title: Finger representation in the cortex of the congenitally blind

abstract: Hand representation in the primary somatosensory cortex (S1) is thought to be shaped by experience. Individuals with congenital blindness rely on their sense of touch for completing daily tasks that in sighted people would be informed by vision, and possess superior tactile acuity. It has therefore been proposed that their S1 hand representation should differ from that of sighted individuals. Alternatively, it has been proposed that the improved tactile acuity in blind individuals is due to cross-modal plasticity, when regions in the occipital and temporal cortex are typically used for processing vision become activated by touch. We probed finger representation using psychophysics and 7T fMRI (1 mm3 resolution) in three individuals with bilateral anophthalmia, a rare condition in which both eyes fail to develop, as well as sighted controls. Despite anophthalmic individuals increased reliance on touch and superior tactile acuity, we found no evidence that they had more pronounced hand representation in S1. This is in line with recent research highlighting the stability of early sensory cortex, despite altered sensorimotor experience in adulthood. Unlike sighted controls, anophthalmic individuals activated the left human middle temporal complex (hMT+) during finger movement. This area did not express any hallmark of typical sensorimotor organisation, suggesting this and previously reported activity does not indicate low-level sensorimotor hand representation. However, left hMT+ contained some single finger information, beyond that found in sighted controls. This latter finding suggests that when the developmentally flexible area hMT+ is unaffected by retinal input, it can acquire novel cross-modal processes, which are potentially unrelated to the areas function in sighted people. As such, our findings highlight the opportunity for other organising principles, beyond domain specific plasticity, in shaping cross-modal reorganisation.


title: Resurrection of human endogenous retroviruses during aging reinforces senescence

abstract: Human endogenous retroviruses (HERVs) are under strict control by the host surveillance system but can become awakened under pathological conditions. Among them, the HERVK family, comprised of the evolutionarily youngest HERVs, is able to transcribe viral genes and producing retrovirus-like particles (RVLPs). However, whether HERVK is mobilized in the aging process and contributes to aging-related pathologies is largely unknown. Using diverse senescence models, we show that epigenetic alterations unlock HERVK expression, which leads to the formation of RVLPs. Derepression of HERVK promotes cellular senescence, while inhibiting HERVK prevents cellular senescence. HERVK RVLPs released from senescent cells or aged individuals are capable of conferring a senescence phenotype to young cells. Conversely, using antibodies to block the HERVK RVLPs abrogates their transmissible pro-senescence effect. Moreover, endogenous retrovirus expression is increased in aged human tissues and serum from the elderly. These findings indicate that the activation of endogenous viruses is part of the driving force of aging.

category: cell biology


title: Reanalysis of deep-sequencing data from Austria points towards a small SARS-COV-2 transmission bottleneck on the order of one to three virions

abstract: An early analysis of SARS-CoV-2 deep-sequencing data that combined epidemiological and genetic data to characterize the transmission dynamics of the virus in and beyond Austria concluded that the size of the viruss transmission bottleneck was large - on the order of 1000 virions. We performed new computational analyses using these deep-sequenced samples from Austria. Our analyses included characterization of transmission bottleneck sizes across a range of variant calling thresholds and examination of patterns of shared low-frequency variants between transmission pairs in cases where de novo genetic variation was present in the recipient. From these analyses, among others, we found that SARS-CoV-2 transmission bottlenecks are instead likely to be very tight, on the order of 1-3 virions. These findings have important consequences for understanding how SARS-CoV-2 evolves between hosts and the processes shaping genetic variation observed at the population level.

category: evolutionary biology


title: Age and Race related changes in Gene Expression during Human PBMC aging

abstract: Human immune system functions over an entire lifetime, yet how and why the immune system becomes less effective with age are not well understood. Here, we characterize peripheral blood mononuclear cells transcriptome from 172 healthy adults with 21~90 years of age using RNA-seq and the weighted gene correlation network analyses (WGCNA). These data reveal a set of insightful gene expression modules and representative gene biomarkers for human immune system aging from Asian and Caucasian ancestry, respectively. Among them, the aging-specific modules show an age-related gene expression variation spike around early-seventies. In addition, it is not known whether Asian and Caucasian immune systems go through similar gene expression changes throughout their lifespan, and to what extent these aging-associated changes are shared among ethnicities. We find the top hub genes including NUDT7, CLPB, OXNAD1 and MLLT3 are shared between Asian and Caucasian aging related modules and further validated in human PBMCs from different age groups. Overall, the impact of age and race on transcriptional variation elucidated from this study provide insights into the transcriptional driver of immune aging.

category: immunology


title: Identification of age and ethnicity specific gene expression biomarkers for immune aging


title: Tetrameric UvrD helicase is located at the E. coli replisome due to frequent replication blocks

abstract: DNA replication in all organisms must overcome nucleoprotein blocks to complete genome duplication. Accessory replicative helicases in Escherichia coli, Rep and UvrD, help replication machinery overcome blocks by removing incoming nucleoprotein complexes or aiding the re-initiation of replication. Mechanistic details of Rep function have emerged from recent live cell studies, however, the activities of UvrD in vivo remain unclear. Here, by integrating biochemical analysis and super-resolved single-molecule fluorescence microscopy, we discovered that UvrD self-associates into a tetramer and, unlike Rep, is not recruited to a specific replisome protein despite being found at approximately 80% of replication forks. By deleting rep and DNA repair factors mutS and uvrA, perturbing transcription by mutating RNA polymerase, and antibiotic inhibition; we show that the presence of UvrD at the fork is dependent on its activity. This is likely mediated by the very high frequency of replication blocks due to DNA bound proteins, including RNA polymerase, and DNA damage. UvrD is recruited to sites of nucleoprotein blocks via distinctly different mechanisms to Rep and therefore plays a more important and complementary role than previously realised in ensuring successful DNA replication.

category: biophysics


title: The last battle of Anne of Brittany: solving mass grave through an interdisciplinary approach (paleopathology, anthropobiology, history, multiple isotopes and radiocarbon dating)

abstract: Mass graves are usually key historical markers with strong incentive for archeological investigations. The identification of individuals buried in mass graves has long benefitted from traditional historical, archaeological, anthropological and paleopathological techniques. The addition of novel methods including genetic, genomic and isotopic geochemistry have renewed interest in solving unidentified mass graves. In this study, we demonstrate that the combined use of these techniques allows the identification of the individuals found in two Breton historical mass graves, where one method alone would not have revealed the importance of this discovery. The skeletons likely belong to soldiers from the two enemy armies who fought during a major event of Breton history: the siege of Rennes in 1491, which ended by the wedding of the Duchess of Brittany with the King of France and signaled the end of the independence of the region. Our study highlights the value of interdisciplinary approaches with a particular emphasis on increasingly accurate isotopic markers. The development of the sulfur isoscape and testing of the triple isotope geographic assignment are detailed in a companion paper [1].

category: ecology


title: Germline activity of the heat shock factor HSF-1 programs the insulin-receptor daf-2 in C. elegans

abstract:
The mechanisms by which maternal stress alters offspring phenotypes remain poorly understood. Here we report that the heat shock transcription factor HSF-1, activated in the C. elegans maternal germline upon stress, epigenetically programs the insulin-like receptor daf-2 by increasing repressive H3K9me2 levels throughout the daf-2 gene. This increase occurs by the recruitment of the C. elegans SETDB1 homolog MET-2 by HSF-1. Increased H3K9me2 levels at daf-2 persist in offspring to downregulate daf-2, activate the C. elegans FOXO ortholog DAF-16 and enhance offspring stress resilience. Thus, HSF-1 activity in the mother promotes the early life programming of the insulin/IGF-1 signaling (IIS) pathway and determines the strategy of stress resilience in progeny.

One Sentence SummaryHSF-1 recruits MET-2 to silence daf-2 and mediate early life programming of C. elegans upon stress


title: A combined EM and proteomic analysis places HIV-1 Vpu at the crossroads of retromer and ESCRT complexes: PTPN23 is a Vpu-cofactor

abstract:
The HIV-1 accessory protein Vpu modulates membrane protein trafficking and degradation to provide evasion of immune surveillance. Targets of Vpu include CD4, HLAs, and BST-2. Several cellular pathways co-opted by Vpu have been identified, but the picture of Vpus itinerary and activities within membrane systems remains incomplete. Here, we used fusion proteins of Vpu and the enzyme ascorbate peroxidase (APEX2) to compare the ultrastructural locations and the proximal proteomes of wild type Vpu and Vpu-mutants. The proximity-omes of the proteins correlated with their ultrastructural locations and placed wild type Vpu near both retromer and ESCRT-0 complexes. Hierarchical clustering of protein abundances across the mutants was essential to interpreting the data and identified Vpu degradation-targets including CD4, HLA-C, and SEC12 as well as Vpu-cofactors including HGS, STAM, clathrin, and PTPN23, an ALIX-like protein. The Vpu-directed degradation of BST-2 required PTPN23 but not the retromer subunits. These data suggest that Vpu directs targets from sorting endosomes to degradation at multi-vesicular bodies via ESCRT-0 and PTPN23.

