously attributed interactions between viperin and a specific biosynthetic enzyme.

category: biochemistry


title: Characterization of SdGA, a cold-adapted glucoamylase from Saccharophagus degradans

abstract: We investigated the structural and functional properties of SdGA, a glucoamylase (GA) from Saccharophagus degradans, a marine bacterium which degrades different complex polysaccharides at high rate. SdGA is composed mainly by a N-terminal GH15_N domain linked to a C-terminal catalytic domain (CD) found in the GH15 family of glycosylhydrolases with an overall structure similar to other bacterial GAs. The protein was expressed in Escherichia coli cells, purified and its biochemical properties were investigated. Although SdGA has a maximum activity at 39{degrees}C and pH 6.0, it also shows high activity in a wide range, from low to mild temperatures, like cold-adapted enzymes. Furthermore, SdGA has a higher content of flexible residues and a larger CD due to various amino acid insertions compared to other thermostable GAs. We propose that this novel SdGA, is a cold-adapted enzyme that might be suitable for use in different industrial processes that require enzymes which act at low or medium temperatures.


title: Probing the SAM Binding Site of SARS-CoV-2 nsp14 in vitro Using SAM Competitive Inhibitors Guides Developing Selective bi-substrate Inhibitors

abstract: The COVID-19 pandemic has clearly brought the healthcare systems world-wide to a breaking point along with devastating socioeconomic consequences. The SARS-CoV-2 virus which causes the disease uses RNA capping to evade the human immune system. Non-structural protein (nsp) 14 is one of the 16 nsps in SARS-CoV-2 and catalyzes the methylation of the viral RNA at N7-guanosine in the cap formation process. To discover small molecule inhibitors of nsp14 methyltransferase (MT) activity, we developed and employed a radiometric MT assay to screen a library of 161 in house synthesized S-adenosylmethionine (SAM) competitive methyltransferase inhibitors and SAM analogs. Among seven identified screening hits, SS148 inhibited nsp14 MT activity with an IC50 value of 70 {+/-} 6 nM and was selective against 20 human protein lysine methyltransferases indicating significant differences in SAM binding sites. Interestingly, DS0464 with IC50 value of 1.1 {+/-} 0.2 M showed a bi-substrate competitive inhibitor mechanism of action. Modeling the binding of this compound to nsp14 suggests that the terminal phenyl group extends into the RNA binding site. DS0464 was also selective against 28 out of 33 RNA, DNA, and protein methyltransferases. The structure-activity relationship provided by these compounds should guide the optimization of selective bi-substrate nsp14 inhibitors and may provide a path towards a novel class of antivirals against COVID-19, and possibly other coronaviruses.


title: TGF-B signaling suppresses TCA cycle metabolism in renal cancer.

abstract: The Warburg effect is one of most-well studied metabolic phenomenon in cancer cells. For the most part, these studies have focused on enhanced rates of glycolysis observed in various models. The presumption has been that mitochondrial metabolism is suppressed. However, recent studies indicate that the extent of mitochondrial metabolism is far more heterogeneous in tumors than originally presumed. One tumor type with suppression of mitochondrial metabolism is renal cell carcinoma (RCC). Prior studies indicate that suppressed TCA cycle enzyme mRNA expression is associated with aggressive RCC. Yet, the mechanisms that regulate the TCA cycle in RCC remain uncharacterized. Here, we demonstrate that loss of TCA cycle enzyme expression is retained in RCC metastatic tissues. Moreover, proteomic analysis demonstrates that reduced TCA cycle enzyme expression is far more pronounced in RCC relative to other tumor types. Loss of TCA cycle enzyme expression is correlated with reduced expression of the transcription factor peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1) which is also lost in RCC tissues. PGC-1 re-expression in RCC cells restores the expression of TCA cycle enzymes in vitro and in vivo and leads to enhanced glucose carbon incorporation into TCA cycle intermediates. Mechanistically, TGF-{beta} signaling, in concert with histone deacetylase 7 (HDAC7), suppresses TCA cycle enzyme expression. In turn, pharmacologic inhibition of TGF-{beta} restores expression of TCA cycle enzyme expression and suppresses tumor growth in an orthotopic model of RCC. Taken together, our findings reveal a novel role for the TGF-{beta} /HDAC7 axis in global suppression of TCA cycle enzymes in RCC and provide novel insight into the molecular basis of altered mitochondrial metabolism in this malignancy.


title: Adequate knowledge of COVID-19 impacts good practices amongst health profession students in the Philippines

abstract:
BackgroundThe spread of the coronavirus disease 2019 (COVID-19) in the Philippines started with its first suspected case on January 22, 2020. The government reacted by imposing several measures including community quarantine, class suspensions, drug therapy and vaccine development, and travel restrictions. This online survey was done amongst Filipino health professions undergraduate students to uncover the relationship between their knowledge, attitude, and practice during this pandemic.

