title: Stability of asymmetric cell division under confinement: A deformable cell model of cytokinesis applied to C. elegans development

abstract:
Cell division during early embryogenesis has been linked to key morphogenic events such as embryo symmetry breaking and tissue patterning. It is thought that boundary conditions together with cell intrinsic cues act as a mechanical "mold", guiding cell division to ensure these events are more robust. We present a novel computational mechanical model of cytokinesis, the final phase of cell division, to investigate how cell division is affected by mechanical and geometrical boundary conditions. The model reproduces experimentally observed furrow dynamics and predicts the volume ratio of daughter cells in asymmetric cell divisions based on the position and orientation of the mitotic spindle. We show that the orientation of confinement relative to the division axis modulates the volume ratio in asymmetric cell division and quantified the mechanical contribution of cortex mechanics, relative to the mechanical properties of the furrow ring. We apply this model to early C. elegans development, which proceeds within the confines of an eggshell, and simulate the formation of the three body axes via sequential (a)symmetric divisions up until the six cell stage. We demonstrate that spindle position and orientation alone can be used to predict the volume ratio of daughter cells during the cleavage phase of development. However, for compression perturbed egg geometries, the model predicts that the change in confinement alone is insufficient to explain experimentally observed differences in cell volume, inferring an unmodeled underlying spindle positioning mechanism. Finally, the model predicts that confinement stabilizes asymmetric cell divisions against bubble-instabilities, which can arise due to elevated mitotic cortical tension.

Author summaryA crucial morphogenic step during early embryonic development is symmetry breaking in the embryo. For C. elegans the formation of the three body axes can be traced back to the six cell stage, where tissue-topology is the result of symmetric and asymmetric divisions. How cell mechanical boundary conditions and cell intrinsic cues influence this process of symmetry breaking is still an open question, as currently, a quantitative mechanical description of cytokinesis in complex architectures is lacking. We developed a simple mechanical model of cell division, incorporated in an existing mechanical cortex model, to simulate cytokinesis in geometrically confined environments. Our approach was able to both capture furrow ring dynamics and predict the volume ratio of daughter cells accurately. By simulating early C. elegans development with different geometrical boundary conditions, we were able to trace back the origin of volume discrepancies between the experimental setups to a quantifiable shift in spindle positioning during cytokinesis. Finally, we showed how embryo confinement partially stabilizes bubble-instabilities that arise during asymmetric cell division during the early cleavage phase.


title: Basic helix-loop-helix pioneer factors interact with the histone octamer to invade nucleosomes and generate nucleosome depleted regions

abstract: Nucleosomes drastically limit transcription factor (TF) occupancy, while pioneer transcription factors (PFs) somehow circumvent this nucleosome barrier. In this study, we compare nucleosome binding of two conserved S. cerevisiae basic helix-loop-helix (bHLH) TFs, Cbf1 and Pho4. A Cryo-EM structure of Cbf1 in complex with the nucleosome reveals that the Cbf1 HLH region can electrostatically interact with exposed histone residues within a partially unwrapped nucleosome. Single molecule fluorescence studies show that the Cbf1 but not the Pho4 HLH region facilitates efficient nucleosome invasion by slowing its dissociation rate relative to DNA through interactions with histones. In vivo studies show that this enhanced binding provided by the Cbf1 HLH region enables nucleosome invasion and ensuing repositioning. These structural, single molecule, and in vivo studies reveal the mechanistic basis of dissociation rate compensation by pioneer factors and how this translates to facilitating chromatin opening inside cells.

category: biophysics


title: Interface resistance of biomolecular condensates

abstract: I.A hallmark of biomolecular condensates formed via liquid-liquid phase separation is the dynamic exchange of condensate components with the surroundings. Such material exchange can be key to condensate function, as the rate of component exchange can impact biochemical reaction rates in the condensates, the speed of response of condensates to a changing environment, and their number and sizes. How is this exchange rate controlled? Intuitively, this rate can be limited by the flux of materials from the dilute phase or by the speed of mixing inside the dense phase. Surprisingly, recent experiments suggest that this rate can also be limited by the dynamics of molecules at the droplet interface, implying the existence of an "interface resistance". Here, we combined theory and simulation to show that an interface resistance can arise when incident molecules contact the interface without entering the dense phase. We find that such "bouncing" occurs for incident molecules that are capable of self-collapse into a non-sticking conformation. Our work highlights the underappreciated role of interface resistance in condensate exchange dynamics, with implications for natural and synthetic systems.


title: Computational Study of Ion Permeation Through Claudin-4 Paracellular Channels

abstract: Claudins (Cldns) form a large family of protein homologs that are essential for the assembly of paracellular tight junctions (TJs), where they form channels or barriers with tissue-specific selectivity for permeants. In contrast to several family members whose physiological role has been identified, Cldn4 remains elusive, despite experimental evidence suggesting that it can form anion-selective TJ channels in the renal epithelium. Computational approaches have recently been employed to elucidate the molecular basis of Cldns function, and hence can help in clarifying Cldn4 role. In this work, we use structural modeling and all-atom molecular dynamics simulations to transfer two previously introduced structural models of Cldn-based paracellular complexes to Cldn4, in order to reproduce a paracellular anion channel. Free energy calculations for ionic transport across the pores allow us to establish the thermodynamic properties driving the ion-selectivity of the structures. While one model shows a cavity permeable to chloride and repulsive to cations, the other forms barrier to the passage of the major physiological ions. Furthermore, our results confirm the charge selectivity role of the residue Lys65 in the first extracellular loop of the protein, rationalizing Cldn4 control of paracellular permeability.


title: Analysis of alternative mRNA splicing in vemuraf-enib-resistant melanoma cells

abstract:
Alternative mRNA splicing is common in cancers. In BRAF V600E mutated malignant melanoma a frequent mechanism of acquired resistance to BRAF inhibitors involves alternative splicing (AS) of BRAF. The resulting shortened BRAF protein constitutively dimerizes and conveys drug resistance. Here, we have analysed AS in SKMEL-239 melanoma cells and a BRAF inhibitor (vemurafenib) resistant derivative that expresses an AS, shortened BRAF V600E transcript. Transcriptome analysis showed differential expression of spliceosome components between the two cell lines. As there is no consensus approach to analysing AS events, we used and compared four common AS softwares based on different principles, DEXSeq, rMATS, ASpli, and LeafCutter. Two of them correctly identified the BRAF V600E AS in the vemurafenib resistant cells. Only 12 AS events were identified by all four softwares. Testing the AS predictions experimentally showed that these overlapping predictions are highly accurate. Interestingly, they identified AS caused alterations in the expression of melanin synthesis and cell migration genes in the vemurafenib resistant cells. This analysis shows that combining different AS analysis approaches produce reliable results and meaningful, biologically testable hypotheses.

Graphic Abstract

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category: cancer biology


title: Analysis of alternative mRNA splicing in vemurafenib-resistant melanoma cells


title: A mathematical model of antibiotic resistance gene flow from livestock and spread amongst humans

abstract:
The evolution and spread of antibiotic resistance poses a major threat to human health. The high level of antibiotic use in the rearing of livestock is contributing to the origin and persistence of antibiotic resistance amongst humans. Understanding how resistance genes spread from livestock to humans and investigating the impact of managing antibiotic use in livestock will be important for guiding strategies to reduce the risk to humans. We have developed a mathematical model of the transmission of resistance genes from livestock to humans and their spread amongst the human population. Using this framework we demonstrate that although resistant zoonotic foodborne infections do not contribute significantly to the annual burden of death, they could be a source of resistance amongst other pathogens, including those that exclusively spread between humans. Amongst these pathogens, only livestock-derived resistant strains that are associated with a net fitness cost would be expected to decline in prevalence following control strategies aimed at reducing the impact on humans of antibiotic use in livestock.

Author SummaryAntibiotics are an essential component of human health care. They are also used in the rearing of livestock for human consumption, which contributes to the development of antibiotic resistant pathogens. Although humans are known to be at risk from antibiotic resistance that evolves amongst livestock, the number of human lives that are at stake remains unclear. Furthermore, the number of lives that could be saved through interventions to reduce antibiotic use in livestock has not been evaluated. Here, we have developed a mathematical framework to explore these questions. Using this framework we explicitly demonstrate that there are too many uncertainties to calculate the number of preventable human deaths. Nevertheless, the importance of reserving new and currently effective antibiotics for human use is clear. Once resistance genes that do not have a fitness disadvantage have spread from livestock to humans, it is too late for interventions targeted at livestock to affect their prevalence in humans in the long term.

category: zoology


title: Enhanced envelope coding following acoustic trauma is detrimental to neural coding of speech in noise

abstract: People with hearing loss struggle understanding speech in noisy backgrounds. Speech-intelligibility models highlight the importance of slow-varying envelopes of speech and noise; however, the physiological basis of impaired perception remains unclear. We provide neurophysiological evidence that, although acoustic trauma enhances both speech and noise envelopes, disruptions in cochlear tonotopicity preferentially enhance neural responses to noise in noisy speech. These results provide mechanistic insights into everyday-communication challenges created by hearing loss.

category: neuroscience


title: Patterns of retrieval-related cortico-striatal connectivity are stable across the adult lifespan

abstract: Memory retrieval effects in the striatum are well documented and robust across a number of experimental paradigms and stimulus materials. However, the functional significance of these effects, and whether they are moderated by age, remains unclear. In the present study, we used fMRI paired with an associative recognition task to examine retrieval effects in the striatum in a large sample of healthy young, middle aged, and older adults. We identified anatomically segregated patterns of enhanced striatal BOLD activity during recollection- and familiarity-based memory judgments. Successful recollection was associated with enhanced BOLD activity in bilateral putamen and nucleus accumbens. Familiarity effects were evident in the head of the caudate nucleus bilaterally. Crucially, none of these effects were reliably moderated by age. Using psychophysiological interaction analyses, we observed a monitoring-related increase in functional connectivity between the caudate and regions of the frontoparietal control network, and between the putamen and bilateral retrosplenial cortex and intraparietal sulcus. In all instances, monitoring-related increases in cortico-striatal connectivity were unmoderated by age. These results suggest that the striatum, and the caudate in particular, couples with the frontoparietal control network to support top-down retrieval monitoring operations, and that the integrity of these effects are preserved in advanced age.


