title: Determinants of multiheme cytochrome extracellular electron transfer uncovered by systematic peptide insertion

abstract: The multiheme cytochrome MtrA enables microbial respiration by transferring electrons across the outer membrane to extracellular electron acceptors. While structural studies have identified residues that mediate MtrA binding to hemes and to other cytochromes that facilitate extracellular electron transfer (EET), the relative importance of these interactions for EET is not known. To better understand EET, we evaluated how insertion of an octapeptide across all MtrA backbone locations affects Shewanella oneidensis MR-1 respiration on Fe(III). EET efficiency was found to be inversely correlated with insertion proximity to the heme prosthetic groups. Mutants with decreased EET also arose from insertions in a subset of the regions that make residue-residue contacts with the porin MtrB, while all sites contacting the extracellular MtrC presented high peptide insertion tolerance. MtrA variants having peptide insertions within the CXXCH motifs that coordinate heme cofactors retained some ability to support respiration on Fe(III), although these variants presented significantly decreased EET. Furthermore, the fitness of cells expressing different MtrA variants under Fe(III)-respiring conditions correlated with anode reduction. The peptide-insertion profile, which represents the first comprehensive sequence-structure-function map for a multiheme cytochrome, implicates MtrA as a strategic protein engineering target for regulating EET.


title: Type two secretion systems secretins are necessary for exopolymeric slime secretion in cyanobacteria and myxobacteria

abstract:
While protein translocation in Gram-negative bacteria is well understood, our knowledge about the translocation of other high-molecular-weight substances is limited. Nozzle-like structures that secrete exopolymeric substances during gliding motility have previously been observed in the outer membranes of cyanobacteria and myxobacteria. Here, we show that these nozzles are composed of the secretins PilQ/GspD, the outer membrane component of the type II and III secretion systems, the type IV pilus apparatus, and filamentous phage extrusion machinery. Our results show for the first time that secretins may be used for secretion of non-proteinaceous polymers in some bacteria, considerably expanding the repertoire of substrates of these multifunctional outer membrane gates. Moreover, we show that gspD is an essential gene in Myxococcus xanthus, which, when depleted, renders this bacterium defective in slime secretion and gliding motility.

SignificanceMany bacteria exhibit gliding motility, movement across surfaces. This motility has been correlated with the deposit of slime trails in their wake. To date, the mechanism of slime secretion has not been understood, and no cell envelope-structures have been identified that are involved in slime secretion during gliding motility. Here, we show that cyanobacteria and myxobacteria use the secretins PilQ/GspD, the outer membrane channels of the T2SS, for slime secretion, which demonstrates a novel cargo transport capacity of these multifunctional outer membrane gates.

category: microbiology


title: CD5L constraints acute and systemic inflammation and can be a novel potent therapeutic agent against sepsis

abstract: The global burden of sepsis, with an estimated 49 million cases and 11 million deaths in 2017, often passes unnoticed to the general public even though it is the direct cause of nearly 20% of all deaths worldwide. This unawareness is perhaps due to misconceptions, or miscoding in the reporting of the ultimate causes of death, as in many diseases it is not the actual infectious agent that causes the biggest harm. Rather, it is the uncontrolled inflammation leading to septic shock that is the most menacing manifestation associated with many infections, and becomes deadly serious once it has passed the stage where anti-microbial drugs no longer have any effect to inactivate or destroy the pathogen. Here we show that the combined anti-bacterial and anti-inflammatory properties of the scavenger receptor cysteine-rich (SRCR) protein CD5L contribute to a remarkable therapeutic effect of the protein to fight sepsis, such that when exogenously administered in C57BL/6 mice with induced lethal-grade sepsis, it can be a very effective curative agent to treat this condition. The resistance conferred by CD5L to polybacterial-induced sepsis using the cecal ligation and puncture (CLP) model is consistent with the reported observations that CD5L physically binds and inactivates diverse species and strains of bacteria. Accordingly, our CD5L-knockout mice are significantly more susceptible to experimentally-induced mid-grade CLP than wild-type animals. We show that CD5L is centered on promoting neutrophil recruitment and activation, overall contributing to reducing the bacteria burden of the animals. However, the dramatic susceptibility of CD5L-deficient animals is not necessarily correlated only with pathogen load, as these mice are also extremely susceptible to sterile sepsis induced by nonlethal doses of LPS. Notwithstanding the observed capacity of CD5L to directly bind to a broad range of pathogens, typical of many PRRs, our evidence suggests that the anti-inflammatory properties of the protein are at least as important as its pathogen-binding potential, and can, and should, be explored to treat the deadly inflammation storm that is sepsis.

category: immunology


title: Parental age at conception on mouse lemurs offspring longevity:sex-specific maternal effects

abstract: Parental age at conception often influences offsprings longevity, a phenomenon referred as the "Lansing effect" described in large variety of organisms. But, the majority of the results refer to the survival of juveniles, mainly explained by an inadequate parental care by the elderly parents, mostly the mothers. Studies on the effect of parental age on offsprings longevity in adulthood remain few, excepted in humans for whom effects of parental age are variable according to statistical models or socioeconomic environments. In a small primate which the longevity reaches up to 12 years, we investigated the effects of parental age at conception on the longevity of offspring (N = 278) issued from parents with known longevity. None of the postnatal parameters, including body mass, influenced offsprings longevity. Mothers age at conception significantly affected offsprings longevity in males but not females. By contrast, fathers age at conception did not influence offsprings longevity. When considering the age of the breeding pairs at conception, the older the mother, the lower the longevity of male offspring with a minimum when the father was aged. No such correlation was observed for female offspring. Lastly, the longevity of female offspring was significantly positively related to the longevity of both parents. Compared with current studies, the surprisingly minor effect of fathers  age and the major impact of mothers age on male offspring survival, despite favourable conditions, were discussed in relation with the highly seasonal reproduction in mouse lemurs.

category: evolutionary biology


title: Seasonality but not photoperiodism affects susceptibility of the two-spotted spider mite, Tetranychus urticae Koch (Acari: Tetranychidae) to pesticides

abstract: Understanding how endogenous and exogenous factors such as annual seasonal rhythm and photoperiodism affect the toxicity of pesticides can help design integrated pest management strategies. The two-spotted spider mite Tetranychus urticae Koch (Acari: Tetranychidae), a worldwide phytophagous pest species distributed in areas with different time zones, is a good model to explore how the photoperiodism and seasonality affect the pesticide toxicity. In this study, we conducted a laboratory experiment from March 2017 to November 2018 where spider mites were reared at three photoperiod regimes in environmentally controlled incubators. The toxicities of two acaricides, propargite and diafenthiruon, were measured on T. urticae every month. To determine potential mechanisms underlying the changes in the acaricide toxicity, we measured body size and total GSTs activity with the toxicity measurements in 2018. Our results showed that the toxicities of the two acaricides were not significantly different among the three photoperiod regimes. However, both had a consistent trend along the season which increased in the spring and summer and decreased in the winter in all photoperiod regimes for two consecutive years, suggesting seasonality be an endogenous factor affecting the susceptibility of the spider mites to pesticide. Pearsons correlation analyses showed only the body size had a weak negative correlation with the acaricide toxicities, suggesting a minor contribution to the higher toxicity from the smaller size of T. urticae. Our study is the first to show that seasonality can have an endogenous effect on the pesticide toxicity, and the results can inform practical insights into the pest management strategies.

category: zoology


title: WDR82 mediated H3K4me3 is associated with tumor proliferation and therapeutic efficacy in pediatric high-grade gliomas

abstract: Pediatric high-grade gliomas (pHGGs) are common malignant brain tumors without effective treatment and poor patient survival. Abnormal posttranslational modification at the histone H3 tail plays critical roles in tumor cell malignancy. We have previously shown that trimethylation of lysine 4 at histone H3 (H3K4me3) plays a significant role in pediatric ependymoma malignancy and is associated with tumor therapeutic sensitivity. Here, we show that H3K4me3 and its methyltransferase WDR82 are elevated in pHGGs. Reduction of H3K4me3 by downregulating WDR82 decreases H3K4me3 promoter occupancy and expression of genes associated with stem cell features, cell proliferation, the cell cycle and DNA damage repair. Reduction of WDR82 mediated H3K4me3 increases the response of pediatric glioma cells to chemotherapy. These findings suggest that WDR82 mediated H3K4me3 is an important determinant of pediatric glioma malignancy and therapeutic response. This highlights the need for a more thorough understanding of the potential of WDR82 as an epigenetic target to increase therapeutic efficacy and improve prognosis for children with malignant gliomas.

category: cancer biology


title: Serotonin sensing by microglia conditions the proper development of neuronal circuits and of social and adaptive skills

abstract:
The proper maturation of emotional and sensory circuits requires a fine tuning of serotonin (5-HT) level during early postnatal development. Consistently, dysfunctions of the serotonergic system have been associated with neurodevelopmental psychiatric diseases, including autism spectrum disorders (ASD). However, the mechanisms underlying the developmental effects of 5-HT remain partially unknown, one obstacle being the action of 5-HT on different cell types.

Here, we focused on microglia, which play a role in brain wiring refinement, and we investigated whether the control of these cells by 5-HT is relevant for neurodevelopment and spontaneous behaviors. Since the main 5-HT sensor in microglia is the 5-HT2B receptor subtype, we prevented 5-HT signaling specifically in microglia by conditionally invalidating Htr2b gene in these cells. We observed that abrogating the serotonergic control of microglia neonatally impacts the phagolysosomal compartment of these cells and their proximity to synapses, and perturbs neuronal circuits maturation. Furthermore, this early ablation of microglial 5-HT2B receptors leads to adult hyperactivity in a novel environment and behavioral defects in sociability and flexibility. Importantly, we show that these behavioral alterations result from a developmental effect, since they are not observed when microglial Htr2b invalidation is induced later, at P30 onward.

