title: The depletion mechanism can actuate bacterial aggregation by self-produced exopolysaccharides and determine species distribution and composition in bacterial aggregates

abstract: Bacteria causing chronic infections are often found in cell aggregates suspended in polymer secretions, and aggregation may be a factor in infection persistence. One aggregation mechanism, called depletion aggregation, is driven by physical forces between bacteria and polymers. Here we investigated whether the depletion mechanism can actuate the aggregating effects of P. aeruginosa exopolysaccharides for suspended (i.e. not surface attached) bacteria, and how depletion affects bacterial inter-species interactions. We found cells overexpressing the exopolysaccharides Pel and Psl, but not alginate remained aggregated after depletion-mediating conditions were reversed. In co-culture, depletion aggregation had contrasting effects on P. aeruginosas interactions with coccus- and rod-shaped bacteria. Depletion caused S. aureus (cocci) and P. aeruginosa (rods) to segregate from each other, S. aureus to resist secreted P. aeruginosa antimicrobial factors, and the species to co-exist. In contrast, depletion aggregation caused P. aeruginosa and Burkholderia sp. to intermix, enhancing type VI secretion inhibition of Burkholderia by P. aeruginosa, leading to P. aeruginosa dominance. These results show that in addition to being a primary cause of aggregation in polymer-rich suspensions, physical forces inherent to the depletion mechanism can actuate the aggregating effects of self-produced exopolysaccharides and determine species distribution and composition of bacterial communities.


title: Ultraviolet-A light increases mitochondrial anti-viral signaling protein in confluent human tracheal cells even at a distance from the light source

abstract: Mitochondrial antiviral signaling (MAVS) protein mediates innate antiviral responses, including responses to certain coronaviruses such as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). We have previously shown that ultraviolet-A (UVA) therapy can prevent virus-induced cell death in human ciliated tracheal epithelial cells (HTEpC) infected with coronavirus-229E, and that UVA treatment results in an increase in intracellular levels of MAVS. In this study, we set out to determine the mechanisms by which UVA light can activate MAVS, and whether local UVA light application can activate MAVS at locations distant from the light source (such as via cell-to-cell communication). MAVS levels were compared in HTEpC exposed to 2 mW/cm2 narrow band (NB)-UVA for 20 minutes and in unexposed controls, at 30-40% and at 100% confluency. MAVS levels were also compared in unexposed HTEpC treated with supernatants or lysates from UVA-exposed cells or from unexposed controls. Also, MAVS was assessed in different sections of confluent monolayer plates where only one section was exposed to NB-UVA. The results show that UVA increases the expression of MAVS protein. Cells in a confluent monolayer exposed to UVA were able to confer an elevation in MAVS in cells adjacent to the exposed section, and even cells in the most distant sections not exposed to UVA. In this study, human ciliated tracheal epithelial cells exposed to UVA demonstrate increased MAVS protein, and also appear to transmit this influence to distant confluent cells not exposed to light.

category: cell biology


title: Harnessing natural variation to identify cis regulators of sex-biased gene expression in a multi-strain mouse liver model

abstract:
Sex differences in gene expression are widespread in the liver, where a large number of autosomal factors act in tandem with growth hormone signaling to regulate individual variability of sex differences in liver metabolism and disease. Here, we compare hepatic transcriptomic and epigenetic profiles of mouse strains C57Bl/6J and CAST/EiJ, representing two subspecies separated by 0.5-1 million years of evolution, to elucidate the actions of genetic factors regulating liver sex differences. We identify 144 protein coding genes and 78 lncRNAs showing strain-conserved sex bias; many have gene ontologies relevant to liver function, are more highly liver-specific and show greater sex bias, and are more proximally regulated than genes whose sex bias is strain-dependent. The strain-conserved genes include key growth hormone-dependent transcriptional regulators of liver sex bias; however, three other transcription factors, Trim24, Tox, and Zfp809, lose sex-biased expression in CAST/EiJ mouse liver. To elucidate these strain specificities in expression, we characterized the strain-dependence of sex-biased chromatin opening and enhancer marks at cis regulatory elements (CREs) within expression quantitative trait loci (eQTL) regulating liver sex-biased genes. Strikingly, 208 of 286 eQTLs with strain-specific, sex-differential effects on expression were associated with a complete gain, loss, or reversal of expression sex differences between strains. Moreover, 166 of the 286 eQTLs were linked to the strain-specific gain or loss of localized sex-biased CREs. Remarkably, a subset of these CREs lacked strain-specific genetic variants yet showed coordinated, strain-dependent sex-biased epigenetic regulation. Thus, we directly link hundreds of strain-specific genetic variants to the high variability in CRE activity and expression of sex-biased genes, and uncover underlying genetically-determined epigenetic states controlling liver sex bias in genetically diverse mouse populations.

Author summaryMale-female differences in liver gene expression confer sex differences in diverse biological processes relevant to human health and disease, but are difficult to model in inbred mice given their identical genetic backgrounds. Outbred mice provide some variability, but cross-strain studies of sex bias in rodents have not been well studied. Here we elucidate the actions of genetic factors regulating liver sex differences in two Diversity Outbred mouse founder mouse strains, C57Bl/6 and CAST/EiJ. We find that many of the strain differences in sex-biased gene expression can be linked to the gain or loss of a cis regulatory element associated with one or more strain-specific sequence variants. Strikingly, in many cases, the associated cis regulatory element lacked strain-specific variants, yet was subject to coordinated, strain-dependent epigenetic regulation. Thus, harnessing the power of naturally occurring genetic diversity of Diversity Outbred mice, we integrated biological data at the genetic, epigenetic, and transcriptomic levels across evolutionary divergent mouse strains to discover hundreds of localized genomic regions that control phenotypic sex differences in the liver. These findings may serve as a model for studies of human genetic variation and the effect of population-wide variation on sex differences in health and disease.

category: genetics


title: Maxicircle architecture and evolutionary insights into Trypanosoma cruzi complex

abstract: We sequenced maxicircles from T. cruzi strains representative of the species evolutionary diversity by using long-read sequencing, which allowed us to uncollapse their repetitive regions, finding that their real lengths range from 35 to 50 kb. T. cruzi maxicircles have a common architecture composed of four regions: coding region (CR), AT-rich region, short (SR) and long repeats (LR). Distribution of genes, both in order and in strand orientation are conserved, being the main differences the presence of deletions affecting genes coding for NADH dehydrogenase subunits, reinforcing biochemical findings that indicate that complex I is not functional in T. cruzi. Moreover, the presence of complete minicircles into maxicircles of some strains lead us to think about the origin of minicircles. Finally, a careful phylogenetic analysis was conducted using coding regions of maxicircles from up to 29 strains, and 1023 single copy nuclear genes from all of the DTUs, clearly establishing that taxonomically T. cruzi is a complex of species composed by group 1 that contains clades A, B and D, and group 2 containing clade C. No significant differences were found in hybrid strains that justify the existence of TcV and Tc VI as separate clades: our results indicate that a unique event of hybridization between TcII and TcIII occurred. Three variants of maxicircles exist in T. cruzi: a, b and c, in correspondence with clades A, B, and C from mitochondrial phylogenies. While A and C carry maxicircles a and c respectively, both clades B and D carry b maxicircle variant; hybrid strains also carry the b- variant. We then propose a new nomenclature that is self-descriptive and makes use of both the phylogenetic relationships and the maxicircle variants present in T. cruzi.

category: genomics


title: Chromatin landscape dynamics in development of the plant parasitic nematode Meloidogyne incognita

abstract:
In model organisms, epigenome dynamics underlies a plethora of biological processes. The role of epigenetic modifications in development and parasitism in nematode pests remains unknown. The root-knot nematode Meloidogyne incognita adapts rapidly to unfavorable conditions, despite its asexual reproduction. However, the mechanisms underlying this remarkable plasticity and their potential impact on gene expression remain unknown. This study provides the first insight into contribution of epigenetic mechanisms to this plasticity, by studying histone modifications in M. incognita. The distribution of five histone modifications revealed the existence of strong epigenetic signatures, similar to those found in the model nematode Caenorhabditis elegans. We investigated their impact on chromatin structure and their distribution relative to transposable elements (TE) loci. We assessed the influence of the chromatin landscape on gene expression at two developmental stages: eggs, and pre-parasitic juveniles. H3K4me3 histone modification was strongly correlated with high levels of expression for protein-coding genes implicated in stage-specific processes during M. incognita development. We provided new insights in the dynamic regulation of parasitism genes kept under histone modifications silencing. In this pioneering study, we establish a comprehensive framework for the importance of epigenetic mechanisms in the regulation of the genome expression and its stability in plant-parasitic nematodes.

Author summaryThe nematode Meloidogyne incognita is one of the most destructive plant parasites worldwide. Its ability to infect a wide range of hosts and its high adaptability contribute to its parasitic success. We investigated the role of epigenetic mechanisms -- specifically post-translational histone modifications -- in the parasitic life cycle. We showed these modifications are linked to gene expression regulation and likely contribute to nematode development and pathogenicity.


title: easyXpress: An R package to analyze and visualize high-throughput C. elegans microscopy data generated using CellProfiler

abstract: High-throughput imaging techniques have become widespread in many fields of biology. These powerful platforms generate large quantities of data that can be difficult to process and visualize efficiently using existing tools. We developed easyXpress to process and review C. elegans high-throughput microscopy data in the R environment. The package provides a logical workflow for the reading, analysis, and visualization of data generated using CellProfilers WormToolbox. We equipped easyXpress with powerful functions to customize the filtering of noise in data, specifically by identifying and removing objects that deviate from expected animal measurements. This flexibility in data filtering allows users to optimize their analysis pipeline to match their needs. In addition, easyXpress includes tools for generating detailed visualizations, allowing the user to interactively compare summary statistics across wells and plates with ease. Researchers studying C. elegans benefit from this streamlined and extensible package as it is complementary to CellProfiler and leverages the R environment to rapidly process and analyze large high-throughput imaging datasets.

category: bioinformatics


title: Hemodynamic molecular imaging of tumor-associated enzyme activity in the living brain.

