title: Physiological alterations in microglial morphology associate with the sleep-wake cycle in a brain region-specific manner

abstract:
Long-term total sleep deprivation induces changes in cortical - and hippocampal microglial morphology that closely resemble the microglial response to the gram-negative bacterial cell wall component lipopolysaccharide (LPS). A recent study found evidence that microglia could modify vigilance-states/sleep, but only few studies investigated microglial throughout the diurnal behavioral inactivity/activity pattern or the naturally occurring sleep-wake cycle, and those who have, only concentrated on the cortical or hippocampal microglia. As microglia demonstrate regional heterogeneity, we compared microglial diurnal morphological alterations in the somatosensory cortex (SC) and dorsal hippocampus (HC) to the basal forebrain (BF), which is a subcortical brain area involved in the regulation of vigilance states.

We collected mouse brain samples every 3h throughout the 24h light-dark-cycle and applied a 3D reconstruction method for the acquired confocal microscopy images for each brain area separately. While microglial regional heterogeneity was evident, stimulation of microglia with LPS caused comparable microglial responses in all brain areas. When comparing microglial features between the 12h light- and dark periods, regional heterogeneity re-appeared. As most of the morphological alterations occurred during the light period-the habitual sleeping period of the mice, we performed polysomnography to study the possible interaction of microglial morphology and sleep. We found that cortical-, but not HC- or BF microglial territory and volume negatively correlated with sleep slow wave activity (SWA), an electroencephalic feature of non-REM sleep (NREMS). Since microglia are sensitive to neuronal activity, we propose that the regional differences reflect vigilance-state specific neuronal activity patterns.

Table of contents image

O_FIG O_LINKSMALLFIG WIDTH=184 HEIGHT=200 SRC="FIGDIR/small/482976v1_ufig1.gif" ALT="Figure 1">
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Cortical-, but not HC- or BF microglial cell volume negatively correlates with non-REM sleep slow wave activity.


title: Human NMDAR autoantibodies disrupt excitatory-inhibitory balance leading to hippocampal network hypersynchrony

abstract: Specific autoantibodies against the NMDA-receptor (NMDAR) GluN1 subunit cause severe and debilitating NMDAR-encephalitis. Autoantibodies induce prototypic disease symptoms resembling schizophrenia, including psychosis and cognitive dysfunction. Using a mouse passive transfer model applying human monoclonal anti-GluN1-autoantibodies, we observed CA1 pyramidal neuron hypoexcitability, reduced AMPA-receptor (AMPAR) signaling, and faster synaptic inhibition resulting in disrupted excitatory-inhibitory balance. Functional alterations were supported by widespread remodeling of the hippocampal proteome, including changes in glutamatergic and GABAergic neurotransmission. At the network level, anti-GluN1-autoantibodies amplified gamma oscillations and disrupted theta-gamma coupling. A data-informed network model revealed that lower AMPAR strength and faster GABAA-receptor current kinetics chiefly account for these abnormal oscillations. As predicted by our model and evidenced experimentally, positive allosteric modulation of AMPARs alleviated aberrant gamma activity and thus reinforced the causative effects of the excitatory-inhibitory imbalance. Collectively, NMDAR-hypofunction-induced aberrant synaptic, cellular, and network dynamics provide new mechanistic insights into disease symptoms in NMDAR-encephalitis and schizophrenia.

category: neuroscience


title: Time-of-day matters - pronounced regional morning-to-evening effects in structural brain metrics

abstract:
In recent decades magnetic resonance imaging (MRI) has established itself as the golden standard for studying human brain structure in health and disease. As a result, it has become increasingly more important to identify factors that may influence study outcomes and contribute to misleading conclusions. With the regional time-of-day (TOD) differences in structural brain metrics utterly neglected and several studies reporting inconsistent TOD changes on the global brain level, this work set out to investigate this phenomenon with voxel-based (VBM) and surface-based morphometry (SBM) using the largest longitudinal dataset to date (N = 77). VBM revealed ubiquitous and often bilaterally symmetric differences in local grey and white matter volume across multiple cortical and subcortical brain regions. The impact of TOD on regional SBM indices was less pronounced than for VBM, and no significant effects were observed for the global volume- and surface-based anatomical metrics. Our findings likely reflect a combination of experience- and circadian-related processes, with the former possibly linked to memory formation. By showing that TOD has a prevalent effect on local anatomical brain metrics, our study underlines the need for this factor to be strictly controlled at the stage of experimental planning and data analysis.

HighlightsO_LINo differences were found for global volume- and surface-based structural metrics
C_LIO_LILocal grey and white matter volume showed widespread time-of-day variability
C_LIO_LISeveral brain regions exhibited surface-based changes between morning and evening
C_LIO_LIFindings likely reflect a combination of experience- and circadian-related processes
C_LI


title: Seasonal changes in membrane structure and excitability in central neurons of goldfish (Carassius auratus) under constant environmental conditions

abstract:
Seasonal modifications in the structure of cellular membranes occur as an adaptive measure to withstand exposure to prolonged environmental change. Little is known about whether such changes may occur independently of external cues, such as photoperiod or temperature, or how they may impact the central nervous system (CNS). We compared membrane properties of central neurons isolated from the retina of goldfish (Carassius auratus), an organism well-adapted to extreme environmental change, during the summer and winter months. Goldfish were maintained in a facility under constant environmental conditions throughout the year. Analysis of whole-retina phospholipid composition using mass spectrometry-based lipidomics revealed a two-fold increase in phosphatidylethanolamine species during the winter, suggesting an increase in cell membrane fluidity. Atomic force microscopy was used to produce localized, nanoscale-force deformation of neuronal membranes. Measurement of Youngs modulus indicated increased membrane stiffness (or decreased elasticity) in neurons isolated during the winter. Voltage-clamp electrophysiology was used to assess physiological changes in neurons between seasons. Winter neurons displayed a hyperpolarized reversal potential (Vrev) and a significantly lower input resistance (Rin) compared to summer neurons. This was indicative of a decrease in membrane excitability during the winter. Subsequent measurement of intracellular Ca2+ activity using Fura-2 microspectrofluorometry confirmed a reduction in action potential activity, including duration and action potential profile, in neurons isolated during the winter. These studies demonstrate chemical and biophysical changes that occur in central neurons of goldfish throughout the year without exposure to seasonal cues, and suggest a novel mechanism of seasonal regulation of CNS activity.

SUMMARY STATEMENTCentral neurons isolated from the retina of goldfish held under constant environmental conditions undergo seasonal changes in membrane structure and excitability.


title: Sex and estrous cycle affect experience-dependent plasticity in mouse primary visual cortex

abstract: Sex hormones can affect cellular physiology and modulate synaptic plasticity, but it is not always clear whether or how sex-dependent differences identified in vitro express themselves as functional dimorphisms in the brain. Historically, most experimental neuroscience has been conducted using only male animals and the literature is largely mute about whether including female mice in will introduce variability due to inherent sex differences or endogenous estrous cycles. Though this is beginning to change following an NIH directive that sex should be included as a factor in vertebrate research, the lack of information raises practical issues around how to design experimental controls and apply existing knowledge to more heterogeneous populations. Various lines of research suggest that visual processing can be affected by sex and estrous cycle stage. For these reasons, we performed a series of in vivo electrophysiological experiments to characterize baseline visual function and experience-dependent plasticity in the primary visual cortex (V1) of male and female mice. We find that sex and estrous stage have no statistically significant effect on baseline acuity measurements, but that both sex and estrous stage have can modulate two mechanistically distinct forms of experience dependent cortical plasticity. We also demonstrate that resulting variability can be largely controlled with appropriate normalizations. These findings suggest that V1 plasticity can be used for mechanistic studies focusing on how sex hormones effect experience dependent plasticity in the mammalian cortex.


title: Biological constraints on stereotaxic targeting of functionally-defined cortical areas

abstract: Understanding computational principles in hierarchically organized sensory systems requires functional parcellation of brain structures and their precise targeting for manipulations. Although brain atlases are widely used to infer area locations in the mouse neocortex, it has been unclear whether stereotaxic coordinates based on standardized brain morphology accurately represent functional domains in individual animals. Here, we used intrinsic signal imaging to evaluate the accuracy of area delineation in the atlas by mapping functionally-identified auditory cortices onto bregma-based stereotaxic coordinates. We found that auditory cortices in the brain atlas correlated poorly with the true complexity of functional area boundaries. Inter-animal variability in functional area locations predicted surprisingly high error rates in stereotaxic targeting with atlas coordinates. This variability was not simply attributed to brain sizes or suture irregularities but instead reflected differences in cortical geography across animals. Our data thus indicate that functional mapping in individual animals is essential for dissecting cortical area-specific roles with high precision.


title: Cholinergic forebrain activation improves cognition, boosts neurotrophin receptors, and lowers Aβ42 levels in the cerebral cortex of 5xFAD mice.