Thus, a primary alteration of 5-HT sensing in microglia, during a critical time window between birth and P30, is sufficient to impair social and flexibility skills. This link between 5-HT and microglia may explain the association between serotonergic dysfunctions and behavioral traits, like impaired sociability and inadaptability to novelty, which are prominent in several psychiatric disorders such as ASD.

category: neuroscience


title: Cold stress upregulates the expression of heat shock proteins and Frost genes, but evolution of cold stress resistance is apparently not mediated through either heat shock proteins or Frost genes in the cold stress selected population

abstract:
The ability to thermal adaptation can alter insects reproductive traits and physiologic response. A number of studies in Drosophila documented the higher expression levels of heat shock proteins (Hsps) and Frost (Fst) genes during the recovery phase of cold shock treatment and suggested that higher expression levels of these genes and lipids can protect from cold stress. However, these genes expression and cold adaptation have not been well studied. Therefore, understanding the molecular and biochemical basis of cold adaptation, we examined the levels of lipid and expression patterns of Hsp22, Hsp23, Hsp40, Hsp68, Hsp70, Hsp 83, and Fst genes under the cold stress or benign condition in the populations of Drosophila melanogaster selected for increased resistance to cold shock.

We observed the significant up-regulation of Hsp22, Hsp23, Hsp40, Hsp68, and Fst genes in the FSB and FCB populations during the recovery phase post cold shock compared to the no shock condition. However, there was not a significant change in the transcript levels of these genes between FSB and FCB under both the cold stress or no shock condition. Additionally, we noticed higher total lipid levels in the females from cold shock treatment than those from no shock treatment. This finding suggests that cold selected populations have different mechanisms to sustain cold stress.


title: Cold stress upregulates the expression of heat shock and Frost genes, but the evolution of cold stress resistance is apparently not mediated through either heat shock or Frost genes in the cold stress selected populations of Drosophila melanogaster


title: High-throughput molecular dynamics-based alchemical free energy calculations for predicting the binding free energy change associated with the common mutations in the spike receptor-binding domain of SARS-CoV-2

abstract: The ongoing pandemic caused by SARS-CoV-2 has gone through various phases. From the initial outbreak the virus has mutated several times, with some lineages showing even stronger infectivity and faster spread than the original virus. Among all the variants, beta, gamma, delta and the latest (omicron) are currently classified as variants of concern (VOC) while the remaining are labelled either as variants of interest (VOI) or variants under monitoring (VUM). In this work, we have focused on the mutations observed in important variants, particularly at the receptor-binding domain (RBD) of the spike protein that is responsible for the interactions with the host ACE2 receptor and binding of antibodies. Studying these mutations is particularly important for understanding the viral infectivity, spread of the disease and for tracking the escape routes of this virus from antibodies. Molecular dynamics (MD) based alchemical free energy calculations have been shown to be very accurate in predicting the free energy change due to a mutation that could have a deleterious or a stabilising effect on the protein itself or its binding affinity to another protein. Here, we investigated the significance of six commonly observed spike RBD mutations on the stability of the spike protein binding to ACE2 by free energy calculations using high throughput MD simulations. For comparison, we also used other (rigorous and non-rigorous) binding free energy prediction methods and compared our results with the experimental data if available. The alchemical free energy-based method consistently predicted the free-energy changes with an accuracy close to {+/-}1.0 kcal/mol when compared with the available experimental values. As per our simulation data the most significant mutations responsible for stabilising the spike RBD interactions with human ACE2 are N501Y and L452R.

category: biophysics


title: MYB12 spatiotemporally represses TMO5/LHW-mediated transcription in the Arabidopsis root meristem

abstract: Transcriptional networks are crucial to integrate various internal and external signals into optimal responses during plant growth and development. Primary root vasculature patterning and proliferation are controlled by a network centred around the basic Helix-Loop-Helix transcription factor complex formed by TARGET OF MONOPTEROS 5 (TMO5) and LONESOME HIGHWAY (LHW), which control cell proliferation and orientation by modulating cytokinin response and other downstream factors. Despite recent progress, many aspects of the TMO5/LHW pathway are not fully understood. In particular, the upstream regulators of TMO5/LHW activity remain unknown. Here, using a forward genetic approach to identify new factors of the TMO5/LHW pathway, we discovered a novel function of the MYB-type transcription factor MYB12. MYB12 physically interacts with TMO5 and dampens the TMO5/LHW-mediated induction of direct target gene expression as well as the periclinal/radial cell divisions. The expression of MYB12 is activated by the cytokinin response, downstream of TMO5/LHW, resulting in a novel MYB12-mediated negative feedback loop that restricts TMO5/LHW activity to ensure optimal cell proliferation rates during root vascular development.

category: plant biology


title: The acid ceramidase/ceramide axis controls parasitemia in Plasmodium yoelii-infected mice by regulating erythropoiesis

abstract: Acid ceramidase (Ac) is part of the sphingolipid metabolism and responsible for the degradation of ceramide. As bioactive molecule, ceramide is involved in the regulation of many cellular processes. However, the impact of cell-intrinsic Ac activity and ceramide on the course of Plasmodium infection remains elusive. Here, we use Ac-deficient mice with ubiquitously increased ceramide levels to elucidate the role of endogenous Ac activity in a murine malaria model. Interestingly, ablation of Ac leads to alleviated parasitemia associated with decreased T cell responses in the early phase of Plasmodium yoelii (P. yoelii) infection. Mechanistically, we identified dysregulated erythropoiesis with reduced numbers of reticulocytes, the preferred host cells of P. yoelii, in Ac-deficient mice. Furthermore, we demonstrate that administration of the Ac inhibitor carmofur to wild type mice has similar effects on P. yoelii infection and erythropoiesis. Notably, therapeutic carmofur treatment after manifestation of P. yoelii infection is efficient in reducing parasitemia. Hence, our results provide evidence for the involvement of Ac and ceramide in controlling P. yoelii infection by regulating red blood cell development.


title: Reorganization of F-actin nanostructures is required for the late phases of SARS-CoV-2 replication in pulmonary cells.

abstract:
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is worldwide the main cause of the COVID-19 pandemic. After infection of human pulmonary cells, intracellular viral replication take place in different cellular compartments resulting in the destruction of the host cells and causing severe respiratory diseases. Although cellular trafficking of SARS-CoV-2 have been explored, little is known about the role of the cytoskeleton during viral replication in pulmonary cells. Here we show that SARS-CoV-2 infection induces dramatic changes of F-actin nanostructures overtime. Ring-like actin nanostructures are surrounding viral intracellular organelles, suggesting a functional interplay between F-actin and viral M clusters during particle assembly. Filopodia-like structures loaded with viruses to neighbour cells suggest these structures as mechanism for cell-to-cell virus transmission. Strikingly, gene expression profile analysis and PKN inhibitor treatments of infected pulmonary cells reveal a major role of alpha-actinins superfamily proteins in SARS-CoV-2 replication. Overall, our results highlight cell actors required for SARS-CoV2 replication that are promises for antiviral targets.

TeaserImpairing regulation of actin filaments inhibits SARS-CoV-2 particle production in human pulmonary cells.


title: Thiopurines inhibit coronavirus Spike protein processing and incorporation into progeny virions

abstract:
There is an outstanding need for broadly acting antiviral drugs to combat emerging viral diseases. Here, we report that thiopurines inhibit the replication of the betacoronaviruses HCoV-OC43 and SARS-CoV-2, and to a lesser extent, the alphacoronavirus HCoV-229E. 6-Thioguanine (6-TG) disrupted early stages of infection, limiting synthesis of full-length and subgenomic HCoV RNAs. Furthermore, consistent with our previous report on the effects of thiopurines on influenza A virus glycoproteins, we observed that 6-TG inhibited accumulation of Spike glycoproteins from diverse HCoVs. Specifically, 6-TG treatment decreased the accumulation of Spike proteins and increased their electrophoretic mobility, consistent with Spike migration following the enzymatic removal of N-linked oligosaccharides with Peptide:N-glycosidase F (PNGaseF). SARS-CoV-2 virus-like particles (VLPs) harvested from 6-TG-treated cells were deficient in Spike. 6-TG treatment had a similar effect on lentiviruses pseudotyped with SARS-CoV-2 Spike; lentiviruses could be harvested from cell supernatants but were deficient in Spike and unable to infect human cells bearing ACE2 receptors. Together, these findings from complementary ectopic expression and infection models strongly indicate that defective Spike trafficking and processing is an outcome of 6-TG treatment. At low micromolar doses, the primary known mode of action of 6-TG is selective inhibition of the small GTPase Rac1. However, we observed that selective chemical inhibitors of the small GTPases Rac1, CDC42 and Rho had no effect on Spike processing and accumulation. The GTPase agonist ML099 countered the effects of 6-TG, suggesting that an unknown GTPase could be the relevant 6-TG-target protein involved in regulating Spike processing and accumulation. Overall, these findings provide important clues about the mechanism of action of a candidate antiviral that can broadly target HCoVs and suggest that small GTPases are promising targets for host-targeted antivirals.