abstract: Molecular imaging could have great utility for detecting, classifying, and guiding treatment of brain disorders, but existing probes offer limited capability for assessing relevant physiological parameters. Here we describe a potent approach for noninvasive mapping of cancer-associated enzyme activity using a molecular sensor that acts on the vasculature, providing a diagnostic readout via local changes in hemodynamic image contrast. The sensor is targeted at the fibroblast activation protein (FAP), an extracellular dipeptidase and clinically relevant biomarker of brain tumor biology. Optimal FAP sensor variants were identified by screening a series of prototypes for responsiveness in a cell-based bioassay. The best variant was then applied for quantitative neuroimaging of FAP activity in rats, where it reveals nanomolar-scale FAP expression by xeno-grafted tumor cells. The activated probe also induces robust hemodynamic contrast in nonhuman primate brain. This work thus demonstrates a translatable strategy for ultrasensitive functional imaging of molecular targets in neuromedicine.

category: bioengineering


title: Neural correlates of semantic number: A cross-linguistic investigation

abstract: One aspect of natural language comprehension is understanding how many of what or whom a speaker is referring to. While previous work has documented the neural correlates of general number comprehension and quantity comparison, we investigate semantic number from a cross-linguistic perspective with the goal of identifying cortical regions involved in distinguishing plural from singular nouns. We use three fMRI datasets in which Chinese, French, and English native speakers listen to an audiobook of a childrens story in their native language. We select these three languages because they differ in their number semantics. While Chinese lacks nominal pluralization, French and English nouns are overtly marked for number. We find a number of known semantic processing regions in common, including dorsomedial prefrontal cortex and the pars orbitalis, in which cortical activation is greater for plural than singular nouns and posit a cross-linguistic role for number in semantic comprehension.

category: neuroscience


title: Analysis of the Neurotropic and Anti-inflammatory Effects of Neuroelectrode Functionalization with a Heparan Sulphate Mimetic

abstract:
Further in the search for biomimicry of the properties analogous to neural tissues, and with an ultimate goal of mitigating electrode deterioration via reactive host cell response and glial scar formation, the bio-functionalisation of PEDOT:PTS neural coating is here presented using a heparan mimetic termed (HM) F6. A sulphated mimetic polyanion, with a potential role in neuromodulation in neurodegenerative diseases, and used here for the first time as neural coating.

This work acts as a first step towards the use of HM biological dopants, to enhance neuroelectrode functionality, to promote neural outgrowth and to maintain minimal glial scar formation in vitro at the neural-interface. Further, this study opens new possibilities for the evaluation of glycan mimetics in neuroelectrode functionalisation.


title: Hierarchical confounder discovery in the experiment-machine learning cycle

abstract: The promise of using machine learning (ML) to extract scientific insights from high dimensional datasets is tempered by the frequent presence of confounding variables, and it behooves scientists to determine whether or not a model has extracted the desired information or instead may have fallen prey to bias. Due both to features of many natural phenomena and to practical constraints of experimental design, complex bioscience datasets tend to be organized in nested hierarchies which can obfuscate the origin of a confounding effect and obviate traditional methods of confounder amelioration. We propose a simple non-parametric statistical method called the Rank-to-Group (RTG) score that can identify hierarchical confounder effects in raw data and ML-derived data embeddings. We show that RTG scores correctly assign the effects of hierarchical confounders in cases where linear methods such as regression fail. In a large public biomedical image dataset, we discover unreported effects of experimental design. We then use RTG scores to discover cross-modal correlated variability in a complex multi-phenotypic biological dataset. This approach should be of general use in experiment-analysis cycles and to ensure confounder robustness in ML models.


title: Phase separation of both a plant virus movement protein and cellular factors support virus-host interactions

abstract:
Phase separation concentrates biomolecules, which should benefit RNA viruses that must sequester viral and host factors during an infection. Here, the p26 movement protein from Pea enation mosaic virus 2 (PEMV2) was found to phase separate and partition in nucleoli and G3BP stress granules (SGs) in vivo. Electrostatic interactions drive p26 phase separation as mutation of basic (R/K-G) or acidic (D/E-G) residues either blocked or reduced phase separation, respectively. During infection, p26 must partition inside the nucleolus and interact with fibrillarin (Fib2) as a pre-requisite for systemic trafficking of viral RNAs. Partitioning of p26 in pre-formed Fib2 droplets was dependent on p26 phase separation suggesting that phase separation of viral movement proteins supports nucleolar partitioning and virus movement. Furthermore, viral ribonucleoprotein complexes containing p26, Fib2, and PEMV2 RNA were formed via phase separation in vitro and could provide the basis for self-assembly in planta. Interestingly, both R/K-G and D/E-G p26 mutants failed to support systemic trafficking of a Tobacco mosaic virus (TMV) vector in Nicotiana benthamiana suggesting that p26 phase separation, proper nucleolar partitioning, and systemic movement are intertwined. p26 also partitioned in SGs and G3BP over-expression restricted PEMV2 accumulation >20-fold. Expression of phase separation-deficient G3BP only restricted PEMV2 5-fold, demonstrating that G3BP phase separation is critical for maximum antiviral activity.

AUTHOR SUMMARYPhase separation of several cellular proteins is associated with forming pathological aggregates and exacerbating neurodegenerative disease progression. In contrast, roles for viral protein phase separation in RNA virus lifecycles are less understood. Here, we demonstrate that the p26 movement protein from Pea enation mosaic virus 2 phase separates and partitions with phase-separated cellular proteins fibrillarin and G3BP. The related orthologue from Groundnut rosette virus has been extensively studied and is known to interact with fibrillarin in the nucleolus as a pre-requisite for virus movement. We determined that basic residues and electrostatic interactions were critical for p26 phase separation. Furthermore, mutation of charged residues prevented the rescue of a movement-deficient Tobacco mosaic virus vector in Nicotiana benthamiana. Stress granules form through phase separation and we found that p26 could partition inside stress granules following heat shock. Phase separation of the stress granule nucleator G3BP was required for maximum antiviral activity and constitutes a host response that is dependent on cellular protein phase separation. Collectively, we demonstrate that phase separation of a plant virus protein facilitates virus-host interactions that are required for virus movement and phase separation of cellular proteins can simultaneously restrict virus replication.

category: microbiology


title: Energy Landscape of the SARS-CoV-2 Reveals Extensive Conformational Heterogeneity

abstract: Cryo-electron microscopy (cryo-EM) has produced a number of structural models of the SARS-CoV-2 spike, already prompting biomedical outcomes. However, these reported models and their associated electrostatic potential maps represent an unknown admixture of conformations stemming from the underlying energy landscape of the spike protein. As for any protein, some of the spikes conformational motions are expected to be biophysically relevant, but cannot be interpreted only by static models. Using experimental cryo-EM images, we present the energy landscape of the spike protein conformations, and identify molecular rearrangements along the most-likely conformational path in the vicinity of the open (so called 1RBD-up) state. The resulting global and local atomic refinements reveal larger movements than those expected by comparing the reported 1RBD-up and 1RBD-down cryo-EM models. Here we report greater degrees of "openness" in global conformations of the 1RBD-up state, not revealed in the single-model interpretations of the density maps, together with conformations that overlap with the reported models. We discover how the glycan shield contributes to the stability of these conformations along the minimum free-energy pathway. A local analysis of seven key binding pockets reveals that six out them, including those for engaging ACE2, therapeutic mini-proteins, linoleic acid, two different kinds of antibodies, and protein-glycan interaction sites, switch conformations between their known apo- and holo-conformations, even when the global spike conformation is 1RBD-up. This is reminiscent of a conformational pre-equilibrium. We found only one binding pocket, namely antibody AB-C135 to remain closed along the entire minimum free energy path, suggesting an induced fit mechanism for this enzyme.

category: biophysics


title: CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes.

abstract: The SARS-CoV-2 protein Nsp2 has been implicated in a wide range of viral processes, but its exact functions, and the structural basis of those functions, remain unknown. Here, we report an atomic model for full-length Nsp2 obtained by combining cryo-electron microscopy with deep learning-based structure prediction from AlphaFold2. The resulting structure reveals a highly-conserved zinc ion-binding site, suggesting a role for Nsp2 in RNA binding. Mapping emerging mutations from variants of SARS-CoV-2 on the resulting structure shows potential host-Nsp2 interaction regions. Using structural analysis together with affinity tagged purification mass spectrometry experiments, we identify Nsp2 mutants that are unable to interact with the actin-nucleation-promoting WASH protein complex or with GIGYF2, an inhibitor of translation initiation and modulator of ribosome-associated quality control. Our work suggests a potential role of Nsp2 in linking viral transcription within the viral replication-transcription complexes (RTC) to the translation initiation of the viral message. Collectively, the structure reported here, combined with mutant interaction mapping, provides a foundation for functional studies of this evolutionary conserved coronavirus protein and may assist future drug design.


title: Structure supports function: informing directed and dynamic functional connectivity with anatomical priors

abstract: The dynamic repertoire of functional brain networks is constrained by the underlying topology of structural connections: the lack of a direct structural link between two brain regions prevents direct functional interactions. Despite the intrinsic relationship between structural (SC) and functional connectivity (FC), integrative and multimodal approaches to combine the two remain limited, especially for electrophysiological data. In the present work, we propose a new linear adaptive filter for estimating dynamic and directed FC using structural connectivity information as priors. We tested the filter in rat epicranial recordings and human event-related EEG data, using SC priors from a meta-analysis of tracer studies and diffusion tensor imaging metrics, respectively. Our results show that SC priors increase the resilience of FC estimates to noise perturbation while promoting sparser networks under biologically plausible constraints. The proposed filter provides intrinsic protection against SC-related false negatives, as well as robustness against false positives, representing a valuable new method for multimodal imaging and dynamic FC analysis.


title: Autophagy gene-dependent intracellular immunity triggered by interferon-γ

abstract:
Genes required for the lysosomal degradation pathway of autophagy play key roles in topologically distinct cellular processes with significant physiologic importance. One of the first-described of these ATG gene-dependent processes is the requirement for a subset of ATG genes in interferon-{gamma} (IFN{gamma})-induced inhibition of norovirus and Toxoplasma gondii replication. Herein we identified new genes that are required for or that negatively regulate this immune mechanism. Enzymes involved in the conjugation of UFM1 to target proteins including UFC1 and UBA5, negatively regulated IFN{gamma}-induced inhibition of norovirus replication via effects of Ern1. IFN{gamma}-induced inhibition of norovirus replication required Wipi2b and Atg9a, but not Becn1 (encoding Beclin1), Atg14, or Sqstm1. The phosphatidylinositol-3-phosphate and ATG16L1 binding domains of WIPI2B were required for IFN{gamma}-induced inhibition of norovirus replication. Both WIPI2 and SQSTM1 were required for IFN{gamma}-induced inhibition of Toxoplasma gondii replication in HeLa cells. These studies further delineate the mechanisms of a programmable form of cytokine-induced intracellular immunity that relies on an expanding cassette of essential ATG genes to restrict the growth of phylogenetically diverse pathogens.