abstract: The biological basis of Alzheimers dementia has been hypothesized in terms of basal forebrain cholinergic decline, and in terms reflecting the neuropathologies surrounding beta amyloid and tau. To shed light on the contributions of these different biological elements, we performed five month intermittent stimulation of the basal forebrain, which projects to the cortical mantle, in 5xFAD Alzheimers model mice and wild-type littermates, and subjected mice to behavioral testing and tissue analysis. The 5xFAD mice performed worse in water maze testing than their littermates. Stimulation improved both classes of mice, and removed performance differences between genotypes by the fifth testing day. Stimulated groups had two to four-fold increases in immunoblot measures of each of the neurotrophin receptors tropomyosin receptor kinase A and B. Stimulation also led to lower tissue A{beta}42 and beta amyloid cleavage enzyme 1 in 5xFAD mice. Despite the lack of strong direct projections from the basal forebrain stimulation region to the hippocampus, the hippocampal tissues in stimulated mice had more nerve growth factor receptor, and lower levels of beta secretase for amyloid. These data support a causal relation between forebrain cholinergic pathways and cognitive decline dependent on A{beta}42. Activation of cholinergic brain pathways improves neurotrophin pathways and reduces A{beta}42 accumulation. The recruitment of both classes of neurotrophin receptors in the process suggests a serine protease cleavage intermediary between cholinergic response and neurotrophin activation.


title: Drawing the experience dynamics of meditation.

abstract: Subjective experiences are hard to capture quantitatively without losing depth and nuance, and subjective report analyses are time-consuming, their interpretation contested. We describe Temporal Experience Tracing, a method that captures relevant aspects of the unified conscious experience over a continuous period of time. The continuous multidimensional description of an experience allows us to computationally reconstruct common experience states. Applied to data from 852 meditations - from novice (n=20) and an experienced (n=12) meditators practising Breathing, Loving-Kindness and Open-Monitoring meditation - we reconstructed four recurring experience states with an average duration of 6:46 min (SD = 5:50 min) and their transition dynamics. Three of the experience states assimilated the three meditation styles practiced, and a fourth experience state represented a common low-motivational,  off-task state for both groups. We found that participants in both groups spent more time in the task-related experience state during Loving Kindness meditation than other meditation styles and were less likely to transition into an  off-task experience state during Loving Kindness meditation than during Breathing meditation. We demonstrate that drawing the dynamics of experience enables the quantitative analysis of subjective experiences, transforming the time dimension of the stream of consciousness from narrative to measurable.


title: Molecular conflicts disrupting centromere assembly contribute to Xenopus hybrid inviability

abstract:
Although central to evolution, the causes of hybrid inviability that drive reproductive isolation are poorly understood. Embryonic lethality occurs when eggs of the frog X. tropicalis are fertilized with either X. laevis or X. borealis sperm. We observed that distinct subsets of paternal chromosomes failed to assemble functional centromeres, causing their mis-segregation during embryonic cell divisions. Core centromere DNA sequence analysis revealed little conservation among the three species, indicating that epigenetic mechanisms that normally operate to maintain centromere integrity are disrupted on specific paternal chromosomes in hybrids. In vitro reactions combining X. tropicalis egg extract with either X. laevis or X. borealis sperm chromosomes revealed that paternally matched or over-expressed centromeric histone CENP-A and its chaperone HJURP could rescue centromere assembly on affected chromosomes in interphase nuclei. However, whereas the X. laevis chromosomes maintained centromeric CENP-A in metaphase, X. borealis chromosomes did not, and also displayed ultra-thin regions containing ribosomal DNA. Both centromere assembly and morphology of X. borealis mitotic chromosomes could be rescued by inhibiting RNA Polymerase I or by preventing collapse of stalled DNA replication forks. These results indicate that specific paternal centromeres are inactivated in hybrids due to disruption of associated chromatin regions that interfere with CENP-A incorporation, at least in some cases due to conflicts between replication and transcription machineries. Thus, our findings highlight the dynamic nature of centromere maintenance and its susceptibility to disruption in vertebrate interspecies hybrids.

ONE SENTENCE SUMMARYCentromere incompatibilities in inviable Xenopus hybrids are sequence-independent and result from disruption of epigenetic pathways required for centromere maintenance.

category: cell biology


title: Individual stochasticity in the life history strategies of animals and plants

abstract: The life histories of organisms are expressed as rates of development, reproduction, and survival. However, individuals may experience differential outcomes for the same set of rates. Such individual stochasticity generates variance around familiar mean measures of life history traits, such as life expectancy and the reproductive number R0. By writing life cycles as Markov chains, we calculate variance and other indices of variability for longevity, lifetime reproductive output (LRO), age at offspring production, and age at maturity for 83 animal and 332 plant populations from the CO_SCPLOWOMADREC_SCPLOW and CO_SCPLOWOMPADREC_SCPLOW matrix databases. We find that the magnitude within and variability between populations in variance indices in LRO, especially, are surprisingly high. We furthermore use principal components analysis to assess how the inclusion of variance indices affects life history constraints. We find that these indices, to a similar or greater degree than the mean, explain the variation in life history strategies among plants and animals.

category: ecology


title: Masculinizer-induced dosage compensation is achieved by transcriptional downregulation of both copies of Z-linked genes in the silkworm, Bombyx mori

abstract: Dosage compensation balances the expression of sex-chromosome-linked genes with autosome-linked genes in the heterogametic sex. The silkworm (Bombyx mori), a lepidopteran model insect, uses the female heterogametic WZ sex determination system. In B. mori, a Z-linked gene, Masculinizer (Masc), is the primary determinant of maleness and dosage compensation. However, it remains unknown whether one of the two Z chromosomes is inactivated or both Z chromosomes are suppressed in B. mori males. Hence, we performed transcriptome analysis using hybrids between two B. mori strains and analyzed the allele-specific expression (ASE) to solve the problem. The ASE analysis revealed that the genes located on the maternal and paternal Z chromosomes are transcriptionally upregulated in Masc knocked down males. Also, our results revealed that two Z chromosomes are transcriptionally downregulated in B. mori males as observed in Caenorhabditis elegans.

category: genetics


title: Cell type-specific prediction of 3D chromatin architecture

abstract: The mammalian genome is spatially organized in the nucleus to enable cell type-specific gene expression. Investigating how chromatin architecture determines this specificity remains a big challenge. Methods for measuring the 3D chromatin architecture, such as Hi-C, are costly and bears strong technical limitations, restricting their widespread application particularly when concerning genetic perturbations. In this study, we present C.Origami, a deep neural network model for predicting de novo cell type-specific chromatin architecture. By incorporating DNA sequence, CTCF binding, and chromatin accessibility profiles, C.Origami achieves accurate cell type-specific prediction. C.Origami enables in silico experiments that examine the impact of genetic perturbations on chromatin interactions, and moreover, leads to the identification of a compendium of cell type-specific regulators of 3D chromatin architecture. We expect Origami - the underlying model architecture of C.Origami - to be generalizable for future genomics studies in discovering novel regulatory mechanisms of the genome.

category: genomics


title: Structural maturation of SYCP1-mediated meiotic chromosome synapsis through conformational remodelling by molecular adapter SYCE3

abstract: In meiosis, a supramolecular protein structure, the synaptonemal complex (SC), assembles between homologous chromosomes to facilitate their recombination. Mammalian SC formation is thought to involve hierarchical zipper-like assembly of an SYCP1 protein lattice that recruits stabilising central element (CE) proteins as it extends. Here, we combine biochemical approaches with separation-of-function mutagenesis in mice to uncover that, rather than stabilising the SYCP1 lattice, the CE protein SYCE3 actively remodels this structure during synapsis. We find that SYCP1 tetramers undergo conformational change into 2:1 heterotrimers upon SYCE3-binding, removing their assembly interfaces and disrupting the SYCP1 lattice. SYCE3 then establishes a new lattice by its self-assembly mimicking the role of the disrupted interface in tethering together SYCP1 dimers. SYCE3 also interacts with CE complexes SYCE1-SIX6OS1 and SYCE2-TEX12, providing a mechanism for their recruitment. Thus, SYCE3 remodels the SYCP1 lattice into a CE-binding integrated SYCP1-SYCE3 lattice to achieve long-range synapsis by a mature SC.

category: biochemistry


title: On-chip engineered human lymphatic microvasculature for physio-/pathological transport phenomena studies

abstract: The human vasculature constitutes an integral part of fluid, protein and cellular transport throughout a variety of physiological processes and pathological events. While the blood vascular system has been the topic of numerous studies in connection to its role in physio-/pathological transport phenomena, our secondary vascular system, the lymphatics, has yet to gain similar attention, in part due to a lack of adequate models to study its biological function. Despite their considerable value, animal models limit the ability to perform parametric studies, whereas current in vitro systems are lacking in physiological mimicry. Here, a microfluidic-based approach is developed that allows for precise control over the transport of growth factors and interstitial fluid flow, which we leverage to recapitulate the in vivo growth of lymphatic capillaries. Using this approach, physiological tissue functionality is validated by characterizing the drainage rate of extracellular solutes and proteins. Finally, lymphatic-immune interactions are studied to affirm inflammation-driven responses by the lymphatics, which recruit immune cells via chemotactic signals, similarly to in vivo, pathological events. Results demonstrate the utility of this platform to study lymphatic biology and disease, as well as use as a screening assay to predict lymphatic absorption of therapeutic biologics.