title: Development of visual cortex in human neonates are selectively modified by postnatal experience

abstract: Experience-dependent cortical plasticity is a pivotal process of human brain development and essential for the formation of most cognitive functions. Although studies found that early visual experience could influence the endogenous development of visual cortex in animals, little is known about such impact on human infants. Using the multi-modal MRI data from developing human connectome project, we revealed the early structural and functional maps in the ventral visual cortex and their development across the first month of age. Particularly, we found the postnatal experience could modulate both the cortical morphology in ventral visual cortex and the functional circuit between bilateral primary visual cortices. But the cortical myelination and overall functional circuits of ventral cortex, particularly that of the high-order visual cortex, developed without significant influence of postnatal experience in such early period. These experience-dependent cortical properties were further validated in the preterm-born infants who have longer postnatal time but immature cortical development at birth. The results confirmed that the development of cortical thickness was dominated by the postnatal experience but the functional circuit might be determined by the overall maturity of visual cortex. These data suggest in human newborns that early postnatal experience shapes the structural and functional development of the visual cortex in selective and organized pattern.


title: High-fidelity dendritic sodium spike generation in human layer 2/3 neocortical pyramidal neurons

abstract: Dendritic computations have a central role in rodent neocortical circuit function, which are signaled into neuronal output by the initiation and propagation of regenerative dendritic spikes. However, it remains poorly explored whether these mechanisms are operational in the human neocortex. To directly examine the dendritic computational properties of the most numerous class of pyramidal neuron in the human and rat neocortex we made simultaneous electrical recordings from the soma and apical dendrites of layer 2/3 pyramidal neurons maintained in acute brain slices of analogous cortical areas under identical experimental conditions. In both species correlated dendritic excitatory input led to the initiation of sodium channel-mediated dendritic spikes with conserved biophysical properties. Dendritic sodium spikes in human and rat layer 2/3 pyramidal neurons could be generated across a similar wide input range, exhibited a similar frequency range of activation, and forward propagated with high fidelity to drive neuronal output to implement stereotyped computations. Our findings therefore reveal that the dendritic computational properties of human layer 2/3 pyramidal neurons are phylogenetically conserved.


title: Integrated single-cell profiling dissects cell-state-specific enhancer landscapes of human tumor-infiltrating T cells.

abstract: Despite extensive studies on the chromatin landscape of exhausted T cells, the transcriptional wiring underlying the heterogeneous functional and dysfunctional states of human tumor-infiltrating lymphocytes (TILs) is incompletely understood. Here, we identify tissue-specific and general gene-regulatory landscapes in the wide breadth of CD8+ TIL functional states covering four cancer entities using single-cell chromatin profiling. We map enhancer-promoter interactions in human TILs by integrating single-cell chromatin accessibility with single-cell RNA-seq data from tumor entity-matching samples, and prioritize key elements by super-enhancer analysis. Our results reveal a human core chromatin trajectory to TIL dysfunction and identify involved key enhancers, transcriptional regulators, and deregulated target genes in this process. Finally, we validate enhancer regulation at immunotherapeutically relevant loci by targeting non-coding regulatory elements with potent CRISPR activators and repressors. In summary, our study provides a framework for understanding and manipulating cell-state-specific gene-regulatory cues from human tumor infiltrating lymphocytes.

category: immunology


title: Bidirectional regulation between AP-1 and SUMO genes modulates inflammatory signaling during Salmonella Typhimurium infection

abstract:
Gram-negative bacterium Salmonella Typhimurium (STm) is the causative agent of gastroenteritis. Among the various gut pathogens, STm is still one of the most frequent culprits posing a significant health challenge. STm utilizes its effector proteins to highjack host cell processes. Alteration of SUMOylation, a post-translational modification mechanism, is one such change caused by STm. STm mediated simultaneous downregulation of SUMO-pathway genes, Ubc9 and PIAS1, is required for an efficient infection. In the present study, the regulation of SUMO pathway genes during STm infection was investigated. Promoters of both UBC9 and PIAS1, were seen to harbor binding motifs of AP-1, Activator protein-1 (c-Jun:c-Fos heterodimers or c-Jun:c-Jun homodimers). Using electrophoretic mobility shift assays, a direct binding of c-Fos to the identified motifs was observed. Perturbation of c-Fos led to changes in expression of Ubc9 and PIAS1, while its SUMO-modifications resulted in differential regulation of its target genes. In line with this, STm infection of fibroblasts with SUMOylation deficient c-Fos (c-FOS-KOSUMO-def-FOS) resulted in uncontrolled activation of target genes, as revealed by 3mRNA-Seq analysis and mathematical modelling, resulting in massive activation of inflammatory pathways. Infection of c-FOS-KOSUMO-def-FOS cells favored STm replication, indicating misdirected immune mechanisms in these cells. Finally, chromatin Immuno-precipitation assays confirmed a context dependent differential binding and release of AP-1 to/from target genes due to its Phosphorylation and SUMOylation respectively. Overall, our data point towards existence of a bidirectional cross-talk between c-Fos and the SUMO pathway and highlighting its importance in AP-1 function relevant to STm infections and beyond.

Author summaryFood borne infections caused Salmonella Typhimurium pose a major health challenge in developing and developed world. Unfortunately, many aspects of Salmonella-host crosstalk still remain unknown. In the current work, using sophisticated computational tools along with cell culture experiments and mathematical modeling, we demonstrate how Salmonella controls SUMOylation, a post-translational modification (PTM) pathway of host. SUMOylation governs fundamental processes of the host cell, and its alteration is required for a successful Salmonella infection. We show that SUMO-pathway genes, Ubc9 and Pias1, are direct target genes of AP-1 transcription factor. C-Fos, a component of AP-1 transcriptionally regulates SUMO-genes by binding to their promoters. During Salmonella infection, a selective activation of target genes of c-Fos was observed. The selective regulation of target genes relied on c-fos PTMs. Experimental perturbation of c-Fos PTMs led to global transcriptional dysregulation including immune hyperactivation. Thus, we show existence of a complex interplay between the SUMO-pathway genes and AP-1 transcription factors which mediate selective gene regulation during Salmonella infection.

category: microbiology


title: The coordination between penicillin-binding protein 1a (PBP1a) and the hydrolytic peptidase DacB determines the integrity of bacterial cell poles

abstract: Peptidoglycan (PG) defines cell shape and protects bacteria against osmotic stress. The growth and integrity of PG require coordinated actions between synthases that insert new PG strands and hydrolases that generate openings to allow the insertion. However, the mechanisms of their coordination remain elusive. Here we show that moenomycin that inhibits a family of PG synthases known as Class-A penicillin-binding proteins (aPBPs), triggers cell lysis despite aPBPs being non-essential for cell integrity. We demonstrate that inhibited PBP1a2, an aPBP, accelerates the degradation of cell poles by DacB, a hydrolytic PG peptidase, in the bacterium Myxococcus xanthus. Moenomycin reduces the mobility of DacB molecules through PBP1a2, potentially promoting the binding between DacB and PG. Conversely, DacB also regulates the distribution and dynamics of aPBPs. These findings reveal the lethal action of moenomycin and suggest that disrupting the coordination between PG synthases and hydrolases could be more lethal than eliminating individual enzymes.


title: Post-transcriptional regulation by copper with a new upstream Open Reading Frame

abstract: Copper is essential to most living beings but also toxic. Bacteria have thus developed homeostatic mechanisms to tightly control its intracellular concentration. The 3-gene operon bp2923-bfrG-bp2921 is down-regulated by copper and notably encodes a TonB-dependent transporter in Bordetella pertussis. We show that the protein encoded by bp2923, which is a member of the DUF2946 family, represents a new type of upstream Open Reading Frame (uORF) involved in post-transcriptional regulation of the downstream genes. In the absence of copper, the entire operon is transcribed and translated. Perception of copper by the nascent bp2923-coded protein via its conserved CXXC motif triggers Rho-dependent transcription termination between the first and second genes by relieving translation arrest on a conserved C-terminal RAPP motif. Homologues of bp2923 are widespread in bacterial genomes, where they head operons predicted to participate in copper homeostasis. This work has unveiled an original mode of genetic regulation by a transition metal and identified a regulatory function for a member of an uncharacterized family of bacterial proteins that we have named CruR, for copper-responsive upstream regulator.


title: Modification of the SUMO activating enzyme subunit SAE2 directs SUMO isoform bias required for mitotic fidelity.

abstract: Protein conjugation with the Small Ubiquitin-like Modifier SUMO1 or the related SUMO2/3 drive changes to protein behaviour. Many substrates are found modified by both SUMO1 and SUMO2/3, while others are modified by one or the other. How isoform specificity is directed is poorly understood. Here we examine modification of the catalytic component of the human SUMO Activation Enzyme, SAE2. We find that an acetylated K164-SAE2 analogue preferentially activates SUMO2 in competition with SUMO1, and that K164-SAE2 discriminates paralogues through their C-terminal regions. We find that K164-SAE2 is deacetylated during mitosis. Mitotic defects in cells expressing an acetylated K164-SAE2 analogue can be corrected by over-expression of SUMO1, suggesting SUMO1 conjugation driven by the deacetylated enzyme supports mitotic fidelity. These surprising data reveal that modification of the SUMO-activating enzyme can bias SUMO paralogue conjugation.

category: molecular biology


title: Pathogen-driven induction of a host transcriptome facilitating epithelial-to-mesenchymal transition

abstract:
Chronic infection of the female reproductive tract by Chlamydia trachomatis can cause fibrotic infertility. Thought to be the product of the immune response to infection, the incidence of fibrosis observed in subclinical or asymptomatic infections remains unexplained. Recent work demonstrates infection induces the pro-fibrotic process of epithelial-to-mesenchymal transition (EMT), but the mechanisms underlying this are unclear. We show the Chlamydia-induced host transcriptome includes targets of YAP, a pro-EMT transcriptional coactivator. We observe increased YAP nuclear translocation and pro-EMT YAP target gene induction during infection, bypassing YAP inhibition by the Hippo kinase cascade, and acting via YAP tyrosine phosphoactivation associated with host Src activity, and the myosin-modulating chlamydial effector CTL0480. Comparing the host transcriptome of a {Delta}CTL0480-mutant infection to wild-type infection revealed consistent reduction in known YAP target expression, as well as attenuated induction of EMT. Our results define a mechanism for Chlamydia-directed modulation of host gene expression, providing insight into chlamydial induction of immune-independent fibrosis.