Author SummaryVpu triggers the degradation or mis-localization of proteins important to the hosts immune response. Vpu acts as an adaptor, linking cellular protein targets to the ubiquitination and membrane trafficking machinery. Vpu has been localized to various cellular membrane systems. By fusing wild type Vpu and Vpu-mutants to the enzyme ascorbate peroxidase, we defined the cellular proteome in proximity to Vpu and correlated this with the proteins location. We found that wild type Vpu is proximal to ESCRT proteins, retromer complexes, and sorting and late endosomal proteins. Functionally, we found that the Vpu-mediated degradation of the innate defense protein BST-2 required PTPN23, an ALIX-like protein, consistent with our observation of Vpus presence at the limiting membranes of multi-vesicular bodies.

category: microbiology


title: Human immunodeficiency reveals GIMAP5 as lymphocyte-specific regulator of senescence

abstract: Elucidating the molecular basis of immunodeficiency diseases is a powerful approach to discovering new immunoregulatory pathways in humans. Here we report 10 affected individuals from 4 families with a new immunodeficiency disease comprising of severe progressive lymphopenia, autoimmunity, immunodeficiency, and liver disease due to recessive loss of function variants in "GTPase of immunity-associated proteins" protein 5 (GIMAP5). We show that the disease involves the progressive loss of naive T lymphocytes and a corresponding increase in antigen-experienced, but poorly functional and replicatively senescent T cells. In vivo treatment of Gimap5-deficient mice with rapamycin (an inhibitor of mTORC1) significantly restores the fraction of naive T lymphocytes. Furthermore, a GIMAP5-deficient human patient who was treated with rapamycin (sirolimus) showed a remarkable reduction in spleen/lymph node size. Together, these observations reveal that GIMAP5 plays a critical role in lymphocyte metabolism which is essential for senescence prevention and immune competence, suggesting that an inhibitor of mTORC1 could be a valuable clinical intervention in treating patients deficient for GIMAP5.


title: The G2-phase enriched lncRNA SNHG26 is necessary for proper cell cycle progression and proliferation

abstract: Long noncoding RNAs (lncRNAs) are involved in the regulation of cell cycle, although only a few have been functionally characterized. By combining RNA sequencing and ChIP sequencing of cell cycle synchronized HaCaT cells we have previously identified lncRNAs highly enriched for cell cycle functions. Based on a cyclic expression profile and an overall high correlation to histone 3 lysine 4 trimethylation (H3K4me3) and RNA polymerase II (Pol II) signals, the lncRNA SNHG26 was identified as a top candidate. In the present study we report that downregulation of SNHG26 affects mitochondrial stress, proliferation, cell cycle phase distribution, and gene expression in cis- and in trans, and that this effect is reversed by upregulation of SNHG26. We also find that the effect on cell cycle phase distribution is cell type specific and stable over time. Results indicate an oncogenic role of SNHG26, possibly by affecting cell cycle progression through the regulation of downstream MYC-responsive genes.

category: molecular biology


title: RGG-motif protein Sbp1 is required for Processing body (P-body) disassembly

abstract: RNA granules are conserved mRNP complexes that play an important role in determining mRNA fate by affecting translation repression and mRNA decay. Processing bodies (P-bodies) harbor enzymes responsible for mRNA decay and proteins involved in modulating translation. Although many proteins have been identified to play a role in P-body assembly, a bonafide disassembly factor remains unknown. In this report, we identify RGG-motif translation repressor protein Sbp1 as a disassembly factor of P-bodies. Disassembly of Edc3 granules but not the Pab1 granules (a conserved stress granule marker) that arise upon sodium azide and glucose deprivation stress are defective in{Delta} sbp1. Disassembly of other P-body proteins such as Dhh1 and Scd6 is also defective in{Delta} sbp1. Complementation experiments suggest that the wild type Sbp1 but not an RGG-motif deletion mutant rescues the Edc3 granule disassembly defect in{Delta} sbp1. We observe that purified Edc3 forms assemblies, which is promoted by the presence of RNA and NADH. Strikingly, addition of purified Sbp1 leads to significantly decreased Edc3 assemblies. Although low complexity sequences have been in general implicated in assembly, our results reveal the role of RGG-motif (a low-complexity sequence) in the disassembly of P-bodies.


title: The Rise of West Nile Virus in Europe: investigatingthe combined effects of climate, land use and economic changes

abstract: West Nile Virus (WNV) has recently emerged as a major public health concern in Europe, its recent expansion also coincided with some remarkable socio-economic and environmental changes, including an economic crisis and some of the warmest temperatures on record. Here we empirically investigate the drivers of this phenomenon at a European wide scale by constructing and analyzing a unique spatial-temporal data-set, that includes data on climate, land-use, the economy, and government spending on environmental related sectors. Drivers and risk factors of WNV were identified by building a conceptual framework, and relationships were tested using a Generalized Additive Model (GAM), which could capture complex non-linear relationships and also account for the spatial and temporal auto-correlation. Some of the key risk factors identified in our conceptual framework, such as a higher percentage of wetlands and arable land, climate factors (higher summer rainfall and higher summer temperatures) were positive predictors of WNV infections. Interestingly, winter temperatures of between 2 {degrees}C and 6 {degrees}C were among some of the strongest predictors of annual WNV infections, one possible explanation for this result is that successful overwintering of infected adult mosquitoes (likely Culex pipiens) is key to the intensity of outbreaks for a given year. Furthermore, lower surface water extent over the summer is also associated with more more intense outbreaks, suggesting that drought, which is known to induce positive changes in WNV prevalence in mosquitoes is also contributing to the upward trend in WNV cases in affected regions. Our indicators representing the economic crisis were also strong predictors of WNV infections, suggesting there is an association between austerity and cuts to key sectors, which could have benefited vector species and the virus during this crucial period. These results, taken in the context of recent winter warming due to climate change, and more frequent droughts, may offer an explanation of why the virus has become so prevalent in Europe.


title: The Rise of West Nile Virus in Southern andSoutheastern Europe: a spatial-temporal analysisinvestigating the combined effects of climate, land use and economic changes


title: Conformity leading self-organised rescue from suboptimally biased risky decision-making

abstract: Given the ubiquity of potentially adverse behavioural bias owing to myopic trial-and-error learning, it seems paradoxical that improvements in decision-making performance through conformist social learning, a process widely considered to be bias amplification, still prevail in animal collective behaviour. Here we show, through model analyses and large-scale interactive behavioural experiments with 585 human subjects, that conformist influence can indeed promote favourable risk taking in repeated experience-based decision making, even though many individuals are systematically biased towards adverse risk aversion. Although strong positive feedback conferred by copying the majoritys behaviour could result in unfavourable informational cascades, our differential equation model of collective behavioural dynamics identified a key role for increasing exploration by negative feedback arising when a weak minority influence undermines the inherent behavioural bias. This  collective behavioural rescue, emerging through coordination of positive and negative feedback, highlights a benefit of collective learning in a broader range of environmental conditions than previously assumed and resolves the ostensible paradox of adaptive collective behavioural flexibility under conformist influences.

category: animal behavior and cognition


title: Conformity leading self-organised rescue from a suboptimal decision-making bias


title: Conformist social learning inoculates against adverse risk aversion


title: Conformist social learning leads to self-organised prevention against adverse bias in risky decision making


title: The contribution of electrostatics to hydrogen exchange in the unfolded protein state

abstract: Although electrostatics have long been recognized to play an important role in hydrogen exchange (HX) with solvent, the quantitative assessment of its magnitude in the unfolded state has hitherto been lacking. This limits the utility of HX as a quantitative method to study protein stability, folding and dynamics. Using the intrinsically disordered human protein -synuclein as a proxy for the unfolded state, we show that a hybrid mean-field approach can effectively compute the electrostatic potential at all backbone amide positions along the chain. From the electrochemical potential a fourfold reduction in hydroxide concentration near the protein backbone is predicted for the C-terminal domain, a prognosis that is in direct agreement with experimentally-derived protection factors from NMR spectroscopy. Thus, impeded HX for the C-terminal region of -synuclein is not the result of intramolecular hydrogen bonding and/or structure formation.


title: Connectome-based individual prediction of cognitive behaviors via the graph propagation network reveals directed brain network topology

abstract: The brain connectome supports the information flow underlying human cognitions and should reflect the individual variability in human cognitive behaviors. Various studies have utilized the brain connectome to predict individual differences in human behaviors. However, traditional studies viewed the brain connectome feature as a vector of one dimension, a method which neglects topological structures of the brain connectome. To utilize topological properties of the brain connectome, we proposed that graph neural network which combines graph theory and neural network can be adopted. Different from previous node-driven graph neural networks that parameterize on the node feature transformation, we designed an edge-driven graph neural network named graph propagation network that parameterizes on the information propagation within the brain connectome. We compared various models in predicting the individual total cognition based on the resting-state functional connectome. The edge-driven graph propagation network showed the highest prediction accuracy and outperformed the node-driven graph neural network and traditional partial least square regression. The graph propagation network also revealed a directed network topology encoding the information flow, indicating that the high-level association cortices are responsible for the information integration underlying the total cognition. These results suggest that the edge-driven graph propagation network can better explore the topological structure of the brain connectome and can serve as a new method to associate the brain connectome and human behaviors.

category: neuroscience


title: High-order interactions maintain or enhance structural robustness of a coffee agroecosystem network

abstract:
The capacity of highly diverse systems to prevail has proven difficult to explain. In addition to methodological issues, the inherent complexity of ecosystems and issues like multicausality, non-linearity and context-specificity make it hard to establish general and unidirectional explanations. Nevertheless, in recent years, high order interactions have been increasingly discussed as a mechanism that benefits the functioning of highly diverse ecosystems and may add to the mechanisms that explain their persistence. Until now, this idea has been explored by means of hypothetical simulated networks. Here, we test this idea using an updated and empirically documented network for a coffee agroecosystem. We identify potentially key nodes and measure network robustness in the face of node removal with and without incorporation of high order interactions. We find that the systems robustness is either increased or unaffected by the addition of high order interactions, in contrast with randomized counterparts with similar structural characteristics. We also propose a method for representing networks with high order interactions as ordinary graphs and a method for measuring their robustness.

HighlightsO_LIThe robustness of a coffee-associated ecological network is either increased or unaffected by the incorporation of high order interactions.
C_LIO_LIA method is proposed for representing high order interactions in ordinary networks.
C_LIO_LIA method is proposed to measure the robustness of networks with high order interactions.
C_LIO_LIHigh order interactions may promote the persistence of diverse ecosystems.
C_LI


title: Pulsatile contractions and pattern formation in excitable active gels

abstract: The actin cortex is an active adaptive material, embedded with complex regulatory networks that can sense, generate, and transmit mechanical forces. The cortex exhibits a wide range of dynamic behaviours, from generating pulsatory contractions and travelling waves to forming organised structures. Despite the progress in characterising the biochemical and mechanical components of the actin cortex, the emergent dynamics of this mechanochemical system is poorly understood. Here we develop a reaction-diffusion model for the RhoA signalling network, the upstream regulator for actomyosin assembly and contractility, coupled to an active actomyosin gel, to investigate how the interplay between chemical signalling and mechanical forces regulate stresses and patterns in the cortex. We demonstrate that mechanochemical feedback in the cortex acts to destabilise homogeneous states and robustly generate pulsatile contractions. By tuning active stress in the system, we show that the cortex can generate propagating contraction pulses, form network structures, or exhibit topological turbulence.


title: Pulsatile contractions and pattern formation in excitable actomyosin cortex


title: Circadian Transcriptomic and Epigenomic Remodeling in Response to Lipid Overload and Human Obesity

abstract:
Aims/hypothesisObesity and elevated circulating lipids may impair metabolism by disrupting the molecular circadian clock. We tested the hypothesis that lipid-overload may interact with the circadian clock and alter the rhythmicity of gene expression through epigenetic mechanisms.