ImportanceInterferon-{gamma} is a critical mediator of cell-intrinsic immunity to intracellular pathogens. Understanding the complex cellular mechanisms supporting robust interferon-{gamma}-induced host defenses could aid in developing new therapeutics to treat infections. Here, we examined the impact of autophagy in the interferon-{gamma} induced host response. We demonstrate that CRISPR-Cas9 screens specifically targeting the autophagy pathway uncover a role for WIPI2 in IFN{gamma}-induced inhibition of Norovirus replication in mouse cells and IFN{gamma} mediated restriction of the Toxoplasma gondii parasitophorous vacuole in human cells. Furthermore, we found perturbation of UFMylation pathway components led to more robust IFN{gamma}-induced inhibition of Norovirus due to ER stress in vitro. Enhancing or inhibiting these dynamic cellular components could serve as a strategy to weaken intracellular pathogens and maintain an effective immune response.


title: Phyllosphere community assembly and response to drought stress on common tropical and temperate forage grasses

abstract:
Grasslands represent a critical ecosystem important for global food production, soil carbon storage, and water regulation. Current intensification and expansion practices add to the degradation of grasslands and dramatically increase greenhouse gas emissions and pollution. Thus, new ways to sustain and improve their productivity are needed. Research efforts focus on the plant-leaf microbiome, or phyllosphere, because its microbial members impact ecosystem function by influencing pathogen resistance, plant hormone production, and nutrient availability through processes including nitrogen fixation. However, little is known about grassland phyllospheres and their response to environmental stress. In this study, globally dominant temperate and tropical forage grass species were grown in a greenhouse under current climate conditions and drought conditions that mimic future climate predictions to understand if (i) plant host taxa influence microbial community assembly, (ii) microbial communities respond to drought stress, and (iii) phyllosphere community changes correlate to changes in plant host traits and stress-response strategies. Community analysis using high resolution sequencing revealed Gammaproteobacteria as the dominant bacterial class, which increased under severe drought stress on both temperate and tropical grasses while overall bacterial community diversity declined. Bacterial community diversity, structure, and response to drought were significantly different between grass species. This community dependence on plant host species correlated with differences in grass species traits, which became more defined under drought stress conditions, suggesting symbiotic evolutionary relationships between plant hosts and their associated microbial community. Further understanding these strategies and the functions microbes provide to plants will help us utilize microbes to promote agricultural and ecosystem productivity in the future.

IMPORTANCEGlobally important grassland ecosystems are at risk of degradation due to poor management practices compounded by predicted increases in severity and duration of drought over the next century. Finding new ways to support grassland productivity is critical to maintaining their ecological and agricultural benefits. Discerning how grassland microbial communities change in response to climate stress will help us understand how plant-microbe relationships may be useful to sustainably support grasslands in the future. In this study, phyllosphere community diversity and composition was significantly altered under drought conditions. The significance of our research is demonstrating how severe climate stress reduces bacterial community diversity, which previously was directly associated with decreased plant productivity. These findings guide future questions about functional plant-microbe interactions under stress conditions, greatly enhancing our understanding of how bacteria can increase food security by promoting grassland growth and resilience.


title: Multiscale light-sheet organoid imaging framework

abstract:
We present an imaging framework capable of turning long term light-sheet imaging of organoids into digital organoids. The framework takes advantage of deep learning techniques to faithfully segment single organoids, their lumen, cells and nuclei in 3D and over long periods of time. In parallel, large lineage trees for each organoid are predicted and corrected to iteratively improve the tracking and segmentation performances over time. To visualize the extracted information, we developed a web-based "Digital Organoid Viewer" that allows a unique understanding of the multivariate and multiscale data by linking 2D lineage trees with the corresponding 3D segmentation meshes.

We also backtracked single cells of interest after fixation obtaining detailed information about their history within the entire organoid context. Furthermore, we show nuclei merging events that arise from cytokinesis failure and that these polyploid never reside in the intestinal crypt, hinting at a tissue scale control and feedback on cellular fidelity. Molecularly, these cytokinesis failures depend on a regenerative state of the organoids and are regulated by Lats1 and RXR and we propose a model of tissue integrity by multi-scale check points. This discovery sheds light on the robustness of a regenerative YAP cellular state, questioning the role of polyploidy in intestinal regeneration.


title: The global rarity of intact coastal regions

abstract: Management of the land-sea interface is considered essential for global conservation and sustainability objectives, as coastal regions maintain natural processes that support biodiversity and the livelihood of billions of people. However, assessments of coastal regions have focused on either strictly the terrestrial or marine realm, and as a consequence, we still have a poor understanding of the overall state of Earths coastal regions. Here, by integrating the terrestrial human footprint and marine cumulative human impact maps, we provide a global assessment of the anthropogenic pressures affecting coastal areas. Just 15.5% of coastal areas globally can be considered having low anthropogenic pressure, mostly found in Canada, Russia, and Greenland. Conversely, 47.9% of coastal regions are heavily impacted by humanity with most countries (84.1%) having >50% of their coastal regions degraded. Nearly half (43.3%) of protected areas across coastal regions are exposed to high human pressures. In order to meet global sustainability objectives, we identify those nations that must undertake greater actions to preserve and restore coastal regions so as to ensure global sustainable development objectives can be met.

category: ecology


title: Tonic endocannabinoid signaling supports sleep through development in both sexes.

abstract: Sleep is an essential behavior that supports brain function and cognition throughout life, in part by acting on neuronal synapses. The synaptic signaling pathways that mediate the restorative benefits of sleep are not fully understood, particularly in the context of development. Endocannabinoids (eCBs) including 2-arachidonyl glycerol (2-AG) and anandamide (AEA), are bioactive lipids that activate cannabinoid receptor, CB1, to regulate synaptic transmission and mediate cognitive functions and many behaviors, including sleep. We used targeted mass spectrometry to measure changes in forebrain synaptic eCBs during the sleep/wake cycle in developing and adult mice. We find that eCBs are downregulated in response to acute sleep deprivation in juvenile mice, while in young adults eCBs are upregulated during the sleep phase in a circadian manner. Next we manipulated the eCB system using selective pharmacology and measured the effects on sleep behavior in developing and adult mice of both sexes using a non-invasive piezoelectric home-cage recording apparatus. Enhancement of eCB signaling through inhibition of 2-AG or AEA degradation, increased dark phase sleep amount and bout length in developing and adult males, but not in females. Inhibition of CB1 by injection of the antagonist AM251 reduced sleep time and caused sleep fragmentation in developing and adult males and females. Our data suggest that males are more sensitive to the sleep promoting effects of enhanced eCBs but that tonic eCB signaling supports sleep behavior through multiple stages of development in both sexes. This work informs the further development of cannabinoid-based therapeutics for sleep disruption.

category: animal behavior and cognition


title: Polymorphisms and gene expression in the almond IGT family are not correlated to variability in growth habit in major commercial almond cultivars

abstract: Almond breeding programs aimed at selecting cultivars adapted to intensive orchards have recently focused on the optimization of tree architecture. This multifactorial trait is defined by numerous components controlled by processes such as hormonal responses, gravitropism and light perception. Gravitropism sensing is crucial to control the branch angle and therefore, the tree habit. A gene family, denominated IGT family after a share conserved domain, has been described as involved in the regulation of branch angle in several species, including rice and Arabidopsis, and even in fruit trees like peach. Here we identified six members of this family in almond: LAZY1, LAZY2, TAC1, DRO1, DRO2, IGT-like. After analyzing their protein sequences in forty-one almond cultivars and wild species, little variability was found, pointing a high degree of conservation in this family. Gene expression was analyzed in fourteen cultivars of agronomical interest comprising diverse tree habit phenotypes. Only LAZY1, LAZY2 and TAC1 were expressed in almond shoot tips during the growing season. No relation was established between the expression profile of these genes and the tree habit. However, some insight has been gained in how LAZY1 and LAZY2 are regulated, identifying the IPA1 almond homologues and other transcription factors involved in hormonal responses as regulators of their expression. Besides, we have found various polymorphisms that could not be discarded as involved in a potential polygenic origin of regulation of architectural phenotypes. Therefore, we have established that unlike many species, IGT family genes do not play a critical role in the control of tree habit in currently commercialized almond cultivars, with other gene families contributing to the variability of these traits.

category: plant biology


title: Beat Perception in Polyrhythms: Time is Structured in Binary Units

abstract: In everyday life, we group and subdivide time to understand the sensory environment surrounding us. Our perceptual system establishes hierarchical structures by nesting different groups of time intervals. Organizing time in units such as diurnal rhythms, phrases, and beat patterns, is fundamental to everyday behavior, speech, and music. When listening to music, we extract rhythmic regularities to create a hierarchical metrical structure that enables us to predict the timing of the next events. Foot tapping and head bobbing to musical rhythms are observable evidence of this process. In the special case of polyrhythms, at least two metrical structures compete to become the reference for these temporal regularities, rendering several possible beats with which we can synchronize our movements. While there is general agreement that tempo, pitch, and loudness influence beat perception in polyrhythms, we focused on the yet neglected influence of beat subdivisions. In three online experiments, 300 participants listened to a range of polyrhythms and tapped their index fingers in time with the perceived beat. The polyrhythms consisted of two simultaneously presented isochronous pulse trains with different ratios (2:3, 2:5, 3:4, 3:5, 4:5, 5:6) and different tempi. For ratios 2:3 and 3:4, we additionally manipulated the pitch of the pulse trains. Results showed a highly robust influence of subdivision grouping on beat perception manifested as a propensity towards beats that are subdivided into two or four equally spaced units, as opposed to beats with three or more complex groupings of subdivisions. Additionally, lower pitched pulse trains were more likely to be perceived as the beat. Our findings suggest that subdivisions, not beats, are the basic unit of beat perception, and that the principle underlying the binary grouping of subdivisions reflects a propensity towards simplicity. This preference for simple grouping is widely applicable to human perception and cognition of time.