Significance StatementOur study presents a means by which C. trachomatis induces pro-EMT gene expression in host epithelial cells, providing an explanation for how subclinical or asymptomatic chlamydial infections frequently result in severe fibrotic sequelae. We identify chlamydial induction of YAP activity as a principal mediator of this effect, and thus a potential therapeutic target for Chlamydia-induced fibrosis. Our finding that the chlamydial effector CTL0480 - previously reported to regulate activity of non-muscle myosin II - promotes YAP activity corroborates recent discoveries indicating YAPs mechanoresponsive function can circumvent its canonical inhibition by the Hippo kinase cascade. Collectively, our data illustrates an underappreciated aspect of the host-pathogen interaction: the downstream consequences of pathogen effector activity on host gene expression.

Summary StatementWe present a means by which Chlamydia trachomatis induces pro-EMT gene expression in the host via Hippo-independent, chlamydial effector-mediated activation of the transcription factor YAP.

category: cell biology


title: Maternal H3K36 and H3K27 HMTs protect germline immortality via regulation of the transcription factor LIN-15B

abstract: Maternally synthesized products play critical roles in development of offspring. A premier example is the C. elegans H3K36 methyltransferase MES-4, which is essential for germline survival and development in offspring. How maternal MES-4 protects germline immortality is not well understood, but its role in H3K36 methylation hinted that it may regulate gene expression in Primordial Germ Cells (PGCs). We tested this hypothesis by profiling transcripts from single pairs of PGCs dissected from wild-type and mes-4 mutant (lacking maternal and zygotic MES-4) newly hatched larvae. We found that mes-4 PGCs display normal turn-on of most germline genes and normal repression of somatic genes, but dramatically up-regulate hundreds of genes on the X chromosome. We demonstrated that X mis-expression is the cause of germline death by generating and analyzing mes-4 mutants that inherited different endowments of X chromosome(s). Intriguingly, removal of the THAP transcription factor LIN-15B from mes-4 mutants reduced X mis-expression and prevented germline death. lin-15B is X-linked and mis-expressed in mes-4 PGCs, identifying it as a critical target for MES-4 repression. The above findings extend to the H3K27 methyltransferase MES-2/3/6, the C. elegans version of Polycomb Repressive Complex 2. We propose that maternal MES-4 and PRC2 cooperate to protect germline survival by preventing synthesis of germline-toxic products encoded by genes on the X chromosome, including the key transcription factor LIN-15B.

category: developmental biology


title: Rapid colour changes in a tiny threatened gecko do not impede computer-assisted individual recognition

abstract: Photo-identification is a non-invasive method used for recognising wild animals with distinctive and stable patterns over time. This method is now widely used for capture-recapture wildlife monitoring. However, in species exhibiting rapid colouration changes, the evolving body patterns can lead to errors in individual recognition. In this study, we assessed the effect of dorsal physiological colour change of the tiny threatened European leaf-toed gecko (Euleptes europaea) on the performance of Wild-ID and Hotspotter, the two most commonly used individual recognition software for wildlife monitoring. We exposed 30 European leaf-toed geckos to several semi-controlled parameters (substrate type, temperature and light from natural diurnal/nocturnal cycles) in order to characterise the extent of variation in dorsal colouration, by standardised reflectance measurements. The colour of the substrate had a significant effect on individual reflectance changes. Body temperature also seemed to significantly affect the reflectance but the experimental conditions did not allow us to clearly distinguish the effect of temperature and light. For each of the 30 geckos, four photographic databases (n = 4*280) were then analysed by both software packages, under two extreme reflectance conditions. Despite the large changes in individual reflectance, Wild-ID and Hotspotter proved to be extremely reliable with a 100% recognition rate. The analysis of similarity scores suggests that Hotspotter is less sensitive to chromatic variation than Wild-ID. We provide here the first evidence that physiological colour change is not a barrier to computer-assisted individual recognition. This study advocates the use of Hotspotter for monitoring populations of European leaf-toed geckos and other saurians that generate significant colouration change over a short time.

category: ecology


title: Distilling complex evolutionary histories with shiftPlot

abstract: Phylogenies form the backbone of many modern comparative methods and are integral components of contemporary science communication. Recent years have seen drastic increases in both the size and complexity of phylogenetic data as computational resources and genetic/trait databases expand. Graphical representations of these massive phylogenetic datasets push against the limits of legibility, often veering closer to artwork than scientific figures optimized to communicate results. While attractive scientific illustrations are certainly a laudable goal, researchers may want to opt for simpler representations to communicate results more concisely. Here, we introduce a new R package, shiftPlot, which implements methods for simplifying and plotting phylogenetic comparative data on discrete traits. Specifically, shiftPlot automatically finds and collapses clades exhibiting the same character state, effectively creating smaller phylogenies that may be more legibly rendered on standard page sizes. Further, these visualizations more clearly communicate evolutionary dynamics by emphasizing state shifts over tip states. While there are undoubtedly situations where this graphical approach will not be suitable (e.g., continuous traits), we believe shiftPlot will prove useful for modern researchers faced with the task of communicating the results of complex phylogenetic analyses.

category: evolutionary biology


title: Novel Murine models of Mania and Depression

abstract: Neuropathological mechanisms triggering manic syndrome or manic episodes in bipolar disorder remain poorly characterised, as the research progress is severely limited by the paucity of appropriate animal models. Here we developed a novel manic mice model by combining a series of chronic unpredictable rhythm disturbances (CURD), which include disruption of circadian rhythm, sleep deprivation, exposure to cone light, with subsequent interference of followed spotlight, stroboscopic illumination, high temperature stress, noise disturbance and foot shock. To validate this novel manic model, we used multiple behavioural and cell biology approaches comparing the CURD-model with healthy controls and depressed mice. The depression model was created by an exposure to an improved chronic unpredictable mild stress, which we defined as chronic unpredictable mild restraint (CUMR). A novel manic mice model induced by environmental stressors and free from genetic or pharmacological interventions will benefit research into pathological mechanisms of mania.

category: animal behavior and cognition


title: Control algorithms underlying the translational optomotor response

abstract:
The optomotor response (OMR) is central to the locomotory behavior in diverse animal species including insects, fish and mammals. Furthermore, the study of the OMR in larval zebrafish has become a key model system for investigating the neural basis of sensorimotor control. However, a comprehensive understanding of the underlying control algorithms is still outstanding. In fish it is often assumed that the OMR, by reducing average optic flow across the retina, serves to stabilize position with respect to the ground. Yet the degree to which this assumption is true, and how this could emerge from the intermittent burst dynamics of larval zebrafish swimming is unclear. Here, we combine detailed computational modeling with a new approach to free-swimming experiments, in which feedback gain - i.e., the degree of sensory feedback produced by swimming - is manipulated by varying the height of larval zebrafish above a moving stimulus. We develop an account of underlying feedback control mechanisms that describes not only bout initiation but also the control of swim speed during bouts. We observe that the degree to which fish stabilize their position is only partial and gain-dependent, suggesting that the OMR may not primarily function in fish to prevent drift. We find the speed profile during bouts follows a fixed temporal pattern independent of bout intensity, suggesting that bout termination and bout duration are not explicitly controlled. We also find that the reverse optic flow, experienced when the fish is swimming faster than the stimulus, plays a minimal role in control of the OMR despite carrying most of the sensory information about self-movement. These results shed new light on the underlying dynamics of the OMR in larval zebrafish and will be crucial for future work aimed at identifying the neural basis of this behavior.

Author SummaryIn many animals vision is central to the control of locomotory behaviors. In particular, innate motor responses to optic flow allow flying animals to react to gusts of air and fish to changes of current. As fish are washed downstream, for example, movement of the riverbed image across the retina evokes forward movement in bouts (short periods of swimming followed by rest periods). It is typically assumed that this translational optomotor response stabilizes the fishs position to prevent it drifting downstream. In larval zebrafish, this response has become a key model system for investigating the neural basis of sensorimotor behaviors in a vertebrate. Here, we combine behavioral experiments and computational modeling to elucidate the underlying control algorithms. We unpick the detailed relationship between visual stimuli and the initiation, termination and intensity of swim bouts. We find initiation and intensity are controlled separately, and that termination is not explicitly controlled. Surprisingly we also found that the degree of stabilization is only partial and varies systematically with height above ground, raising questions of the function of this response. These findings shed new light on the underlying dynamics which will be crucial for future work to identify the neural basis of this behavior.


title: Long-term memory in frog-eating bats

abstract:
Long-term memory has clear advantages but also has neurological and behavioral costs1-3. Given these opposing selection pressures, understanding how long memories last can shed light on how memory enhances or constrains animals abilities to exploit their niches. Although testing memory retention in wild animals is difficult, it is important because captive conditions do not reflect the complex cognitive demands of wild environments, and long-term captivity changes the brain4 (past studies on nonhuman long-term memory are reviewed in Table S1). Here, we trained wild-caught frog-eating bats (Trachops cirrhosus) to find prey by flying to a novel acoustic cue, released them back into the wild, and then re-captured some of them 1-4 years later. When re-tested, all eight  experienced bats that previously learned the novel prey sounds flew to those sounds within seconds, whereas 17 naive bats tested with the same sounds showed weak responses. Experienced bats also showed behavior indicating generalization of memories between novel sounds and rewards over time. The frog-eating bats remarkably long memory for novel acoustic cues indicates that an ability to remember rarely encountered prey may be advantageous for this predator, and suggests hitherto unknown cognitive abilities in bats.