AUTHOR SUMMARYThe COVID-19 pandemic has ignited efforts to repurpose existing drugs as safe and effective antivirals. Rather than directly inhibiting viral enzymes, host-targeted antivirals inhibit host cell processes to indirectly impede viral replication and/or stimulate antiviral responses. Here, we describe a new antiviral mechanism of action for the FDA-approved thiopurine 6-thioguanine. We demonstrate that this thiopurine is a pro-drug that must be metabolized by host enzymes to gain antiviral activity. We show that it can inhibit the replication of several human coronaviruses, including SARS-CoV-2, at least in part by interfering with the processing and accumulation of Spike glycoproteins, thereby impeding assembly of infectious progeny viruses. We provide evidence implicating host cell GTPase enzymes in the antiviral mechanism of action.


title: SARS-CoV-2 Omicron variant is more stable than the ancestral strain on various surfaces

abstract: The Omicron BA.1 SARS-CoV-2 variant of concern spreads quickly around the world and outcompetes other circulating strains. We examined the stability of this SARS-CoV-2 variant on various surfaces and revealed that the Omicron variant is more stable than its ancestral strain on smooth and porous surfaces.


title: More or less deadly? A mathematical model that predicts SARS-CoV-2 evolutionary direction.

abstract: SARS-CoV-2 has caused tremendous deaths world wild. It is of great value to predict the evolutionary direction of SARS-CoV-2. In this paper, we proposed a novel mathematical model that could predict the evolutionary trend of SARS-CoV-2. We focus on the mutational effects on viral assembly capacity. A robust coarse-grained mathematical model is constructed to simulate the virus dynamics in the host body. Both virulence and transmissibility can be quantified in this model. The relationship between virulence and transmissibility can be simulated. A delicate equilibrium point that optimizing the transmissibility can be numerically obtained. Based on this model, we predict the virulence of SARS-CoV-2 might further decrease, accompanied by an enhancement of transmissibility. However, this trend is not continuous; its virulence will not disappear but remains at a relatively stable range. We can also explain the cross-species transmission phenomenon of certain RNA virus based on this model. A small-scale model which simulates the virus packing process is also proposed. It can be explained why a small number of mutations would lead to a significant divergence in clinical performance, both in the overall particle formation quantity and virulence. This research provides a mathematical attempt to elucidate the evolutionary driving force in RNA virus evolution.


title: Evolutionary safety of death by mutagenesis

abstract: Nucleoside analogs are a major class of antiviral drugs. Some act by increasing the viral mutation rate causing "death by mutagenesis" of the virus. Their mutagenic capacity, however, may lead to an evolutionary safety concern. We define evolutionary safety as a probabilistic assurance that the treatment will not generate an increased number of epidemiologically concerning mutated virus progeny. We develop a mathematical framework to estimate the total mutant load produced with and without mutagenic treatment. We predict rates of appearance of virus mutants as a function of the timing of treatment and the immune competence of patients, employing various assumptions about the vulnerability of the viral genome and its potential to generate undesired phenotypes. We focus on the case study of Molnupiravir, which is an FDA-approved treatment against COVID-19. We estimate that Molnupiravir is narrowly evolutionarily safe, subject to the current estimate of parameters. Evolutionary safety can be improved by restricting treatment to individuals with a low clearance rate and by designing treatments that lead to a greater increase in mutation rate. We report a simple rule to determine the fold-increase in mutation rate required to obtain evolutionary safety which is also applicable to other pathogen-treatment combinations.


title: Processing Stage Flexibility of the SNARC effect: Task Relevance or Magnitude Relevance?

abstract:
Previous studies have shown that the processing stage of the spatial-numerical association of response codes (SNARC) effect was flexible. Two recent studies by Nan et al. (2021) and Yan et al. (2021) used the same experimental paradigm to check whether the SNARC effect occurred in the semantic-representation stage but reached contradictory conclusions, showing that the SNARC effect was influenced by a magnitude Stroop effect in a magnitude comparison task but not by a parity Stroop effect in a parity judgment task. The two studies had two distinct operational factors: the task type (magnitude comparison task or parity judgment task, with the numerical magnitude information task-relevant or task-irrelevant) and the semantic representation stage-related interference information (magnitude or parity Stroop effect, with the interference information magnitude-relevant or magnitude-irrelevant). To determine which factor influenced the SNARC effect, in the present study, the Stroop effect was switched in the two tasks based on the previous studies. The findings of four experiments consistently showed that the SNARC effect was not influenced by the parity Stroop effect in the magnitude comparison task but was influenced by the magnitude Stroop effect in the parity judgment task. Combined with the results of Nan et al. (2021) and Yan et al. (2021), the findings indicated that regardless of the task type or the task-relevance of numerical magnitude information, magnitude-relevant interference information was the primary factor to affect the SNARC effect. Furthermore, a two-stage processing model that explained the observed flexibility of the SNARC effect was proposed and discussed.

Public Significance StatementPrevious studies have shown that the spatial-numerical association of response codes (SNARC) effect is flexible in the direction and processing stage. The task type and interference information might be two influential factors for the flexibility of the SNARC effect. The present study reported that magnitude-relevant interference information, regardless of task type, was a crucial role to affect the SNARC effect. Moreover, a two-stage processing model was proposed to reveal the processing pathway of the SNARC effect and provided a possible explanation for the longstanding debate about the processing stage of the SNARC effect.

category: animal behavior and cognition


title: Impact of Autocalibration Method on Accelerated Echo-Planar Imaging of the Cervical Spinal Cord at 7T

abstract:
PurposeThe spinal cord contains sensorimotor neural circuits of scientific and clinical interest. However, spinal cord fMRI is significantly more technically demanding than brain fMRI due primarily to its proximity to the lungs. Accelerated EPI at 7T is particularly vulnerable to k-space phase inconsistencies induced by motion or B0 fluctuation, during either autocalibration signal (ACS) or timeseries acquisition. For 7T brain fMRI, sensitivity to motion and B0 fluctuation can be reduced using a re-ordered segmented EPI ACS based on the fast low-angle excitation echo-planar technique (FLEET). However, respiration-induced B0 fluctuations (exceeding 100Hz at C7) are greater, and fewer k-space lines per slice are required, for cervical spinal cord fMRI at 7T, necessitating a separate evaluation of ACS methods.

MethodsWe compared 24-line single-shot EPI, and 48-line two-shot segmented EPI, two-shot FLEET, and GRE-based ACS acquisition methods, performed under various physiological conditions, in terms of temporal SNR (tSNR) and prevalence of artifacts in GRAPPA-accelerated EPI of the cervical spinal cord at 7T.

ResultsSegmented EPI and FLEET ACS produce images with nearly identical patterns of severe image artifacts. GRE and single-shot EPI ACS consistently produce images free from significant artifacts, and tSNR is significantly greater for GRE ACS, particularly in lower slices where through-slice dephasing is most severe.

ConclusionGRE and single-shot EPI ACS acquisition methods, which are robust to respiration-induced phase errors between k-space segments, produce images with fewer and less severe artifacts than either FLEET or conventionally segmented EPI for accelerated EPI of the cervical spinal cord at 7T.

category: bioengineering


title: Open modification searching of SARS-CoV-2-human protein interaction data reveals novel viral modification sites

abstract: The outbreak of the SARS-CoV-2 coronavirus, the causative agent of the COVID-19 disease, has led to an ongoing global pandemic since 2019. Mass spectrometry can be used to understand the molecular mechanisms of viral infection by SARS-CoV-2, for example, by determining virus-host protein-protein interactions (PPIs) through which SARS-CoV-2 hijacks its human hosts during infection, and to study the role of post-translational modifications (PTMs). We have reanalyzed public affinity purification mass spectrometry data using open modification searching to investigate the presence of PTMs in the context of the SARS-CoV-2 virus-host PPI network. Based on an over two-fold increase in identified spectra, our detected protein interactions show a high overlap with independent mass spectrometry-based SARS-CoV-2 studies and virus-host interactions for alternative viruses, as well as previously unknown protein interactions. Additionally, we identified several novel modification sites on SARS-CoV-2 proteins that we investigated in relation to their interactions with host proteins. A detailed analysis of relevant modifications, including phosphorylation, ubiquitination, and S-nitrosylation, provides important hypotheses about the functional role of these modifications during viral infection by SARS-CoV-2.

category: bioinformatics


title: A rich get richer effect governs intracellular condensate size distributions

abstract: Phase separation of biomolecules into condensates has emerged as a ubiquitous mechanism for intracellular organization and impacts many intracellular processes, including reaction pathways through clustering of enzymes and their intermediates. Precise and rapid spatiotemporal control of reactions by condensates requires tuning of their sizes. However, the physical processes that govern the distribution of condensate sizes remain unclear. Here, we utilize a combination of synthetic and native condensates to probe the underlying physical mechanisms determining condensate size. We find that both native nuclear speckles and FUS condensates formed with the synthetic Corelet system obey an exponential size distribution, which can be recapitulated in Monte Carlo simulations of fast nucleation followed by coalescence. By contrast, pathological aggregation of cytoplasmic Huntingtin polyQ protein exhibits a power-law size distribution, with an exponent of -1.41 {+/-} 0.02. These distinct behaviors reflect the relative importance of nucleation and coalescence kinetics: introducing continuous condensate nucleation into the Monte Carlo coarsening simulations gives rise to polyQ-like power-law behavior. We demonstrate that the emergence of power-law distributions under continuous nucleation reflects a "rich get richer" effect, whose extent may play a general role in the determination of condensate size distributions.


title: Welfare concerns for mounted load carrying by working donkeys in Pakistan

abstract: Working donkeys (Equus asinus) are vital to peoples livelihoods. They are essential for carrying goods, however globally, overloading is one of the primary welfare concerns of working donkeys. We studied mounted load carrying by donkeys and associated factors in Pakistan. A cross-sectional study of donkey owners (n = 332) was conducted, and interviews were undertaken based on a questionnaire. Owners estimated that the median weight of their donkeys was 110kg (interquartile range (IQR) 100-120kg), and that they carried a median mounted load of 81.5kg (IQR 63-99kg). We found that 87.4% of donkeys carried a load above 50% of their bodyweight ratio (BWR), the median BWR carried was 77.1% (IQR 54.5-90.7%), and 25.3% of donkeys carried above 90% BWR. Donkeys that were loaded at more than 50% BWR were more likely to sit, compared to donkeys loaded with less weight (p=0.01). Donkeys working in peri-urban and urban areas were more likely to carry a greater BWR than donkeys working in rural areas (P<0.001), as were those carrying construction materials or bricks, compared to agricultural materials (p=0.004). Age (p=0.03) and breed (p=0.01) were also associated with carrying a higher weight. Overloading based on current recommendations (50% BWR) was common, with the majority (87.4%) of donkeys reported to carry more than the recommended 50% limit. This survey provides evidence of on-the-ground working practices and factors associated with mounted load carrying, which is critical for developing evidence-based recommendations for loading, in order to improve the welfare of working donkeys.

category: scientific communication and education


title: Comparison of individualized behavioral predictions across anatomical, diffusion and functional connectivity MRI

abstract:
A fundamental goal across the neurosciences is the characterization of relationships linking brain anatomy, functioning, and behavior. Although various MRI modalities have been developed to probe these relationships, direct comparisons of their ability to predict behavior have been lacking. Here, we compared the ability of anatomical T1, diffusion and functional MRI (fMRI) to predict behavior at an individual level. Cortical thickness, area and volume were extracted from anatomical T1 images. Diffusion Tensor Imaging (DTI) and approximate Neurite Orientation Dispersion and Density Imaging (NODDI) models were fitted to the diffusion images. The resulting metrics were projected to the Tract-Based Spatial Statistics (TBSS) skeleton. We also ran probabilistic tractography for the diffusion images, from which we extracted the stream count, average stream length, and the average of each DTI and NODDI metric across tracts connecting each pair of brain regions. Functional connectivity (FC) was extracted from both task and resting-state fMRI. Individualized prediction of a wide range of behavioral measures were performed using kernel ridge regression, linear ridge regression and elastic net regression. Consistency of the results were investigated with the Human Connectome Project (HCP) and Adolescent Brain Cognitive Development (ABCD) datasets. In both datasets, FC-based models gave the best prediction performance, regardless of regression model or behavioral measure. This was especially true for the cognitive domain. Furthermore, all modalities were able to predict cognition better than other behavioral domains. Combining all modalities improved prediction of cognition, but not other behavioral domains. Finally, across all behaviors, combining resting and task FC yielded prediction performance similar to combining all modalities. Overall, our study suggests that in the case of healthy children and young adults, behaviorally-relevant information in T1 and diffusion features might reflect a subset of the variance captured by FC.