category: bioengineering


title: iPheGWAS : an intelligent computational framework to integrate and visualise genome-phenome wide association studies

abstract: Estimating the genetic correlations by LDSC is computationally demanding and visualising multiple GWAS results along with their genetic relationships is restricted. This study developed iPheGWAS, a novel approach which applied hierarchical clustering to GWAS summary statistics to (i) calculate their genetic relatedness, and (ii) enable three-dimensional visualisation of multiple ordered GWAS plots. Simulation and real-world data analysis demonstrated that when investigating genetic relationships among multiple phenotypes, iPheGWAS can deliver comparable results with LDSC but with 8 times faster computational speed. It can also provide novel findings in studying genetically-correlated comorbidities, such as mental illness and rheumatoid arthritis.

category: bioinformatics


title: vissE: A versatile tool to identify and visualise higher-order molecular phenotypes from functional enrichment analysis

abstract:
Functional analysis of high throughput experiments using pathway analysis is now ubiquitous. Though powerful, these methods often produce thousands of redundant results owing to knowledgebase redundancies upstream. This scale of results hinders extensive exploration by biologists and often leads to investigator biases due to previous knowledge and expectations. To address this issue, we present vissE, a flexible network-based analysis method that summarises redundancies into biological themes and provides various analytical modules to characterise and visualise them with respect to the underlying data, thus providing a comprehensive view of the biological system. We demonstrate vissEs versatility by applying it to three different technologies: bulk, single-cell and spatial transcriptomics. Applying vissE to a factor analysis of a breast cancer spatial transcriptomic data, we identified stromal phenotypes that support tumour dissemination. Its adaptability allows vissE to enhance all existing gene-set enrichment and pathway analysis workflows, removing investigator bias from molecular discovery.

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title: Protein-Ligand Interaction Graphs: Learning from Ligand-Shaped 3D Interaction Graphs to Improve Binding Affinity Prediction

abstract:
Graph Neural Networks (GNNs) have recently gained in popularity, challenging molecular fingerprints or SMILES-based representations as the predominant way to represent molecules for binding affinity prediction. Although simple ligand-based graphs alone are already useful for affinity prediction, better performance on multi-target datasets has been achieved with models that incorporate 3D structural information. Most recent advances utilize complex GNN architectures to capture 3D protein-ligand information by incorporating ligand-interacting protein atoms as additional nodes in the graphs; or by building a second protein-based graph in parallel. This expands the graph considerably while obfuscating the shape of the underlying ligand, diminishing the advantage that GNNs have when encoding molecular structures. There is therefore a need for a simple and elegant molecular graph representation that retains the topology of the ligand while simultaneously encoding 3D protein-ligand interactions.

We present Protein-Ligand Interaction Graphs (PLIGs): a simple way of representing atom-atom contacts of 3D protein-ligand complexes as node features for GNNs. PLIGs featurize an atom node in the molecular graph by describing each atoms properties as well as all atom-atom contacts made with protein atoms within a distance threshold. The edges of the graph are therefore identical to ligand-based graphs, but the nodes encode the 3D protein-ligand contacts. Since PLIGs are applicable to any GNN architecture, we have benchmarked their performance with six different GNN architectures, and compared them to conventional ligand-based graphs and fingerprint-based multi-layer perceptron (MLP) models using the CASF-2016 benchmark set where we found PLIG-based Graph Attention Networks (GATNet) to be the best performing model ({rho}=0.84, RMSE=1.22 pK). In summary, we created a novel graph-based representation that incorporates 3D structural information into the node features of ligand-shaped molecular graphs. The PLIG representation is simple, elegant, flexible and easily customizable, opening up many possibilities of incorporating other 2D and 3D properties into the graph.

AccessThe code and implementation for PLIGs and all models can be found at github.com/MarcMoesser/Protein-Ligand-Interaction-Graphs.


title: Soft disorder modulates the assembly path of protein complexes

abstract: We ordered the entire set of X-ray crystallographic structures in the Protein Data Bank into hierarchies of progressive interactions involving identical or very similar protein chains, obtaining 40 205 hierarchies of protein complexes with an increasing number of partners. We then studied these hierarchies as a proxy for assembly pathways in protein complex formation. The database was used to show statistically that new interfaces, upon protein complex oligomerization, tend to be observed on residues that have been characterized as softly disordered (flexible, amorphous, or intrinsically disordered) in simpler complexes, i.e. structures with fewer partners and preceding the newly oligomerized complex in the hierarchy. Furthermore, we observe that the location of soft disorder changes place in the sequence as the number of partners increases. Our results unveil the existence of a general mechanism of protein assembly involving soft disorder that modulates and orders the way protein complexes are assembled. Since soft disorder regions are highly correlated with interactions in protein complexes, this work highlights the difficulty of predicting the structure of large protein complexes from sequence, and underscores the importance of coupling soft disorder predictors with the next generation of complex structure predictors. Finally, we investigate the relationship between Alphafold2s structure prediction confidence metric pLDDT on unbound structures and soft disorder, showing a strong correlation between Alphafold2s low-confidence residues and the union of all soft disorder regions observed throughout the interaction hierarchy, paving the way for the use of the pLDDT metric as a proxy for interface prediction and assembly paths.


title: An actin-like filament from Clostridium botulinum exhibits a novel mechanism of filament dynamics

abstract: Here, we report the discovery of a ParM protein from Clostridium botulinum (CBg-ParM), which forms a double-stranded polar filament. CBg-ParM is promiscuous in hydrolyzing nucleotides, showing robust activities for GDP, ADP, and AMPPNP in addition to ATP and GTP. CBg-ParM shares many similarities in its basic filament architecture with actin, however it does not depolymerize after nucleotide hydrolysis and Pi release, as observed for actin or other ParMs. Instead of destabilizing the filament, the Pi release induces a large lateral strand shift of ~2.5 nm. We identified the ParR (CBg-ParR) that acts as a nucleation factor in the initial stage of polymerization, similar to ParR from the Escherichia coli ParM-R1 plasmid. CBg-ParR also functions as a depolymerization factor, probably by recognizing the structural change in the CBg-ParM filament after Pi release, exhibiting a new mechanism for accelerated turnover of the ParM filament. Thus, CBg-ParM is thus a unique actin homolog with novel filament dynamics and nucleotide hydrolysis mechanisms.

category: biophysics


title: Meta analysis and experimental re-evaluation of the Boyle van 't Hoff relation with osmoregulation modelled by linear elastic principles and ion osmolyte leakage

abstract: In this study we challenge the paradigm of using the Boyle van t Hoff (BvH) relation to relate cell size as a linear function of inverse extracellular osmotic pressure for short time periods (~5 to 30 mins). We present alternative models that account for mechanical resistance (turgor model) and ion-osmolyte leakage (leak model), which is not accounted for by the BvH relation. To test the BvH relation and the alternative models, we conducted a meta-analysis of published BvH datasets, as well as new experiments using a HepG2 cell line. Our meta-analysis showed that the BvH relation may be assumed of the hypertonic region but cannot be assumed a priori over the hyper- and hypotonic region. Both alternative models perform better than the BvH relation but are nearly indistinguishable when plotted. The return to isotonic conditions plot indicated neither alternative model accurate predicts return volumes for HepG2 cells. However, a combined turgor-leak model accurately predicts both the BvH plot and the return to isotonic conditions plot. Moreover, this turgor-leak model provides a facile method to estimate the membrane-cortex Youngs modulus and the cell membrane permeability to intracellular ions/osmolytes during periods of osmotic challenge, and predicts a novel passive method of volume regulation without the need for ion pumps.


title: A comprehensive analysis of immune landscape of Indian triple negative breast cancer

abstract:
BackgroundTriple-negative breast cancer (TNBC) is a heterogeneous disease with a significant clinical challenge. TNBC alarmingly comprises 25-30% of breast cancers in India compared with only 10-15% in the West. However, immunotherapy was approved for high-risk early-stage TNBCs in the West. Hence, a long-standing question is whether Indian TNBCs immunologically and clinically resemble Western TNBCs such that they respond similarly to immunotherapies. Here we sought to elucidate the immune landscape of Indian TNBCs for the first time, compare them to Western disease and associate them with clinical parameters, cellular types/signaling, and immunotherapy response.

MethodsWe profiled 730 immune genes in 88 retrospective Indian TNBC samples using NanoString platform, clustered them into subtypes using a machine-learning approach, and compared them with Western TNBCs (n=422; public datasets). Subtype-specific gene signatures were identified, followed by clinicopathological, immune cell type, and pathway (multiomics) analyses. We also assessed responses to (cross-cancer) immunotherapy. Tumor-infiltrating lymphocytes (TILs) and pan-macrophage marker were evaluated using hematoxilin-eosin staining and immunohistochemistry, respectively.