O_TBL View this table:
org.highwire.dtl.DTLVardef@15a8294org.highwire.dtl.DTLVardef@132eb3forg.highwire.dtl.DTLVardef@1f29583org.highwire.dtl.DTLVardef@135dff2org.highwire.dtl.DTLVardef@19cfa_HPS_FORMAT_FIGEXP  M_TBL O_FLOATNOTable S1:C_FLOATNO O_TABLECAPTIONStudies of animal memory durations documenting memories of months or years. Memory duration = the longest duration demonstrated in the study. Wild or captive = where animals spent the time of memory retention; some "captive" animals were originally wild caught. Context = the ecological context and memory task being tested. 2-AFC = Two-alternative forced choice.

C_TABLECAPTION C_TBL


title: Prioritized single-cell proteomics reveals molecular and functional polarization across primary macrophages

abstract:
Major aims of single-cell proteomics include increasing the consistency, sensitivity, and depth of protein quantification, especially for proteins and modifications of biological interest. To simultaneously advance all of these aims, we developed prioritized Single Cell ProtEomics (pSCoPE). pSCoPE ensures duty-cycle time for analyzing prioritized peptides across all single cells (thus increasing data consistency) while analyzing identifiable peptides at full duty-cycle, thus increasing proteome depth. These strategies increased the quantified data points for challenging peptides and the overall proteome coverage about 2-fold. pSCoPE enabled quantifying proteome polarization in primary mouse macrophages and linking it to phenotypic variability in endocytic activity. Proteins annotated to phagosome maturation and proton transport showed concerted variation for both untreated and lipopolysaccharide-treated macrophages, indicating a conserved axis of polarization. pSCoPE further quantified proteolytic products, suggesting a gradient of cathepsin activities within a treatment condition. pSCoPE is easily accessible and likely to benefit many applications, especially mechanistic analysis seeking to focus on proteins of interest without sacrificing proteome coverage.

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category: bioengineering


title: Engineering Principles and Algorithmic Design Synthesis for Ultracompact Bio-Hybrid Perfusion Chip

abstract: Bioinspired 3D microfluidic systems that combine vascularization with extracellular matrix architectures of organotypic geometry, composition and biophysical traits can help advance our understanding of microorgan physiology. Here, two-photon stereolithography is adopted to fabricate freestanding perfusable 3D cell scaffolds with micrometer resolution from gelatin methacryloyl hydrogel derived from extracellular matrix protein. As a proof of concept, we introduce an ultracompact bio-hybrid chip layout to demonstrate perfusion and cell seeding of double-digit m proteinaceous channels. This perfusion chip consists of a standardized microfluidic interface fabricated from standard resin and a GM10 bioink channel printed atop of this interface. In addition, we demonstrate that algorithmic design synthesis can recapitulate intact alveoli and capillary networks with tunable design parameters to implement vascularized alveolar tissue models. This approach will allow for a systematic investigation of cell-cell and tissue dynamics in response to defined structural, mechanical and bio-molecular cues and is ultimately scalable to fabricate organ-on-a-chip systems.


title: Proteochemometric method for pIC50 prediction of Flaviviridae

abstract: Viruses remain an area of concern despite constant development of antiviral drugs and therapies. One of the contributors among others is the flaviviridae family of viruses. Like other spaces, antiviral peptides (AVP) are gaining importance for studying flaviviridae family. Along with antiviral properties of peptides, information about bioactivity takes it even closer to accurate predictions of peptide capabilities. Experimental identification of bioactivity of each potential peptide is an expensive and time consuming task. Computational methods like Proteochemometric modelling (PCM) are promising for prediction of bioactivity based on peptide and target sequence. The additional edge PCM methods bring in is the aspect of considering both peptide and target properties instead of only looking at peptide properties. In this study, we propose prediction of pIC50 for AVP against flaviviridae family target proteins. The target proteins were manually curated from literature. Here we utilize the PCM descriptors as peptide descriptors, target descriptors and cross term descriptors. We observe taking peptide and target information improves the results qualitatively and gives better pIC50 predictions. The R2 and MAPE values are 0.85 and 8.44 % respectively

category: bioinformatics


title: GPCR-IFP: A Web Server for Analyzing G-Protein Coupled Receptor-Ligand Fingerprint Interaction from Experimental Structures

abstract: G-protein coupled receptors (GPCRs) are interesting targets for a broad range of drugs. The comprehensions of the interactions mode between GPCRs and their ligands remains to be resolved. Here, we present GPCR-IFP, a web server which drives to gather experimental information supports a better understanding of ligand-receptor interaction and the chemical space. Despite the vast chemical library used for drug discovery, the structures of ligands for a particular receptor share some common molecular features. Thus, we foraged to collect all experimental structures of GPCRs and analyzed protein-ligand interactions which resulted in important unique patterns for both agonist and antagonist. All those results can be analyzed and visualized in GPCR-IFP, a friendly-used webserver.


title: Extracting physical characteristics of higher-order chromatin structures from 3D image data

abstract: AO_SCPLOWBSTRACTC_SCPLOWHigher-order chromatin structures have functional impacts on gene regulation and cell identity determination. Using high-throughput sequencing (HTS)-based methods like Hi-C, active or inactive compartments and open or closed topologically associating domain (TAD) structures can be identified on a cell population level. Recently developed high-resolution three-dimensional (3D) molecular imaging techniques such as 3D electron microscopy with in situ hybridization (3D-EMSIH) and 3D structured illumination microscopy (3D-SIM) enable direct detection of physical representations of chromatin structures in a single cell. However, computational analysis of 3D image data with explainability and interpretability on functional characteristics of chromatin structures is still challenging. We developed Extracting Physical-Characteristics from Images of Chromatin Structures (EPICS), a machine-learning based computational method for processing high-resolution chromatin 3D image data. Using EPICS on images produced by 3D-EMISH or 3D-SIM techniques, we generated more direct 3D representations of higher-order chromatin structures, identified major chromatin domains, and determined the open or closed status of each domain. We identified several high-contributing features from the model as the major physical characteristics that define the open or closed chromatin domains, demonstrating the explainability and interpretability of EPICS. EPICS can be applied to the analysis of other high-resolution 3D molecular imaging data for spatial genomics studies. The R and Python codes of EPICS are available at https://github.com/zang-lab/epics.


title: Hsp multichaperone complex buffers pathologically modified Tau

abstract: Alzheimers disease is a neurodegenerative disorder in which misfolding and aggregation of pathologically modified Tau is critical for neuronal dysfunction and degeneration. The two central chaperones Hsp70 and Hsp90 coordinate protein homeostasis, but the nature of the interaction of Tau with the Hsp70/Hsp90 machinery has remained enigmatic. Here we show that Tau is a high-affinity substrate of the human Hsp70/Hsp90 machinery. Complex formation involves extensive intermolecular contacts, blocks Tau aggregation and depends on Taus aggregation-prone repeat region. The Hsp90 co-chaperone p23 directly binds Tau and stabilizes the multichaperone/substrate complex, whereas the E3 ubiquitin-protein ligase CHIP efficiently disassembles the machinery targeting Tau to proteasomal degradation. Because phosphorylated Tau binds the Hsp70/Hsp90 machinery but is not recognized by Hsp90 alone, the data establish the Hsp70/Hsp90 multichaperone complex as a critical regulator of Tau in neurodegenerative diseases.


title: Topological action potentials in engineered tissues

abstract: Due to the nonlinear current-voltage relations of ion channels, an interface between two tissues can have very different bioelectrical properties compared to either tissue on its own. Here we show experimentally that gap junction-coupled interfaces between non-excitable tissues can be electrically excitable. This topologically protected excitability occurs over a far larger range of ion channel expression levels than does excitability in the bulk. Topological excitations at tissue interfaces can cause local elevations in calcium concentration, possibly providing a bioelectrical mechanism for interface sensing. As in condensed matter physics, topological excitations in electrophysiology constitute a distinct class of phenomena which may show exotic and novel properties.


title: Gene expression signature of castrate resistant prostate cancer

abstract:
Prostate gland is a highly androgen dependent gland and hence the first line of treatment for metastatic prostate cancer happens to be androgen ablation. This is achieved by multiple non-surgical methods. However, most of these cancers although respond well initially, become resistant to androgen ablation sooner or later. These cancers then become extremely aggressive and difficult to treat, thereby drastically affect the patient prognosis. The purpose of this project was to identify a gene expression signature for castrate resistant prostate cancer which may aid in identification of mechanisms responsible for castrate resistance. For this purpose, we have collected patient samples belonging to a. Control group; b. Castrate Sensitive group and c. Castrate resistant group. Gene expression profiling has been done on these samples using RNA-seq and several differentially expressed genes identified between the castrate sensitive and resistant groups. We have also identified some genes which are expressed in the castrate resistant group alone, which is of interest since these may have an implication in evolution of castrate resistance and also prognosis.