MethodsWe determined the effect of the saturated fatty acid palmitate on circadian transcriptomics and examined the impact on histone H3 lysine K27 acetylation (H3K27ac) and the regulation of circadian rhythms in primary human skeletal muscle myotubes. Total H3 abundance and histone H3K27ac was assessed in vastus lateralis muscle biopsies from obese and normal weight men.

ResultsPalmitate disrupted transcriptomic rhythmicity in myotubes. Genes that lost or gained rhythmicity after palmitate treatment were involved in metabolic processes, protein translation and transport, and transcriptional regulation. Histone H3K27ac, a marker of active gene enhancers, was modified by palmitate treatment in myotubes, but not in skeletal muscle from men with obesity.

Conclusion/interpretationPalmitate disrupts transcriptomic rhythmicity and modifies histone H3K27ac in circadian manner, suggesting acute lipid-overload alters the epigenetic state of skeletal muscle. Our results indicate that dietary saturated fatty acids impart post-transcriptional modifications to histone proteins and regulate circadian transcriptomics.

category: physiology


title: Targeted comodulation supports flexible and accurate decoding in V1

abstract: Sensory-guided behavior requires reliable encoding of stimulus information in neural responses, and task-specific decoding through selective combination of these responses. The former has been the topic of intensive study, but the latter remains largely a mystery. We propose a framework in which shared stochastic modulation of task-informative neurons serves as a label to facilitate downstream decoding. Theoretical analysis and computational simulations demonstrate that a decoder that exploits such a signal can achieve flexible and accurate readout. Using this theoretical framework, we analyze behavioral and physiological data obtained from monkeys performing a visual orientation discrimination task. The responses of recorded V1 neurons exhibit strongly correlated modulation. This modulation is stronger in those neurons that are most informative for the behavioral task and it is substantially reduced in a control condition where recorded neurons are uninformative. We demonstrate that this modulator label can be used to improve downstream decoding within a small number of training trials, consistent with observed behavior. Finally, we find that the trial-by-trial modulatory signal estimated from V1 populations is also present in the activity of simultaneously recorded MT units, and preferentially so if they are task-informative, supporting the hypothesis that it serves as a label for the selection and decoding of relevant downstream neurons.


title: The periodic axon membrane skeleton leads to high-density sodium nanodomains but does not impact action potentials

abstract: Recent work has established that axons have a periodic skeleton structure comprising of azimuthal actin rings connected via longitudinal spectrin tetramer filaments. This structure endows the axon with structural integrity and mechanical stability. Additionally, voltage-gated sodium channels follow the periodicity of the active-spectrin arrangement, spaced [~]190 nm segments apart. The impact of this periodic sodium channel arrangement on the generation and propagation of action potentials is unknown. To address this question, we simulated an action potential using the Hodgkin-Huxley formalism in a cylindrical compartment but instead of using a homogeneous distribution of voltage-gated sodium channels in the membrane, we applied the experimentally determined periodic arrangement. We found that the periodic distribution of voltage-gated sodium channels does not significantly affect the generation or propagation of action potentials, but instead leads to high-density sodium channel nanodomains. This work provides a foundation for future studies investigating the role of the voltage-gated sodium channel periodic arrangement in the axon.


title: Clinical Phage Microbiology:A suggested framework and recommendations for the in-vitro matching steps of phage therapy

abstract:
Personalized-phage-therapy is a promising solution for the emerging crisis of bacterial infections that fail to be eradicated by conventional antibiotics.

One of the most crucial elements of personalized-phage-therapy is the proper matching of phages and antibiotics to the target bacteria in a given clinical setting. However, to date, there is no consensus guideline for laboratory procedures that enable in vitro evaluation of phages intended for treatment.

In this work, we suggest a framework and strategies identify appropriate phages and combine them with antibiotics in clinical microbiology laboratories. This framework, which we term here "Clinical Phage Microbiology" is based on our experience and other previously reported cases of both, successful and failed phage treatments.

Additionally, we discuss troubleshooting methodologies for possible pitfalls and special cases that may need to be assessed before treatment including interactions with the host immune system, biofilms, and polymicrobial infections.

We believe that the "Clinical Phage Microbiology" pipeline presented here should serve as the basis for standardization of laboratory protocols to match phages for personalized therapy.


title: Potassium isomerized linoleate satisfies EPA MB-35-00 for surface disinfection of Candida auris (AR-0381)

abstract: Four distinct lots of Potassium Isomerized Linoleate, 442 mM or 141 mg/ml (within the cosmetic-cleanser and commercial-soap acceptable concentration ranges but much greater than physiologic conditions), showed greater than 5 log kill rates (total) for Candida auris (AR-0381) for all carriers during 5 separate procedural runs of EPA MB-35-00. After exposing the inoculated stainless-steel carriers to the plant-oil soap for 1, 2, or 10 minute(s), we recovered no Candida auris on these tested carriers. Control carriers with phosphate-buffered saline applied, recovered 5.0-6.8 Log of colony-forming units per carrier.


title: Structure guided engineering of a cold active esterase expands substrate range though a stabilisation mutation that allows access to a buried water chamber

abstract: Cold active esterases represent an important class of enzymes capable of undertaking useful chemical transformations at low temperatures. EstN7 from Bacillus cohnii represents a true psychrophilic esterase with a temperature optimum below 20{degrees}C. We have recently determined the structure of EstN7 and have used this knowledge to understand substrate specificity and expands its substrate range through protein engineering. Substrate range is determined by a plug at the end of acyl binding pocket that blocks access to a buried water filled cavity, so limiting EstN7 to turnover of C2 and C4 substrates. Data mining revealed a potentially important commercial reaction, conversion of triacetin to only the 1,2-glyceryl diacetate isomer, which the EstN7 could achieve. Residues M187, N211 and W206 were identified as plug residues. M187 was identified as the key plug residue but mutation to alanine destabilised the structure as whole. Another plug mutation, N211A had a stabilising effect on EstN7 and suppressed the destabilising M187A mutation. The M187A-N211A variant had the broadest substrate range, capable of hydrolysing a C8 substrate. Thus, the structure of EstN7 together with focused engineering has provided new insights into the structural stability and substrate specificity that allowed expansion of substrate range.

category: biochemistry


title: Aging predisposes B cells to malignancy by activating c-Myc and perturbing the genome and epigenome

abstract: While cancer is an age-related disease, most studies focus on genetically engineered younger mouse models. Here, we uncover how cancer develops as a consequence of the naturally aged immune system in mice. B-cell lymphoma frequently occurs in aged mice and is associated with increased cell size, splenomegaly, and a novel clonal B-cell population. Age-emergent B cells clonally expand outside of germinal centers driven by somatic mutations, activated c-Myc and hypermethylated promoters, and both genetically and epigenetically recapitulate human follicular and diffuse-large B-cell lymphomas. Mechanistically, mouse cancerous B cells originate from age-associated B cells, which are atypical memory B cells. Age-associated B cells secrete a spectrum of proinflammatory cytokines and activate paracrinally the expression of c-Myc in surrounding B cells. Although clonal B cells are a product of an aging microenvironment, they evolve being self-sufficient and support malignancy when transferred into young mice. Inhibition of mTOR and c-Myc attenuates premalignant changes in B cells during aging and emerges as a therapeutic strategy to delay the onset of age-related lymphoma. Together, we uncover how aging generates cancerous B cells, characterize a model that captures the origin of spontaneous cancer during aging and identify interventions that may postpone age-associated lymphoma.

category: cancer biology


title: Integrative analysis reveals aged clonal B cells, microenvironment and c-Myc activation in the origin of age-related lymphoma


title: The proximal proteome of 17 SARS-CoV-2 proteins links to disrupted antiviral signaling and host translation

abstract:
Viral proteins localize within subcellular compartments to subvert host machinery and promote pathogenesis. To study SARS-CoV-2 biology, we generated an atlas of 2422 human proteins vicinal to 17 SARS-CoV-2 viral proteins using proximity proteomics. This identified viral proteins at specific intracellular locations, such as association of accessary proteins with intracellular membranes, and projected SARS-CoV-2 impacts on innate immune signaling, ER-Golgi transport, and protein translation. It identified viral protein adjacency to specific host proteins whose regulatory variants are linked to COVID-19 severity, including the TRIM4 interferon signaling regulator which was found proximal to the SARS-CoV-2 M protein. Viral NSP1 protein adjacency to the EIF3 complex was associated with inhibited host protein translation whereas ORF6 localization with MAVS was associated with inhibited RIG-I 2CARD-mediated IFNB1 promoter activation. Quantitative proteomics identified candidate host targets for the NSP5 protease, with specific functional cleavage sequences in host proteins CWC22 and FANCD2. This data resource identifies host factors proximal to viral proteins in living human cells and nominates pathogenic mechanisms employed by SARS-CoV-2.