ResultsWe identified three robust and similarly distributed TNBC immune transcriptome subtypes (Subtypes-1-3) in Indian women, and they are represented correspondingly in Western TNBCs and associated with well-known TNBC subtypes. Irrespective of the ethnicity, Subtype-1 harbored tumor microenvironmental and anti-tumor immune events associated with smaller tumors, younger age, and a better prognosis. Subtype-1 mainly represented basal-like/claudin-low breast cancer and immunomodulatory TNBC subtypes. Subtype-1 showed an increase in a cascade of events, including damage-associated molecular patterns, acute inflammation, Th1 responses, T-cell receptor-related and chemokine-specific signaling, antigen presentation, and viral-mimicry pathways. Subtype-1 was significantly (p<0.05) associated with pre-menopausal women, dense TILs and responses and/or improved prognosis to anti-PD-L1 and MAGEA3 immunotherapies. Subtype-2 was enriched for Th2/Th17 responses, CD4+ regulatory cells, basal-like/mesenchymal subtypes, and an intermediate prognosis. Subtype-3 patients expressed innate immune genes/proteins, including those representing macrophages and neutrophils, and had poor survival.

ConclusionWe identified three immune-specific TNBC subtypes in Indian patients with differential clinical and immune behaviors, which largely overlapped with the Western TNBC cohorts. This study suggests cancer immunotherapy in TNBC may work similarly in both populations. Hence, this may expedite pharmaceutical adoption of immunotherapy to Indian TNBC patients.

category: cancer biology


title: Application of high-throughput, high-depth, targeted single-nucleus DNA sequencing in pancreatic cancer

abstract: Despite insights gained by bulk DNA sequencing of cancer it remains challenging to resolve the admixture of normal and tumor cells, and/or of distinct tumor subclones; high throughput single-cell DNA sequencing circumvents these and brings cancer genomic studies to higher resolution. However, its application has been limited to liquid tumors or a small batch of solid tumors, mainly because of the lack of a scalable workflow to process solid tumor samples. Here we optimized a highly automated nuclei extraction workflow that achieved fast and reliable targeted single-nucleus DNA library preparation of 38 samples from 16 pancreatic adenocarcinoma (PDAC) patients, with an average library yield per sample of 2867 single nuclei. We demonstrate that this workflow not only performs well using low cellularity or low tumor purity samples but reveals novel genomic evolution patterns of PDAC as well.


title: Systematic analysis uncovers SYK dependency in NF1LoF melanoma cells

abstract: The loss of function (LoF) of NF1 is the third most frequent mutation that drives hyperactivated RAS and tumor growth in >10% of melanomas. NF1LoF melanoma cells, however, do not show consistent sensitivity to individual MEK, ERK, or PI3K/mTOR inhibitors. Here, we perform a targeted kinase inhibitor screen and identify a tool compound, named MTX-216, to be highly effective in blocking NF1LoF melanoma cells. Single-cell analysis links drug-induced cytotoxicity to effective co-suppression of proliferation marker Ki-67 and the ribosomal S6 phosphorylation, an integrator of multiple RAS-mediated signaling pathways. Using a combination of kinome selectivity assay, transcriptomic analysis, and genetic experiments, we find the anti-tumor efficacy of MTX-216 to be dependent on its ability to inhibit not only PI3K (its nominal target) but also SYK, and suppression of a group of genes that regulate mitochondrial electron transport chain and whose expression is associated with poor survival in NF1LoF melanoma patients. Furthermore, combinations of inhibitors targeting either MEK or PI3K/mTOR with an independent SYK kinase inhibitor or SYK knockdown show favorable effects. These studies provide a path to exploit SYK dependency to selectively block NF1LoF melanoma cells.


title: A photoswitchable ligand targeting β1-adrenoceptor enables light-control of the cardiac rhythm

abstract: Catecholamine-triggered {beta}-adrenoceptor ({beta}-AR) signaling is essential for the correct functioning of the heart. Although both {beta}1- and {beta}2-AR subtypes are expressed in cardiomyocytes, drugs selectively targeting {beta}1-AR have proven this receptor as the main target for the therapeutic effects of beta blockers in heart. Here, we report a new strategy for the spatiotemporal control of {beta}1-AR activation by means of light-regulated drugs with a high level of {beta}1-/{beta}2-AR selectivity. All reported molecules allow for an efficient real time optical control of receptor function in vitro. Moreover, using confocal microscopy we demonstrate that the binding of our best hit, pAzo-2, can be reversibly photocontrolled. Strikingly, pAzo-2 also enables a dynamic cardiac rhythm management on alive zebrafish larvae using light, thus highlighting the therapeutic and research potential of the developed photoswitches. Overall, this work provides the first proof of precise control of the therapeutic target {beta}1-AR in native environments using light.

category: pharmacology and toxicology


title: Dietary Lipid Oxidization Products Alter Growth, Adiposity and Gut Microbial Ecology in Prepubertal Porcine Model

abstract: Elevated levels of dietary fats in westernized diets, associated with increased risk of obesity and other chronic diseases, are increasingly consumed by children in the United States. Cooking practices such as high heat frying and increased use of oxidizable sources of fats have introduced high levels of lipid oxidation products (LOPs) into these diets. The effects of these highly reactive dietary compounds on human biology are largely unstudied, especially in the gut where these compounds are likely present at higher concentrations. Given that the gut microbiome can be influenced by dietary components and then in turn have a systemic impact, we investigated the effects of consuming LOPs on gut bacterial and fungal communities and on growth and body composition during the prepubertal period in a porcine model. The presence of LOPs in the high fat diet reduced growth and body fat gain in the model. The gut microbiome was uniquely altered by both high fat and the presence of LOPs, with notable changes in the abundances of Turicibacterales, Spriochaetales, RF39, Lactobacillales and Erysipelotrichales. The mycobiome was dominated by Kazachstania, a porcine specific yeast, which was only minimally influenced by the dietary regimen. Application of machine learning identified dietary fat and LOPs as strong predictors of body fat. The genus Methanobrevibacter was the key microbial predictor of body fat. This study highlights the need for further studies on the biological effects of LOPs which have become ubiquitous in human, livestock and pet diets in developed countries.

category: physiology


title: The Receptor Kinase FER Mediates Phase Separation of Glycine-Rich RNA-Binding Protein 7 to Confer Temperature Resilience in Arabidopsis

abstract: Temperature fluctuations repress plant growth. Although glycine-rich RNA-binding proteins (GRPs) and cold shock proteins (CSPs) have been implicated in cold adaptation, their physiological roles in the response to temperature fluctuations are largely unknown. The receptor kinase FERONIA (FER), a master regulator of cell growth, phosphorylates GRP7 within its intrinsically disordered region to modulate mRNA alternative splicing in the nucleus. Here we show that natural variations at a GRP7 residue phosphorylated by FER influences GRP7 liquid-liquid phase separation (LLPS), aiding Arabidopsis to grow over a wider temperature range. LLPS of GRP7 in the cytoplasm leads to the formation of stress granules that recruits RNAs, along with the translation machinery component eIF4E1 and mRNA chaperones, CSP1 and CSP3, to inhibit translation. Mutations in FER and the GRP7-LLPS-recruited components attenuate root growth under temperature shift conditions. Our findings illustrate the roles of GRP7 LLPS in improving plant root capacity to withstand temperature fluctuations.

category: plant biology


title: Widespread hybridization between invasive bleak (Alburnus alburnus) and native Iberian chubs (Squalius spp.): a neglected threat

abstract: Hybridization between native and exotic species is a major conservation issue. In Iberian rivers, which are simultaneously among the most invaded and diverse ecosystems, harboring a high proportion of endemic fishes, this issue is becoming highly concerning. To date, hybridization has been reported to occur between the invasive bleak Alburnus alburnus and the endemic chubs Squalius alburnoides and S. pyrenaicus, in some scattered locations. However, the bleak is increasingly spreading in the region, potentially increasing the risks of hybridization with these and other Squalius species. To gather a more comprehensive picture on the current extension of hybridization, we compiled and mapped records on hybrids between bleak and chubs collected by multiple research teams in different ongoing projects in the Portuguese territory, and genetically assessed the hybrid identity of specimens in an area of sympatry between bleak and S. carolitertii, using nuclear and mitochondrial markers. We found that hybridization with bleak is widespread in several Portuguese river basins and involves at least three endemic chubs, S. alburnoides, S. pyrenaicus and S. carolitertii. This may have serious consequences, including not only waste of reproductive effort and damage of genetic integrity, but also putative shifts on the reproductive dynamics of the Squalius system, which includes endemic hybrids, reproducing sexually and nonsexually. Hybridization should be recognized as a significant impact of biological invasions, and we recommend that future studies should characterize the fitness of hybrids and their ecological and genetic interactions with parental Iberian fish, to elucidate effective conservation measures.

category: zoology


title: A sporadic Alzheimer's blood-brain barrier model for developing ultrasound-mediated delivery of Aducanumab and anti-Tau antibodies.

abstract:
RationaleThe blood-brain barrier (BBB) is a major impediment to therapeutic intracranial drug delivery for the treatment of neurodegenerative diseases, including Alzheimers disease (AD). Focused ultrasound applied together with microbubbles (FUS+MB) is a novel technique to transiently open the BBB and increase drug delivery. Evidence suggests that FUS+MB is safe, however the effects of FUS+MB on human BBB cells, especially in the context of AD, remain sparsely investigated.