MethodsCross-sectional data were obtained from an online survey done on students of medicine, dentistry, optometry, rehabilitative sciences, and pharmacy.

ResultsAt a response rate of 100% (n=1257), the results show that healthcare profession students in the Philippines have good knowledge (87.6%) and practices (63.6%) regarding COVID-19, yet attitude (63.6%) was just passable. This study also shows that a strong correlation exists between knowledge and practice concerning the current pandemic, r(2) = 0.08, P = 0.004.

ConclusionAdequate knowledge of COVID-19 impacts good practices of avoiding crowded places and misuse of steam inhalation amongst health profession students in the Philippines. Knowledge and practice pertaining to the current pandemic have been found to be good, but attitude remains low.

category: scientific communication and education


title: SMAD4 governs a feedforward regulation of the TGF-beta effects in CD8 T cells that contributes to preventing chronic intestinal inflammation

abstract: SMAD4, a key mediator of TGF-{beta} signaling, plays a crucial role in T cells to prevent chronic gut inflammation. However, the molecular mechanisms underlying this control remain elusive. Using different genetic and epigenetic approaches, we unexpectedly reveal that SMAD4 in CD8 T cells prevents chronic intestinal inflammation by a feedforward mechanism that is TGF-{beta}-independent. Prior to any TGF-{beta}-receptor engagement, SMAD4 acts as an active and basal repressor of epigenetic, transcriptional and functional TGF-{beta} imprinting in CD8 T cells. Thus, in sharp opposition to total TGF-{beta} signaling deletion, SMAD4 deletion impairs naive CD8 T cell effector predisposition but promotes CD8 T cell accumulation and epithelial retention by promoting their response to IL-7 and their expression of integrins such as Itgae. Besides, SMAD4 deletion unleashes the induction of a wide range of TGF-{beta}-signaling-repressors such as Smad7, Ski, Skil, and Smurf2 and hampers TGF-{beta}-mediated CD8 T cell immunosuppression. Mechanistically, prior to any TGF-{beta} signal, SMAD4 binds to the loci of several TGF-{beta}-target genes, and by regulating histone acetylation, represses their expression. The massive gut epithelial colonization, associated with their escape from the immunoregulatory TGF-{beta} effects overtakes their poor effector preconditioning and elicits microbiota-driven chronic epithelial CD8 T cell activation. Hence, in an anticipatory manner, independently of TGF-{beta}, SMAD4 governs a feedforward regulation of TGF-{beta} effects in CD8 T cells, preventing chronic intestinal inflammation.


title: Bayesian analysis of source tracking markers to estimate the effects of an urban sanitation intervention on human fecal contamination in Mozambique

abstract:
Fecal source tracking (FST) may be useful to assess pathways of fecal contamination in domestic environments and to estimate the impacts of water, sanitation, and hygiene (WASH) interventions in low-income settings. We measured two non-specific and two human-associated fecal indicators in water, soil, and surfaces before and after a shared latrine intervention from low-income households in Maputo, Mozambique participating in the Maputo Sanitation (MapSan) trial. Up to a quarter of households were impacted by human fecal contamination, but trends were unaffected by improvements to shared sanitation facilities. The intervention reduced E. coli gene concentrations in soil but did not impact culturable E. coli or the prevalence of human FST markers in a difference-in-differences analysis. Using a novel Bayesian hierarchical modeling approach to account for human marker diagnostic sensitivity and specificity, we revealed a high amount of uncertainty associated with human FST measurements and intervention effect estimates. The field of microbial source tracking would benefit from adding measures of diagnostic accuracy to better interpret findings, particularly when FST analyses convey insufficient information for robust inference. With improved measures, FST could help identify dominant pathways of human and animal fecal contamination in communities and guide implementation of effective interventions to safeguard health.

SYNOPSISAn urban sanitation intervention had minimal and highly uncertain effects on human fecal contamination after accounting for fecal indicator sensitivity and specificity.

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title: Impacts of an urban sanitation intervention on fecal indicators and the prevalence of human fecal contamination in Mozambique