Author SummarySARS-CoV-2 is the latest pathogenic coronavirus to emerge as a public health threat. We create a database of proximal host proteins to 17 SARS-CoV-2 viral proteins. We validate that NSP1 is proximal to the EIF3 translation initiation complex and is a potent inhibitor of translation. We also identify ORF6 antagonism of RNA-mediate innate immune signaling. We produce a database of potential host targets of the viral protease NSP5, and create a fluorescence-based assay to screen cleavage of peptide sequences. We believe that this data will be useful for identifying roles for many of the uncharacterized SARS-CoV-2 proteins and provide insights into the pathogenicity of new or emerging coronaviruses.


title: Developmental depression-facilitation shift controls excitation-inhibition balance

abstract: Changes in the short-term dynamics of excitatory synapses over development have been observed throughout cortex, but their purpose and consequences remain unclear. Here, we propose that developmental changes in synaptic dynamics buffer the effect of slow inhibitory long-term plasticity, allowing for continuously stable neural activity. Using computational modelling we demonstrate that early in development excitatory short-term depression quickly stabilises neural activity, even in the face of strong, unbalanced excitation. We introduce a model of the commonly observed developmental shift from depression to facilitation and show that neural activity remains stable throughout development, while inhibitory synaptic plasticity slowly balances excitation, consistent with experimental observations. Our model predicts changes in the input responses from phasic to phasic-and-tonic and more precise spike timings. We also observe a gradual emergence of synaptic working memory mediated by short-term facilitation. We conclude that the developmental depression-to-facilitation shift may control excitation-inhibition balance throughout development with important functional consequences.


title: Machine learning to predict the source of campylobacteriosis using whole genome data

abstract:
Campylobacteriosis is among the worlds most common foodborne illnesses, caused predominantly by the bacterium Campylobacter jejuni. Effective interventions require determination of the infection source which is challenging as transmission occurs via multiple sources such as contaminated meat, poultry, and drinking water. Strain variation has allowed source tracking based upon allelic variation in multi-locus sequence typing (MLST) genes allowing isolates from infected individuals to be attributed to specific animal or environmental reservoirs. However, the accuracy of probabilistic attribution models has been limited by the ability to differentiate isolates based upon just 7 MLST genes. Here, we broaden the input data spectrum to include core genome MLST (cgMLST) and whole genome sequences (WGS), and implement multiple machine learning algorithms, allowing more accurate source attribution. We increase attribution accuracy from 64% using the standard iSource population genetic approach to 71% for MLST, 85% for cgMLST and 78% for kmerized WGS data using machine learning. To gain insight beyond the source model prediction, we use Bayesian inference to analyse the relative affinity of C. jejuni strains to infect humans and identified potential differences, in source-human transmission ability among clonally related isolates in the most common disease causing lineage (ST-21 clonal complex). Providing generalizable computationally efficient methods, based upon machine learning and population genetics, we provide a scalable approach to global disease surveillance that can continuously incorporate novel samples for source attribution and identify fine-scale variation in transmission potential.

Author summaryC. jejuni are the most common cause of food-borne bacterial gastroenteritis but the relative contribution of different sources are incompletely understood. We traced the origin of human C. jejuni infections using machine learning algorithms that compare the DNA sequences of bacteria sampled from infected people, contaminated chickens, cattle, sheep, wild birds and the environment. This approach achieved improvement in accuracy of source attribution by 33% over existing methods that use only a subset of genes within the genome and provided evidence for the relative contribution of different infection sources. Sometimes even very similar bacteria showed differences, demonstrating the value of basing analyses on the entire genome when developing this algorithm that can be used for understanding the global epidemiology and other important bacterial infections.

category: bioinformatics


title: Recruitment of KRAS downstream target ARL4C to membrane protrusions accelerates pancreatic cancer cell invasion.

abstract: Pancreatic cancer (PC) has a high mortality rate due to metastasis. Whereas KRAS is mutated in most PC patients, controlling KRAS or its downstream effectors has not been succeeded clinically. ARL4C is a small G protein whose expression is induced by the Wnt and EGF-RAS pathways. In the present study, we found that ARL4C is frequently overexpressed in PC patients and showed that its unique localization to membrane protrusions is required for cancer cell invasion. IQGAP1 was identified as a novel interacting protein for ARL4C. ARL4C recruited IQGAP1 and its downstream effector, MMP14, to membrane protrusions. Specific localization of ARL4C, IQGAP1, and MMP14 was the active site of invasion, which induced degradation of the extracellular matrix. Moreover, subcutaneously injected antisense oligonucleotide (ASO) against ARL4C into tumor-bearing mice suppressed metastasis of PC. These results suggest that ARL4C-IQGAP1-MMP14 signaling is activated at membrane protrusions of PC cells.


title: Topography and motion of the acid-sensing ion channel intracellular domains

abstract: Acid-sensing ion channels (ASICs) are trimeric cation-selective channels activated by decreases in extracellular pH. The intracellular N and C terminal tails of ASIC1 influence channel gating, trafficking, and signaling in ischemic cell death. Despite several x-ray and cryo-EM structures of the extracellular and transmembrane segments of ASIC1, these important intracellular tails remain unresolved. Here we describe the coarse topography of the cASIC1 intracellular domains determined by FRET, measured using either fluorescent lifetime imaging or patch clamp fluorometry. We find the C terminal tail projects into the cytosol by approximately 35 [A] and that the N and proximal segment of the C tail from the same subunits are closer than adjacent subunits. Using pH-insensitive fluorescent proteins, we fail to detect any relative movement between the N and C tails upon extracellular acidification but do observe axial motions of the membrane proximal segments towards the plasma membrane. Taken together, our study furnishes a coarse topographic map of the ASIC intracellular domains while providing directionality and context to intracellular conformational changes induced by extracellular acidification.


title: Deep Brain Stimulation for Parkinson's Disease Induces Spontaneous Cortical Hypersynchrony In Extended Motor and Cognitive Networks

abstract: The mechanism of action of deep brain stimulation (DBS) for Parkinsons disease remains unclear. Studies have shown that DBS decreases pathological beta hypersynchrony between the basal ganglia and motor cortex. However, little is known about DBSs effects on long range corticocortical synchronization. Here, we use machine learning combined with spectral graph theory to compare resting-state cortical connectivity between the off and on-stimulation states and compare these differences to healthy controls. We found that turning DBS on increased high beta and gamma band coherence in a cortical circuit spanning the motor, occipitoparietal, middle temporal, and prefrontal cortices. We found no significant difference between DBS-off and controls in this network with multivariate pattern classification showing that the brain connectivity pattern in control subjects is more like those during DBS-off than DBS-on. These results show that therapeutic DBS increases spontaneous high beta-gamma synchrony in a network that couples motor areas to broader cognitive systems.


title: Chronic Stress Alters Astrocyte Morphology in Mouse Prefrontal Cortex

abstract:
BackgroundNeuromorphological changes are consistently reported in the prefrontal cortex (PFC) of patients with stress-related disorders and in rodent stress models, but the effects of stress on astrocyte morphology and potential link to behavioral deficits are relatively unknown.

MethodsTo answer these questions, transgenic mice expressing green fluorescent protein (GFP) under the glial fibrillary acid protein (GFAP) promotor were subjected to 7, 21 or 35 days of chronic restraint stress (CRS). CRS induced behavioral effects on anhedonia- and anxiety-like behaviors were measured using the sucrose intake and the PhenoTyper tests, respectively. PFC GFP+ or GFAP+ cells morphology was assessed using Sholl analysis and associations with behavior were determined using correlation analysis.

ResultsCRS-exposed male and female mice displayed anxiety-like behavior at 7, 21 and 35 days and anhedonia-like behavior at 35 days. Analysis of GFAP+ cell morphology revealed significant atrophy of distal processes following 21 and 35 days of CRS. CRS induced similar decreases in intersections at distal radii for GFP+ cells, accompanied by increased proximal processes. In males, the number of intersections at the most distal radius step significantly correlated with anhedonia-like behavior (r=0.622, p<0.05) for GFP+ cells and with behavioral emotionality calculated by z-scoring all behavioral measured deficits (r=-0.667, p<0.05). Similar but not significant correlations were observed in females. No correlation between GFP+ cell atrophy with anxiety-like behavior was found.

ConclusionChronic stress exposure induces a progressive atrophy of cortical astroglial cells, potentially contributing to maladaptive neuroplastic and behavioral changes associated with stress-related disorders.


title: DeTOKI identifies and characterizes the dynamics of chromatin topologically associating domains in a single cell

abstract: The human genome has a dynamic, well-organized hierarchical 3D architecture, including megabase-sized topologically associating domains (TAD). TADs are a key structure of the genome regulating nuclear processes, such as gene expression, DNA replication and damage repair. However, owing to a lack of proper computational tools, TADs have still not been systematically and reliably surveyed in single cells. In the present work, we developed a new algorithm to decode TAD boundaries that keep chromatin interaction insulated (deTOKI) from ultra-sparse Hi-C data. By nonnegative matrix factorization, this novel algorithm seeks out for regions that insulate the genome into blocks with minimal chance of clustering. We found that deTOKI outperformed competing tools and that it reliably identified TADs with single-cell Hi-C (scHi-C) data. By applying deTOKI, we found that domain structures are prevalent in single cells. Further, although domain structures are highly dynamic between cells, TADs adhere to the ensemble, suggesting tight regulation of single-cell TADs. Finally, we found that the insulation properties of TAD boundaries have major effect on the epigenetic landscape in individual cells. In sum, deTOKI serves as a powerful tool for profiling TADs in single cells.


title: Chromatin accessibility changes at intergenic regions associates with ovarian cancer drug resistance

abstract: We have investigated how genomic distribution of chromatin accessibilities alter during acquisition of resistance to carboplatin-based chemotherapy using matched ovarian cell lines from high grade serous ovarian cancer (HGSOC) patients before and after becoming clinically resistant to platinum-based chemotherapy. Resistant lines show altered chromatin accessibility at intergenic regions, but less so at gene promoters. Super-enhancers, as defined by clusters of cis-regulatory elements, at these intergenic regions show chromatin changes that are associated with altered expression of linked genes, with enrichment for genes involved in the Fanconi anemia/BRCA DNA damage response pathway. Further, genome-wide distribution of platinum adducts associates with the chromatin changes observed and distinguish sensitive from resistant lines. In the resistant line, we observe fewer adducts around gene promoters and more adducts at intergenic regions. Thus, chromatin changes at intergenic regulators of gene expression are associated with in vivo derived drug resistance and Pt-adduct distribution in patient-derived HGSOC drug resistance models.