title: Brainstem cholinergic modulation of the thalamocortical activity in urethane anesthetized mice.

abstract: In mammals, sleep consists in the recurrence of two main stages the rapid eye movement (REM) sleep and the slow wave sleep (SWS). The full expression of sleep rhythms requires an intact thalamocortical loop, and its modulation by neuromodulators such as acetylcholine. A high tone of acetylcholine is observed during REM sleep while a low tone of acetylcholine modulates the cortical slow waves during SWS. Brainstem Cholinergic neurons activity correlates with cortical sleep stages but these neurons do not project directly to the cortex. Instead, they could contribute to cortically-recorded sleep stage modulation via a thalamic relay, in particular via the midline thalamic nuclei. Focusing on the brainstem LDTg cholinergic neurons, I investigated how midline thalamic single unit activity and cortical sleep-like stages are modulated during optogenetic-induced activation or silencing of LDTg cholinergic neurons in urethane anesthetized mice. Thalamic neurons were more active during REM-like than SWS-like stages. Bursting activity predominated during SWS-like while tonic firing was prominent during REM-like stage. Optogenetic silencing of the brainstem LDTg cholinergic neurons abolished REM-like stages and reduced tonic spiking of thalamic neurons. Moreover, during SWS-like, silent Down states were prolonged and thalamic tonic spiking during Up states was reduced. Stimulation of the brainstem LDTg cholinergic neurons had a mild effect on thalamic activity even though tonic discharge was increased. Surprisingly, optogenetic stimulation abolished as well REM-like stages maybe through compensatory mechanisms.


title: Temporal fine structure influences voicing confusions for consonant identification in multi-talker babble

abstract: To understand the mechanisms of speech perception in everyday listening environments, it is important to elucidate the relative contributions of different acoustic cues in transmitting phonetic content. Previous studies suggest that the envelope of speech in different frequency bands conveys most speech content, while the temporal fine structure (TFS) can aid in segregating target speech from background noise. However, the role of TFS in conveying phonetic content beyond what envelopes convey for intact speech in complex acoustic scenes is poorly understood. The present study addressed this question using online psychophysical experiments to measure the identification of consonants in multi-talker babble for intelligibility-matched intact and 64-channel envelope-vocoded stimuli. Consonant confusion patterns revealed that listeners had a greater tendency in the vocoded (versus intact) condition to be biased toward reporting that they heard an unvoiced consonant, despite envelope and place cues being largely preserved. This result was replicated when babble instances were varied across independent experiments, suggesting that TFS conveys voicing information beyond what is conveyed by envelopes for intact speech in babble. Given that multi-talker babble is a masker that is ubiquitous in everyday environments, this finding has implications for the design of assistive listening devices such as cochlear implants.


title: Absolute proteome quantification in the gas-fermenting acetogen Clostridium autoethanogenum

abstract: Microbes that can recycle one-carbon (C1) greenhouse gases into fuels and chemicals are vital for the biosustainability of future industries. Acetogens are the most efficient known microbes for fixing carbon oxides CO2 and CO. Understanding proteome allocation is important for metabolic engineering as it dictates metabolic fitness. Here, we use absolute proteomics to quantify intracellular concentrations for >1,000 proteins in the model-acetogen Clostridium autoethanogenum grown on three gas mixtures. We detect prioritisation of proteome allocation for C1 fixation and significant expression of proteins involved in the production of acetate and ethanol as well as proteins with unclear functions. The data also revealed which isoenzymes are important. Integration of proteomic and metabolic flux data demonstrated that enzymes catalyse high fluxes with high concentrations and high in vivo catalytic rates. We show that flux adjustments were dominantly accompanied with changing enzyme catalytic rates rather than concentrations. Our work serves as a reference dataset and advances systems-level understanding and engineering of acetogens.

category: systems biology


title: Analysis of the Role of N-glycosylation in Cell-surface expression, Function and Binding Properties of SARS-CoV-2 receptor ACE2

abstract:
Human angiotensin I-converting enzyme 2 (hACE2) is a type-I transmembrane glycoprotein that serves as the major cell entry receptor for SARS-CoV and SARS-CoV-2. The viral spike (S) protein is required for attachment to ACE2 and subsequent virus-host cell membrane fusion. Previous work has demonstrated the presence of N-linked glycans in ACE2. N-glycosylation is implicated in many biological activities, including protein folding, protein activity, and cell surface expression of biomolecules. However, the contribution of N-glycosylation to ACE2 function is poorly understood. Here, we examined the role of N-glycosylation in the activity and localization of two species with different susceptibility to SARS-CoV-2 infection, porcine ACE2 (pACE2) and hACE2. The elimination of N-glycosylation by tunicamycin (TM) treatment or mutagenesis, showed that N-glycosylation is critical for the proper cell surface expression of ACE2 but not for its carboxiprotease activity. Furthermore, nonglycosylable ACE2 localized predominantly in the endoplasmic reticulum (ER) and not at the cell surface. Our data also revealed that binding of SARS-CoV and SARS-CoV-2 S protein to porcine or human ACE2 was not affected by deglycosylation of ACE2 or S proteins, suggesting that N-glycosylation plays no role in the interaction between SARS coronaviruses and the ACE2 receptor. Impairment of hACE2 N-glycosylation decreased cell to cell fusion mediated by SARS-CoV S protein but not SARS-CoV-2 S protein. Finally, we found that hACE2 N-glycosylation is required for an efficient viral entry of SARS-CoV/SARS-CoV-2 S pseudotyped viruses, which could be the result of low cell surface expression of the deglycosylated ACE2 receptor.

ImportanceElucidating the role of glycosylation in the virus-receptor interaction is important for the development of approaches that disrupt infection. In this study, we show that deglycosylation of both ACE2 and S had a minimal effect on the Spike-ACE2 interaction. In addition, we found that removal of N-glycans of ACE2 impaired its ability to support an efficient transduction of SARS-CoV and SARS-CoV-2 S pseudotyped viruses. Our data suggest that the role of deglycosylation of ACE2 on reducing infection is likely due to a reduced expression of the viral receptor on the cell surface. These findings offer insight into the glycan structure and function of ACE2, and potentially suggest that future antiviral therapies against coronaviruses and other coronavirus-related illnesses involving inhibition of ACE2 recruitment to the cell membrane could be developed.


title: Mechanosensitivity of amoeboid cells crawling in 3D

abstract:
Efficient immune-responses require migrating leukocytes to be in the right place at the right time. When crawling through the body amoeboid leukocytes must traverse complex three-dimensional tissue-landscapes obstructed by extracellular matrix and other cells, raising the question how motile cells adapt to mechanical loads to overcome these obstacles. Here we reveal the spatio-temporal configuration of cortical actin-networks rendering amoeboid cells mechanosensitive in three-dimensions, independent of adhesive interactions with the microenvironment. In response to compression, Wiskott-Aldrich syndrom protein (WASp) assembles into dot-like structures acting as nucleation sites for actin spikes that in turn push against the external load. High precision targeting of WASp to objects as delicate as collagen fibers allows the cell to locally and instantaneously deform its viscoelastic surrounding in order to generate space for forward locomotion. Such pushing forces are essential for fast and directed leukocyte migration in fibrous and cell-packed tissues such as skin and lymph nodes.

In BriefWASp-driven actin spikes counter compressive loads of crowded tissue-landscapes.


title: Pseudohypoxic HIF pathway activation dysregulates collagen structure-function in human lung fibrosis

abstract: Extracellular matrix (ECM) stiffening with downstream activation of mechanosensitive pathways is strongly implicated in fibrosis. We previously reported that altered collagen nanoarchitecture is a key determinant of pathogenetic ECM structure-function in human fibrosis (Jones et al., 2018). Here, through human tissue, bioinformatic and ex vivo studies we show that hypoxia-inducible factor (HIF) pathway activation is a critical pathway for this process regardless of oxygen status (pseudohypoxia). Whilst TGF{beta} increased rate of fibrillar collagen synthesis, HIF pathway activation was required to dysregulate post-translational modification of fibrillar collagen, promoting  bone-type cross-linking, altering collagen nanostructure, and increasing tissue stiffness. In vitro, knock down of Factor Inhibiting HIF (FIH) or oxidative stress caused pseudohypoxic HIF activation in normal fibroblasts. In contrast, endogenous FIH activity was reduced in fibroblasts from patients with lung fibrosis in association with significantly increased normoxic HIF pathway activation. In human lung fibrosis tissue, HIF mediated signalling was increased at sites of active fibrogenesis whilst subpopulations of IPF lung mesenchymal cells had increases in both HIF and oxidative stress scores. Our data demonstrate that oxidative stress can drive pseudohypoxic HIF pathway activation which is a critical regulator of pathogenetic collagen structure-function in fibrosis.


title: Implicit Laplacian of Enhanced Edge (ILEE): An unguided quantitative cytoskeletal imaging algorithm

abstract: The eukaryotic cytoskeleton plays essential roles in cell signaling and trafficking, which is broadly associated with immunity and diseases of human and plants. To date, most analyses aiming at defining the temporal and spatial dynamics of the cytoskeleton have relied on qualitative and quantitative analysis of fluorescence images to describe cytoskeletal function. While state-of-the-art, these approaches have limitations: the diverse shape and brightness of the cytoskeleton cause considerable inaccuracy in both human-driven and automated approaches, and the widely adopted image projection process (3D to 2D) leads to bias and information loss. Here, we describe the development and application of Implicit Laplacian of Enhanced Edge (ILEE), an unguided approach that uses a 2D/3D-compatible local thresholding algorithm for the quantitative evaluation of cytoskeletal status and organization at high performance. Using ILEE, we constructed a Python library to enable automated cytoskeletal image analysis, providing numerous biologically-interpretable indices measuring the density, bundling, severing, branching, and directionality of the cytoskeleton. The data presented herein demonstrate that ILEE resolves the defects of classic cytoskeleton analysis approaches, enables the measurement of novel cytoskeletal features, and yields quantitatively descriptive data with superior accuracy, stability, and robustness. We released the ILEE algorithm as an open-source library and further developed a Google Colab interface as a community resource.