MethodsHere we generated BBB cells (induced brain endothelial cells (iBECs) and astrocytes (iAstrocytes)) from apolipoprotein E gene allele E4 (APOE4, high AD risk) and allele E3 (APOE3, lower AD risk) carrying patient-derived induced pluripotent stem cells (iPSCs). We then developed a human sporadic AD BBB cell platform to investigate the effects of FUS+MB on BBB cells and screen for the delivery of two potentially therapeutic AD antibodies.

ResultsWe utilized this robust and reproducible human BBB model to demonstrate increased delivery of therapeutic AD antibodies across the BBB following FUS+MB treatment, including an analogue of Aducanumab (AduhelmTM; anti-amyloid-{beta}) and a novel anti-Tau antibody RNF5. Our results also demonstrate the safety of FUS+MB indicated by minimal changes in the cell transcriptome as well as little or no changes in cell viability and inflammatory responses within the first 24 h post FUS+MB. Finally, we report a more physiologically relevant hydrogel-based 2.5D BBB model as a key development for FUS+MB-mediated drug delivery screening, with potentially higher translational utility.

ConclusionOur results demonstrate an important translatable patient BBB cell model for identifying FUS+MB-deliverable drugs and screening for cell- and patient-specific effects of FUS+MB, accelerating the use of FUS+MB as a therapeutic modality in AD.

One Sentence SummaryFocused ultrasound increases the in vitro delivery of therapeutic antibodies Aducanumab and anti-Tau in a sporadic Alzheimers disease patient-derived blood-brain barrier cell model.


title: Oxytocin via oxytocin receptor excites neurons in the endopiriform nucleus of juvenile mice

abstract:
The neuropeptide oxytocin (OXT) modulates social behaviors across species and may play a developmental role for these behaviors and their mediating neural pathways. Despite having high, stable levels of OXT receptor (OXTR) ligand binding from birth, endopiriform nucleus (EPN) remains understudied. EPN integrates olfactory and gustatory input and has bilateral connections with several limbic areas. Because the role of OXTR signaling in EPN is unknown, we sought to provide anatomical and electrophysiological information about OXTR signaling in mouse EPN neurons. Using in situ hybridization, we found that most EPN neurons co-express Oxtr mRNA and the marker for VGLUT1 and are thus glutamatergic cells. Based on high levels of OXTR ligand binding in EPN, we hypothesized that oxytocin application would modulate activity in these cells as measured by whole-cell patch-clamp electrophysiology. Bath application of OXT and an OXTR specific ligand (TGOT) increased the excitability of EPN neurons in wild-type, but not in OXTR-knockout tissue. These results show an effect of OXT on a presumably glutamatergic cell population within EPN. Given the robust, relatively stable OXTR expression in EPN throughout life, OXTR in this multi-sensory and limbic integration area may be important for modulating activity in response to an array of social or other salient stimuli throughout the lifespan and warrants further study.

Significance statementThere is a high level of oxytocin receptor (OXTR) expression in the mouse endopiriform nucleus (EPN) throughout development, however little is known about the effect of oxytocin on these neurons. We show here that Oxtr mRNA co-expresses mainly with VGLUT1, a glutamatergic cell marker. Using OXTR-EGFP mice to identify EPN, we show that OXT has a mainly excitatory effect on EPN neurons. Thus, activity in EPN neurons may be modulated by OXT during exposure to salient or social stimuli throughout development and this could affect development of behavioral responses during social exposure.


title: Impaired peri-olfactory Cerebrospinal Fluid clearance mediated cognitive decline after dyssomnia

abstract: Animal experiments have demonstrated the dependency of CSF clearance function on age and sleep, which partially underlay the cognitive decline in the elderly. However, evidence is lacking in humans mainly due to limited method to assess CSF clearance function. We aimed to image CSF clearance pathways in human brain by dynamic MRI with intrathecal contrast agent as a CSF tracer. We performed T1-weighted and T2-fluid attenuated inversion recovery imaging with equal sequence parameters before and at multiple time points after intrathecal injection of contrast agent to visualize the putative meningeal lymphatic pathway, peri-olfactory nerve pathway and peri-optic nerve pathway. We defined the CSF clearance function as the percentage change in signal unit ratio of critical locations in these pathways from baseline to 39 hours after intrathecal injection. CSF clearance through the putative meningeal lymphatic and peri-neural pathways were clearly visualized in all 85 patients. The CSF clearance function of meningeal lymphatic and peri-neural pathways were reduced with aging (all P < 0.05). The CSF clearance function through peri-olfactory nerve pathway was positive correlated with sleep quality and cognitive function (both P < 0.05). Moreover, the CSF clearance function through peri-olfactory nerve pathway mediated the association of sleep quality with cognitive function (percent change in {beta} [bootstrap 95% confidence interval]: 35% [-0.220, -0.003]). The study shows promise for dynamic MRI with intrathecal injection of contrast agent as a method to assess CSF clearance function through putative peri-neural pathways, and interprets the impaired clearance through putative peri-olfactory nerve pathway may explain the cognitive decline in patients with dyssomnia.


title: Taste quality interactions and transformations in a sensorimotor circuit

abstract: Taste detection and hunger state dynamically regulate the decision to initiate feeding. To study how context-appropriate feeding decisions are generated, we combined synaptic resolution circuit reconstruction with targeted genetic access to specific neurons to elucidate a gustatory sensorimotor circuit for feeding initiation in adult Drosophila melanogaster. This circuit connects gustatory sensory neurons to proboscis motor neurons through three intermediate layers. Most neurons in this pathway are necessary and sufficient for proboscis extension, a feeding initiation behavior, and respond selectively to sugar taste detection. Pathway activity is amplified by hunger signals that act at select second-order neurons to promote feeding initiation in food-deprived animals. In contrast, the feeding initiation circuit is inhibited by a bitter taste pathway that impinges on premotor neurons, illuminating a local motif that weighs sugar and bitter taste detection to adjust behavioral outcome. Together, these studies reveal central mechanisms for the integration of external taste detection and internal nutritive state to flexibly execute a critical feeding decision.


title: Taste quality and hunger interactions in a feeding sensorimotor circuit


title: Emergence of hyper insecticide-resistant dengue vectors in Indochina Peninsula: threats of concomitant knockdown resistance mutations

abstract:
Aedes aegypti (Linnaeus, 1762) is the main mosquito vector for dengue and other arboviral infectious diseases. Control of this important vector highly relies on the use of insecticides, especially pyrethroids. Nevertheless, the development of pyrethroid resistance is a major obstacle to mosquito/disease control worldwide. Here, we focused on the mutations in the target site of pyrethroid insecticides, voltage-sensitive sodium channel (Vssc), and found that Ae. aegypti collected from Vietnam has the L982W allele in the Vssc at a high frequency (>79%). L982W mutation is located in the highly conserved region of Vssc that is associated with sodium-ion selectivity and permeation rate. Strains having the L982W allele showed similar or even higher levels of resistance to pyrethroids than those having V1016G, a typical knockdown resistance allele in Asia. Furthermore, concomitant mutations L982W+F1534C and V1016G+F1534C were confirmed, and strains having these multiple Vssc mutations exhibited incomparably higher levels of pyrethroid resistance than any other field population ever reported. Molecular modeling analysis confirmed that these concomitant mutant alleles could interfere with approaching pyrethroid to Vssc. Remarkably, >90% of Vssc of Ae. aegypti were occupied by these hyper insecticide-resistant haplotypes in Phnom Penh city, Cambodia. Analysis of whole Vssc coding genes suggested that Vsscs have evolved into stronger resistant forms efficiently through gene recombination events. At this point, L982W has never been detected in Vssc of Ae. aegypti from any other neighboring countries. We strongly emphasize the need to be vigilant about these strong resistance genes spreading to the world through Indochina Peninsula.