title: Small-molecule inhibitors of the RNA m6A demethylase FTO potently support the survival of dopamine neurons

abstract: The fat mass and obesity-associated protein (FTO), an RNA N6-methyladenosine (m6A) demethylase, is an important regulator of central nervous system development, neuronal signalling and disease. We present here the target-tailored development and biological characterization of small-molecule inhibitors of FTO. The active compounds were identified using high-throughput molecular docking and molecular dynamics screening of the ZINC compound library. In FTO binding and activity-inhibition assays the two best inhibitors demonstrated Kd = 185 nM; IC50 = 1.46 M (compound 2) and Kd = 337 nM; IC50 = 28.9 M (compound 3). Importantly, the treatment of mouse midbrain dopamine neurons with the compounds promoted cellular survival and rescued them from growth factor deprivation induced apoptosis already at nanomolar concentrations. Moreover, these inhibitors demonstrated good blood-brain-barrier penetration in the model system, 31.7% and 30.8%, respectively. The compounds 2 and 3 protected dopamine neurons with greater potency than our recently developed alkylation repair homolog protein 5 (AlkBH5) m6A demethylase inhibitors. Inhibition of m6A RNA demethylation by small-molecule drugs, as presented here, has therapeutic potential and provides tools for the identification of disease-modifying m6A RNAs in neurogenesis and neuroregeneration. Further refinement of the lead compounds identified in this study, can also lead to unprecedented breakthroughs in the treatment of neurodegenerative diseases.


title: Regression QSAR Models for Predicting HIV-1 Integrase Inhibitors

abstract: The Human Immunodeficiency Virus (HIV) infection is a global pandemic that has claimed 33 million lives to date. One of the most efficacious treatment for naive or pre-treated HIV patients is with the HIV integrase strand transfer inhibitors (INSTIs). However, given that HIV treatment is life-long, the emergence of HIV-1 strains resistant to INSTIs is an imminent challenge. In this work, we showed two best regression QSAR models that were constructed using a boosted Random Forest algorithm [Formula] and a boosted K* algorithm [Formula] to predict the pIC50 values of INSTIs. Subsequently, the regression QSAR models were deployed against the Drugbank database for drug repositioning. The top ranked compounds were further evaluated for their target engagement activity using molecular docking studies and their potential as INSTIs evaluated from our literature search. Our study offers the first example of a large-scale regression QSAR modelling effort for discovering highly active INSTIs to combat HIV infection.

category: pharmacology and toxicology


title: Identification of host antiviral genes differentially induced by clinically diverse strains of Tick-Borne Encephalitis Virus

abstract:
Tick Borne Encephalitis Virus (TBEV) is an important human arthropod-borne virus, which causes tick-borne encephalitis (TBE), an acute viral infection of the central nervous system (CNS) that causes neurological symptoms of varying severity. TBEV is prevalent in large parts of central- and northern-Europe as well as Northern Asia, and strains of varying pathogenicity have been described. Both host and viral specific characteristics have been postulated to determine the outcome of TBEV infection, but the exact basis of their clinical variability remains undefined.

Here, we report the generation of Spinach RNA aptamer labelled TBEV replicons of high (Hypr) and low (Vs) pathogenicity isolates and perform the first direct comparison of both strains in cell culture. We show that pathogenic Hypr replicates to higher levels than Vs in mammalian cells, but not in arthropod cells, and that the basis of this difference maps to the NS5 region, encoding the methyltransferase and RNA polymerase. For both Hypr and Vs strains, NS5 and the viral genome localized to defined intracellular structures typical of positive strand RNA viruses, but Hypr was associated with significant activation of IRF-3, caspase-3 and caspase-8, whilst Vs activated Akt, affording protection against caspase-mediated apoptosis. Activation of TIAR and the formation of cytoplasmic stress granules were an additional early feature of Vs but not Hypr replication. Taken together, these findings highlight NS5 and novel host cell responses as key underling factors for the differential clinical characteristics of TBEV strains.

ImportanceTick-borne encephalitis virus (TBEV) is an emerging virus of the flavivirus family spread by ticks. Tick bite can transfer the virus and lead to a febrile infection, Tick-borne encephalitis, of varying severity. There is no specific therapeutic treatment and control in endemic areas is by vaccination. The basis of the different pathologies shown following TBEV infection, from mild to fatal, is not clear although the virus genotype clearly has a role. Mapping the basis of their differential effects would allow focus on the stages of the replication cycle responsible, which might guide the development of therapeutic interventions or the creation of purposefully attenuated strains as candidate vaccines.


title: Cleavage of Braun lipoprotein Lpp from the bacterial peptidoglycan by a paralog of L,D-transpeptidases, LdtF

abstract:
Gram-negative bacterial cell envelope is made up of an outer membrane (OM), an inner membrane (IM) that surrounds the cytoplasm, and a periplasmic space between the two membranes containing peptidoglycan (PG or murein). PG is an elastic polymer that forms a mesh-like sacculus around the IM protecting cells from turgor and environmental stress conditions. In several bacteria including E. coli, the OM is tethered to PG by an abundant OM lipoprotein, Lpp (or Braun lipoprotein) that functions to maintain the structural and functional integrity of the cell envelope. Since its discovery Lpp has been studied extensively and although L,D-transpeptidases, the enzymes that catalyse the formation of PG-Lpp linkages have been earlier identified, it is not known how these linkages are modulated. Here, using genetic and biochemical approaches, we show that LdtF (formerly yafK), a newly-identified paralog of L,D-transpeptidases in E. coli is a murein hydrolytic enzyme that catalyses cleavage of Lpp from the PG sacculus. LdtF also exhibits glycine-specific carboxypeptidase activity on muropeptides containing a terminal glycine residue. LdtF is earlier presumed to be an L,D-transpeptidase; however, our results show that it is indeed an L,D-endopeptidase that hydrolyses the products generated by the L,D-transpeptidases. To summarize, this study describes the discovery of a murein endopeptidase with a hitherto unknown catalytic specificity that removes the PG-Lpp cross-links suggesting a role for LdtF in regulation of PG-OM linkages to maintain the structural integrity of the bacterial cell envelope.

Significance statementBacterial cell walls contain a unique protective exoskeleton, peptidoglycan, which is a target of several clinically important antimicrobials. In Gram-negative bacteria, peptidoglycan is covered by an additional lipid layer, outer membrane that serves as permeability barrier against entry of toxic molecules. In some bacteria, an extremely abundant lipoprotein, Lpp staples outer membrane to peptidoglycan to maintain the structural integrity of the cell envelope. In this study, we identify a previously unknown peptidoglycan hydrolytic enzyme that cleaves Lpp from the peptidoglycan sacculus and show how the outer membrane-peptidoglycan linkages are modulated in Escherichia coli. Overall, this study helps in understanding the fundamental bacterial cell wall biology and in identification of alternate drug targets for development of new antimicrobials.


title: Nuclear Hormone Receptor NHR-49 controls a HIF-1-independent hypoxia adaptation pathway in Caenorhabditis elegans

abstract: The response to insufficient oxygen (hypoxia) is orchestrated by the conserved Hypoxia-Inducible Factor (HIF). However, HIF-independent hypoxia response pathways exist that act in parallel to HIF to mediate the physiological hypoxia response. Here, we describe a HIF-independent hypoxia response pathway controlled by Caenorhabditis elegans Nuclear Hormone Receptor NHR-49, an orthologue of mammalian Peroxisome Proliferator-Activated Receptor alpha (PPAR). We show that nhr-49 is required for worm survival in hypoxia and is synthetic lethal with hif-1 in this context, demonstrating that these factors act independently. RNA-seq analysis shows that in hypoxia nhr-49 regulates a set of genes that are hif-1-independent, including autophagy genes that promote hypoxia survival. We further show that Nuclear Hormone Receptor nhr-67 is a negative regulator and Homeodomain-interacting Protein Kinase hpk-1 is a positive regulator of the NHR-49 pathway. Together, our experiments define a new, essential hypoxia response pathway that acts in parallel to the well-known HIF-mediated hypoxia response.

category: genetics


title: Cryo-EM study on the homo-oligomeric ring formation of yeast TRiC/CCT subunits reveals TRiC ring assembly mechanism

abstract: The complex eukaryotic chaperonin TRiC/CCT helps maintain cellular protein homeostasis, however, its assembly mechanism remains largely unknown. To address the subunit specificity in TRiC assembly, we express each of the individual yeast TRiC subunit in E. coli. Our cryo-EM structural study and biochemical analyses demonstrate that CCT1/2/6 can form TRiC-like homo-oligomeric double ring (HR) complex, however ATP-hydrolysis cannot trigger their ring closure; after deletion of the long N-terminal extension, CCT5 can form the closed double-ring structure; while CCT3/4/7/8 cannot form the HRs. It appears that CCT1 forms a HR in a unique spiral configuration, and ATP-hydrolysis can drive it to re-assemble with an inserted extra subunit-pair. Our data suggest that CCT5 could be the leading subunit in ATP-hydrolysis-driven TRiC ring closure. Moreover, we demonstrate that ADP is sufficient to trigger the assembly of the HRs and TRiC from the assembly intermediate micro-complex form. Our study reveals that through evolution, the more ancestral subunits may have evolved to take more responsibilities in TRiC ring assembly, and we propose a possible assembly mechanism of TRiC involving subunit-pair insertion. Collectively, our study gives hints on the structural basis of subunit specificity in TRiC assembly and cooperativity, beneficial for future TRiC-related therapeutic strategy development.


title: Discovery of a AhR flavonoid agonist that counter-regulates ACE2 expression in rodent models of inflammation and attenuates ACE2-SARS-CoV2 interaction in vitro

abstract: The severe acute respiratory syndrome (SARS)-CoV-2, a newly emerged coronavirus first identified in 2019, is the pathogenetic agent od Corona Virus Induced Disease (COVID)19. The virus enters the human cells after binding to the angiotensin converting enzyme (ACE) 2 receptor in target tissues. ACE2 expression is induced in response to inflammation. The colon expression of ACE2 is upregulated in patients with inflammatory bowel disease (IBD), highlighting a potential risk of intestinal inflammation in promoting viral entry in the human body. Because mechanisms that regulate ACE2 expression in the intestine are poorly understood and there is a need of anti-SARS-CoV2 therapies, we have settled to investigate whether natural flavonoids might regulate the expression of ACE2 in intestinal models of inflammation. The results of these studies demonstrated that pelargonidin, a natural flavonoid bind and activates the Aryl hydrocarbon Receptor (AhR) in vitro and reverses intestinal inflammation caused by chronic exposure to high fat diet or to the intestinal braking-barrier agent DSS in a AhR-dependent manner. In these two models, development of colon inflammation associated with upregulation of ACE2 mRNA expression. Colon levels of ACE2 mRNA were directly correlated with TNF mRNA levels. In contrast to ACE2 the angiotensin 1-7 receptor MAS was downregulated in the inflamed tissues. Molecular docking studies suggested that pelargonidin binds a fatty acid binding pocket on the receptor binding domain of SARS-CoV2 Spike protein. In vitro studies demonstrated that pelargonidin significantly reduces the binding of SARS-CoV2 Spike protein to ACE2 and reduces the SARS-CoV2 replication in a concentration-dependent manner. In summary, we have provided evidence that a natural flavonoid might hold potential in reducing intestinal inflammation and ACE2 induction in the inflamed colon in a AhR-dependent manner.