HighlightsO_LIFC predicts behavior better than anatomical and diffusion features
C_LIO_LICognition is predicted better than other behavioral domains regardless of modality
C_LIO_LICombining resting & task FC improves prediction as much as combining all modalities
C_LIO_LIFindings were replicated over 3 regression models and 2 datasets
C_LI


title: Introducing RELAX (the Reduction of Electroencephalographic Artifacts): A fully automated pre-processing pipeline for cleaning EEG data - Part 2: Application to Event-Related Potentials

abstract:
Electroencephalography (EEG) is commonly used to examine neural activity time-locked to the presentation of a stimulus, referred to as an Event-Related Potential (ERP). However, EEG is also influenced by non-neural artifacts, which can confound ERP comparisons. Artifact cleaning can reduce artifacts, but often requires time-consuming manual decisions. Most automated cleaning methods require frequencies <1Hz to be filtered out of the data, so are not recommended for ERPs (which often contain <1Hz frequencies). In our companion article, we introduced RELAX (the Reduction of Electroencephalographic Artifacts), an automated and modular cleaning pipeline that reduces artifacts with Multiple Wiener Filtering (MWF) and/or wavelet enhanced independent component analysis (wICA) applied to artifact components detected with ICLabel (wICA_ICLabel) (Bailey et al., 2022). To evaluate the suitability of RELAX for data cleaning prior to ERP analysis, multiple versions of RELAX were compared to four commonly used EEG cleaning pipelines. Cleaning performance was compared across a range of artifact cleaning metrics and in the amount of variance in ERPs explained by different conditions in a Go-Nogo task. RELAX with MWF and wICA_ICLabel cleaned the data the most effectively and produced amongst the most dependable ERP estimates. RELAX with wICA_ICLabel only or MWF_only may detect experimental effects better for some ERP measures. Importantly, RELAX can high-pass filter data at 0.25Hz, so is applicable to analyses involving ERPs. The pipeline is easy to implement via EEGLAB in MATLAB and is freely available on GitHub. Given its performance, objectivity, and ease of use, we recommend RELAX for EEG data cleaning.

The MATLAB code, the supplementary materials, and a simple instruction manual explaining how to implement the RELAX pipeline can be downloaded from https://github.com/NeilwBailey/RELAX/releases. A condition of use of the pipeline is that the version of the pipeline used is referred to as RELAX_[pipeline], for example "RELAX_MWF_wICA" or "RELAX_wICA_ICLabel", and that the current paper be cited, as well as the dependencies used. These dependencies are likely to include: EEGLAB (Delorme & Makeig, 2004), fieldtrip (Oostenveld et al., 2011), the MWF toolbox (Somers et al., 2019), fastICA (Hyvarinen, 1999), wICA (Castellanos & Makarov, 2006), ICLabel (Pion-Tonachini et al., 2019), and PREP (Bigdely-Shamlo et al., 2015)

See our companion article for the application of RELAX to the study of oscillatory power (Bailey et al., 2022).


title: Sepsis-induced brain state instability

abstract: Sepsis-associated brain dysfunction (SABD) is a frequent severe complication of sepsis and the systemic inflammatory response syndrome. It is associated with high mortality and a majority of survivors suffer long-term neurological consequences. Here, we studied the effects of SABD on oscillatory brain states in an acute rat model of sepsis induced by high dose LPS (10 mg/kg). To focus on intrinsically generated brain state dynamics, we used a urethane model that spares oscillatory activity in REM- and NREM-like sleep states. Soon after the intraperitoneal LPS injection we observed a robust fragmentation of both oscillatory states resulting in a three-fold increase in the number of state transitions that lasted for several hours, although the overall time spent in either state did not change. Analysis of power spectra showed opposing shifts in low frequency oscillations (1-9 Hz) that resulted in increased similarity between both states in 2-D state space. The described spectral characteristics of sepsis-induced EEG state instability might point to a mechanism underlying severe sleep fragmentation as described both in sepsis patients and in SABD animal models.


title: Lingering neural representations of past task features adversely affect future behavior

abstract: During goal-directed behavior, humans purportedly form and retrieve so called  event files - conjunctive representations that link context-specific information about stimuli, their associated actions, and the expected action-outcomes. The automatic formation - and later retrieval - of such conjunctive  event file representations can substantially facilitate efficient action selection. However, recent behavioral work suggests that these event-files may also adversely affect future behavior, especially when action requirements have changed between successive instances of the same task context (e.g., during task-switching). Here, we directly tested this hypothesis through a recently developed method that allows measuring the strength of the neural representations of context-specific stimulus-action conjunctions (i.e., event files). Thirty-five male and female adult humans performed a task-switching paradigm while undergoing EEG recordings. Replicating previous behavioral work, we found that changes in action requirements between two spaced repetitions of the same task incurred a significant reaction time cost. By combining multi-variate pattern analysis and representational similarity analysis of the EEG recordings with linear mixed-effects modeling of trial-to-trial behavior, we then found that the magnitude of this behavioral cost was directly proportional to the strength of the conjunctive representation formed during the most recent previous exposure to the same task - i.e., the most recent  event file. This confirms that the formation of conjunctive representations of specific task contexts, stimuli, and actions in the brain can indeed adversely affect future behavior. Moreover, these findings demonstrate the potential of neural decoding of complex task set representations towards the prediction of behavior beyond the current trial.


title: Hippocampal Interneuronal Dysfunction and Hyperexcitability in Porcine Model of Concussion

abstract: Cognitive impairment is a common symptom following mild traumatic brain injury (mTBI or concussion) and can persist for years in some individuals. While the underlying mechanisms driving these impairments remain unknown, structural changes in the hippocampus post-mTBI have been reported in human patients, as well as electrophysiological changes in rodents following impact models of TBI. In addition, slice preparations from a closed-head, rotational acceleration injury (RAI) in swine showed reduced axonal function and hippocampal circuitry disruption. However, electrophysiological changes in neurons and their subtypes have not been examined. Using in vivo electrophysiology techniques, we examined the laminar oscillatory field potentials and single unit activity in the intact hippocampal network at 7 days post-RAI in anesthetized minipigs. Concussion altered the electrophysiological properties of pyramidal cells and interneurons differently in area CA1. Specifically, while firing rate and burst occurrence of CA1 interneurons were significantly decreased post-mTBI, these parameters were unchanged in putative CA1 pyramidal cells. However, pyramidal CA1 cells in TBI animals were significantly less entrained to hippocampal gamma (40 - 80 Hz) oscillations. In addition, stimulation of the Schaffer collaterals revealed hyperexcitability in the laminar CA1 response post-mTBI. Finally, computational simulations suggest that the reported changes in interneuronal firing rate and action potentials may be due to alterations in voltage-gated sodium channels. These data demonstrate that a single concussion can lead to significant neuronal and circuit level changes in the hippocampus, and that the loss of pyramidal gamma entrainment and changes in interneuronal firing may be important contributors to cognitive dysfunction following mTBI.


title: Hippocampal Interneuronal Dysfunction and Hyperexcitability in a Porcine Model of Concussion


title: Non-literal language processing is jointly supported by the language and Theory of Mind networks: Evidence from a novel meta-analytic fMRI approach

abstract:
Going beyond the literal meaning of utterances is key to communicative success. However, the mechanisms that support non-literal inferences remain debated. We use a novel meta-analytic approach to evaluate the contribution of linguistic, social-cognitive, and executive mechanisms to non-literal interpretation. We identified 74 fMRI experiments (n=1,430 participants) from 2001-2021 that contrasted non-literal language comprehension with a literal control condition, spanning ten phenomena (e.g., metaphor, irony, indirect speech). Applying the activation likelihood estimation approach to the 825 activation peaks yielded six left-lateralized clusters. We then evaluated the locations of both the individual-study peaks and the clusters against probabilistic functional atlases (cf. macroanatomy, as is typically done) for three candidate brain networks--the language-selective network (Fedorenko et al., 2011), which supports language processing, the Theory of Mind (ToM) network (Saxe & Kanwisher, 2003), which supports social inferences, and the domain-general Multiple-Demand (MD) network (Duncan, 2010), which supports executive control. These atlases were created by overlaying individual activation maps of participants who performed robust and extensively validated  localizer tasks (n=806 for language; n=198 for ToM; n=691 for MD). The analysis revealed that both the individual-study peaks and the ALE clusters fell primarily within the language network and the ToM network. These results suggest that non-literal processing is supported by both i) mechanisms that process literal linguistic meaning, and ii) mechanisms that support general social inference. They thus undermine a strong divide between literal and non-literal aspects of language and challenge the claim that non-literal processing requires additional executive resources.