Significance StatementThe high frequency (>78%) of the L982W allele was detected at the target site of the pyrethroid insecticide, the voltage-sensitive sodium channel (Vssc) of Aedes aegypti collected from Vietnam and Cambodia. Haplotypes having concomitant mutations L982W+F1534C and V1016G+F1534C were also confirmed in both countries, and their frequency was high (>90%) in Phnom Penh, Cambodia. Strains having these haplotypes exhibited substantially higher levels of pyrethroid resistance than any other field population ever reported. The L982W mutation has never been detected in any country of the Indochina Peninsula except Vietnam and Cambodia, but it may be spreading to other areas of Asia, which can cause an unprecedentedly serious threat to the control of dengue fever as well as other Aedes-borne infectious diseases.


title: Measuring the response to visually presented faces in the human lateral prefrontal cortex

abstract: Neuroimaging studies have identified multiple face-selective areas. In the current study we compared the functional response of the face area in the lateral prefrontal cortex to that of other face-selective areas. In Experiment 1 participants (N=32) were scanned viewing videos containing faces, bodies, scenes, objects, and scrambled objects. We identified a face-selective area in the right inferior frontal gyrus (rIFG). In Experiment 2 participants (N=24) viewed the videos or static images. Results showed that the rIFG, posterior superior temporal sulcus (pSTS) and occipital face area (OFA) exhibited a greater response to moving than static faces. In Experiment 3 participants (N=18) viewed face videos presented in the contralateral and ipsilateral visual fields. Results showed that the face areas in the IFG and pSTS responded equally to faces in both visual fields, while the OFA and fusiform face area (FFA) showed a contralateral bias. These experiments suggest two conclusions; firstly, in all three experiments the face area in the IFG was not as reliably identified as face areas in the occipitotemporal cortex. Secondly, the similarity of the response patterns in the IFG and pSTS face areas suggests that the areas are functionally connected, a conclusion consistent with neuroanatomical and functional connectivity evidence.


title: Interpreting dynamics of neural activity after dimensionality reduction

abstract: Recorded activity of cortical neurons during behavior is often analyzed with dimensionality reduction methods. The resulting oscillatory trajectories have been interpreted as signatures of latent oscillatory dynamical systems. Here we show that oscillatory trajectories arise as a consequence of the horseshoe effect after applying dimensionality reduction methods on signals that approximately exhibit continuous variation in time, regardless of whether latent oscillatory dynamical systems are present or not. We show that task-relevant information is instead contained in deviations between oscillatory trajectories, which we account for by introducing a new model that goes beyond the dichotomy between representational and dynamical systems models of neural activity. Our findings help interpret the results of dimensionality reduction analyses.


title: Evoking the N400 Event-Related Potential (ERP) Component Using a Publicly Available Novel Set of Sentences with Semantically Incongruent or Congruent Eggplants (Endings).

abstract: During speech comprehension, the ongoing context of a sentence is used to predict sentence outcome by limiting subsequent word likelihood. Neurophysiologically, violations of context-dependent predictions result in amplitude modulations of the N400 event-related potential (ERP) component. While N400 is widely used to measure semantic processing and integration, no publicly-available auditory stimulus set is available to standardize approaches across the field. Here, we developed an auditory stimulus set of 404 sentences that utilized the semantic anomaly paradigm, provided cloze probability for all stimuli, and was developed for both children and adults. With 20 neurotypical adults, we validated that this set elicits robust N400s, as well as two additional semantically-related ERP components: the late positivity component and the recognition potential. This stimulus set and the 20 high-density (128-channel) electrophysiological datasets are made publicly available here to promote data sharing and reuse. Future studies that use this stimulus set to investigate sentential semantic comprehension in both control and clinical populations may benefit from the increased comparability and reproducibility within this field of research.


title: Multimodal single-cell profiling of intrahepatic cholangiocarcinoma defineshyperactivated Tregs as a potential therapeutic target

abstract: The quality of the immune infiltrate of intrahepatic cholangiocarcinoma (iCCA), a rare, yet aggressive tumor of the biliary tract, remains poorly characterized, limiting development of successful immunotherapies. We used high-dimensional flow cytometry to characterise the T cell and myeloid compartments of iCCA comparing these with their tumor-free peritumoral and circulating counterparts. We found poor infiltration of putative tumor-specific CD39+ CD8+ T cells accompanied by abundant infiltration of hyperactivated CD4+ regulatory T cells (Tregs), whose frequency in relation to that of CD4+ CD69+ T cells and conventional type 2 dendritic cells was associated with poor prognosis. Single-cell RNA-sequencing identified an altered network of transcription factors in iCCA-infiltrating compared to peritumoral T cells, suggesting reduced effector functions by tumor-infiltrating CD8+ T cells and enhanced immunosuppression by CD4+ Tregs. Specifically, we found that expression of mesenchyme homeobox 1 (MEOX1) was highly enriched in tumor-infiltrating Tregs, and demonstrated that MEOX1 overexpression is sufficient to reprogram circulating precursors to acquire the transcriptional and epigenetic landscape of tumorinfiltrating Tregs. Interfering with hyperactivated Tregs should be thus explored to enhance antitumor immunity in iCCA.

category: immunology


title: PTEN is required for human Treg suppression of costimulation

abstract: Regulatory T cell (Treg) therapy is under clinical investigation for the treatment of transplant rejection, autoimmune disease, and graft-versus-host disease. With the advent of genome editing, attention has turned to reinforcing Treg function for therapeutic benefit. A hallmark of Tregs is dampened activation of PI3K-AKT signalling, of which PTEN is a major negative regulator. Loss-of-function studies of PTEN, however, have not conclusively shown a requirement for PTEN in upholding Treg function and stability. Using CRISPR-based genome editing in human Tregs, we show that PTEN ablation does not cause a global defect in Treg function and stability; rather, it selectively blocks their ability to suppress antigen-presenting cells. PTEN-KO Tregs exhibit elevated glycolytic activity, upregulate FOXP3, maintain a Treg phenotype, and have no discernable defects in lineage stability. Functionally, PTEN is dispensable for human Treg-mediated inhibition of T cell activity in vitro and in vivo but is required for suppression of costimulatory molecule expression by antigen-presenting cells. These data are the first to define a role for a signalling pathway in controlling a subset of human Treg activity. Moreover, they point to the functional necessity of PTEN-regulated PI3K-AKT activity for optimal human Treg function.


title: Newly synthesized mRNA escapes translational repression during the acute phase of the mammalian unfolded protein response

abstract: Endoplasmic Reticulum (ER) stress, caused by the accumulation of misfolded proteins in the ER, elicits a homeostatic mechanism known as the Unfolded Protein Response (UPR). The UPR reprograms gene expression to promote adaptation to chronic ER stress. The UPR comprises an acute phase involving inhibition of bulk protein synthesis and a chronic phase of transcriptional induction coupled with the partial recovery of protein synthesis. However, the role of transcriptional regulation in the acute phase of the UPR is not well understood. Here we analyzed the fate of newly synthesized mRNA encoding the protective and homeostatic transcription factor X-box binding protein 1 (XBP1) during this acute phase. We have previously shown that global translational repression induced by the acute UPR was characterized by decreased translation and increased stability of XBP1 mRNA. We demonstrate here that this stabilization is independent of new transcription. In contrast, we show XBP1 mRNA newly synthesized during the acute phase accumulates with long poly(A) tails and escapes translational repression. Inhibition of nascent RNA polyadenylation during the acute phase decreased cell survival with no effect in unstressed cells. Furthermore, during the chronic phase of the UPR, levels of XBP1 mRNA with long poly(A) tails decreased in a manner consistent with co-translational deadenylation. Finally, additional pro-survival, transcriptionally-induced mRNAs show similar regulation, supporting the broad significance of the pre-steady state UPR in translational control during ER stress. We conclude that the biphasic regulation of poly(A) tail length during the UPR represents a previously unrecognized pro-survival mechanism of mammalian gene regulation.

category: molecular biology


title: Hippo Signaling Cofactor, WWTR1, at the Crossroads of Human Trophoblast Progenitor Self-Renewal and Differentiation.

abstract:
Healthy progression of human pregnancy relies on cytotrophoblast progenitor (CTB) self-renewal and their differentiation towards multi-nucleated syncytiotrophoblasts (STBs) and invasive extravillous trophoblasts (EVTs). However, underlying molecular mechanisms that fine-tune CTB self-renewal or direct their differentiation towards STBs or EVTs during human placentation are poorly defined. Here, we show that hippo signaling cofactor WW Domain Containing Transcription Regulator 1 (WWTR1) is a master regulator of trophoblast fate choice during human placentation. Using human trophoblast stem cells (human TSCs), primary CTBs and human placental explants, we demonstrate that WWTR1 promotes self-renewal in human CTBs and is essential for their differentiation to EVTs. In contrast, WWTR1 prevents induction of STB fate in undifferentiated CTBs. Our single-cell RNA-sequencing analyses in first-trimester human placenta along with mechanistic analyses in human TSCs revealed that WWTR1 fine-tunes trophoblast fate by directly regulating Wnt signaling components. Importantly, our analyses of placentae from pathological pregnancies show that extreme preterm birth (gestational time [≤]28weeks) and intrauterine growth restriction along with preeclampsia (IUGR/PE) are often associated with loss of WWTR1 expression in CTBs. In summary, our findings establish a critical importance of WWTR1 at the crossroads of human trophoblast progenitor self-renewal vs. differentiation. It plays positive instructive roles to promote CTB self-renewal and EVT differentiation and safeguards undifferentiated CTBs from obtaining the STB fate.