title: Eye-Region Specific Ribbon Tuning Supports Distinct Modes of Synaptic Transmission in Same-Type Cone-Photoreceptors

abstract: Many sensory systems use ribbon-type synapses to transmit their signals to downstream circuits. The properties of this synaptic transfer fundamentally dictate which aspects in the original stimulus will be accentuated or suppressed, thereby partially defining the detection limits of the circuit. Accordingly, sensory neurons have evolved a wide variety of ribbon geometries and vesicle pool properties to best support their diverse functional requirements. However, the need for diverse synaptic functions does not only arise across neuron types, but also within. Here we show that UV-cones, a single type of photoreceptor of the larval zebrafish eye, exhibit striking differences in their synaptic ultrastructure and consequent calcium to glutamate transfer function depending on their location in the eye. We arrive at this conclusion by combining serial section electron microscopy and simultaneous "dual-colour" 2-photon imaging of calcium and glutamate signals from the same synapse in vivo. We further use the functional dataset to fit a cascade-like model of the ribbon synapse with different vesicle pool sizes, transfer rates and other synaptic properties. Exploiting recent developments in simulation-based inference, we obtain full posterior estimates for the parameters and compare these across different retinal regions. The model enables us to extrapolate to new stimuli and to systematically investigate different response behaviours of various ribbon configurations. We also provide an interactive, easy-to-use version of this model as an online tool. Overall, we show that already on the synaptic level of single neuron types there exist highly specialized mechanisms which are advantageous for the encoding of different visual features.


title: Distinct Synaptic Transfer Functions in Same-Type Photoreceptors


title: Evaluating the reliability of human brain white matter tractometry

abstract: The validity of research results depends on the reliability of analysis methods. In recent years, there have been concerns about the validity of research that uses diffusion-weighted MRI (dMRI) to understand human brain white matter connections in vivo, in part based on reliability of the analysis methods used in this field. We defined and assessed three dimensions of reliability in dMRI-based tractometry, an analysis technique that assesses the physical properties of white matter pathways: (1) reproducibility, (2) test-retest reliability and (3) robustness. To facilitate reproducibility, we provide software that automates tractometry (https://yeatmanlab.github.io/pyAFQ). In measurements from the Human Connectome Project, as well as clinical-grade measurements, we find that tractometry has high test-retest reliability that is comparable to most standardized clinical assessment tools. We find that tractometry is also robust: showing high reliability with different choices of analysis algorithms. Taken together, our results suggest that tractometry is a reliable approach to analysis of white matter connections. The overall approach taken here both demonstrates the specific trustworthiness of tractometry analysis and outlines what researchers can do to demonstrate the reliability of computational analysis pipelines in neuroimaging.


title: Hidden information on protein function in censuses of proteome foldedness

abstract:
Methods that assay protein foldedness with proteomics have generated censuses of protein folding stabilities in biological milieu. Surprisingly, different censuses poorly correlate with each other. Here, we show that methods targeting foldedness through monitoring amino acid sidechain reactivity also detect changes in conformation and ligand binding. About one quarter of cysteine or methionine sidechains in proteins in mammalian cell lysate increase in reactivity upon chemical denaturant titration consistent with two-state unfolding. Paradoxically, up to one third decreased reactivity, which were enriched in proteins with functions relating to unfolded protein stress. One protein, chaperone HSPA8, displayed changes arising from ligand and cofactor binding. Unmasking this hidden information should improve efforts to understand both folding and the remodeling of protein function directly in complex biological settings.

One Sentence SummaryWe show that proteome folding stability censuses are ill-defined because they earmark hidden information on conformation and ligand binding.


title: Rats spontaneously perceive global motion direction of drifting plaids

abstract: Computing global motion direction of extended visual objects is a hallmark of primate high-level vision. Although neurons selective for global motion have also been found in mouse visual cortex, it remains unknown whether rodents can combine multiple motion signals into global, integrated percepts. To address this question, we trained two groups of rats to discriminate either gratings (G group) or plaids (i.e., superpositions of gratings with different orientations; P group) drifting horizontally along opposite directions. After the animals learned the task, we applied a visual priming paradigm, where presentation of the target stimulus was preceded by the brief presentation of either a grating or a plaid. The extent to which rat responses to the targets were biased by such prime stimuli provided a measure of the spontaneous, perceived similarity between primes and targets. We found that gratings and plaids, when uses as primes, were equally effective at biasing the perception of plaid direction for the rats of the P group. Conversely, for G group, only the gratings acted as effective prime stimuli, while the plaids failed to alter the perception of grating direction. To interpret these observations, we simulated a decision neuron reading out the representations of gratings and plaids, as conveyed by populations of either component or pattern cells (i.e., local or global motion detectors). We concluded that the findings for the P group are highly consistent with the existence of a population of pattern cells, playing a functional role similar to that demonstrated in primates. We also explored different scenarios that could explain the failure of the plaid stimuli to elicit a sizable priming magnitude for the G group. These simulations yielded testable predictions about the properties of motion representations in rodent visual cortex at the single-cell and circuitry level, thus paving the way to future neurophysiology experiments.


title: Intra-helical salt bridge contribution to membrane protein insertion

abstract: Salt bridges between negatively (D, E) and positively charged (K, R, H) amino acids play an important role in protein stabilization. This has a more prevalent effect in membrane proteins where polar amino acids are exposed to a very hydrophobic environment. In transmembrane (TM) helices the presence of charged residues can hinder the insertion of the helices into the membrane. This can sometimes be avoided by TM region rearrangements after insertion, but it is also possible that the formation of salt bridges could decrease the cost of membrane integration. However, the presence of intra-helical salt bridges in TM domains and their effect on insertion has not been properly studied yet. In this work, we use an analytical pipeline to study the prevalence of charged pairs of amino acid residues in TM -helices, which shows that potentially salt-bridge forming pairs are statistically over-represented. We then selected some candidates to experimentally determine the contribution of these electrostatic interactions to the translocon-assisted membrane insertion process. Using both in vitro and in vivo systems, we confirm the presence of intra-helical salt bridges in TM segments during biogenesis and determined that they contribute between 0.5-0.7 kcal/mol to the apparent free energy of membrane insertion ({Delta}Gapp). Our observations suggest that salt bridge interactions can be stabilized during translocon-mediated insertion and thus could be relevant to consider for the future development of membrane protein prediction software.


title: Myo-inositol Oxygenase Overexpression Rescues Vitamin C Deficient Arabidopsis (vtc) Mutants

abstract:
Biosynthesis of O_SCPLOWLC_SCPLOW-ascorbate (AsA) in plants is carried out by a complex metabolic network, which involves O_SCPLOWDC_SCPLOW-mannose/O_SCPLOWLC_SCPLOW-galactose, O_SCPLOWDC_SCPLOW-galacturonate, O_SCPLOWLC_SCPLOW-gulose, and myo-inositol as main precursors. Arabidopsis lines over-expressing enzymes in the myo-inositol pathway have elevated AsA, accumulate more biomass of both aerial and root tissues, and are tolerant to abiotic stresses as shown by manual and digital phenotyping. We crossed myo-inositol oxygenase (MIOX4) over-expressers with two low-vitamin C mutants (vtc1-1 and vtc2-1) encoding enzymes involved in O_SCPLOWDC_SCPLOW-mannose/O_SCPLOWLC_SCPLOW-galactose route. The purpose of developing these crosses was to test MIOX4s ability to restore the low AsA phenotype in mutants, and to assess the contribution of individual biosynthetic pathways to abiotic stress tolerance. We used a powerful high-throughput phenotyping platform for detailed phenotypic characterization of the Arabidopsis crosses with visible, fluorescence, near-infrared and infrared sensors. We combined digital phenotyping with photosynthetic parameters and soil water potential measurements. Our results show that MIOX4 is able to restore the AsA content of the mutants and the restored lines (vtc+MIOX4) show high AsA, enhanced growth rate, accumulate more biomass, and display healthier chlorophyll fluorescence and water content profiles compared to controls.

HighlightsConstitutive expression of a myo-inositol oxygenase restored vitamin C deficient (vtc mutants). The restored lines have elevated ascorbate content and are tolerant to abiotic stresses. Under normal and abiotic stress conditions, the restored lines have enhanced biomass and increased water retention.


title: Spatiospectral brain networks reflective of improvisational experience

abstract: Musical improvisers are trained to categorize certain musical structures into functional classes, which is thought to facilitate improvisation. Using a novel auditory oddball paradigm (Goldman et al., 2020) which enables us to disassociate a deviant (i.e. musical cord inversion) from a consistent functional class, we recorded scalp EEG from a group of musicians who spanned a range of improvisational and classically trained experience. Using a spatiospectral based inter and intra network connectivity analysis, we found that improvisers showed a variety of differences in connectivity within and between large-scale cortical networks compared to classically trained musicians, as a function of deviant type. Inter-network connectivity in the alpha band, for a time window leading up to the behavioural response, was strongly linked to improvisation experience, with the default mode network acting as a hub. Spatiospectral networks post response were substantially different between improvisers and classically trained musicians, with greater inter-network connectivity (specific to the alpha and beta bands) seen in improvisers whereas those with more classical training had largely reduced inter-network activity (mostly in the gamma band). More generally, we interpret our findings in the context of network-level correlates of expectation violation as a function of subject expertise, and we discuss how these may generalize to other and more ecologically valid scenarios.