Significance StatementNon-literal language is pervasive in communication. Past work has linked non-literal language understanding to language comprehension, social inference, and executive control, which selectively draw on the language, Theory of Mind (ToM), and Multiple Demand (MD) brain networks, respectively. Using a novel meta-analytic approach, we leverage  probabilistic functional atlases for these networks--created using fMRI data from hundreds of participants performing validated functional  localizers--to interpret activations for non-literal>literal contrasts from 74 past fMRI studies (1,430 participants, 825 activation peaks). Unlike traditional meta-analyses, which rely on anatomy for interpretation, this approach enables inferences about cognitive processes. We find that activations fall within the language and ToM networks, but not the MD network, undermining the role of executive control in non-literal interpretation.


title: Dissecting the Role of the Human Microbiome in COVID-19 via Metagenome-assembled Genomes

abstract: Coronavirus disease 2019 (COVID-19), primarily a respiratory disease caused by infection with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is often accompanied by gastrointestinal symptoms. However, little is known about the relation between the human microbiome and COVID-19, largely due to the fact that previous studies fail to provide high taxonomic resolution to identify microbes that likely interact with SARS-CoV-2 infection. Here we used whole-metagenome shotgun sequencing data together with assembly and binning strategies to reconstruct metagenome-assembled genomes (MAGs) from a total of 514 nasopharyngeal and fecal samples of patients with COVID-19 and controls. We reconstructed a total of 11,584 medium-and high-quality microbial MAGs and obtained 5,403 non-redundant MAGs (nrMAGs) with strain-level resolution. We found that, thanks to the high taxonomic resolution of nrMAGs, the gut microbiome signatures can accurately distinguish COVID-19 cases from healthy controls and predict the progression of COVID-19. Moreover, we identified a set of nrMAGs with a putative causal role in the clinical manifestations of COVID-19 and revealed their functional pathways that potentially interact with SARS-CoV-2 infection. The presented results highlight the importance of incorporating the human gut microbiome in our understanding of SARS-CoV-2 infection and disease progression. The genomic content of nrMAGs presented here has the potential to inform microbiome-based therapeutic developments for COVID-19 progression and post-COVID conditions.


title: The Plasmodium falciparum CCCH zinc finger protein ZNF4 plays an important role in gametocyte exflagellation through the regulation of male gametocyte enriched transcripts

abstract:
CCCH zinc finger proteins (ZFPs) function mainly as RNA-binding proteins (RBPs) where they play a central role in the mRNA metabolism. Over 27 CCCH-ZFPs are encoded in the genome of the human malaria parasite Plasmodium falciparum, the causative agent of malaria tropica. However, little is known about their functions. In this study, we characterize one member of the PfCCCH-ZFP named ZNF4. We show that ZNF4 is highly expressed in mature gametocytes where it predominantly localizes to the cytoplasm. Targeted gene disruption of ZNF4 showed no significant effect in asexual blood stage replication and gametocyte development while male gametocyte exflagellation was significantly impaired leading to reduced malaria transmission in the mosquito. Comparative transcriptomics between wildtype (WT) and the ZNF4-deficient line (ZNF4-KO) demonstrated the de-regulation of about 473 genes (274-upregulated and 199 down-regulated) in mature gametocytes. Most of the down-regulated genes show peak expression in mature gametocyte with male enriched genes associated to the axonemal dynein complex formation and cell projection organization highly affected, pointing to the phenotype in male gametocyte exflagellation. Up-regulated genes are associated to ATP synthesis. Our combine data therefore indicate that ZNF4 is a CCCH zinc finger protein which plays an important role in male gametocyte exflagellation through the regulation of male gametocyte enriched genes.

Author SummaryCCCH ZFPs have gained significant interest due to their ability to interact with RNA and control different RNA metabolic processes. The role of CCCH ZFPs in the malaria parasite Plasmodium falciparum has not been well studied. In this study we report the functional characterization of a PfCCCH-ZFP named ZNF4. Using mouse anti-ZNF4 antisera and a ZNF4-HA tag parasite line we show that the protein is mainly expressed in the cytosol of mature gametocytes. To determine the function of ZNF4, we generated a ZNF4 knockout parasite line and we found that the asexual blood stages and gametocytes developed normally while the ability of the male gametocytes to exflagellate as well as the further development of the parasite in the mosquito was significantly impaired. Interestingly, when the transcriptome of mature gametocytes of the ZNF4-KO was compared to the WT, down-regulated genes were mainly male gametocyte enriched genes associated to processes involved in gametocyte exflagellation such axonemal dynein complex formation and cell projection organization indicating that ZNF4 plays an important role in male gametocyte exflagellation through the regulation of male gametocyte enriched transcripts.

category: cell biology


title: BMAL1 and MEX3A co-regulate intestinal stem cell succession

abstract: Chemotherapeutic agents, such as 5-fluorouracil (5-FU), often induce intestinal mucositis due to toxicity to rapidly dividing intestinal stem cells (ISCs). Drug delivery at different times of day can alter 5-FU toxicity; however, the underlying biology is unclear. We found that homeostasis and succession between two ISC types, fast proliferating Lgr5+ crypt base columnar (CBC) cells and stress-resistant +4 cells (Bmi1+), are controlled by the circadian clock transcription factor BMAL1 and the BMAL1-regulated RNA-binding protein MEX3A via both direct transcriptional regulation and post-transcriptional control of Lgr5 mRNA stability. Bmal1 knockout in Lgr5+ CBCs reduced MEX3A expression and CBC numbers but increased Bmi1 expression in the crypts. Timing 5-FU delivery when crypt cells had low Lgr5 but peak level of Bmi1 protected ISCs from apoptosis. Together, these findings identify a novel role of BMAL1 in ISC homeostasis and provide a biological explanation for chronotherapeutic chemoprotection.


title: ITS-based assessment of Madagascar's fungal diversity and arrival of EcM fungi to the island

abstract:
Madagascar is known for its high diversity and endemism of Fauna and Flora, which makes it particularly interesting for research on diversity and evolution. Fungi, however, have been largely overlooked, and whether fungi exhibit the same patterns as animals and plants has yet to be further examined.

We collected fungal sporocarps and ectomycorrhizal (EcM) roots during opportunistic surveys in five forests in Madagascar and generated a dataset of fungal Internal Transcribed Spacer (ITS) DNA sequences. We analysed them together with all publicly available fungal ITS DNA sequences. We identified 620 Operational Taxonomic Units (OTUs) from Madagascar, 10% of which contained only sequences from our surveys. We found 292 OTUs belonging to EcM species with /russula-lactarius, /boletus, /tomentella-telephora, /cortinarius and /amanita as the most abundant EcM lineages. Overall, sixty percent of all the fungi and 81% of the EcM species found are endemic to Madagascar. Lastly, we conducted a phylogenetic analysis using all the OTUs in Amanitaceae, Boletaceae and Russulaceae families to elucidate their relative timing of arrival in Madagascar. We found that the EcM species from Madagascar in the three families diverged recently (less than 34 mya), long after the separation of India and Madagascar (88 mya), which is consistent with a dispersal mediated process of arrival on the island. Our study provides the first comprehensive view of the current state of knowledge of EcM fungi in Madagascar represented by molecular data useful for ecological and evolutionary studies.

category: ecology


title: ITS-based assessment of Madagascar's fungal diversity and arrival of ectomycorrhizal fungi to the island


title: Iterative deletion of gene trees detects extreme biases in distance-based phylogenomic coalescent analyses

abstract: Summary coalescent methods offer an alternative to the concatenation (supermatrix) approach for inferring phylogenetic relationships from genome-scale datasets. Given huge datasets, broad congruence between contrasting phylogenomic paradigms is often obtained, but empirical studies commonly show some well supported conflicts between concatenation and coalescence results and also between species trees estimated from alternative coalescent methods. Partitioned support indices can help arbitrate these discrepancies by pinpointing outlier loci that are unjustifiably influential at conflicting nodes. Partitioned coalescence support (PCS) recently was developed for summary coalescent methods, such as ASTRAL and MP-EST, that use the summed fits of individual gene trees to estimate the species tree. However, PCS cannot be implemented when distance-based coalescent methods (e.g., STAR, NJst, ASTRID, STEAC) are applied. Here, this deficiency is addressed by automating computation of  partitioned coalescent branch length (PCBL), a novel index that uses iterative removal of individual gene trees to assess the impact of each gene on every clade in a distance-based coalescent tree. Reanalyses of five phylogenomic datasets show that PCBL for STAR and NJst trees helps quantify the overall stability/instability of clades and clarifies disagreements with results from optimality-based coalescent analyses. PCBL scores reveal severe  missing taxa,  apical nesting,  misrooting, and  basal dragdown biases. Contrived examples demonstrate the gross overweighting of outlier gene trees that drives these biases. Because of interrelated biases revealed by PCBL scores, caution should be exercised when using STAR and NJst, in particular when many taxa are analyzed, missing data are non-randomly distributed, and widespread gene-tree reconstruction error is suspected. Similar biases in the optimality-based coalescent method MP-EST indicate that congruence among species trees estimated via STAR, NJst, and MP-EST should not be interpreted as independent corroboration for phylogenetic relationships. Such agreements among methods instead might be due to the common defects of all three summary coalescent methods.


title: Immediate perturbation of DNA methylation upon acute prenatal alcohol exposure in the mouse developing brain cortex

abstract:
The reshaping of the DNA methylome landscape after prenatal alcohol exposure (PAE) has been well-documented in the adult brain, therefore a long time after the end of the exposure. However, the question of the immediate deposition or loss of DNA methylation marks in the prenatal neocortex, just after the end of PAE has not yet been directly addressed, genome widely.

Using a binge-drinking-like model of PAE and capture of the DNA methylome, we have identified differentially methylated regions (DMRs) that are established immediately, within two hours after the end of PAE. Remarkably, these DMRs are prominently and statistically associated with: (i) enhancers that are active in the brain, associated with GO terms of importance for neurogenesis, neurodevelopment, and neuronal differentiation; (ii) genes that, in physiological conditions show dynamic gain in chromatin accessibility and/or upregulation of their expression in the time-window of exposure; (iii) imprinted genes and members of protocadherin genes clusters, two gene families playing key roles in neurodevelopment, whose mono-allelically expression is regulated by DNA methylation and impaired upon PAE. We observed that DMR-containing mono-allelically expressed genes, as well as other genes important for neurodevelopment, are also immediately upregulated upon PAE, suggesting that these early DNA methylation perturbations are thus highly susceptible to rapidly alter gene expression after PAE.