We have compared this with data from The Cancer Genome Atlas (TCGA). Using criteria such as overall survival, disease free survival, progression free survival and biochemical recurrence, we have identified genes which may have relevance in progression to castrate resistance and in prognosis. Functional annotation of these genes may give an insight into the mechanism of development of castrate resistance.


title: Extracellular matrix guidance determines proteolytic and non-proteolytic cancer cell patterning

abstract: Metastatic tumor cell invasion into interstitial tissue is a mechanochemical process that responds to tissue cues and further involves proteolytic remodeling of the tumor stroma. How matrix density, tissue guidance and the ability of proteolytic tissue remodeling cooperate and determine decision-making of invading tumor cells in complex-structured three-dimensional (3D) tissue remains unclear. We here developed a collagen-based invasion assay containing a guiding interface of low collagen density adjacent to randomly organized 3D fibrillar lattice and examined the invasion of melanoma cells from multicellular spheroids in response to matrix density, guidance cues and collagenolysis. After 48 hours of culture, two invasion niches developed, (i) sheet-like collective migration along the interface and (ii) single cell- and strand-like invasion into randomly organized 3D matrix. High collagen density impeded migration into the random matrix, whereas migration along a high-density collagen interface was increased compared to the low-density matrix assay. In silico analysis predicted that facilitated interface migration in high-density matrix depended on physical guidance without collagen degradation, whereas migration into randomly organized matrix was strongly dependent on collagenolysis. When tested in 3D culture, inhibition of matrix metalloprotease (MMP)-mediated collagen degradation compromised migration into random matrix in dependence of density, whereas interface-guided migration remained effective. In conclusion, with increasing tissue density, matrix cues bordered by dense matrix, but not randomly organized matrix, support effective MMP-independent migration. This identifies the topology of interstitial tissue a primary determinant of switch behaviors between MMP-dependent and MMP-independent cancer cell invasion.


title: No evidence of induced skin cancer or other skin abnormalities after long term (66 week) chronic exposure to 222-nm far-UVC radiatio

abstract: Far-UVC radiation, typically defined as 200-235 nm, has similar or greater anti-microbial efficacy compared to conventional 254-nm germicidal radiation. In addition, biophysical considerations of the interaction of far-UVC with tissue, as well as multiple short-term safety studies in animal models and humans, suggest that far-UVC exposure may be safe for skin and eye tissue. Nevertheless, the potential for skin cancer after chronic long-term exposure to far-UVC has not been studied. Here, we assessed far-UVC induced carcinogenic skin changes and other pathological dermal abnormalities in 96 SKH-1 hairless mice of both sexes that were exposed to average daily dorsal skin doses of 396 mJ/cm2, 126 mJ/cm2 or 56 mJ/cm2 of 222 nm far-UVC radiation for 66 weeks, 5 days per week, 8 hours per day, as well as similarly-treated unexposed controls. No evidence for increased skin cancer, abnormal skin growths, or incidental skin pathology findings was observed in the far-UVC exposed mice. In addition, there were no significant changes in morbidity or mortality. The findings from this study support the long-term safety of long-term chronic exposure to far-UVC radiation, and therefore its potential suitability as a practical anti-microbial approach to reduce airborne viral and bacterial loads in occupied indoor settings.


title: Humans trade-off energetic cost with fatigue avoidance while walking

abstract: Metabolic cost minimization is widely regarded as the principal optimality criterion that governs walking. Minimizing muscle activation has, nevertheless, outperformed energy optimization in simulating human gait and predicting certain gait behaviors. The highly coupled nature of metabolic and muscle activation costs makes it difficult to empirically discern the interrelationship between these objectives. We implemented a unique experimental design that pits metabolic cost against muscle activation costs estimated from electromyography of seven lower limb muscles. Healthy adults (N=10) selected between walking on a treadmill incline versus walking in a crouched posture (that disproportionately affected activation cost), forcing a choice between minimizing metabolic cost or activation cost. When experiencing these Competing-Cost-Pairs, participants systematically protected their activation cost at the expense of high metabolic power ([Formula]; 19% penalty, p<0.05). This held true when activation cost was expressed as the sum of the muscle activations squared ([Formula]; 66% saving, p<0.05) and as the maximal activation across muscles ([Formula]; 44% saving, p<0.05), both of which penalize overburdening any individual muscle and thus indicate fatigue avoidance. Activation cost, expressed as the sum of muscle volume-normalized activation [Formula], more closely models energy use and was also protected by the participants decision (23% saving, p<0.05) demonstrating that activation was, at best, an inaccurate proxy signal for metabolic energy. Energy minimization was only observed when there was no adverse effect on muscle activation. By decoupling metabolic and activation costs, we provide the first empirical evidence of humans embracing non-energetic optimality in favor of a clearly defined alternate neuromuscular objective.

category: physiology


title: Mesembryanthemum crystallinum plasma membrane root aquaporins are regulated via clathrin-coated vesicles in response to salt stress

abstract:
The regulation of PIP-type aquaporins in the roots of plants has been identified as an important aspect in salinity tolerance. However, the molecular and cellular details underlying this process in halophytes remain unclear. Using free flow electrophoresis and label-free proteomics, we report that the increased abundance of PIPs at the plasma membrane of Mesembryanthemum crystallinum roots under salinity conditions is regulated by clathrin-coated vesicles (CCVs). To understand this regulation, we analyzed several components of the M. crystallinum CCVs complexes: clathrin light chain (McCLC) and subunits 1 and 2 of the adaptor complex (McAP1 and McAP2). Co-localization analyses revealed the association between McPIP1;4 and McAP2 and between McPIP2;1 and McAP1, observations corroborated by mbSUS assays, suggesting that aquaporin abundance at the PM is under the control of CCVs. The ability of McPIP1;4 and McPIP2;1 to form homo- and hetero-oligomers was tested and confirmed, as well as their activity as water channels. Also, we found increased phosphorylation of McPIP2;1 only at plasma membrane in response to salt stress. Our results prompt how root PIPs from halophytes are regulated through CCVs trafficking and phosphorylation, impacting their localization, transport activity and abundance under salinity conditions.

One-sentence summaryAbundance of plasma membrane aquaporins in M. crystallinum roots increases in response to salinity via a clathrin-coated vesicle-dependent mechanism.

category: plant biology


title: DUF581-9 (At2g44670; FLZ3) negatively regulates SnRK1 activity by interference with T-loop phosphorylation

abstract: In plants, SUCROSE NON-FERMENTING RELATED KINASE 1 (SnRK1) is a key energy-sensor that orchestrates large-scale transcriptional reprogramming to maintain cellular homeostasis under energy deficit. SnRK1 activity is under tight negative control, although the exact mechanisms leading to its activation are far from being understood. We show that the Arabidopsis DOMAIN OF UNKNOWN FUNCTION (DUF581) protein DUF581-9/FLZ3 binds to the catalytic SnRK1 subunit KIN10 to inhibit its activation by GRIK-dependent T-loop phosphorylation. Overexpression of DUF581-9 in Arabidopsis dampens SnRK1 signalling and interferes with adaptation to dark-induced starvation. The presence of DUF581-9 significantly reduced SnRK1 activity in protoplasts and in vitro. This was accompanied by a reduction in T175 T-loop phosphorylation and also diminished KIN10 auto-phosphorylation. Furthermore, DUF581-9 reduced binding of the up-stream activating kinase GRIK2 to KIN10, explaining the reduced KIN10 T-loop phosphorylation. Ectopically expressed DUF581-9 protein was rapidly turned over by the proteasome when Arabidopsis plants were subjected to starvation treatment, likely releasing its inhibitory activity on the SnRK1 complex. Taken together, our results support a model in which DUF581-9 negatively regulates SnRK1 activity under energy sufficient conditions. Turnover over of the protein provides a rapid way for SnRK1 activation under energy deficit without the need of de-novo protein synthesis.


title: Water influx is required for CD4+ T cell activation and T cell-dependent antibody responses

abstract:
Signaling from the T cell antigen receptor (TCR) on CD4+ T cells triggers the adaptive immune response by inducing T cell activation, proliferation, and differentiation. However, TCR signaling pathways are incompletely understood. Unexpectedly, we demonstrate that WNK1, a kinase previously implicated in osmoregulation in the kidney, is required for T-dependent antibody responses. We show that WNK1-OXSR1-STK39-dependent water influx through AQP3 is required for TCR signaling in CD4+ T cells and for entry into cell cycle. Additionally, by preventing ATR activation this signaling pathway is required for T cells to progress through the G2 phase of the cell cycle. Thus, TCR signaling via WNK1, OXSR1, STK39 and AQP3 leads to water entry that is essential for CD4+ T cell proliferation and hence T cell-dependent antibody responses.

One Sentence SummaryT cell antigen receptor signaling via the WNK1 kinase causes water entry which is essential for CD4+ T cell proliferation.


title: Plasma iron controls neutrophil production and function

abstract: Low plasma iron (hypoferremia) induced by hepcidin is a conserved inflammatory response that protects against infections but inhibits erythropoiesis. How hypoferremia influences leukocytogenesis is unclear. Using proteomic data, we predicted that neutrophil production would be profoundly more iron-demanding than generation of other white blood cell types. Accordingly in mice, hepcidin-mediated hypoferremia substantially reduced numbers of granulocytes but not monocytes, lymphocytes or dendritic cells. Neutrophil rebound after anti-GR1-induced neutropenia was blunted during hypoferremia, but was rescued by supplemental iron. Similarly, hypoferremia markedly inhibited pharmacologically-stimulated granulopoiesis mediated by GCSF and inflammation-induced accumulation of neutrophils in the spleen and peritoneal cavity. Furthermore, hypoferremia specifically altered neutrophil effector functions, suppressing antibacterial mechanisms but enhancing mitochondrial ROS-dependent NETosis associated with chronic inflammation. Notably, antagonising endogenous hepcidin during acute inflammation enhanced production of neutrophils. We propose plasma iron modulates the profile of innate immunity by controlling monocyte-to-neutrophil ratio and neutrophil activity in a therapeutically targetable system.


title: DISTINCTIVE FEATURES OF THE RESPIRATORY SYNCYTIAL VIRUS PRIMING LOOP COMPARED TO OTHER NON-SEGMENTED NEGATIVE STRAND RNA VIRUSES

abstract:
De novo initiation by viral RNA-dependent RNA polymerases often requires a polymerase priming residue, located within a priming loop, to stabilize the initiating NTPs. Polymerase structures from three different non-segmented negative strand RNA virus (nsNSV) families revealed putative priming loops in different conformations, and an aromatic priming residue has been identified in the rhabdovirus polymerase. In a previous study of the respiratory syncytial virus (RSV) polymerase, we found that Tyr1276, the L protein aromatic amino acid residue that most closely aligns with the rhabdovirus priming residue, is not required for RNA synthesis but two nearby residues, Pro1261 and Trp1262, were required. In this study, we examined the roles of Pro1261 and Trp1262 in RNA synthesis initiation. Biochemical studies showed that substitution of Pro1261 inhibited RNA synthesis initiation without inhibiting back-priming, indicating a defect in initiation. Biochemical and minigenome experiments showed that the initiation defect incurred by a P1261A substitution could be rescued by factors that would be expected to increase the stability of the initiation complex, specifically increased NTP concentration, manganese, and a more efficient promoter sequence. These findings indicate that Pro1261 of the RSV L protein plays a role in initiation, most likely in stabilizing the initiation complex. However, we found that substitution of the corresponding proline residue in a filovirus polymerase had no effect on RNA synthesis initiation or elongation. These results indicate that despite similarities between the nsNSV polymerases, there are differences in the features required for RNA synthesis initiation.