title: Modeling SARS-CoV-2 nsp1-5'-UTR complex via the extended ensemble simulations

abstract: Nonstructural protein 1 (nsp1) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a 180-residue protein that blocks translation of host mRNAs in SARS-CoV-2-infected cells. Although it is known that SARS-CoV-2s own RNA evades nsp1s host translation shutoff, the molecular mechanism underlying the evasion was poorly understood. We performed an extended ensemble molecular dynamics simulation to investigate the mechanism of the viral RNA evasion. Simulation results showed that the stem loop structure of the SARS-CoV-2 RNA 5-untranslated region (SL1) is recognized by both nsp1s globular region and intrinsically disordered region. The recognition presumably enables selective translation of viral RNAs. Cluster analysis of the binding mode and detailed analysis of the binding poses revealed several residues involved in the SL1 recognition mechanism. The simulation results imply that the nsp1 C-terminal helices are lifted from the 40S ribosome upon the binding of SL1 to nsp1, unblocking translation of the viral RNA.


title: Modeling the SARS-CoV-2 nsp1--5'-UTR complex via extended ensemble simulations


title: SIRT1 regulates sphingolipid metabolism and neural differentiation of mouse embryonic stem cells through c-Myc- SMPDL3B

abstract: Sphingolipids are important structural components of cell membranes and prominent signaling molecules controlling cell growth, differentiation, and apoptosis. Sphingolipids are particularly abundant in the brain, and defects in sphingolipid degradation are associated with several human neurodegenerative diseases. However, molecular mechanisms governing sphingolipid metabolism remain unclear. Here we report that sphingolipid degradation is under transcriptional control of SIRT1, a highly conserved mammalian NAD+-dependent protein deacetylase, in mouse embryonic stem cells (mESCs). Deletion of SIRT1 results in accumulation of sphingomyelin in mESCs, primarily due to reduction of SMPDL3B, a GPI-anchored plasma membrane bound sphingomyelin phosphodiesterase. Mechanistically, SIRT1 regulates transcription of Smpdl3b through c-Myc. Functionally, SIRT1 deficiency-induced accumulation of sphingomyelin increases membrane fluidity and impairs neural differentiation in vitro and in vivo. Our findings discover a key regulatory mechanism for sphingolipid homeostasis and neural differentiation, further imply that pharmacological manipulation of SIRT1-mediated sphingomyelin degradation might be beneficial for treatment of human neurological diseases.


title: A crosswalk to align the GSS and NIH grants databases based on university names

abstract: Notable reports over the past dozen years have recommended the federal government and others improve data collection on the research workforce in the United States. The federal government already collects a wealth of data, but important datapoints, like the number of biomedical postdocs working in the U.S., for example, are still not well defined. Furthermore, of the data that are collected, differences in collection method and data naming conventions, like inconsistent naming of universities, hinders our ability to merge information across different datasets. Here I describe the creation of three macros meant to align the National Center for Science and Engineering Statistics Survey of Graduate Students and Postdoctorates in Science and Engineering (GSS) with NIH grants databases based on consolidating university names under a single name common to both databases. Aligning these databases will allow for a deeper understanding of how various federal and university policies affect the number trainees, grants, and funding at individual institutions.

category: scientific communication and education


title: ELOF1 is a transcription-coupled DNA repair factor that directs RNA polymerase II ubiquitylation

abstract: Cells employ transcription-coupled repair (TCR) to eliminate transcription-blocking DNA lesions. The binding of the TCR-specific repair factor CSB triggers DNA damage-induced ubiquitylation of RNA polymerase II (RNAPII) at a single lysine (K1268) by the CRL4CSA ubiquitin ligase. However, how the CRL4CSA ligase is specifically directed toward the K1268 site is unknown. Here, we identify ELOF1 as the missing link that facilitates RNAPII ubiquitylation, a key signal for the assembly of downstream repair factors. This function requires its constitutive interaction with RNAPII close to the K1268 site, revealing ELOF1 as a specificity factor that positions CRL4CSA for optimal RNAPII ubiquitylation. Furthermore, drug-genetic interaction screening reveals an unanticipated compensatory TCR pathway in which ELOF1 together with known factors DOT1L and HIRA protect CSB-deficient cells from collisions between transcription and replication machineries. Our study provides a genetic framework of the transcription stress response and reveals key insights into the molecular mechanism of TCR.


title: Pax3 induces neural circuit repair through a developmental program of directed axon outgrowth.

abstract: Repairing damaged or dysfunctional human brain circuits remains an ongoing challenge for biomedical science. While surviving neuronal networks can be reorganised after lesion, for example by neurotrophins, these new connections are disorganised and rarely produce clinical improvement. Here we investigate how to promote axonal growth while retaining correct cellular targeting. We show that, in response to brain-derived neurotrophic factor (BDNF) in target-tissue, potential reinnervating neurons upregulate Pax3. Pax3 in turn increases polysialic acid-neural cell adhesion molecule (PSA-NCAM) on their axon terminals, facilitating their outgrowth and pathfinding, and resulting in correctly-targeted neural circuit repair in the mature nervous system. This is a novel role for Pax3, which we confirmed by showing its expression in afferent neurons is essential for spontaneous and BDNF-induced reinnervation in the developing and mature brains, respectively. Together these results suggest that Pax3 contributes to a repair program, in which axon growth is promoted and direction signaling maintained. These data advance our understanding for accurately rebuilding neural circuits: restricting growth-promotion to potential afferent neurons, as opposed to stimulating the whole circuit, allows axon growth without impairing its guidance.


title: Pax3 repairs a neural circuit through a program of directed axon outgrowth


title: Pathogenic tau accelerates aging-associated activation of transposable elements in the mouse central nervous system

abstract: Transposable elements comprise almost half of the mammalian genome. A growing body of evidence suggests that transposable element dysregulation accompanies brain aging and neurodegenerative disorders, and that transposable element activation is neurotoxic. Recent studies have identified links between pathogenic forms of tau, a protein that accumulates in Alzheimer disease and related tauopathies, and transposable element-induced neurotoxicity. Starting with transcriptomic analyses, we find that age- and tau-induced transposable element activation occurs in the mouse brain. Among transposable elements that are activated at the RNA level in the context of brain aging and tauopathy, we find that the endogenous retrovirus (ERV) class of retrotransposons is particularly enriched. We show that protein encoded by Intracisternal A-particle, a highly active mouse ERV, is elevated in brains of tau transgenic mice. We further demonstrate that brains of tau transgenic mice contain increased DNA copy number of transposable elements, raising the possibility that these elements actively retrotranspose in the context of tauopathy. Taken together, our study lays the groundwork for future mechanistic studies focused on transposable element regulation in the aging mouse brain and in mouse models of tauopathy, while providing support for therapeutic approaches targeting transposable element activation for Alzheimer disease and related tauopathies.


title: Can we fish on stocks that need rebuilding? Illustrating the trade-offs between stock conservation and fisheries considerations

abstract: In the Northeast Atlantic, advice for many fish stocks follows the ICES MSY approach, where a zero catch will be recommended if the stock is below its limit reference point, Blim, and cannot rebuild in the short-term. How-ever, zero catch advice are rarely implemented by managers. This study used medium-term stochastic forecasts with harvest control rules (HCRs) to investigate the consequences of allowing reduced fishing below Blim. We applied the method to western Baltic herring and North Sea cod, two contrasting species currently estimated below Blim. We show that the minimum rebuilding probability of 95% required by the MSY approach could be impossible to reach in the short-to medium-term. When this is the case, a lower probability may need to be considered instead in the short-term. Recruitment is the largest source of uncertainty in stock response to management, and can exceed differences between HCRs. Reference points should be estimated in accordance with current recruitment levels if they are to be used for short-term advice or as realistic rebuilding targets. For both stocks, it is possible to keep fishing at reduced levels for similar cumulative catch, SSB and risk on the stock in the medium-term compared to no catch below Blim. Medium-term trade-offs between stock conservation and fisheries considerations may be needed when fishery closure cannot be implemented in practice.


title: Efficient in vivo genome editing mediated by stem cells-derived extracellular vesicles carrying designer nucleases

abstract: Precise genome editing using designer nucleases (DNs), such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeat/Cas9 (CRISPR/Cas9) system, has become a method of choice in a variety of biological and biomedical applications in recent years. Notably, efficacy of these systems is currently under scrutiny in about 50 clinical trials. Although high DNs activity in various cell types in vitro has already been achieved, efficient in vivo genome editing remains a challenge. To solve this problem, we employed stem cells-derived extracellular vesicles (EVs) as carriers of DNs. We used umbilical cord-derived mesenchymal stem cells (UC-MSCs) and induced pluripotent stem cells (iPSCs) as EV-producer cells, since they are both applied in regenerative medicine. In our proof-of-concept studies, we achieved up to 50% of EGFP marker gene knockout in vivo using EVs carrying either ZFN, TALEN or the CRISPR/Cas9 system, particularly in the liver. Importantly, we obtained almost 50% of modified alleles in the liver of the experimental animals, when targeting the Pcsk9 gene, whose overexpression is implicated in hypercholesterolemia. Taken together, our data provide strong evidence that stem cells-derived EVs constitute a robust tool in delivering DNs in vivo, which may be harnessed to clinical practice in the future.

category: bioengineering


title: Human Astrocytes Exhibit Tumor Microenvironment-, Age-, and Sex-Related Transcriptomic Signatures

abstract:
Astrocytes are dynamic cells with important roles in brain function and neurological disease. There are notable species differences between human astrocytes and commonly used animal models. However, changes of the molecular attributes of human astrocytes across disease states, sex, and age are largely unknown, which is a barrier in understanding human astrocyte biology and its potential involvement in neurological diseases. To better understand the properties of human astrocytes, we acutely purified astrocytes from the cerebral cortices of over 40 humans across various ages, sexes, and disease states. We performed RNA sequencing to generate transcriptomic profiles of these astrocytes and identified genes associated with these biological variables. Here, we identified a robust transcriptomic signature of human astrocytes in the tumor-surrounding microenvironment, including upregulation of proliferation processes, along with downregulation of genes involved in ionic homeostasis and synaptic function, suggesting involvement of peri-tumor astrocytes in tumor-associated neural circuit dysfunction. In aging, we also found downregulation of synaptic regulators and upregulation of markers of astrocyte reactivity, while in maturation we identified changes in ionic transport with implications for calcium signaling. In addition, we identified some of the first transcriptomic evidence of sexual dimorphism in human cortical astrocytes, which has implications for observed sex differences across many neurological disorders. Overall, genes involved in synaptic function exhibited dynamic changes in multiple conditions. This data provides powerful new insights into human astrocyte biology in several biologically relevant states, that will aid in generating novel testable hypotheses about homeostatic and reactive astrocytes in humans.