DMRs in imprinted and protocadherin genes have been previously identified, both in the adult rodent brain prior-exposed to alcohol prenatally, and in cohorts of children diagnosed with fetal alcohol spectrum disorders (FASD). Our study thus strongly suggests that the DNA methylation profiles of key regulatory regions of these gene families are very quickly disturbed after the PAE and that these immediate altered regions could be persistently affected long after the stress. This strongly reinforces their potential as future biomarkers of PAE.

Ethical issuesThe breeding and treatments of wild type C57BL/6N mice, used for the experimental protocols described in this study have been approved by the Institutional Animal Care and Use Ethical Committee of the Paris University (registration number CEEA-40). The project has been recorded under the following reference by the Ministere de lEnseignement Superieur et de la Recherche (#2016040414515579). All efforts were made to reduce stress and pain to animals.

category: genomics


title: A Dynamic Bottom-Up Saliency Detection Method for Still Images

abstract:
IntroductionExisting saliency detection algorithms in the literature have ignored the importance of time. They create a static saliency map for the whole recording time. However, bottom-up and top-down attention continuously compete and the salient regions change through time. In this paper, we propose an unsupervised algorithm to predict the dynamic evolution of bottom-up saliency in images.

MethodWe compute the variation of low-level features within non-overlapping patches of the input image. A patch with higher variation is considered more salient. We use a threshold to ignore less salient parts and create a map. A weighted sum of this map and its center of mass is calculated to provide the saliency map. The threshold and weights are set dynamically. We use the MIT1003 and DOVES datasets for evaluation and break the recording to multiple 100ms or 500ms-time intervals. A separate ground-truth is created for each interval. Then, the predicted dynamic saliency map is compared to the ground-truth using Normalized Scanpath Saliency, Kullback-Leibler divergence, Similarity, and Linear Correlation Coefficient metrics.

ResultsThe proposed method outperformed the competitors on DOVES dataset. It also had an acceptable performance on MIT1003 especially within 0-400ms after stimulus onset.

ConclusionThis dynamic algorithm can predict an images salient regions better than the static methods as saliency detection is inherently a dynamic process. This method is biologically-plausible and in-line with the recent findings of the creation of a bottom-up saliency map in the primary visual cortex or superior colliculus.


title: Neuroendocrinology of the lung revealed by single cell RNA sequencing

abstract: Pulmonary neuroendocrine cells (PNECs) are sensory epithelial cells that transmit airway status to the brain via sensory neurons and locally via CGRP and GABA. Several other neuropeptides and neurotransmitters have been detected in various species, but the number, targets, functions, and conservation of PNEC signals are largely unknown. We used scRNAseq to profile hundreds of the rare mouse and human PNECs. This revealed >40 PNEC neuropeptide and peptide hormone genes, most cells expressing unique combinations of 5-18 genes. Peptides are packaged in separate vesicles, release presumably regulated by the distinct, multimodal combinations of sensors expressed by each PNEC. Expression of cognate receptors predicts an array of local targets, and we show the new PNEC signal angiotensin directly activates innervating sensory neurons. Many signals lack lung targets so may have endocrine activity like those of PNEC- derived carcinoid tumors. PNECs are an extraordinarily rich and diverse signaling hub rivaling the enteroendocrine system.


title: Correlation of biomechanics and cancer cell phenotype by combined Brillouin and Raman spectroscopy of U87-MG glioblastoma cells

abstract: The elucidation of biomechanics furthers understanding of brain tumor biology. Brillouin spectroscopy is a new optical method that addresses viscoelastic properties down to subcellular resolution in contact-free manner. Moreover, it can be combined with Raman spectroscopy to obtain co-localized biochemical information. Here, we applied co-registered Brillouin and Raman spectroscopy to U87-MG human glioblastoma cells in vitro. Using 2D and 3D cultures, we related biomechanical properties with local biochemical composition at subcellular level, as well as cell phenotype. Brillouin and Raman mapping of adherent cells showed that the nucleus and nucleoli are stiffer than the perinuclear region and the cytoplasm. The biomechanics of cell cytoplasm is affected by culturing conditions, i.e. cells grown as spheroids being stiffer than adherent cells. Inside the spheroids, the presence of lipid droplets as assessed by Raman spectroscopy reveals higher Brillouin shifts which is not related to local stiffness increase, but due to a higher refractive index combined with a lower mass density. This highlights the importance of locally defined biochemical reference data for a correct interpretation of the Brillouin shift of cells and tissue in future studies investigating the biomechanics of brain tumor models by Brillouin spectroscopy.


title: Reliable one-step assessment of IGHV mutational status and gene mutations in Chronic Lymphocytic Leukemia by capture-based high throughput sequencing.

abstract:
Proper management of chronic lymphocytic leukemia (CLL) patients requiring therapy relies on two important prognostic and theranostic molecular features: respectively, the mutational status of tumoral cells immunoglobulin heavy chain variable domain (IGHV) and the characteristics of TP53. Both these (immuno)genetic analyses require multiple time-consuming amplification and sequencing techniques by Sanger or HTS. The capture-HTS technology, allowing to select regions of interest, represents an attractive alternative and has already been applied for the detection of clonality in lymphoproliferative disorders. Here, a single-step capture design was developed to concomitantly investigate for IGHV and TP53. This was applied to a training retrospective (n=14) and a validation prospective (n=91) cohorts of CLL patients. The training cohort demonstrated the robustness of the method by comparison with the classical Sanger sequencing technology (100% identical results) for the IGHV mutational status. This consistency was confirmed for the first 59 patients of the validation cohort. Overall, the IGHV status of whole population (n=103) was accurately identified. Simultaneously, deletion or mutations of TP53 were identified from the same capture-library and HTS-sequencing run for each patient. This novel approach provides, in a single assay, useful answers about the molecular landscape of CLL patients, allowing for a documented choice of therapy.

Graphical abstract

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title: Interferon regulatory factor 3 upregulates the Treg recruitment factor CCL22 in response to double-stranded DNA in cancer cells

abstract: Cancer immunotherapy holds great promise for the treatment of solid tumors, but its effectiveness is hindered by the recruitment of regulatory T cells (Tregs), which inhibit anti-tumor immune responses. We report here that cytosolic dsDNA, a characteristic of many cancer cells, upregulates expression of the Treg-recruitment chemokine CCL22 in multiple types of malignant epithelial cells. We also identified that interferon regulatory factor 3 (IRF3) is a key regulator of CCL22 in response to dsDNA. Both IRF3 and NF-{kappa}B are activated downstream of the stimulator of interferon genes (STING), a primary effector protein responding to multiple cytosolic dsDNA sensors. IRF3 activation by STING triggers robust expression of type I interferons, which can boost anti-tumor immune responses. Thus, STING agonists have been used clinically to activate IRF3 during immunotherapy. However, STING activation in some cases is reported to paradoxically foster a pro-tumor, immunosuppressive environment. Our finding that IRF3 regulates CCL22 in response to dsDNA suggests a possible mechanism contributing to STING-mediated immunosuppression. In addition, we found that cultured cancer cells appear able to evolve mechanisms to co-opt nucleic acid sensing pathways to upregulate CCL22, suggesting that these pathways may contribute to acquired immune evasion in tumors with increased cytosolic dsDNA.


title: Homophilic wiring principles underpin neuronal network topology in vitro

abstract: Economical efficiency has been a popular explanation for how networks organize themselves within the developing nervous system. However, the precise nature of the economic negotiations governing this self-organization remain unclear. We approach this problem by combining high-density microelectrode array (HD-MEA) recordings, which allow for detailed characterization of the ongoing extracellular electrical activity of individual neurons in vitro, with a generative modeling approach capable of simulating network formation. The best fitting model uses a homophilic generative wiring principle in which neurons form connections to other neurons with similar connectivity patterns to themselves. This homophily-based mechanism for neuronal network emergence accounts for a wide range of observations that are described, but not sufficiently explained, by traditional analyses of network topology. Using rodent and human monolayer and organoid cultures, we show that homophilic generative mechanisms account for the topology of emerging cellular functional connectivity, representing an important wiring principle and determining factor of neuronal network formation in vitro.


title: Vocalization categorization behavior explained by a feature-based auditory categorization model

abstract: Vocal animals produce multiple categories of calls with high between- and within-subject variability, over which listeners must generalize to accomplish call categorization. The behavioral strategies and neural mechanisms that support this ability to generalize are largely unexplored. We previously proposed a theoretical model that accomplished call categorization by detecting features of intermediate complexity that best contrasted each call category from all other categories. We further demonstrated that some neural responses in the primary auditory cortex were consistent with such a model. Here, we asked whether a feature-based model could predict call categorization behavior. We trained both the model and guinea pigs on call categorization tasks using natural calls. We then tested categorization by the model and guinea pigs using temporally and spectrally altered calls. Both the model and guinea pigs were surprisingly resilient to temporal manipulations, but sensitive to moderate frequency shifts. Critically, model performance quantitatively matched guinea pig behavior to a remarkable degree. By adopting different model training strategies and examining features that contributed to solving specific tasks, we could gain insight into possible strategies used by animals to categorize calls. Our results validate a model that uses the detection of intermediate-complexity contrastive features to accomplish call categorization.


title: Introducing RELAX (the Reduction of Electroencephalographic Artifacts): A fully automated pre-processing pipeline for cleaning EEG data - Part 1: Algorithm and Application to Oscillations

abstract: Electroencephalographic (EEG) data is typically contaminated with non-neural artifacts which can confound the results of experiments. Artifact cleaning approaches are available, but often require time-consuming manual input and significant expertise. Advancements in artifact cleaning often only address a single artifact, are only compared against a small selection of pre-existing methods, and seldom assess whether a proposed advancement improves experimental outcomes. To address these issues, we developed RELAX (the Reduction of Electroencephalographic Artifacts), an automated EEG cleaning pipeline implemented within EEGLAB that reduces all artifact types. RELAX cleans continuous data using Multiple Wiener filtering [MWF] and/or wavelet enhanced independent component analysis [wICA] applied to artifacts identified by ICLabel [wICA_ICLabel]). Several versions of RELAX were tested using three datasets containing a mix of cognitive and resting recordings (N = 213, 60 and 23 respectively). RELAX was compared against six commonly used EEG cleaning approaches across a wide range of artifact cleaning quality metrics, including signal-to-error and artifact-to-residue ratios, measures of remaining blink and muscle activity, and the amount of variance explained by experimental manipulations after cleaning. RELAX with MWF and wICA_ICLabel showed amongst the best performance for cleaning blink and muscle artifacts while still preserving neural signal. RELAX with wICA_ICLabel (and no MWF) may perform better at detecting the effect of experimental manipulations on alpha oscillations in working memory tasks. The pipeline is easy to implement in MATLAB and freely available on GitHub. Given its high cleaning performance, objectivity, and ease of use, we recommend RELAX for data cleaning across EEG studies.