title: Implicit Laplacian of Enhanced Edge: An Unguided Algorithm for Accurate and Automated Quantitative Analysis of Cytoskeletal Images


title: Generation and timing of graded responses to morphogen gradients

abstract: Morphogen gradients are known to subdivide a naive cell field into distinct zones of gene expression. Here we examine whether morphogens can also induce a graded response within such domains. To this end we explore the role of the Dorsal protein nuclear gradient along the dorso-ventral axis in defining the graded pattern of actomyosin constriction that initiates gastrulation in early Drosophila embryos. Two complementary mechanisms for graded accumulation of mRNAs of critical zygotic target genes were identified. First, activation of target-gene expression expands over time from the ventral-most region of high nuclear Dorsal to lateral regions where the levels are lower, due to a Dorsal-dependent priming probability of transcription sites. Thus, sites that are activated earlier will lead to more mRNA accumulation. Second, once the sites are primed, the rate of Pol II loading is also dependent on Dorsal levels. Morphological restrictions require that translation of the graded mRNA be delayed until completion of embryonic cell formation. Such timing is achieved by large introns, that provide a delay in production of the mature mRNAs.

category: developmental biology


title: Prediction of gene expression from regulatory sequence composition enhances transcriptome-wide association studies

abstract: Transcriptome-wide association studies (TWAS) can prioritize trait-associated genes by finding correlations between a trait and the genetically regulated component of gene expression. A basic ingredient of a TWAS is a regression model, typically trained in an external reference data set, used to impute the genetically-regulated expression. We devised a model that improves the accuracy of the imputation by using, as predictors, not the genotypes directly but rather the sequence composition of the proximal gene regulatory region, expressed as its profile of affinities for a set of position weight matrices. When trained on 48 tissues from GTEx, the regression model showed improved performance compared with models regressing expression directly on the genotype. We imputed the expression levels in genotyped individuals from the ADNI data set, and used the imputed expression to perform a TWAS. We also developed a method to perform the TWAS based on summary statistics from genome-wide association studies, and applied it to 11 complex traits from the UK Biobank. The greater accuracy in the prediction of gene expression allowed us to report hundreds of new gene-phenotype association candidates.


title: Super-Resolution Imaging by Dual Iterative Structured Illumination Microscopy

abstract: Three-dimensional (3D) multicolor super-resolution imaging in the 50-100 nm range in fixed and living cells remains challenging. We extend the resolution of structured illumination microscopy (SIM) by an improved nonlinear iterative reconstruction algorithm that enables 3D multicolor imaging with improved spatiotemporal resolution at low illumination intensities. We demonstrate the performance of dual iterative SIM (diSIM) imaging cellular structures in fixed cells including synaptonemal complexes, clathrin coated pits and the actin cytoskeleton with lateral resolutions of 60-100 nm with standard fluorophores. Furthermore, we visualize dendritic spines in 70 {micro}m thick brain slices with an axial resolution < 200 nm. Finally, we image dynamics of the endoplasmatic reticulum and microtubules in living cells with up to 255 frames/s.


title: The Drosophila gene smoke alarm regulates nociceptor-epidermis interactions and thermal nociception behavior

abstract: The detection and processing of noxious sensory input depends on the proper growth and function of nociceptor sensory neurons in the peripheral nervous system. In Drosophila melanogaster, the class IV (cIV) multidendritic dendritic arborization (md-da) neurons detect noxious stimuli through their highly branched dendrites that innervate the epidermis of the larval body wall. Here, we describe requirements of a previously uncharacterized gene named smoke alarm (smal), a discoidin domain receptor, in cIV md-da dendrite morphogenesis and nociception behavior. We find that smal mutant larvae exhibit thermal hyperalgesia that is fully rescued with a BAC transgene containing smal. Consistent with this phenotype, a smal reporter gene was expressed in nociceptors and other peripheral sensory neurons. Smal::GFP protein localized to punctate structures throughout the cIV md-da neurons. We further show that smal loss-of-function results in reduced nociceptor dendrite branching. Interestingly, mammalian homologues of smal act as collagen receptors, and we find that smal mutant dendrites showed an increase in epidermal cell ensheathment relative to animals that are wild type for smal. Based on this phenotype we propose that Smal protein function is required for attachment of dendrites to the extracellular matrix (ECM) and the loss of this activity results in thermal hyperalgesia.


title: mRNA vaccine-induced SARS-CoV-2-specific T cells recognize B.1.1.7 and B.1.351 variants but differ in longevity and homing properties depending on prior infection status

abstract: While mRNA vaccines are proving highly efficacious against SARS-CoV-2, it is important to determine how booster doses and prior infection influence the immune defense they elicit, and whether they protect against variants. Focusing on the T cell response, we conducted a longitudinal study of infection-naive and COVID-19 convalescent donors before vaccination and after their first and second vaccine doses, using a high-parameter CyTOF analysis to phenotype their SARS-CoV-2-specific T cells. Vaccine-elicited spike-specific T cells responded similarly to stimulation by spike epitopes from the ancestral, B.1.1.7 and B.1.351 variant strains, both in terms of cell numbers and phenotypes. In infection-naive individuals, the second dose boosted the quantity and altered the phenotypic properties of SARS-CoV-2-specific T cells, while in convalescents the second dose changed neither. Spike-specific T cells from convalescent vaccinees differed strikingly from those of infection-naive vaccinees, with phenotypic features suggesting superior long-term persistence and ability to home to the respiratory tract including the nasopharynx. These results provide reassurance that vaccine-elicited T cells respond robustly to emerging viral variants, confirm that convalescents may not need a second vaccine dose, and suggest that vaccinated convalescents may have more persistent nasopharynx-homing SARS-CoV-2-specific T cells compared to their infection-naive counterparts.

category: immunology


title: mRNA vaccine-induced T cells respond identically to SARS-CoV-2 variants of concern but differ in longevity and homing properties depending on prior infection status


title: Polymerization of C9 enhances bacterial cell envelope damage and killing by membrane attack complex pores

abstract: Complement proteins can form Membrane Attack Complex (MAC) pores that directly kill Gram-negative bacteria. MAC pores assemble by stepwise binding of C5b, C6, C7, C8 and finally C9, which can polymerize into a transmembrane ring of up to 18 C9 monomers. It is still unclear if the assembly of a polymeric-C9 ring is necessary to sufficiently damage the bacterial cell envelope to kill bacteria, because a robust way to specifically prevent polymerization of C9 has been lacking. In this paper, polymerization of C9 was prevented without affecting the binding of C9 to C5b-8 by locking the first transmembrane helix domain of C9. We show that polymerization of C9 strongly enhanced bacterial cell envelope damage and killing by MAC pores for several Escherichia coli and Klebsiella strains. Moreover, we show that polymerization of C9 is impaired on complement-resistant E. coli strains that survive killing by MAC pores. Altogether, these insights are important to understand how MAC pores kill bacteria and how bacterial pathogens can resist MAC-dependent killing.


title: Dissecting the clonality of I1 plasmids using ORF-based binarized structure network analysis of plasmids (OSNAp)

abstract: Phylogenetic relationship of 97 I1 plasmids harboring blaCTX-M genes encoding extended-spectrum beta-lactamase (ESBL) was analyzed using the ORF-based binarized structure network analysis of plasmids (OSNAp). The majority of plasmids carrying blaCTX-M-1 or blaCTX-M-8, ESBL genes primarily associated with domestic animals, were clonal. On the other hand, plasmids carrying blaCTX-M-14 or blaCTX-M-15, identified from both humans and domestic animals, were diverse in their contents. The findings suggest that circulation of I1 plasmids among humans and animals may contribute to their diversity.


title: Phage-resistant bacteria reveal a role for potassium in root colonization

abstract: Bacteriophage predation is an important factor in bacterial community dynamics and evolution. Phage-bacteria interaction has mainly been studied in lab cultures, while dynamics in natural habitats, and especially in the plant root niche are underexplored. To better understand this process, we characterized infection of the soil bacterium B. subtilis NCBI 3610 by the lytic phage SPO1 during growth in LB medium and compared it to root colonization. Resistance in vitro was primarily through modification of the phage receptor. However, this type of resistance reduced the ability to colonize the root. From a line that survived phage infection while retaining the ability to colonize the root, we identified a plant-specific phage resistance mechanism involving potassium (K+) ion influx modulation and enhanced biofilm formation.


title: Delayed DNA replication in haploid human embryonic stem cells

abstract:
Haploid human embryonic stem cells (ESCs) provide a powerful genetic system but diploidize at high rates. We hypothesized that diploidization results from aberrant DNA replication. To test this, we profiled DNA replication timing in isogenic haploid and diploid ESCs. The greatest difference was the earlier replication of the X chromosome in haploids, consistent with the lack of X chromosome inactivation. Surprisingly, we also identified 21 autosomal regions that had dramatically delayed replication in haploids, extending beyond the normal S phase and into G2/M. Haploid-delays comprised a unique set of quiescent genomic regions that are also under-replicated in polyploid placental cells. The same delays were observed in female ESCs with two active X chromosomes, suggesting that increased X chromosome dosage may cause delayed autosomal replication. We propose that incomplete replication at the onset of mitosis could prevent cell division and result in re-entry into the cell cycle and whole genome duplication.