SIGNIFICANCEHuman pregnancy relies on formation of the transient organ placenta and trophoblast cells are the major building blocks of the placenta. A defect in trophoblast progenitor self-renewal or their differentiation is associated with either pregnancy loss or pathological pregnancies, yet underlying molecular mechanisms that regulate trophoblast differentiation are poorly understood. In this study, we discovered that WWTR1, a transcription cofactor and a component of conserved Hippo signaling pathway, optimizes trophoblast progenitor self-renewal and is essential for their differentiation into the invasive extravillous trophoblast cell lineage. Our findings establish WWTR1 as a critical regulator for success in human placentation and progression of a healthy pregnancy.

category: developmental biology


title: Climate biogeography of Arabidopsis thaliana: linking distribution models, individual performance, and life history

abstract:
AIMThe role of environmental conditions in limiting species distributions is often hypothesized, but it is challenging to gather large-scale data to demonstrate environmental impacts on individual performance. The past and present biogeography of model organisms is key context to understanding how environment shapes species genetic and phenotypic diversity.

LOCATIONGlobal

TAXONArabidopsis thaliana ("Arabidopsis")

METHODSWe fit occurrence records to climate data, and then projected the distribution of Arabidopsis under last glacial maximum, current, and future climates. We confronted model predictions with individual performance measured on 2,194 herbarium specimens, and we asked whether predicted suitability was associated with life-history variation measured on 898 natural accessions.

RESULTSThe most important climate variables constraining the Arabidopsis distribution were winter cold in northern and high elevation regions and summer heat in southern regions. Herbarium specimens from regions with lower habitat suitability in both northern and southern regions were smaller, supporting the hypothesis that the distribution of Arabidopsis is constrained by climate-associated factors. Climate anomalies partly explained interannual variation in herbarium specimen size, but these did not closely correspond to local limiting factors identified in the distribution model. Late-flowering genotypes were absent from the lowest suitability regions, suggesting slower life histories are only viable closer to the center of the realized niche. We identified glacial refugia farther north than previously recognized, as well as refugia concordant with previous population genetic findings. Lower latitude populations, known to be genetically distinct, are most threatened by future climate change. The recently colonized range of Arabidopsis was well-predicted by our native-range model applied to certain regions but not others, suggesting it has colonized novel climates.

MAIN CONCLUSIONSIntegration of distribution models with performance data from vast natural history collections is a route forward for testing hypotheses about species distributions and their relationship with evolutionary fitness across large scales.


title: Flipped elevational pattern of pollination mode in tropical versus temperate Americas

abstract:
AimAbiotic factors, such as temperature and precipitation, vary markedly along elevational gradients, and can in turn, shape key biotic interactions, such as herbivory and pollination. Despite the well-known effects of climatic conditions on pollinator activity and efficiency, we know little about the role of climate in pollinator shifts in animal-pollinated plants at broad geographic scales. Here we investigate patterns of altitudinal turnover in pollination mode across the Americas, with a focus on the most common pollinators (bees and hummingbirds). Specifically, we test Crudens classic hypothesis that plants are likely to shift to bird pollination at high elevations because endothermic pollinators are more reliable in cold and rainy conditions.

LocationAmericas

Time periodCurrent

Major taxa studied2232 plant taxa from 26 clades

MethodsWe collated information on pollination mode (1262 insect-pollinated, 970 vertebrate-pollinated) for the study taxa from the literature, and used GBIF occurrence data to estimate median distributions and bioclimatic attributes of each species. We used (phylogenetic) GLMMs to test for associations between pollination mode and ecogeographic variables.

ResultsTo our surprise, we found flipped elevational patterns of insect- and vertebrate-pollination strategies across latitudes, with vertebrate pollination dominating at high elevations in the tropics, but not in temperate zones. We term this pattern the  Tropical flip. We recovered a strong association of vertebrate-pollinated plants with moist, forested habitats across latitudes, while insect-pollinated plants were often found in cool and dry or warm and moist conditions.

Main conclusionsAltitudinal gradients in temperature may not serve as a universal explanation for shifts among endothermic insect and ectothermic vertebrate pollination. Instead, strong abiotic niche differentiation among insect- and vertebrate-pollinated plants, along with competition for pollination niche space, has likely shaped the  tropical flip.


title: Identifying the C. elegans vulval transcriptome

abstract: Development of the C. elegans vulva is a classic model of organogenesis. This system, which starts with six equipotent cells, encompasses diverse types of developmental event, including developmental competence, multiple signaling events to control precise and faithful patterning of three cell fates, execution and proliferation of specific cell lineages, and a series of sophisticated morphogenetic events. Early events have been subjected to extensive mutational and genetic investigations and later events to cell biological analyses. We infer the existence of dramatically changing profiles of gene expression that accompanies the observed changes in development. Yet except from serendipitous discovery of several transcription factors expressed in dynamic patterns in vulval lineages, our knowledge of the transcriptomic landscape during vulval development is minimal. This study describes the composition of a vulva-specific transcriptome. We used tissue specific harvesting of mRNAs via immunoprecipitation of epitope-tagged poly(A) binding protein, PAB-1, heterologously expressed by a promoter known to express GFP in vulval cells throughout their development. The identified transcriptome was small but tightly interconnected. From this data set we identified several genes with identified functions in development of the vulva and validated more with promoter-GFP reporters of expression. For one target, lag-1, promoter-GFP expression was limited but fluorescent tag of the endogenous protein revealed extensive expression. Thus, we have identified a transcriptome of the C. elegans as a launching pad for exploration of functions of these genes in organogenesis.


title: Classification of plant growth-promoting bacteria inoculation status and prediction of growth-related traits in tropical maize using hyperspectral image and genomic data

abstract:
Recent technological advances in high-throughput phenotyping have created new opportunities for the prediction of complex traits. In particular, phenomic prediction using hyper-spectral reflectance could capture various signals that affect phenotypes genomic prediction might not explain. A total of 360 inbred maize lines with or without plant growth-promoting bacterial inoculation management under nitrogen stress were evaluated using 150 spectral wavelengths ranging from 386 to 1021 nm and 13,826 single-nucleotide polymorphisms. Six prediction models were explored to assess the predictive ability of hyperspectral and genomic data for inoculation status and plant growth-related traits. The best models for hyperspectral prediction were partial least squares and automated machine learning. The Bayesian ridge regression and BayesB were the best performers for genomic prediction. Overall, hyper-spectral prediction showed greater predictive ability for shoot dry mass and stalk diameter, whereas genomic prediction was better for plant height. The prediction models that simultaneously accommodated both hyperspectral and genomic data resulted in a predictive ability as high as that of phenomics or genomics alone. Our results highlight the usefulness of hyperspectral-based phenotyping for management and phenomic prediction studies.

Core ideasO_LIHyperspectral reflectance data can classify plant growth-promoting bacteria inoculation status
C_LIO_LIPhenomic prediction performs better than genomic prediction depending on the target phenotype
C_LIO_LIAutoML is a promising approach for automating hyperparameter tuning for classification and prediction
C_LI


title: SNP calling parameters have minimal impact on population structure and divergence time estimates for the rice blast fungus

abstract:
ObjectivesAccurate single-nucleotide polymorphisms (SNP) calls are crucial for robust evolutionary and population genetic inferences in genomic analyses. Such inferences can reveal the time-scales and processes associated with the emergence and spread of pandemic plant pathogens, such as the rice blast fungus Magnaporthe oryzae (Syn. Pyricularia oryzae). However, the specificity and sensitivity of SNP calls depend on the filtering parameters applied to the data. Here, we used a benchmarking approach to evaluate the impact of SNP calling on different population genetic analyses of the rice blast fungus, namely genetic clustering, topology of phylogenetic reconstructions and estimation of evolutionary rates.