Author SummaryRSV has a significant impact on human health. It is the major cause of respiratory disease in infants and exerts a significant toll on the elderly and immunocompromised. RSV is a member of the Mononegavirales, the non-segmented, negative strand RNA viruses (nsNSVs). Like other viruses in this order, RSV encodes an RNA dependent RNA polymerase, which is responsible for transcribing and replicating the viral genome. Due to its essential role during the viral replication cycle, the polymerase is a promising candidate target for antiviral inhibitors and so a greater understanding of the mechanistic basis of its activities could aid antiviral drug development. In this study, we identified an amino acid residue within the RSV polymerase that appears to stabilize the RNA synthesis initiation complex and showed that it plays a role in both transcription and RNA replication. However, the corresponding residue in a different nsNSV polymerase does not appear to play a similar role. This work reveals a key feature of the RSV polymerase but identifies differences with the polymerases of other related viruses.


title: Genetic and environmental drivers of large-scale epigenetic variation in Thlaspi arvense

abstract:
Natural plant populations often harbour substantial heritable variation in DNA methylation. However, a thorough understanding of the genetic and environmental drivers of this epigenetic variation requires large-scale and high-resolution data, which currently exist only for a few model species. Here, we studied 207 lines of the annual weed Thlaspi arvense (field pennycress), collected across a large latitudinal gradient in Europe and propagated in a common environment. By screening for variation in DNA sequence and DNA methylation using whole-genome (bisulfite) sequencing, we found significant epigenetic population structure across Europe. Average levels of DNA methylation were strongly context-dependent, with highest DNA methylation in CG context, particularly in transposable elements and in intergenic regions. Residual DNA methylation variation within all contexts was associated with genetic variants, which often co-localized with annotated methylation machinery genes but also with new candidates. Variation in DNA methylation was also significantly associated with climate of origin, with methylation levels being higher in warmer regions and lower in more variable climates. Finally, we used variance decomposition to assess genetic versus environmental associations with differentially methylation regions (DMRs). We found that while genetic variation was generally the strongest predictor of DMRs, the strength of environmental associations increased from CG to CHG and CHH, with climate-of-origin as the strongest predictor in about one third of the CHH DMRs. In summary, our data show that natural epigenetic variation in Thlaspi arvense is significantly associated with both DNA sequence and environment of origin, and that the relative importance of the two factors strongly depends on the sequence context of DNA methylation. T. arvense is an emerging biofuel and winter cover crop; our results may hence be relevant for breeding efforts and agricultural practices in the context of rapidly changing environmental conditions.

Author SummaryVariation within species is an important level of biodiversity, and it is key for future adaptation. Besides variation in DNA sequence, plants also harbour heritable variation in DNA methylation, and we want to understand the evolutionary significance of this epigenetic variation, in particular how much of it is under genetic control, and how much is associated with the environment. We addressed these questions in a high-resolution molecular analysis of 207 lines of the common plant field pennycress (Thlaspi arvense), which we collected across Europe, propagated under standardized conditions, and sequenced for their genetic and epigenetic variation. We found large geographic variation in DNA methylation, associated with both DNA sequence and climate of origin. Genetic variation was generally the stronger predictor of DNA methylation variation, but the strength of environmental association varied between different sequence contexts. Climate-of-origin was the strongest predictor in about one third of the differentially methylated regions in the CHH context, which suggests that epigenetic variation may play a role in the short-term climate adaptation of pennycress. As pennycress is currently being domesticated as a new biofuel and winter cover crop, our results may be relevant also for agriculture, particularly in changing environments.


title: Spatial transcriptomics reveal markers of histopathological changes in Duchenne muscular dystrophy mouse models

abstract: Duchenne muscular dystrophy (DMD) is caused by mutations in the DMD gene, leading to lack of dystrophin. Chronic muscle damage eventually leads to histological alterations in skeletal muscles. The identification of genes and cell types driving tissue remodeling is a key step to develop effective therapies. Here we use spatial transcriptomics in two DMD mouse models differing in disease severity to identify gene expression signatures underlying skeletal muscle pathologies and directly link this to the muscle histology. Deconvolution analysis allowed the identification of cell types contributing to histological alterations. We show how the expression of specific genes is enriched in areas of muscle regeneration (Myl4, Sparc, Hspg2), fibrosis (Vim, Fn1, Thbs4) and calcification (Bgn, Ctsk, Spp1). Finally, our analysis of differentiation dynamics in the severely affected D2-mdx muscle shows a subset of the muscle fibers are predicted to become affected in its future state. Genes associated with tissue remodeling could enable to design new diagnostic and therapeutic strategies for DMD.

category: genomics


title: DNA co-methylation has a stable structure and is related to specific aspects of genome regulation

abstract:
BackgroundDNA methylation (DNAm) is an epigenetic mark that can be used to understand interindividual variability in genomic regulation, and it is influenced by many genetic and environmental factors. Co-methylation between DNAm sites is a known phenomenon but the full architecture of relationships between the approximately 450,000 (450k) sites most commonly measured in epidemiological studies has not been described. We investigate whether the cis and trans interindividual co-methylation structure amongst the 450k sites changes across the lifecourse, whether it differs between UK-born White and Pakistani individuals, and how it may be related to genome regulation.

ResultsWe find stability across the life course (birth to adolescence), across cohorts, and between two ethnic groups. Highly correlated DNAm sites in close proximity are highly heritable, influenced by nearby genetic variants (cis mQTLs), and are enriched for transcription factor (TF) binding sites related to regulation of short RNAs essential for cellular function transcribed by RNA polymerase III. Highly correlated sites that are either distant, or on different chromosomes, are driven by both common and unique environmental factors, and methylation at these sites is less likely to be driven by genotype. They are enriched for a multitude of TF binding sites and for inter-chromosomal chromatin contact sites, suggesting that DNA co-methylation of distant sites may be related to long-range cooperative TF interactions.

ConclusionsWe conclude that DNA co-methylation, especially in cis, has a stable structure from birth to adolescence and between white British and Pakistani individuals. We hypothesise that co-methylation may have roles in genome regulation in humans, including 3D chromatin architecture. The stable structure we have identified might have implications for the future design and interpretation of epigenetic studies.


title: Technology applications in bovine gait analysis: a scoping review

abstract: Quantitative bovine gait analysis using technology has evolved significantly over the last two decades. However, subjective methods of gait assessment using visual locomotion scoring remain the primary on-farm and experimental approach. The objective of this review is to map research trends in quantitative bovine gait analysis and to explore the technologies that have been utilized to measure biomechanical parameters of gait. A scoping literature review was conducted according to PRISMA guidelines. A search algorithm based on PICO framework generated three components - bovine, gait, and technology - to address our objectives. Three online databases were searched for original work published from January 2000 to June 2020. A two-step screening process was then conducted, starting with the review of article titles and abstracts based on inclusion criteria. A remaining 125 articles then underwent a full-text assessment, resulting in 82 final articles. Thematic analysis of research aims resulted in four major themes among the studies: gait/claw biomechanics, lameness detection, intervention/comparison, and system development. Lameness detection (55 % of studies) was the most common reason for technology use. Studies in the field of bovine gait analysis used three main technologies: force and pressure platforms (FPP), vision-based systems (VB), and accelerometers. FPP were the first and most popular technologies to evaluate bovine gait and were used in 58.5 % of studies. They include force platforms, pressure mapping systems, and weight distribution platforms. The second most applied technology was VB (34.1 % of studies), which predominately consists of video analysis and image processing systems. Accelerometers, another technological method to measure gait characteristics, were used in 14.6 % of studies. A strong demand for automatic lameness detection influences the path of development for quantitative gait analysis technologies. Although progress has been made, more research is needed to achieve more accurate, practical, and user-friendly technologies.


title: Female reproductive fluid composition differs based on mating system in Peromyscus mice

abstract: Post-copulatory sexual selection is theorized to favor female traits that allow them to control sperm use and fertilization, leading to the prediction that female reproductive traits that influence sperm migration should differ between polyandrous and monogamous species. Here we exploit natural variation in the female mating strategies of closely related Peromyscus mice to compare female traits that influence sperm motility - the viscosity, pH, and calcium concentration of fluids in the reproductive tract - between polyandrous and monogamous species. We find that the viscosity and pH, but not calcium concentration, of fluids collected from both the uterus and the oviduct significantly differ between species based on mating system. Our results demonstrate the existence of a viscosity gradient within the female reproductive tract that increases in monogamous species but decreases in polyandrous species. Both species have a more alkaline environment in the uterus than oviduct, but only in the polyandrous species did we observe a decrease in calcium in the distal end of the tract. These results suggest that fluid viscosity and pH in the female reproductive tracts of these mice may be influenced by post-copulatory sexual selection and provide a promising potential mechanism for female sperm control given their importance in modulating sperm behavior.


title: Projective LDDMM: Spatially Reconstructing a Story of Rostrally-Dominant Tau in Alzheimer's Disease

abstract: Since Braaks initial histological observations, it has been recognized that Alzheimers disease (AD) neurofibrillary tangles (NFTs) appear in the medial temporal lobe (MTL) of the brain very early in the disease course. MRI-based shape diffeomorphometry markers have demonstrated pre-clinical AD changes in the MTL but it has not been possible to confirm that these MRI changes correspond to the presence of NFTs. Here, we present a method termed Projective LDDMM for aligning sparse measurement profiles of AD pathology (i.e., 2D digital histology images) with 3D MRI. We reconstruct measures of 2D NFT density in the dense metric of 3D MRI, using the Mai Paxinos Atlas coordinates for two cases of advanced AD. Analyses reveal the highest levels of NFT density in the rostral third (10-15 mm) of the hippocampus and the adjoining regions of the entorhinal cortex and amygdala. These findings emphasize the selective vulnerability of MTL subregions in AD, and suggest that high resolution MRI methods might benefit from focusing on the rostral MTL to more closely link these MRI images to AD neuropathology.