HighlightsO_LIDNA replication timing of haploid ESCs profiled by WGS
C_LIO_LIExtreme replication timing delays in haploid ESCs at unique genomic regions
C_LIO_LIReplication delays associate with X-chromosome dosage in multiple systems
C_LIO_LIReplication delayed regions correspond to underreplication in mouse polyploid cells
C_LI


title: Comparative transcriptomic analysis reveals translationally relevant processes in mouse models of malaria

abstract: Recent initiatives to improve translation of findings from animal models to human disease have focussed on reproducibility but quantifying the relevance of animal models remains a challenge. Here we use comparative transcriptomics of blood to evaluate the systemic host response and its concordance between humans with different clinical manifestations of malaria and five commonly used mouse models. Plasmodium yoelii 17XL infection of mice most closely reproduces the profile of gene expression changes seen in the major human severe malaria syndromes, accompanied by high parasite biomass, severe anemia, hyperlactatemia, and cerebral microvascular pathology. However, there is also considerable discordance of changes in gene expression between species and across all models, indicating that the relevance of biological mechanisms of interest in each model should be assessed before conducting experiments. Our data will aid selection of appropriate models for translational malaria research, and the approach is generalizable to other disease models.


title: A comprehensive landscape of 60S ribosome biogenesis factors

abstract: Eukaryotic ribosome biogenesis is facilitated and regulated by numerous ribosome biogenesis factors (RBFs). High-resolution cryo-EM maps have defined the molecular interactions of RBFs during maturation, but many transient and dynamic interactions, particularly during early assembly, remain uncharacterized. Using quantitative proteomics and crosslinking coupled to mass spectrometry (XL-MS) data from a extensive set of pre-ribosomal particles, we derived a comprehensive and time-resolved interaction map of RBF engagement during 60S maturation. A novel filter that efficiently eliminates false positive interactions and integration of our MS data with known structural information allowed us to localize 22 unmapped RBFs to specific biogenesis intermediates and to identify 9 proteins that represent potentially new RBFs. Our analysis reveals an extensive interaction network for the casein kinase complex in 60S maturation and elucidates the timing and molecular function of 60S engagement by DEAD-box ATPases. Our data provide a powerful resource for future studies of 60S ribosome biogenesis.

category: biochemistry


title: Comparative Transcriptome Profiling of High and Low oil yielding Santalum album L.

abstract: East Indian Sandalwood (Santalum album L.) is highly valued for its heartwood and its oil. There have been no efforts to comparative study of high and low oil yielding genetically identical sandalwood trees grown in similar climatic condition. Thus we intend to study a genome wide transcriptome analysis to identify the corresponding genes involved in high oil biosynthesis in S. album. In this study, 15 years old S. album (SaSHc and SaSLc) genotypes were targeted for analysis to understand the contribution of genetic background on high oil biosynthesis in S. album. A total of 28,959187 and 25,598869 raw PE reads were generated by the Illumina sequencing. 2.12 million and 1.811 million coding sequences were obtained in respective accessions. Based on the GO terms, functional classification of the CDS 21262, & 18113 were assigned into 26 functional groups of three GO categories; (4,168; 3,641) for biological process (5,758;4,971) cellular component and (5,108;4,441) for molecular functions. Total 41,900 and 36,571 genes were functionally annotated and KEGG pathways of the DEGs resulted 213 metabolic pathways. In this, 14 pathways were involved in secondary metabolites biosynthesis pathway in S. album. Among 237 cytochrome families, nine groups of cytochromes were participated in high oil biosynthesis. 16,665 differentially expressed genes were commonly detected in both the accessions (SaHc and SaSLc). The results showed that 784 genes were upregulated and 339 genes were downregulated in SaHc whilst 635 upregulated 299 downregulated in SaSLc S. album. RNA-Seq results were further validated by quantitative RT-PCR. Maximum Blast hits were found to be against Vitis vinifera. From this study we have identified additional number of cytochrome family in SaHc. The accessibility of a RNA-Seq for high oil yielding sandalwood accessions will have broader associations for the conservation and selection of superior elite samples/populations for further genetic improvement program.


title: Optimal Chemotherapy Scheduling for Non-Genetic Drug Resistance

abstract: One of the most difficult challenges in cancer therapy is the emergence of drug resistance within tumors. Sometimes drug resistance can emerge as the result of mutations and Darwinian selection. However, recently another phenomenon has been discovered, in which tumor cells switch back and forth between drug-sensitive and pre-resistant states. Upon exposure to the drug, sensitive cells die off, and pre-resistant cells become locked in to a state of permanent drug resistance. In this paper, we explore the implications of this transient state switching for therapy scheduling. We propose a model to describe the phenomenon and estimate parameters from experimental melanoma data. We then compare the performance of continuous and alternating drug schedules, and use sensitivity analysis to explore how different conditions affect the efficacy of each schedule. We find that for our estimated parameters, a continuous therapy schedule is optimal. However we also find that an alternating schedule can be optimal for other, hypothetical parameter sets, depending on the difference in growth rate between pre-drug and post-drug cells, the delay between exposure to the drug and emergence of resistance, and the rate at which pre-resistant cells become resistant relative to the rate at which they switch back to the sensitive state.


title: de novo identification of maximally deregulated subnetworks based on multi-omics data with DeRegNet

abstract:
BackgroundWith a growing amount of (multi-)omics data being available, the extraction of knowledge from these datasets is still a difficult problem. Classical enrichment-style analyses require predefined pathways or gene sets that are tested for significant deregulation to assess whether the pathway is functionally involved in the biological process under study. De novo identification of these pathways can reduce the bias inherent in predefined pathways or gene sets. At the same time, the definition and efficient identification of these pathways de novo from large biological networks is a challenging problem.

ResultsWe present a novel algorithm, DeRegNet, for the identification of maximally deregulated subnetworks on directed graphs based on deregulation scores derived from (multi-)omics data. DeRegNet can be interpreted as maximum likelihood estimation given a certain probabilistic model for de-novo subgraph identification. We use fractional integer programming to solve the resulting combinatorial optimization problem. We can show that the approach outperforms related algorithms on simulated data with known ground truths. On a publicly available liver cancer dataset we can show that DeRegNet can identify biologically meaningful subgraphs suitable for patient stratification. DeRegNet is freely available as open-source software.

ConclusionThe proposed algorithmic framework and its available implementation can serve as a valuable heuristic hypothesis generation tool contextualizing omics data within biomolecular networks.


title: De novo identification of maximally deregulated subnetworks based on multi-omics data with DeRegNet


title: Patterns of serum immune biomarkers during elephant endotheliotropic herpesvirus viremia in Asian and African elephants

abstract: Hemorrhagic disease (HD) caused by a group of elephant endotheliotropic herpesviruses (EEHV) is one of the leading causes of death for young elephants in human care. These viruses are widespread and typically persist latently in adult elephants with no negative effects; however, in juvenile Asian and more recently young African elephants, the onset of disease can be rapid and the mortality rate high. Measuring biomarkers associated with the immune response could be beneficial to understanding underlying disease processes, as well as the management of infection and HD. The goal of this study was to measure acute phase proteins and cytokines in serum collected from elephants infected with EEHV (13 Asian and 1 African) and compare concentrations according to presence, severity and outcome of disease. Serum amyloid A (SAA) and haptoglobin (HP) were higher in elephants with EEHV viremia than those without; concentrations increased with increasing viral load, and were higher in fatal cases compared to those that survived. In Asian elephants, SAA was also higher during EEHV1 viremia compared to EEHV5. Cytokine concentrations were typically low, and no statistical differences existed between groups, perhaps due to insufficient assay sensitivity in this age group. However, in individuals with detectable levels, longitudinal profiles indicated changes in tumor necrosis factor alpha (TNF-) and interleukin-2 (IL-2) that may reflect an immune response to EEHV infection. These results highlight the potential benefit of measuring circulating biomarker concentrations, such as APPs and cytokines, to improve our understanding of EEHV viremia and HD, assist with monitoring the progression of disease and determining the impact of interventions.


title: Fluorescence-Activated Droplet Sorting of Polyethylene terephthalate Degrading Enzymes

abstract: Enzymes that can decompose synthetic plastics such as polyethylene terephthalate (PET) are urgently needed. However, a bottleneck remains due to a lack of techniques for detecting and sorting environmental microorganisms with vast diversity and abundance. Here, we developed a fluorescence-activated droplet sorting (FADS) pipeline for high-throughput screening of PET-degrading microorganisms or enzymes (PETases). The pipeline comprises three steps: generation and incubation of droplets encapsulating single cells, picoinjection of fluorescein dibenzoate (FDBz) as the fluorogenic probe, and screening of droplets to obtain PET-degrading cells. We characterized critical factors associated with this method, including specificity and sensitivity for discriminating PETase from other enzymes. We then optimized its performance and compatibility with environmental samples. The system was used to screen a wastewater sample from a PET textile mill. We successfully obtained PET-degrading species from nine different genera. Moreover, two putative PETases from isolates Kineococcus endophyticus Un-5 and Staphylococcus epidermidis Un-C2-8 were genetically derived, heterologously expressed, and preliminarily validated for PET-degrading activities. We speculate that the FADS pipeline can be widely adopted to discover new PET-degrading microorganisms and enzymes in various environments and may be utilized in the directed evolution of PETases using synthetic biology.


title: Fluorescence-Activated Droplet Sorting of Polyethylene terephthalate-degrading Enzymes


title: Evaluation of Machine Learning predictions of a highly resolved long time series of Chlorophyll-a concentration

abstract: Pelagic Chlorophyll-a concentrations are key for evaluation of the environmental status and productivity of marine systems. In this study, chlorophyll-a concentrations for the Helgoland Roads Time Series were modeled using a number of measured water and environmental parameters. We chose three common Machine Learning algorithms from the literature: Support Vector Machine Regressor, Neural Networks Multi-layer Perceptron Regressor and Random Forest Regressor. Results showed that Support Vector Machine Regressor slightly outperformed other models. The evaluation with a test dataset and verification with an independent validation dataset for chlorophyll-a concentrations showed a good generalization capacity, evaluated by the root mean squared errors of less than 1 g L-1. Feature selection and engineering are important and improved the models significantly, as measured in performance, improving by a minimum of 48% the adjusted R2. We tested SARIMA in comparison and found that the univariate nature of SARIMA does not allow for better results than the Machine Learning models. Additionally, the computer processing time needed was much higher (prohibitive) for SARIMA.


title: The cerebellum as a moderator of negative bias of facial expression processing in depressive patients

abstract:
BackgroundNegative bias--a mood-congruent bias in emotion processing--is an important aspect of major depressive disorder (MDD), and such a bias in facial expression recognition has a significant effect on patients social lives. Neuroscience research shows abnormal activity in emotion-processing systems regarding facial expressions in MDD. However, the neural basis of negative bias in facial expression processing has not been explored directly.