Significance StatementAstrocytes are an abundant class of cells playing integral roles in the central nervous system. Astrocyte dysfunction is implicated in a variety of human neurological diseases. Yet our knowledge of astrocytes is largely based on mouse studies. Direct knowledge of human astrocyte biology remains limited. Here, we present transcriptomic profiles of human cortical astrocytes, and we identified molecular differences associated with age, sex, and disease state. We found changes suggesting involvement of peritumor astrocytes in tumor-associated neural circuit dysfunction, aging-associated decline in astrocyte-synapse interactions, ionic transport changes with brain maturation, and some of the first evidence of sexual dimorphism in human astrocytes. These data provide necessary insight into human astrocyte biology that will improve our understanding of human disease.


title: Dynamic arrest and aging of biomolecular condensates are regulated by low-complexity domains, RNA and biochemical activity

abstract:
Biomolecular condensates require suitable material properties to properly carry out their function. Yet, modulators that affect the material properties of condensates have remained largely unexplored.

Here we apply Differential Dynamic Microscopy (DDM) to probe the material properties of an in vitro model of processing bodies (P-bodies) consisting of condensates formed by the DEAD-box ATPase Dhh1 in the presence of ATP and RNA. DDM allows us to measure the viscosity of liquid droplets and to distinguish between liquid-like and gel- or glass-like condensates. By applying this single-droplet technique we show that condensates within the same population exhibit a distribution of material properties, which can be drastically affected by several modulators such as the low-complexity domains (LCDs) of the protein, the protein/RNA ratio, the type of RNA as well as the enzymatic activity.

In particular, we show that structured RNA leads to a large fraction of dynamically arrested condensates with respect to unstructured polyuridylic acid (polyU), emphasizing the role of RNA structure in condensate dynamics. We further demonstrate that the ageing of the condensates and the formation of gel or glass-like structures is reduced by promoting the enzymatic ATPase activity of Dhh1 and the rate of droplet formation and dissolution.

Our study shows that not only the reversible formation and dissolution of condensates but also their material properties are regulated on several levels, and that biochemical activity and material turnover can be important to maintain fluid-like properties over time.


title: Modeling of DNA binding to the condensin hinge domain using molecular dynamics simulations guided by atomic force microscopy

abstract: The condensin protein complex compacts chromatin during mitosis using its DNA-loop extrusion activity. Previous studies proposed scrunching and loop-capture models as molecular mechanisms for the loop extrusion process, both of which assume the binding of double-strand (ds) DNA to the so-called hinge domain formed at the interface of the condensin subunits Smc2 and Smc4. However, how the hinge domain contacts dsDNA has remained unknown, potentially due to its conformational plasticity. Here, we conducted atomic force microscopy imaging of the budding yeast condensin holo-complex and used this data as basis for coarse-grained molecular dynamics simulations to model the hinge structure in a transient open conformation. We then simulated the dsDNA binding to open and closed hinge conformations, predicting that dsDNA binds to the outside surface when closed and to the outside and inside surfaces when open. Our simulations also suggested that the hinge can close around dsDNA bound to the inside surface. The conformational change of the hinge domain might be essential for the dsDNA binding regulation and play important roles in condensin-mediated DNA-loop extrusion.


title: IL-10 driven memory T cell survival and Tfh differentiation promote HIV persistence

abstract: Mechanisms regulating HIV persistence are complex and not well understood. Increased IL-10 levels were positively associated with HIV reservoir in blood and lymph nodes (LN) of treated HIV aviremic individuals. In LNs, B cells, regulatory T cells, follicular T helper cells (Tfh), monocytes and macrophages contributed to the frequencies of IL10+ cells. Cells with HIV DNA in LNs were in close proximity to IL-10+ cells and/or had the active form of STAT3, the transcription downstream of IL-10. Gene signatures and proteins associated to cell survival, Co-inhibitory receptors expression, maintenance of memory T cells, immune metabolism and Tfh frequencies were all modulated by IL-10 and associated with HIV reservoir persistence. In vitro, STAT3 knockout or neutralization of IL-10, reverted all the aforementioned pathways and resulted in 10-fold decay in HIV reservoir. Collectively, these results provide strong evidence for a pivotal role of IL-10 in HIV persistence, and a potential therapeutic strategy for HIV cure.


title: Bortezomib inhibits lung fibrosis and fibroblast activation without proteasome inhibition

abstract: The FDA-approved proteasomal inhibitor bortezomib (BTZ) has attracted interest for its potential anti-fibrotic actions. However, neither its in vivo efficacy in lung fibrosis nor its dependence on proteasome inhibition has been conclusively defined. Herein, we identify that therapeutic administration of BTZ in a mouse model of pulmonary fibrosis diminished the severity of fibrosis without reducing proteasome activity in the lung. Under conditions designed to mimic this lack of proteasome inhibition in vitro, it reduced fibroblast proliferation, differentiation into myofibroblasts, and collagen synthesis. It promoted de-differentiation of myofibroblasts and overcame their characteristic resistance to apoptosis. Mechanistically, BTZ inhibited kinases important for fibroblast activation while inducing expression of dual-specificity phosphatase 1 or DUSP1, and knockdown of DUSP1 abolished its anti-fibrotic actions in fibroblasts. Our findings identify a novel proteasome-independent mechanism of anti-fibrotic actions for BTZ and support its therapeutic repurposing for pulmonary fibrosis.


title: Bi-phasic dynamics of the mitochondrial DNA mutation m.3243A>G in blood: An unbiased, mutation level-dependent model implies positive selection in the germline.

abstract: The A-to-G point mutation at position 3243 in the human mitochondrial genome (m.3243A>G) is the most common pathogenic mtDNA variant responsible for disease in humans. It is widely accepted that m.3243A>G levels decrease in blood with age, and correction representing ~2% annual decline is often applied to account for this change in mutation level. Here we report that recent data indicate the dynamics of m.3243A>G are far more complex and depend on the blood mutation level in a bi-phasic way. As a consequence, the traditional 2% correction, which is adequate  on average, creates opposite predictive biases at high and low mutation levels. Thus, overall accuracy of traditional correction depends on the proportion of individuals with high and low mutant levels in the dataset. Unbiased age correction is needed to circumvent these drawbacks of the standard model. We propose to abolish both biases by using an approach where correction depends on mutation level in biphasic way, to account for the biphasic dynamics of m.3243A>G in blood. The significance of removing bias was further tested using germline selection as a model, in which we detected mutation patterns consistent with the possibility of positive selection for m.3243A>G. We conclude that use of bi-phasic approach will greatly improve the predictive accuracy of modelling data for changes in mtDNA mutations in the germline and in somatic cells during aging.

category: genomics


title: Guest-host supramolecular assembly of injectable hydrogel fibers for cell encapsulation

abstract: The fibrous architecture of the extracellular matrix (ECM) is recognized as an integral regulator of cell function. However, there is an unmet need to develop mechanically robust biomaterials mimicking nanofibrous tissue topography that are also injectable to enable minimally invasive delivery. In this study we have developed a fibrous hydrogel composed of supramolecularly-assembled hyaluronic acid (HA) nanofibers that exhibits mechanical integrity, shear-thinning, rapid self-healing, and cytocompatibility. HA was modified with methacrylates to permit fiber photocrosslinking following electrospinning and either  guest adamantane or  host {beta}-cyclodextrin groups to guide supramolecular fibrous hydrogel assembly. Analysis of fibrous hydrogel rheological properties showed that the mixed guest-host fibrous hydrogel was more mechanically robust (6.6 {+/-} 2.0 kPa, storage modulus (G')) than unmixed guest hydrogel fibers (1.0 {+/-} 0.1 kPa, G') or host hydrogel fibers (1.1 {+/-} 0.1 kPa, G') separately. The reversible nature of the guest-host supramolecular interactions also allowed for shear-thinning and self-healing behavior as demonstrated by cyclic deformation testing. Human mesenchymal stromal cells (hMSCs) encapsulated in fibrous hydrogels demonstrated satisfactory viability following injection and after seven days of culture (> 85%). Encapsulated hMSCs were more spread and elongated when cultured in viscoelastic guest-host hydrogels compared to non-fibrous elastic controls, with hMSCs also showing significantly decreased circularity in fibrous guest-host hydrogels compared to non-fibrous guest-host hydrogels. Together, these data highlight the potential of this injectable fibrous hydrogel platform for cell and tissue engineering applications requiring minimally invasive delivery.


title: Brief report: Attentional Bias towards Social Interactions during Viewing of Naturalistic Scenes

abstract: Human visual attention is readily captured by the social information in scenes. Multiple studies have shown that social areas of interest (AOIs) such as faces and bodies attract more attention than non-social AOIs (e.g. objects or background). However, whether this attentional bias is moderated by the presence (or absence) of a social interaction remains unclear. Here, the gaze of 70 young adults was tracked during the free viewing of 60 naturalistic scenes. All photographs depicted two people, who were either interacting or not. Analyses of dwell time revealed that more attention was spent on human than background AOIs in the interactive pictures. In non-interactive pictures, however, dwell time did not differ between AOI type. In the time-to-first-fixation analysis, humans always captured attention before other elements of the scene, although this difference was slightly larger in interactive than non-interactive scenes. These findings confirm the existence of a bias towards social information in attentional capture, and suggest that the presence of social interaction may be important in inducing a similar social bias in attentional engagement. Together with previous research using less naturalistic stimuli, these findings suggest that social interactions carry additional social value that guides ones perceptual system.


title: A novel reticular oscillator in the brainstem synchronizes neonatal crying with breathing

abstract: Human speech can be divided into short, rhythmically-timed elements, similar to syllables within words. Even our cries and laughs, as well as the vocalizations of other species, are periodic. However, the cellular and molecular mechanisms underlying the tempo of mammalian vocalizations remain unknown. Here we describe rhythmically-timed neonatal mouse vocalizations that occur within single breaths, and identify a brainstem node that structures these cries, which we name the intermediate reticular oscillator (iRO). We show that the iRO acts autonomously and sends direct inputs to key muscles in order to coordinate neonatal vocalizations with breathing, as well as paces and patterns these cries. These results reveal that a novel mammalian brainstem oscillator embedded within the conserved breathing circuitry plays a central role in the production of neonatal vocalizations.