title: Ubiquitous lognormal distribution of neuron densities across mammalian cerebral cortex

abstract: Numbers of neurons and their spatial variation are fundamental organizational features of the brain. Despite the large corpus of data available in the literature, the statistical distributions of neuron densities within and across brain areas remain largely uncharacterized. Here, we show that neuron densities are compatible with a lognormal distribution across cortical areas in several mammalian species. We find that this also holds true for uniformly sampled regions across cortex as well as within cortical areas. Our findings uncover a new organizational principle of cortical cytoarchitecture. The ubiquitous lognormal distribution of neuron densities adds to a long list of lognormal variables in the brain.


title: Prefrontal PV interneurons facilitate attention and are linked to attentional dysfunction in a mouse model of absence epilepsy

abstract: Absence seizures are characterized by brief periods of unconsciousness accompanied by a lapse in motor function that can occur hundreds of times throughout the day. Outside of these frequent moments of unconsciousness, approximately a third of patients experience treatment-resistant attention impairments. Convergent evidence suggests prefrontal cortex (PFC) dysfunction may underlie attention impairments in affected patients. To test this, we use a combination of slice physiology, fiber photometry, electrocorticography (ECoG), optogenetics, and behavior in the Scn8a+/- mouse model of absence epilepsy. In these mice, we find decreased parvalbumin interneuron (PVIN) recruitment in the medial PFC (mPFC) in vitro and hypoactivity during cue presentation in vivo that is linked to attention dysfunction. Further, we find that low levels of mPFC PVIN activity are predictive of poorer performance in WT littermates. This highlights cue-evoked PVIN activity as an important mechanism for attention and suggests PVINs may represent a therapeutic target for cognitive comorbidities in absence epilepsy.


title: Biocompatible polymers for scalable production of human neural organoids

abstract: The generation of neural organoids from human pluripotent stem cells holds great promise in modeling disease and screenings drugs, but current approaches are difficult to scale due to undesired organoid fusion. Here, we develop a scalable neural organoid platform by screening biocompatible polymers that prevent fusion of organoids cultured in suspension. We show that addition of one inexpensive polysaccharide enables straightforward screening of 298 FDA-approved drugs and teratogens for growth defects using over 2,400 cortical organoids.


title: Transcriptomic similarity in the mouse and human brain

abstract: The ever-increasing use of mouse models in preclinical neuroscience research calls for an improvement in the methods used to translate findings between mouse and human brains. Using openly accessible brain-wide transcriptomic data sets, we evaluated the similarity of mouse and human brain regions on the basis of homologous gene expression. Our results suggest that mouse-human homologous genes capture broad patterns of neuroanatomical organization, but that the resolution of cross-species correspondences can be improved using a novel supervised machine learning approach. Using this method, we demonstrate that sensorimotor subdivisions of the neocortex exhibit greater similarity between species, compared with supramodal sub-divisions, and that mouse isocortical regions separate into sensorimotor and supramodal clusters based on their similarity to human cortical regions. We also find that mouse and human striatal regions are strongly conserved, with the mouse caudoputamen exhibiting an equal degree of similarity to both the human caudate and putamen.


title: Whole-brain comparison of rodent and human brains using spatial transcriptomics


title: Impact of maternal protein restriction on hypoxia-inducible factor (HIF) expression in male fetal kidney development

abstract:
BackgroundThe kidney ontogenesis is the most structurally affected by gestational protein restriction, reducing close to 30% of their functional units. The reduced nephron number is predictive of hypertension and cardiovascular dysfunctions generally observed in the adult age of most fetal programming models. We demonstrate HIF-1 predicts molecular pathway changes may be associated with the decreased nephron numbers in the 17 gestational days (17GD) low protein (LP) intake male fetal kidney compared to regular protein (NP) progeny intake. Here, we evaluated the predicted targets and related pathways in the fetal kidneys of 17-GD LP offspring to elucidate the molecular modulations during nephrogenesis.

MethodsPregnant Wistar rats were allocated into two groups: NP (regular protein diet -17%) or LP (diet-6%). Taking into account miRNA transcriptome sequencing previous study (miRNA-Seq) in 17-GD male offspring kidneys using previously described methods, was investigated predicted target genes and proteins, in particular, related to HIF-1 pathway by RT-qPCR and immunohistochemistry.

Results and conclusionsThe current study data supported that nephron onset impairment in the 17-DG fetuss kidney, programmed by gestational low-protein intake, is, at least in part, related to alterations in the HIF-1 signaling pathway. Factors that facilitate the transposition of HIF-1 to the mesenchymal cells nucleus, such as NOS, Ep300, and HSP90, may have an essential role in this regulatory process. This alteration leads to the inhibition of adaptive responses to the adverse environment, secondary to an increase in ungraded HIF-1, possibly associated with a reduction in the transcription factor elF-4 and proteins of their respective signaling pathways. Consequently, we may suggest an early maturation process of renal cells, inhibition of nephron progenitor cell division, and reduction of renal functional units in the offspring of rats submitted to severe gestational protein restriction.


title: A single amino acid transporter controls the uptake of priming-inducing beta-amino acids and the associated trade-off between induced resistance and plant growth.

abstract: Selected beta-amino acids, such as beta-aminobutyric acid (BABA) and R-beta-homoserine (RBH), can prime plants for resistance against broad-spectrum diseases. Here, we describe a genome-wide screen of fully annotated Arabidopsis T-DNA insertion lines for impaired in RBH-induced immunity (iri) against the downy mildew pathogen Hyaloperonospora arabidopsidis, yielding 104 lines that were partially affected and 4 lines that were completely impaired in RBH-induced resistance. The iri1-1 mutant phenotype could be confirmed by an independent T-DNA insertion in the same gene, encoding the high-affinity amino acid transporter LHT1. Using uptake experiments with IRI1/LHT1-expressing yeast cells and mass spectrometry-based quantification of RBH and BABA in leaves of mutant and over-expression lines of IRI1/LHT1, we demonstrate that IRI1/LHT1 acts as the main transporter for cellular uptake and systemic distribution of RBH and BABA. Subsequent characterisation of mutant and over-expression lines of IRI1/LHT1 for induced resistance and growth responses revealed that the level of IRI1/LHT1 expression determines the trade-off between induced resistance and plant growth by RBH and BABA.


title: Alpha-mannosidase-2 modulates arbovirus infection in a pathogen- and Wolbachia-specific manner in Aedes aegypti mosquitoes

abstract: Multiple Wolbachia strains can block pathogen infection, replication, and/or transmission in Aedes aegypti mosquitoes under both laboratory and field conditions. However, Wolbachia effects on pathogens can be highly variable across systems and the factors governing this variability are not well understood. It is increasingly clear that the mosquito host is not a passive player in which Wolbachia governs pathogen transmission phenotypes; rather, the genetics of the host can significantly modulate Wolbachia-mediated pathogen blocking. Specifically, previous work linked variation in Wolbachia pathogen blocking to polymorphisms in the mosquito alpha-mannosidase 2 (Man2) gene. Here we use CRISPR-Cas9 mutagenesis to functionally test this association. We developed Man2 knockouts and examined effects on both Wolbachia and virus levels, using both dengue virus (DENV; Flaviviridae) and Mayaro virus (MAYV; Togaviridae). Wolbachia titers were significantly elevated in Man2 knockout (KO) mosquitoes, but there were complex interactions with virus infection and replication. In Wolbachia-uninfected mosquitoes, the Man2 KO mutation was associated with decreased DENV titers, but in a Wolbachia-infected background, the Man2 KO mutation significantly modulated virus blocking. In contrast, the Man2 KO mutation significantly increased MAYV replication in Wolbachia-uninfected mosquitoes and did not affect Wolbachia-mediated virus blocking. These results demonstrate that Man2 modulates arbovirus infection in Ae. aegypti mosquitoes in a pathogen- and Wolbachia-specific manner, and that Wolbachia-mediated pathogen blocking is a complex phenotype dependent on the mosquito host genotype and the pathogen. These results have significant impact for the design and use of Wolbachia-based strategies to control vector-borne pathogens.


title: Establishment of an efficient transformation and CRISPR/Cas9-mediated gene editing system in Chinese local planting cassava (Manihot esculenta Crantz) cultivar SC8

abstract: Cassava starch is a widely used raw material for industrial production. South Chinese cassava cultivar 8 (Manihot esculenta Crantz cv. SC8) is one of the main locally planted cultivars. In this study, an efficient transformation system for cassava SC8 mediated with Agrobacterium strain LBA4404 was presented for the first time, in which the factors of Agrobacterium strain cell infection (density OD600 = 0.65), 250 {micro}M acetosyringone induction, and agro-cultivation with wet friable embryogenic callus (FEC) for 3 days in dark conditions were found to increase the transformation efficiency through the binary vector pCAMBIA1304 harboring GUS- and GFP-fused genes driven by the CaMV35S promoter. Based on the optimized transformation protocol, approximately 120-140 independent transgenic lines per mL settled FEC cell volume (SCV) by gene transformation in approximately five months, and 45.83% homozygous mono-allelic mutations of the MePDS gene with a YAO promoter-driven CRISPR/Cas9 system were generated. This study will open a more functional avenue for the genetic improvement of cassava SC8.


title: Combining quadrat, rake and echosounding to estimate submerged aquatic vegetation biomass at the ecosystem scale

abstract: Measuring freshwater submerged aquatic (SAV) biomass at large spatial scales is challenging and no single technique can cost effectively accomplish this while maintaining accuracy. We propose to combine and intercalibrate accurate quadrat-scuba diver technique, fast rake sampling and large scale echosounding. We found that the relationship between quadrat and rake biomass is moderately strong (R2 = 0.62, RMSECV = 2.19 g/m2) and varies with substrate type and SAV growth form. Rake biomass was also successfully estimated from biovolume10 and its error (R2 = 0.53, RMSECV = 5.95 g/m2), a biomass proxy derived from echosounding, at a resolution of 10 m radius from rake sampling point. However, the relationship was affected by SAV growth form, depth, acoustic data quality and wind conditions. Sequential application of calibrations yielded predictions in agreement with quadrat observations, but echosounding predictions underestimated biomass in shallow areas (< 1.5 m) while outperforming point estimation in deep areas (> 3 m). Whole-system biomass was more accurately estimated by calibrated echosounding than rake point surveys, owing to the large sample size and better representation of spatial heterogeneity of echosounding. We recommend developing as a one-time event a series of quadrat and rake calibration equations for each growth form and substrate type. Because the relationship between biovolume and biomass depends on SAV growth form, rake and echosounding calibration needs to be conducted frequently. With the two calibrations, rake can thus be used as a rapid ground truthing or in shallow areas where echosounding is inadequate.


title: Transcriptomic analysis of the C3-CAM transition in Cistanthe longiscapa, a drought tolerant plant in the Atacama Desert

abstract:
One of the most outstanding plant species during the blooming of the Atacama Desert is the annual plant Cistanthe longiscapa. This plant can perform CAM photosynthesis, but the ecophysiological and molecular mechanisms that this plant uses to withstand the extreme conditions it inhabits in the field are unknown.