MethodsSixteen patients with MDD and twenty-three healthy controls (HC) who underwent an fMRI scan during an explicit facial emotion task with happy to sad faces were selected. We identified brain areas in which the MDD and HC groups showed different correlations between the behavioral negative bias scores and functional activities.

ResultsBehavioral data confirmed the existence of a higher negative bias in the MDD group. Regarding the relationship with neural activity, higher activity of happy faces in the posterior cerebellum was related to a higher negative bias in the MDD group, but lower negative bias in the HC group.

LimitationsThe sample size was small, and the possible effects of medication were not controlled for in this study.

ConclusionsWe confirmed a negative bias in the recognition of facial expressions in patients with MDD. fMRI data suggest the cerebellum as a moderator of facial emotion processing, which biases the recognition of facial expressions toward their own mood.


title: Common neural bases for processing speech prosody and music: An integrated model

abstract:
It is shared notion that speech and music processing share some commonalities. Brain bioelectrical activity was recorded in healthy participants listening to music obtained by digitally transforming real speech into melodies played by viola. Sentences were originally pronounced with a positive or negative affective prosody. The researchs aim was to investigate if the emotional content of music was extracted similarly to how the affective prosody of speech is processed.

EEG was recorded from 128 electrodes in 20 healthy students. Participants had to detect rare neutral piano sounds while ignoring viola melodies. Stimulus negative valence increased the amplitude of frontal P300 and N400 ERP components while a late inferior frontal positivity was enhanced in response to positive melodies. Similar ERP markers were previously found for processing positive and negative music, vocalizations and speech. Source reconstruction applied to N400 showed that negative melodies engaged the right superior temporal gyrus and right anterior cingulate cortex, while positive melodies engaged the left middle and inferior temporal gyrus and the inferior frontal cortex. An integrated model is proposed depicting a possible common circuit for processing the emotional content of music, vocalizations and speech, which might explain some universal and relatively innate brain reaction to music.


title: Spatiotemporal specificity of correlated DNA methylation and gene expression pairs across different human tissues and stages of brain development

abstract: DNA methylation (DNAm) that occurs on promoter regions is primarily considered to repress gene expression. Previous studies indicated that DNAm could also show positive correlations with gene expression. Both DNAm and gene expression profiles are known to be tissue- and development-specific. This study aims to investigate how DNAm and gene expression are coordinated across different human tissues and developmental stages, as well as the biological significance of such correlations. By analyzing 2,239 samples with both DNAm and gene expression data in the same human subjects obtained from six published datasets, we evaluated the correlations between gene and CpG pairs (GCPs) at cis-regions and compared significantly correlated GCPs (cGCPs) across different tissues and brains at different age groups. A total of 37,363 cGCPs were identified in the six datasets; approximately 38% of the cGCPs were positively correlated. The majority (>90%) of cGCPs were tissue- or development-specific. We also observed that the correlation direction can be opposite in different tissues and ages. Further analysis highlighted the importance of cGCPs for their cellular functions and potential roles in complex traits and human diseases. For instance, early developmental brain possessed a highly unique set of cGCPs that were associated with neurogenesis and psychiatric disorders. By assessing the epigenetic factors involved in cGCPs, we discovered novel regulatory mechanisms of positive cGCPs distinct from negative cGCPs, which were related to multiple factors, such as H3K27me3, CTCF, and JARD2. The catalog of cGCPs compiled can be used to guide functional interpretation of genetic and epigenetic studies.


title: Inferring population structure in biobank-scale genomic data

abstract: Inferring the structure of human populations from genetic variation data is a key task in population and medical genomic studies. While a number of methods for population structure inference have been proposed, current methods are impractical to run on biobank-scale genomic datasets containing millions of individuals and genetic variants. We introduce SCOPE, a method for population structure inference that is orders of magnitude faster than existing methods while achieving comparable accuracy. SCOPE infers population structure in about a day on a dataset containing one million individuals and variants as well as on the UK Biobank dataset containing 488,363 individuals and 569,346 variants. Furthermore, SCOPE can leverage allele frequencies from previous studies to improve the interpretability of population structure estimates.


title: Lipid Droplets and Ferritin Heavy Chain: a Devilish Liaison in Cancer Radioresistance

abstract: Although much progress has been made in cancer treatment, the molecular mechanisms underlying cancer radioresistance (RR) as well as the biological characteristic of radioresistant cancer cells still need to be clarified. In this regard, we discovered that breast, bladder, lung, neuroglioma and prostate 6 Gy X-ray resistant cells were characterized by an increase of Lipid Droplet (LD) number and that the cells containing highest LDs showed the highest clonogenic potential after irradiation. Moreover, we observed that LD content was tightly connected with the iron metabolism and in particular with the presence of the ferritin heavy chain (FTH1). In fact, breast and lung cancer cells silenced for the FTH1 gene showed a reduction in the LD numbers and, by consequence, became radiosensitive. FTH1 restoration as well as iron-chelating treatment by Deferoxamine were able to restore the LD amount and RR. Overall, these results provide evidence of a novel molecular mechanism behind RR in which LDs and FTH1 are tightly connected to each other, a synergistic effect which might be worth deeply investigating in order to make cancer cells more radiosensitive and improve the efficacy of radiation treatments.

category: cancer biology


title: Comparison of Approaches to Transcriptomic Analysis in Multi-Sampled Tumors

abstract: Intratumoral heterogeneity is a well-documented feature of human cancers associated with outcome and treatment resistance. However, a heterogeneous tumor transcriptome contributes an unknown level of variability to analyses of differentially expressed genes that may contribute to phenotypes of interest, including treatment response. Although current clinical practice and the vast majority of research studies use a single sample from each patient, decreasing costs in sequencing technologies and computing costs have made repeated-measures analyses increasingly economical. Repeatedly sampling the same tumor increases the statistical power of differentially expressed gene analysis that is indispensable towards downstream analysis and also increases ones understanding of within-tumor variance that may affect conclusions. Here, we compared five different methods for analyzing gene expression profiles derived from repeated sampling of human prostate tumors in two separate cohorts of patients. We also benchmarked the sensitivity of generalized linear models to linear mixed models for identifying differentially expressed genes contributing to relevant prostate cancer pathways based on a ground truth model.


title: Short-Duration RAGE Antagonism Transiently Disrupts Tendon Homeostasis and does not Alter Diabetic Tendon Healing

abstract: Obesity and type II Diabetes Mellitus (T2DM) have substantial pathological effects on tendon homeostasis, including loss of collagen organization and increased risk of tendon rupture. Moreover, following rupture or acute injury, the healing process is impaired by T2DM. We have previously demonstrating that restoring normal metabolic function in a murine model of obesity/ T2DM is insufficient to blunt or reverse the progression of diabetic tendinopathy, indicating the need for identification of novel therapeutic approaches to both maintain tendon homeostasis, and to improve the healing process. RAGE, the Receptor for Advanced Glycation Endproducts has been implicated as a key driver of several diabetic pathologies. We have demonstrated that pharmacological antagonism of RAGE is sufficient to partially improve tendon healing in non-diabetic animals. Therefore, in the current study we tested the efficacy of blunted RAGE signaling, via treatment with a RAGE Antagonist Peptide (RAP), to improve tendon healing in the context of T2DM. While our study did not find a beneficial effect of short-term RAP treatment on the healing process of T2DM mice, we did identify several important challenges brought about by this model of diet-induced obesity and T2DM. Both high fat (HFD) and low fat diet (LFD) feeding shifted the temporal molecular profile of healing compared to standard laboratory chow fed mice. Moreover, RAP treatment resulted in a transient disruption in homeostasis in the contralateral control tendons of both HFD and LFD mice, and this was due to a potential interaction with the systemic response to tendon injury as this response was not observed in HFD and LFD fed mice that did not undergo tendon repair surgery. Collectively, these data highlight the complications associated with models of diet induced obesity, and the lean control diets that should be considered in future studies.

category: pathology


title: Cannabinoid tetrad effects of oral Δ9-tetrahydrocannabinol (THC) and cannabidiol (CBD) in male and female rats: sex, dose-effects and time course evaluations

abstract: Rationale The legalization of medicinal use of Cannabis sativa in most US states and the removal of hemp from the Drug Enforcement Agency (DEA) controlled substances act has resulted in a proliferation of products containing {Delta}9-tetrahydrocannabinol (THC) and cannabidiol (CBD) for oral consumption (e.g., edibles, oils and tinctures) that are being used for recreational and medicinal purposes. Objective This study examined the effects of cannabinoids THC and CBD when administered orally on measures of pain sensitivity, body temperature, locomotor activity, and catalepsy (i.e., cannabinoid tetrad) in male and female Sprague Dawley rats. Methods Rats (N=24, 6 per sex/drug group) were administered THC (1-20 mg/kg), CBD (3-30 mg/kg), or sesame oil via oral gavage. Thermal and mechanical pain sensitivity (tail flick assay, von Frey test), rectal measurements for body temperature, locomotor activity, and the bar-test of catalepsy were completed. A separate group of rats (N=8/4 per sex) were administered morphine (5-20 mg/kg; intraperitoneal, IP) and evaluated for pain sensitivity as a positive control. Results We observed classic tetrad effects of antinociception, hypothermia, hyper- and hypolocomotion, and catalepsy after oral administration of THC that were long lasting (>7 hours). CBD modestly increased mechanical pain sensitivity and produced sex-dependent effects on body temperature and locomotor activity. Conclusions Oral THC and CBD produced long lasting effects, that differed in magnitude and time course when compared with other routes of administration. Examination of cannabinoid effects administered via different routes of administration, species, and in both males and females is critical to enhance translation.

category: pharmacology and toxicology


title: Early life gut microbiome dynamics mediate maternal effects of infant growth in vervet monkeys

abstract:
BackgroundMaternal parity is associated with variation in infant growth across mammals, but the mechanisms underlying this relationship are unclear. Given emerging links between growth and the microbiome, and the importance of maternal microbiota in establishing this community, the assembly of the infant gut microbiome may be a mediator of parity effects on infant growth.