title: Methionine uptake via SLC43A2 transporter is essential for regulatory T lymphocyte survival

abstract: It is increasingly clear that cell death, survival or growth decisions of T lymphocyte subsets depend on interplay between cytokine-dependent and metabolic processes. What the metabolic requirements of T regulatory cells (Tregs) for their survival are, and how these requirements are satisfied remain to be fully understood. In this study, we identified a necessary requirement of methionine uptake and utilization for Tregs survival upon interleukin 2 (IL-2) deprivation. Activated Tregs have high methionine uptake and consumption to S-adenosyl methionine (SAM) and S-adenosyl homocysteine (SAH). This methionine uptake is essential for Tregs survival, and is regulated by Notch1 activity. Notch1 controls the expression of the solute carrier protein SLC43A2 transporter during IL-2 deprivation. SLC43A2 is necessary for sufficient methionine uptake, and determines Tregs viability upon IL-2 withdrawal. Collectively, we identify a specifically regulated mechanism of methionine import in Tregs that is necessary for the survival of these cells. This highlights the need for methionine availability and metabolism in contextually regulating cell death in an immunosuppressive population of T lymphocytes.


title: Phospholipase Cβ2 Promotes Vascular Endothelial Growth Factor Induced Vascular Permeability

abstract:
BackgroundRegulation of vascular permeability (VP) is critical to maintaining tissue metabolic homeostasis. Vascular endothelial growth factor (VEGF) is a key stimulus of VP in acute and chronic diseases including ischemia reperfusion injury, sepsis and cancer. Identification of novel regulators of VP would allow for the development of effective targeted therapeutics for patients with unmet medical need.

MethodsIn vitro and in vivo models of VEGFA-induced vascular permeability, pathological permeability, quantitation of intracellular calcium release and cell entry, and PIP2 levels were evaluated with and without modulation of PLC{beta}2.

ResultsGlobal knock-out of PLC{beta}2 in mice resulted in blockade of VEGFA-induced vascular permeability in vivo and trans-endothelial permeability in primary lung endothelial cells. Further work in an immortalized human microvascular cell line modulated with stable knock-down of PLC{beta}2 recapitulated the observations in the mouse model and primary cell assays. Additionally, loss of PLC{beta}2 limited both intracellular release and extracellular entry of calcium following VEGF stimulation as well as reduced basal and VEGFA-stimulated levels of PIP2 compared to control cells. Finally, loss of PLC{beta}2 in both a hyperoxia induced lung permeability model and a cardiac ischemia:reperfusion model resulted in improved animal outcomes when compared to WT controls.

ConclusionsThe results implicate PLC{beta}2 as a key positive regulator of VEGF-induced VP through regulation of both calcium flux and PIP2 levels at the cellular level. Targeting of PLC{beta}2 in a therapeutic setting may provide a novel approach to regulating vascular permeability in patients.

Graphic Abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

HighlightsO_LIPLC{beta}2 promotes VEGFA induced vascular permeability.
C_LIO_LILoss of PLC{beta}2 prevents VEGFA vascular permeability via repression of cellular calcium flux and membrane PIP2 levels.
C_LIO_LILoss of PLC{beta}2 reduces vascular permeability and improves outcomes in a hyperoxic lung damage model and a cardiac ischemia:reperfusion model in vivo.
C_LIO_LITargeting PLC{beta}2 inhibition may lead to a novel therapeutic for diseases such as stroke and myocardial infarction.
C_LI


title: Lymphangiocrine signals are required for proper intestinal repair after cytotoxic injury

abstract: The intestinal epithelium undergoes continuous renewal and has an exceptional capacity to regenerate after injury. Maintenance and proliferation of intestinal stem cells (ISCs) is regulated by their surrounding niche, largely through Wnt signaling. However, it remains undetermined which niche cells produce signals during different injury states, and the role of endothelial cells (ECs) as a component of the ISC niche during homeostasis and after injury has been underappreciated. Here, we show that lymphatic endothelial cells (LECs) reside in proximity to crypt epithelial cells and secrete molecules that support epithelial renewal and repair. The LECs are an essential source of Wnt signaling in the small intestine, as loss of LEC-derived Rspo3 leads to a lower number of stem and progenitor cells and hinders recovery after cytotoxic injury. Together, our findings identify LECs as an essential niche component for optimal intestinal recovery after cytotoxic injury.


title: Interconnection between molecular regulators in LMNA related muscular dystrophy

abstract: Nuclear lamina is composed of different A-type and B-type lamin proteins and acts as major regulator of DNA replication, transcription, heterochromatin-euchromatin machinery. The majority of mutations in A type lamin are associated with some forms of muscular dystrophies,that majorly distinguishable by a common clinical feature : progressive skeletal muscle wasting. This speculates impaired skeletal muscle differentiation during development and after injury with the influence of myriad of signalling pathways. The molecular mechanism behind phenotypes of lamin A associated muscular dystrophies are still elusive . Here, we used genome wide expression analysis platform during the differentiation of murine C2C12 skeletal muscle cells to investigate the factors have been attributed to the disease. We compared the expression levels of the components of pathways that indicates important role of skeletal muscle as well as identified gene regulatory networks at two different time points of muscle differentiation in wild type and mutant cells. We also report significant perturbations in the expression and activation of Wnt signalling pathway in mutant cells among 40 dysregulated signalling pathways , presenting pronounced regulation of normal downstream myogenic signalling . Finally, with this largest data sets we evaluate in depth characterization of molecular effectors for myogenic differentiation, which could allow greater insight into development of therapeutic strategies for the remission of patients with LMNA linked muscle - related pathologies.


title: Inter-microscope comparability of dental microwear texture data obtained from obtained from different optical profilometers.

abstract: Dental microwear texture analysis has become a well-established approach for dietary inference and reconstruction of mammals and other tetrapods, both extant and extinct. As the amount of available data grows immensely, researchers could benefit from combining data gathered by others to perform meta-analyses. However, different devices used to capture three-dimensional surface scans for DMTA are known to produce variation even when measuring the same surface. Here we compare DMTA data of 36 guinea pigs that received different diets in a controlled feeding experiment, measured on a confocal disc-scanning and a confocal laser-scanning microscope. We are testing different pre-analysis filtering protocols to mitigate differences. We find inter-microscopes and filter-related differences for the majority of analysed 41 DMTA parameters. Certain microscope-specific filter routines resulted in less differences than other pre-analysis protocols. We further identify DMTA parameters which were stable regardless of microscope or pre-analysis treatment. Overall, the results obtained on both microscopes show the same dietary differentiation between guinea pig feeding groups, which supports that DMTA is a suitable method to obtain repeatable, objective dietary inferences. We finally propose a roadmap to enhance data exchange and inter-lab comparability and collaboration in the future.


title: Inter-microscope comparability of dental microwear texture data obtained from different optical profilometers.


title: MOSAIC: A Unified Trait Database to Complement Structured Population Models

abstract:
O_LIThe ecological sciences have joined the big data revolution. However, despite exponential growth in data availability, broader interoperability amongst datasets is still needed to unlock the potential of open access. The interface of demography and functional traits is well-positioned to benefit from said interoperability. Trait-based ecological approaches have been criticised because of their inability to predict fitness components, the core of demography; likewise, demographic approaches are data-hungry, and so using traits as ecological shortcuts to understanding and forecasting population viability could offer great value.
C_LIO_LIHere, we introduce MOSAIC, an open-access trait database that unlocks the demographic potential stored in the COMADRE, COMPADRE, and PADRINO open-access databases. MOSAIC data have been digitised and curated through a combination of existing datasets and additional taxonomic and/or trait records sourced from primary literature. In its first release, MOSAIC (v. 1.0.0) includes 14 trait fields for 300 animal and plant species: biomass, height, growth determination, regeneration, sexual dimorphism, mating system, hermaphrodism, sequential hermaphrodism, dispersal capacity, type of dispersal, mode of dispersal, dispersal classes, volancy, and aquatic habitat dependency. MOSAIC also includes species-level phylogenies for 1,359 species and population-specific climate data where locations are recorded.
C_LIO_LIUsing MOSAIC, we highlight a taxonomic mismatch of widely used trait databases with existing structured population models. Despite millions of trait records available in open-access databases, taxonomic overlap between open-access demographic and trait databases is <5%. We identify where traits of interest to ecologists can benefit from database integration and start to quantify traits that are poorly quantified (e.g., growth determination, modularity).
C_LIO_LIThe MOSAIC database evidences the importance of improving interoperability in open-access efforts in ecology as well as the need for complementary digitisation to fill targeted taxonomic gaps. In addition, MOSAIC highlights emerging challenges associated with the disparity between locations where different trait records are sourced.
C_LI


title: Origin and persistence of polymorphism in loci targeted by disassortative preference: a general model

abstract: The emergence and persistence of polymorphism within populations generally requires specific selective regimes. Here, we develop an unifying theoretical framework to explore how disassortative mating can generate and maintain polymorphism at the targeted loci. To this aim, we model the dynamics of alleles at a single locus A in a population of haploid individuals, where reproductive success depends on the combination of alleles carried by the parents at locus A. Our theoretical study of the model confirms that the conditions for the persistence of a given level of allelic polymorphism depend on the relative reproductive advantages among pairs of individuals. Interestingly, equilibria with unbalanced allelic frequencies were shown to emerge from successive introduction of mutants.We then investigate the role of the function linking allelic divergence to reproductive advantage on the evolutionary fate of alleles within population. Our results highlight the significance of the shape of this function on both the number of alleles maintained and their level of genetic divergence. Large number of alleles are maintained with substantial turn-over among alleles when disassortative advantage slowly increases when allelic differentiation becomes large. In contrast, few highly differentiated alleles are predicted to be maintained when genetic differentiation has a strong effect on disassortative advantage. These opposite effects predicted by our model shed light on the levels of allelic differentiation and polymorphism empirically observed in loci targeted by disassortative mate choice.