Morphological and ecophysiological traits were studied and leaf samples at dawn/dusk times were collected from three sites distributed across an increasing south to north arid gradient, to evaluate CAM expression and transcriptomic differences, and search for links between photosynthetic path and abiotic response.

Plants from the different sites presented significant differences in nocturnal leaf acid accumulation, isotopic carbon ratio ({delta}13C), succulence and other four traits that clearly indicated a spectrum of CAM photosynthesis intensity that correlated with aridity intensity. The differential gene expression analysis among Dawn vs Dusk between sampling sites showed higher gene expression in the arid northern site (3991 v/s 2293) with activation of regulatory processes associated with abscisic acid and circadian rhythm.

The analysis highlights clear ecophysiological differences and the requirement of a strong rewiring of the gene expression to allow a transition from a weak into a strong CAM in C. longiscapa.


title: Timely sleep coupling: spindle-slow wave synchrony is linked to early amyloid-β burden and predicts memory decline

abstract: Sleep alteration is a hallmark of ageing and emerges as a risk factor for Alzheimers disease (AD). While the fine-tuned coalescence of sleep microstructure elements may influence age-related cognitive trajectories, its association with AD processes is not fully established. Here, we investigated whether the coupling of spindles and slow waves is associated with early amyloid-beta (A{beta}) brain burden, a hallmark of AD neuropathology, and cognitive change over 2 years in 100 healthy individuals in late-midlife (50-70y; 68 women). We found that, in contrast to other sleep metrics, earlier occurrence of spindles on slow-depolarisation slow waves is associated with higher medial prefrontal cortex A{beta} burden (p=0.014, r2{beta}*=0.06), and is predictive of greater longitudinal memory decline (p=0.032, r2{beta}*=0.07). These findings unravel early links between sleep, AD-related processes and cognition and suggest that altered coupling of sleep microstructure elements, key to its mnesic function, contributes to poorer brain and cognitive trajectories in ageing.


title: Inka2, a novel Pak4 inhibitor, regulates actin dynamics in dendritic spine development

abstract: The actin filament is a fundamental part of the cytoskeleton defining cell morphology and regulating various physiological processes, including filopodia formation and dendritic spinogenesis of neurons. Serine/threonine-protein kinase Pak4, an essential effector, links Rho GTPases to control actin polymerization. Previously, we identified the Inka2 gene, a novel mammalian protein exhibiting sequence similarity to Inka1, which serves as a possible inhibitor for Pak4. Although Inka2 is dominantly expressed in the nervous system and involved in focal-adhesion dynamics, its molecular role remains unclear. Here, we found that Inka2-iBox directly binds to Pak4 catalytic domain to suppress actin polymerization. Inka2 promoted actin depolymerization and inhibited the formation of cellular protrusion caused by Pak4 activation. We further generated the conditional knockout mice of the Inka2 gene. The beta-galactosidase reporter indicated the preferential Inka2 expression in the dorsal forebrain neurons. Cortical pyramidal neurons of Inka2-/- mice exhibited decreased density and aberrant morphology of dendritic spines with marked activation/phosphorylation of downstream molecules of Pak4 signal cascade, including LIMK and cofilin. These results uncovered the unexpected function of endogenous Pak4 inhibitor in neurons. Unlike Inka1, Inka2 is a critical mediator for actin reorganization required for dendritic spine development.


title: COVID-19 patients have increased levels of membrane-associated and soluble CD48

abstract:
COVID-19 is a respiratory-centered systemic disorder caused by SARS-CoV-2. The disease can progress into a severe form causing acute lung injury.

CD48 is a co-signaling receptor, existing as both membrane-bound and soluble forms reported to be dysregulated in several inflammatory conditions. Therefore, we reasoned that CD48 could be deregulated in COVID-19 as well.

Here we analyzed CD48 expression in autoptic sections and peripheral blood leukocytes and sera of COVID-19 patients by gene expression profiling (HTG(R) autoimmune panel), immunohistochemistry, flow cytometry and ELISA.

Lung tissue of COVID-19 patients showed increased CD48 mRNA expression and infiltration of CD48+ lymphocytes. In the peripheral blood, mCD48 was considerably increased on all evaluated cells, and additionally, sCD48 levels were significantly higher in COVID-19 patients independently of disease severity. Considering the alterations of mCD48 and sCD48, a specific role for CD48 in COVID-19 can be assumed, suggesting it as a potential target for therapy.


title: Pre-exposure to mRNA-LNPs reprograms adaptive and innate immune responses in an inheritable fashion

abstract: Billions of SARS-CoV-2 mRNA-LNP vaccine doses have already been administered to humans. However, we lack a comprehensive understanding of the immune effects of this platform. Here we bring experimental evidence that pre-exposure to mRNA-LNPs or its LNP component has effects on both innate and adaptive immune responses. Pre-exposure to mRNA-LNPs led to long-term, platform-specific inhibition of the adaptive immune responses. As such, mice responded with lower antibody responses when exposed the second time to the mRNA-LNP platform, but with undisturbed adaptive immune responses to protein-based Alum or AddaVax-adjuvanted vaccines. On the other hand, we report that after pre-exposure to mRNA-LNPs, resistance of mice to heterologous infections with influenza virus and Candida albicans is likely enhanced. Interestingly, mice pre-exposed to mRNA-LNPs can pass down the acquired immune traits to their offspring, providing better protection. In summary, the mRNA-LNP vaccine platform induces long-term immunological changes that can affect both humoral responses and heterologous protection against infections. More studies are needed to understand in-depth the mechanisms responsible for these effects.


title: Single-cell multiomics atlas of organoid development uncovers longitudinal molecular programs of cellular diversification of the human cerebral cortex

abstract: Realizing the full utility of brain organoids as experimental systems to study human cortical development requires understanding whether organoids replicate the cellular and molecular events of this complex process precisely, reproducibly, and with fidelity to the embryo. Here we present a comprehensive single-cell transcriptomic, epigenetic, and spatial atlas of human cortical organoid development, comprising over 610,000 cells, spanning initial generation of neural progenitors through production of differentiated neuronal and glial subtypes. We define the lineage relationships and longitudinal molecular trajectories of cortical cell types during development in organoids, and show that developmental processes of cellular diversification in organoids correlate closely to endogenous ones, irrespective of metabolic state. Using this data, we identify genes with predicted human-specific roles in lineage establishment, and discover a developmental origin for the transcriptional diversity of human callosal projection neurons, a population that has undergone dramatic expansion and diversification during human evolution. Our work provides a comprehensive, single-cell molecular map of human corticogenesis in vitro, identifying developmental trajectories and molecular mechanisms associated with human cellular diversification.


title: Glial control of sphingolipid levels sculpts diurnal remodeling of sleep circuitry

abstract: Structural plasticity in the brain often necessitates dramatic remodeling of neuronal processes and attendant reorganization of both the cytoskeleton and plasma membrane. While cytoskeletal restructuring has been studied extensively, how changes in specific lipids might orchestrate structural plasticity remain incompletely understood. We show that specific glial cells in Drosophila produce Glucocerebrosidase (GBA) to locally catabolize sphingolipids, critical components of neuronal membranes. Defects in sphingolipid catabolism drive lysosomal dysfunction, causing Gba1b mutants to harbor protein aggregates that cycle across circadian time, are regulated by neural activity and the circadian clock, and plateau with age. Moreover, cell-specific perturbations reveal that sphingolipid catabolism is necessary for neurites in sleep circuits to extend and retract across the day, and for sleep behavior. Critically, reprogramming the temporal pattern of GBA expression in sleep-circuit neurons is sufficient to invert the membrane remodeling cycle. Thus, dynamic changes in sphingolipid levels instruct the diurnal pattern of neuronal plasticity.


title: Synapses in oligodendrocyte precursor cells are dynamic and contribute to Ca2+ activity

abstract: Cell-cell interactions are critical to central nervous system (CNS) structure and function. Direct neuron-neuron interactions occur via synapses, but only one type of neuron-glia synapse is known to exist: those formed between neurons (pre-) and oligodendrocyte precursor cells (OPCs) (post-)1,2. These synapses are thought to bridge neuronal activity to OPCs, which are critical for developmental myelination and adult motor learning3. However, the composition and assembly of neuron-OPC synapses and their in vivo functions remain largely unclear. Here, using zebrafish to label postsynaptic organizers PSD-95 and Gephyrin in OPCs, we found that synapses in OPCs possess dynamic assembly properties and are developmentally regulated. We also found that synapses and voltage-gated Ca2+ channels (VGCCs) play important roles in driving intrinsic OPC Ca2+ activity that occurs mainly in microdomains, while evoked synaptic release has a limited role that diminishes through development. Finally, disrupting a key synaptic gene, neuroligin3b, specifically in OPCs impairs OPC differentiation and subsequent myelination. Our results establish an in vivo model of dynamic neuron-OPC synapses mediating intrinsic OPC Ca2+ activity and impacting OPC differentiation, pointing to plastic neuron-OPC interactions and synapse-dependent and -independent Ca2+ pathways in OPCs.