ResultsHere, we analyzed 118 fecal and milk samples from mother-infant vervet monkey dyads across the first 6 months postpartum in a population with high growth-associated infant mortality. Despite poorer milk production, infants born to low parity females were larger at 6 months of age than their counterparts and exhibited divergent patterns in gut microbiome assembly. Gut microbiome alpha diversity increased rapidly from the first days of life to 4 months old in all infants, but infants born to low parity females exhibited reduced gut microbiome alpha diversity during early life. At the taxonomic level, infants broadly exhibited a shift from Bacteroides fragilis to Prevotella dominance. Infants of low parity females housed more B. fragilis in their guts, and B. fragilis dominance drove reduced alpha diversity. Maternal vertical transmission to the infant gut was greater from milk than from the maternal gut, and was greatest among infants born to low parity females. B. fragilis was 15-fold more abundant in milk than in the maternal gut and was greater in the milk of low parity females, suggesting that milk may be the primary maternal reservoir of B. fragilis. Path analyses demonstrated that both infant gut alpha diversity and B. fragilis mediated parity effects on postnatal growth: infants were larger at 6 months old if they exhibited reduced alpha diversity and a greater relative abundance of B. fragilis during early life.

ConclusionThe first days of life are a critical period of infant gut microbiome organization during which the establishment of a less diverse, milk-oriented microbial community abundant in B. fragilis promotes growth among infants born to reproductively inexperienced females.

category: physiology


title: The role of network interactions in opioid analgesia

abstract: Opioids are potent analgesic drugs with widespread cortical, subcortical and spinal targets. In particular, the central pain system comprising ascending and descending pain pathways has high opioid receptor densities and is thus crucial for opioid analgesia. Here, we investigated effects of the opioid remifentanil in a large sample (n=78) of healthy male participants using combined cortico-spinal fMRI. This approach offers the possibility to measure BOLD responses simultaneously in the brain and spinal cord allowing us to investigate the role of cortico-spinal coupling in opioid analgesia. Our data show that opioids altered activity in regions involved in pain processing such as somatosensory regions including the spinal cord and pain modulation such as prefrontal regions. Moreover, coupling strength along the descending pain system, i.e. between the medial prefrontal cortex, periaqueductal gray and spinal cord was stronger in participants who reported stronger analgesia during opioid treatment while the reversed pattern was observed in the control group. These results indicate that coupling along the descending pain pathway is a potential mechanism of opioid analgesia and can differentiate between opioid analgesia and unspecific reductions in pain such as habituation.


title: Cortico-spinal coupling along descending pain system differentiates between opioid and saline treatment in healthy participants


title: Orexin A excites the rat olivary pretectal nucleus via OX2 receptor in a daily manner

abstract:
Pronounced environmental changes between the day and night forced living organisms to evolve specialised mechanisms organising their daily physiology, named circadian clocks. Currently, it has become clear that the master clock in the suprachiasmatic nuclei of the hypothalamus is not an exclusive brain site to generate daily rhythms. Indeed, several brain areas, including the subcortical visual system have been recently shown to change their neuronal activity across the daily cycle. Here we focus our investigation on the olivary pretectal nucleus (OPN) - a retinorecipient structure primarily involved in the pupillary light reflex. Using the multi-electrode array technology ex vivo we provide evidence for OPN neurons to elevate their firing during the behaviourally quiescent light phase. Additionally, we report the robust sensitivity to orexin A via the identified OX2 receptor in this pretectal centre, with higher responsiveness noted during the night. Interestingly, we likewise report a daily variation in the response to PAC1 receptor activation, with implications for the convergence of orexinergic and visual input on the same OPN neurons. Altogether, our report is first to suggest a daily modulation of the OPN activity via intrinsic and extrinsic mechanisms, organising its temporal physiology.

GRAPHICAL ABSTRACT

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=159 SRC="FIGDIR/small/443625v1_ufig1.gif" ALT="Figure 1">
View larger version (20K):
org.highwire.dtl.DTLVardef@97ec8eorg.highwire.dtl.DTLVardef@2b5eeforg.highwire.dtl.DTLVardef@165d985org.highwire.dtl.DTLVardef@1abb7c9_HPS_FORMAT_FIGEXP  M_FIG C_FIG HIGHLIGHTSO_LINeurons in the olivary pretectal nucleus (OPN) increase their firing during the day
C_LIO_LIOrexin A robustly excites the OPN via the OX2 receptor
C_LIO_LIOrexin A and the activation of PAC1 receptor are more effective during the night
C_LI


title: Dysfunctions of the paraventricular hypothalamic nucleus induce hypersomnia in human and mice

abstract: Hypersomnolence disorder (HD) is characterized by excessive sleep, which is a common sequela following stroke, infections or tumorigenesis. HD was traditionally thought to be associated with lesions of wake-promoting nuclei. However, lesion of a single, even two or more wake-promoting nucleuses simultaneously did not exert serious HD. The specific nucleus and neural circuitry for HD remain unknown. Here, we observed that three patients with lesions around the paraventricular nucleus of the hypothalamus (PVH) showed hypersomnolence lasting more than 20 h per day and their excessive sleep decreased with the recovery of the PVH area. Therefore, we hypothesized that the PVH might play an essential role in the occurrence of HD. Using multichannel electrophysiological recording and fiber photometry, we found that PVHvglut2 neurons were preferentially active during wakefulness. Chemogenetic activation of PVHvglut2 neurons potently induced 9-h wakefulness, and PVHCRH, PVHPDYN and PVHOT neuronal activation also exerted wakefulness. Most importantly, ablation of PVHvglut2 neurons drastically induced hypersomnia-like behaviors (30.6% reduction in wakefulness). These results indicate that dysfunctions of the PVH is crucial for physiological arousal and pathogenesis underlying HD.


title: Neuron specific ablation of eIF5A or deoxyhypusine synthase leads to impairment in development and cognitive functions in mice

abstract:
Eukaryotic initiation factor 5A (eIF5A) is an essential factor with a unique amino acid, hypusine, required for its activity. Hypusine is formed exclusively in eIF5A by a post-translational modification involving two enzymes, deoxyhypusine synthase (DHPS) and deoxyhypusine hydroxylase (DOHH). Each of the three genes, Eif5a, Dhps or Dohh is required for mouse embryonic development. Variants in EIF5A or DHPS were recently identified as the genetic basis underlying certain rare neurodevelopmental disorders in humans. To investigate the roles of eIF5A and DHPS in brain development, we have generated four conditional knockout mouse strains using the Emx1-Cre or Camk2a-Cre strain and examined the effects of temporal- and region-specific deletion of Eif5a or Dhps. The conditional deletion of Dhps or Eif5a by Emx1 promotor driven Cre expression (E.9.5, cortex and hippocampus) led to gross defects in forebrain development, reduced growth and premature death. On the other hand, the conditional deletion of Dhps or Eif5a by Camk2a-promoter driven Cre expression (postnatal, mainly in the CA1 region of hippocampus) did not lead to global developmental defects; rather, these knockout animals exhibited severe impairment in spatial learning, contextual learning and memory, when subjected to the Morris Water Maze test and a contextual learning test. In both models, the Dhps knockout mice displayed more severe impairment than their Eif5a knockout counterparts. The observed defects in brain, global development or cognitive functions most likely result from translation errors due to a deficiency in active, hypusinated eIF5A. Our study underscores the important roles of eIF5A and DHPS in neurodevelopment.

SignificanceeIF5A, an essential translation factor, is the only protein that undergoes a unique posttranslational modification, that converts lysine to hypusine by conjugation of the aminobutyl moiety from the polyamine spermidine. Hypusine biosynthesis occurs by two enzymatic steps involving deoxyhypusine synthase (DHPS) and deoxyhypusine hydroxylase (DOHH). Mutations in EIF5A or DHPS have been associated with rare neurodevelopmental disorders in humans. To understand the mechanisms underlying the pathogenesis of the disease, we generated mutant mice with brain-specific deletions of Eif5a or Dhps. The Eif5a and Dhps conditional knockout mice exhibited impairment in brain development, growth and cognitive functions. These animal models may serve as useful tools in the development of therapies against the eIF5A- or DHPS-associated neurodevelopmental disorders.


title: Parallel processing of olfactory and mechanosensory information in the honeybee antennal lobe.

abstract: We report that airflow produces a complex activation pattern in the antennal lobes of the honeybee Apis mellifera. Glomerular response maps provide a stereotypical code for the intensity and the dynamics of mechanical stimuli that is superimposed on the olfactory code. We show responses to modulated stimuli suggesting that this combinatorial code could provide information about the intensity, direction, and dynamics of the airflow during flight and waggle dance communication.


title: Generalizable predictive modeling of semantic processing ability from functional brain connectivity

abstract: Semantic processing (SP) is one of the critical abilities of humans for representing and manipulating meaningful and conceptual information. Neuroimaging studies of SP typically collapse data from many subjects, but both its neural organization and behavioral performance vary between individuals. It is not yet understood whether and how the individual variabilities in neural organizations contribute to the individual differences in SP behaviors. Here we aim to identify the neural signatures underlying SP variabilities by analyzing individual functional connectivity (FC) patterns based on a large-sample Human Connectome Project (HCP) dataset and rigorous predictive modeling. We used a two-stage predictive modeling approach to build an internally cross-validated model and to test the models generalizability with unseen data from different HCP sub-populations and task states as well as other out-of-sample datasets that are independent of the HCP. FC patterns within a putative semantic brain network were significantly predictive of individual SP scores summarized from five semantic tasks. This cross-validated predictive model can be used to predict unseen HCP data. The model generalizability was enhanced with FCs in language tasks than resting state and other task states and was better for females than males. The model constructed from the HCP dataset can be generalized to two independent cohorts that participated in different semantic tasks. FCs connecting to the Perisylvian language network show the most reliable contributions to predictive modeling and the out-of-sample generalization. These findings contribute to our understanding of the neural sources of individual differences in SP, which potentially lay the foundation for personalized education and improve intervention practice for patients with SP and language deficits.