title: Putting life history theory to the test - the estimation of reproductive values from field data

abstract: Quantifying fitness is important to understand adaptive evolution. Reproductive values are useful for making fitness comparisons involving different categories of individuals, like males and females. By definition, the reproductive value of a category is the expected per capita contribution of the members of that category to the gene pool of future generations. Life history theory reveals how reproductive values can be determined from life-history parameters, but this requires matrix algebra. Recently, a more intuitive, pedigree-based method has become popular. It estimates genetic contributions of individuals to future generations by tracking their descendants. Here we compare both methods. We implement various life-history scenarios (for which the "true" reproductive values can be calculated) in individual-based simulations, use this data to estimate reproductive values with both methods, and compare the results with the true reproductive values. We show that the pedigree-based estimation of reproductive values is either systematically biased (and hence inaccurate), or very imprecise. This holds even for simple life histories and under idealized conditions. The traditional algebraic method estimates reproductive values with accuracy, and the precision of estimates can be determined by sensitivity analyses. However, these estimates can be biased as well when they are based on inadequate life-history models.


title: Accelerating Minimap2 for accurate long read alignment on GPUs

abstract:
BackgroundLong read sequencing technology is becoming increasingly popular for Precision Medicine applications like variant calling from Whole Genome Sequencing (WGS) and for metagenomics applications like microbial abundance estimation. Minimap2 is the state-of-the-art aligner and mapper used by the leading long read sequencing technologies, today. However, Minimap2 is very slow for long noisy reads. 60-70% of the run-time on a CPU comes from the highly sequential chaining step in Minimap2. On the other hand, most Point-of-Care computational workflows in long read sequencing use Graphics Processing Units (GPUs). We present minimap2-accelerated (mm2-ax), a heterogeneous design for sequence mapping and alignment where the compute intensive chaining step of minimap2 is sped up on the GPU and demonstrate its time and cost benefits.

ResultsWe extract better intra-read parallelism from chaining without loosing mapping accuracy by forward transforming Minimap2s chaining algorithm. Further, we utilize the high memory available on modern cloud instances for better performance on the GPU by converting a sparse vector which defines the chaining workload to a dense one in order to optimize for better arithmetic intensity (more operations per byte of data fetched from high-latency global memory) on the GPU. We also optimize for better workload balancing, data locality and minimal branch divergence on the GPU. We show mm2-ax on an NVIDIA A100 GPU improves the chaining step with 12.6 - 5X speedup and 9.44 - 3.77X speedup : costup over the fastest version of Minimap2, mm2-fast, benchmarked on a single Google Cloud Platform instance of 30 SIMD cores.

Conclusionsmm2-ax is minimap2 sped-up on GPU without losing mapping accuracy. mm2-ax executable is made available at: https://doi.org/10.5281/zenodo.6374533.


title: Fear of the new? Geckos hesitate to attack novel prey, feed near objects and enter a novel space

abstract: Neophobia, the fear of novelty, is an ecologically important response which enables animals to avoid potentially harmful situations. Low levels of neophobia have been linked to elevated dispersal/ migration, invasiveness and living in human modified landscapes albeit only in birds and mammals. In this study, we assessed neophobia in captive Tokay geckos (Gekko gecko). We expected to find low neophobia in our geckos because they are invasive and adopt well to anthropogenic environments. This species is, however, also both predator and prey in the wild which might select for higher neophobia. We tested neophobia in three contexts: attacking novel prey, foraging near novel objects and entering a novel space. We aimed to quantify (1) neophobia in these contexts, (2) individual consistency across trials using different novel stimuli, and (3) correlation of individual responses across the three contexts. We found that geckos hesitate to attack novel prey and prey close to objects (familiar and novel). Geckos hesitated the most when entering novel space and repeatability of behaviour across contexts was low (R = 0.12) indicating that neophobia might not be a single trait. The strength of a neophobic response can indicate how anxious or curious an individual is. This test has great potential to help answer questions about how captivity, enrichment, rearing environment and cognition affect fear responses in different contexts in lizards. By studying reptiles, we can better understand the universality of what is known about the causes leading to difference in neophobia across individuals and species.


title: URB597 induces aggression in adult Lister Hooded rats

abstract:
The endocannabinoid system has been implicated in both social and cognitive processing. The endocannabinoid metabolism inhibitor, URB597, dose-dependently improves non-social memory in adult Wistar and Sprague Dawley rats, whereas its effect on social interaction (SI) is affected by both rat strain and drug dose. Lister Hooded rats consistently respond differently to drug treatment in general compared with albino strains. This study sought to investigate the effects of different doses of URB597 on social and non-social memory in Lister Hooded rats, as well as analysing the behavioural composition of the SI.

Males were tested for novel object recognition (NOR), social preference (between an object and an unfamiliar rat), social novelty recognition (for a familiar vs unfamiliar rat) and SI with an unfamiliar rat. URB597 (0.1 or 0.3 mg/kg) or vehicle was given 30 minutes before testing. During SI testing, total interaction time was assessed along with time spent on aggressive and explorative behaviours.

Lister Hooded rats displayed expected non-social and social memory and social preference, which was not affected by URB597. During SI, URB597 did not affect total interaction time. However, the high dose increased aggression, compared to vehicle, and decreased anogenital sniffing, compared to the low dose of URB597. In summary, URB597 did not affect NOR, social preference or social recognition memory but did have subtle behavioural effects during SI in Lister hooded rats.

These findings highlight the importance of considering strain as well as the composition of behaviour when investigating drug effects on social behaviour.


title: The Vaccinia virus chondroitin sulfate binding protein drives host membrane curvature to facilitate fusion

abstract: Virus binding serves to define virus tropism and species specificity1. Virus binding proteins are classically considered as facilitators of cell surface attachment prior to receptor engagement and virus internalization. For efficient entry vaccinia virus (VACV) - the prototypic poxvirus - relies on four binding proteins and an eleven-protein entry fusion complex (EFC)2. We recently demonstrated that VACV binding and fusion proteins are organized into distinct functional domains, with localization of EFC proteins to virion tips directly influencing membrane fusion activity3. However, the relationship between virus binding protein distribution, virion binding orientation and subsequent membrane fusion remain unexplored. Here, we show that virus binding proteins guide side-on virion binding and promote curvature of the host membrane towards EFC-containing virion tips to facilitate virus fusion. Using a cell-derived membrane-bleb model system together with super-resolution and electron microscopy we found that side-bound VACV virions induce membrane invagination in the presence of low pH. Repression or deletion of individual binding proteins revealed that three of four contribute to binding orientation, amongst which the chondroitin sulphate binding protein, D8, is required for host membrane bending. Consistent with low-pH dependent macropinocytic entry of vaccinia virus4,5, loss of D8 prevents virion-associated macropinosome membrane bending, disrupts fusion pore formation and infection kinetics. Our results extend the role of viral binding proteins from mere attachment factors to active participants in successful viral membrane fusion and further illustrate the influence of virus protein architecture on successful infection.


title: Voltage-Sensing Phosphatase (VSP) Regulates Endocytosis-Dependent Nutrient Absorption in Chordate Enterocytes

abstract:
Voltage-sensing phosphatase (VSP) is a unique membrane protein that translates membrane electrical activities into the changes of phosphoinositide profiles. VSP orthologs from various species have been intensively investigated toward their biophysical properties, primarily using a heterologous expression system. In contrast, the physiological role of VSP in native tissues remains largely unknown. Here we report that zebrafish VSP (Dr-VSP) is functionally expressed on the endomembranes of lysosome-rich enterocytes (LREs) that mediate dietary protein absorption via endocytosis in the zebrafish mid-intestine. Dr-VSP-deficient LREs were remarkably defective in forming endosomal vacuoles after initial uptake of dextran and mCherry. Dr-VSP-deficient zebrafish exhibited growth restriction and higher mortality during the critical period when zebrafish larvae rely primarily on exogenous feeding via intestinal absorption. Furthermore, our comparative study on marine invertebrate Ciona intestinalis VSP (Ci-VSP) revealed co-expression with endocytosis-associated genes in absorptive epithelial cells of the Ciona digestive tract, corresponding to zebrafish LREs. These findings signify a crucial role of VSP in regulating endocytosis-dependent nutrient absorption in specialized enterocytes across animal species.

Summary statementVoltage-sensing phosphatase (VSP) is identified in absorptive enterocytes, revealing its crucial role in promoting endocytosis and nutrient absorption during early development.


title: NAK associated protein 1 is required to activate Tank binding kinase 1 to regulate mitosis

abstract: Mitosis is a precisely regulated cellular mechanism that governs fundamental processes like embryogenesis, development, and tissue regeneration. Prenatal mitotic errors can cause birth defects, including neurodevelopmental disorders, congenital heart disease, and miscarriage, whereas postnatal abnormal cell division leads to early tissue aging and tumorigenesis. Aberrant expression of the serine/threonine kinase, TANK-Binding Kinase 1 (TBK1), is associated with several types of cancers, such as glioblastomas, breast, and lung cancers. However, its role in normal cell division is not well understood. To better define mechanistically how TBK1 is activated during mitosis, we identified NAK-associated protein 1 (NAP1/AZI2) to be essential for mitosis. Loss of NAP1 reduces mitosis and cell proliferation resulting in the accumulation of multinucleated cells phenocopying the loss of TBK1. NAP1 is further responsible for the activation of TBK1 at centrosomes of dividing cells and required for proper mitotic progression. Furthermore, NAP1 expression during mitosis is mediated by the ubiquitin proteasome system. We have uncovered a distinct function for the NAP1-TBK1 complex during mitosis, completely novel from its previously known function in innate immunity.