ResultsTo benchmark SNP calling parameters, we generated a gold standard set of validated SNPs by sequencing nine M. oryzae genomes with both Illumina short-reads and Oxford Nanopore Technologies (ONT). We used the gold standard set of SNPs to identify the SNP calling parameter configuration that maximizes sensitivity and specificity. We found that the choice of parameter configurations can substantially change the number of ascertained SNPs, preferentially affecting SNPs segregating at low population frequency. However, SNP calling parameter configurations did not significantly affect the clustering of isolates in clonal lineages, the monophyly of each clonal lineage, and the estimation of evolutionary rates. We leverage the evolutionary rates obtained from each SNP calling parameter configuration to generate divergence time estimates that take into account the uncertainty associated with both the estimation of evolutionary rates and SNP calling. Our analysis indicates that M. oryzae clonal lineage expansions took place ~300 years ago.


title: Behavioral differences among domestic cats in the response to cat-attracting plants and their volatile compounds reveal a potential distinct mechanism of action for actinidine

abstract: It has been known for centuries that cats respond euphorically to Nepeta cataria (catnip). Recently, we have shown that Lonicera tatarica (Tatarian honeysuckle), Actinidia polygama (silver vine) and Valeriana officinalis (valerian) can also elicit this "catnip response". The aim of this study was to learn if the behavior seen in response to these plants is similar to the response to catnip. Furthermore, we studied if these responses are fixed or if there are differences between cats. While nepetalactone was identified decades ago as the molecule responsible for the "catnip response", we know that this volatile is found almost exclusively in catnip. Therefore, we also aimed to identify other compounds in these alternative plants that can elicit the blissful behavior in cats. Bioassays with 6 cats were performed in a stress-free environment, where 6 plants and 13 single compounds were each tested for at least 100 and 17 hours, respectively. All responses were video recorded and BORIS software was used to analyze the cats behavior. Both response duration and behavior differed significantly between the cats. While individual cats had preferences for particular plants, the behavior of individual cats was consistent among all plants. About half a dozen lactones similar in structure to nepetalactone were able to elicit the "catnip response", as were the structurally more distinct molecules actinidine and dihydroactinidiolide. Most cats did not respond to actinidine, whereas those who did, responded longer to this volatile than any of the other secondary plant metabolites, and different behavior was observed. Interestingly, dihydroactinidiolide was also found in excretions and secretions of the red fox, making this the first report of a compound produced by a mammal, that can elicit the "catnip response". A range of different cat-attracting compounds was detected by chemical analysis of plant materials but differences in cat behavior could not be directly related to differences in chemical composition of the plants. Together with among other results of habituation / dishabituation experiments, this indicates that additional cat-attracting compounds may be present in the plant materials that remain to be discovered. Collectively, these findings suggest that both the personality of the cat and genetic variation in the genes encoding olfactory receptors may play a role in how cats respond to cat-attracting plants. Furthermore, the data suggest a potential distinct mechanism of action for actinidine.

category: animal behavior and cognition


title: Disentanglement of Entropy and Coevolution using Spectral Regularization

abstract: The rise in the number of protein sequences in the post-genomic era has led to a major breakthrough in fitting generative sequence models for contact prediction, protein design, alignment, and homology search. Despite this success, the interpretability of the modeled pairwise parameters continues to be limited due to the entanglement of coevolution, phylogeny, and entropy. For contact prediction, post-correction methods have been developed to remove the contribution of entropy from the predicted contact maps. However, all remaining applications that rely on the raw parameters, lack a direct method to correct for entropy. In this paper, we investigate the origins of the entropy signal and propose a new spectral regularizer to down weight it during model fitting. We find the added regularizer to GREMLIN, a Markov Random Field or Potts model, allows for the inference of a sparse contact map without loss in precision, meanwhile improving interpretability, and resolving overfitting issues important for sequence evaluation and design.


title: GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species

abstract:
BackgroundMany wild species have suffered drastic population size declines over the past centuries, which have led to  genomic erosion processes characterized by reduced genetic diversity, increased inbreeding, and accumulation of harmful mutations. Yet, genomic erosion estimates of modern-day populations often lack concordance with dwindling population sizes and conservation status of threatened species. One way to directly quantify the genomic consequences of population declines is to compare genome-wide data from pre-decline museum samples and modern samples. However, doing so requires computational data processing and analysis tools specifically adapted to comparative analyses of degraded, ancient or historical, DNA data with modern DNA data as well as personnel trained to perform such analyses.

ResultsHere, we present a highly flexible, scalable, and modular pipeline to compare patterns of genomic erosion using samples from disparate time periods. The GenErode pipeline uses state-of-the-art bioinformatics tools to simultaneously process whole-genome re-sequencing data from ancient/historical and modern samples, and to produce comparable estimates of several genomic erosion indices. No programming knowledge is required to run the pipeline and all bioinformatic steps are well-documented, making the pipeline accessible to users with different backgrounds. GenErode is written in Snakemake and Python3 and uses Conda and Singularity containers to achieve reproducibility on high-performance compute clusters. The source code is freely available on GitHub (https://github.com/NBISweden/GenErode).

ConclusionsGenErode is a user-friendly and reproducible pipeline that enables the standardization of genomic erosion indices from temporally sampled whole genome re-sequencing data.


title: Acid-Base Homeostasis and Implications to the Phenotypic Behaviors of Cancer

abstract: Acid-base homeostasis is a fundamental property of living cells and its persistent disruption in human cells can lead to a wide range of diseases. We have conducted computational modeling and analysis of transcriptomic data of 4750 human tissue samples of nine cancer types in the TCGA database. Built on our previous study, we have quantitatively estimated the (average) production rate of OH- by cytosolic Fenton reactions, which continuously disrupt the intracellular pH homeostasis. Our predictions indicate that all or a subset of 43 reprogrammed metabolisms (RMs) are induced to produce net protons (H+) at comparable rates of Fenton reactions to keep the intracellular pH stable. We have then discovered that a number of well-known phenotypes of cancers, including increased growth rate, metastasis rate and local immune cell composition, can be naturally explained in terms of the Fenton reaction level and the induced RMs. This study strongly suggests the possibility to have a unified framework for studies of cancer-inducing stressors, adaptive metabolic reprogramming, and cancerous behaviors. In addition, strong evidence is provided to demonstrate that a popular view of that Na+/H+ exchangers, along with lactic acid exporters and carbonic anhydrases are responsible for the intracellular alkalization and extracellular acidification in cancer may not be justified.


title: Comparative analysis of MERFISH spatial transcriptomics with bulk and single-cell RNA sequencing

abstract: Spatial transcriptomics extends single cell RNA sequencing (scRNA-seq) technologies by providing spatial context for cell type identification and analysis. In particular, imaging-based spatial technologies such as Multiplexed Error-Robust Fluorescence In Situ Hybridization (MERFISH) can achieve single-cell resolution, allowing for the direct mapping of single cell identities to spatial positions. Nevertheless, because MERFISH produces an intrinsically different data type than scRNA-seq methods, a technical comparison between the two modalities is necessary to ascertain how best to integrate them. Here, we used the Vizgen MERSCOPE platform to perform MERFISH on mouse liver and kidney tissues and compared the resulting bulk and single-cell RNA statistics with those from the existing Tabula Muris Senis cell atlas. We found that MERFISH produced measurements that quantitatively reproduced the bulk RNA-seq and scRNA-seq results, with some minor differences in overall gene dropout rates and single-cell transcript count statistics. Finally, we explored the ability of MERFISH to identify cell types, and found that it could independently resolve distinct cell types and spatial structure in both liver and kidney. Computational integration with the Tabula Muris Senis atlas using scVI and scANVI did not noticeably enhance these results. We conclude that compared to scRNA-seq, MERFISH provides a quantitatively comparable method for measuring single-cell gene expression, and that efficient gene panel design allows for robust identification of cell types with intact spatial information without the need for computational integration with scRNA-seq reference atlases.


title: POSITIVE RATE DEPENDENT ACTION POTENTIAL PROLONGATION BY MODULATING POTASSIUM ION CHANNELS

abstract: Pharmacological agents that prolong action potential duration (APD) to a larger extent at slow rates than at the fast excitation rates typical of ventricular tachycardia exhibit reverse rate dependence. Reverse rate dependence has been linked to the lack of efficacy of class III agents at preventing arrhythmias. In this report we show that, in computer models of the ventricular action potential, APD prolongation by accelerating phase 2 repolarization (by increasing IKs) and decelerating phase 3 repolarization (by blocking IKr and IK1) results in a robust positive rate dependence (i.e., larger APD prolongation at fast rates than at slow rates). In contrast, APD prolongation by blocking a specific potassium channel type results in reverse rate dependence or a marginal positive rate dependence. Interventions that result in a strong positive rate dependence tend to decrease the repolarization reserve because they require substantial IK1 block. However, limiting IK1 block to [~]50% results in a strong positive rate dependence with moderate decrease in repolarization reserve. In conclusion, the use of a combination of IKs activators and IKr and IK1 blockers could result in APD prolongation that potentially maximizes anti-arrhythmic effects (by maximizing APD prolongation at fast excitation rates) and minimizes pro-arrhythmic effects (by minimizing APD prolongation at slow excitation rates).


title: Behavioral benefits of spatial attention explained by multiplicative gain, not receptive field shifts, in a neural network model

abstract: Attention allows us to focus sensory processing on behaviorally relevant aspects of the visual world. Directing attention has been associated with a number of changes in sensory representation including multiplicative gain as well as shifts in the size and location of neuron receptive fields in early visual cortex. But, which, if any, of these physiological effects can account for the behavioral benefits of attention? Here we use a large scale computational model of primate visual cortex to perform a set of experiments in which we decouple changes in spatial tuning from changes in gain. We show that increased gain at cued locations in a neural network observer model mimics the improvement of human subjects on an attentional task with a spatial cue. Increasing gain resulted in changes in receptive field size and location similar to physiological effects, yet when we forced the model to use only these spatial tuning changes the model failed to produce any behavioral benefit. Instead, we found that gain alone was both necessary and sufficient to explain behavioral improvement during attention. Our results suggest that receptive field shifts are a result of the signal gain that boosts behavioral performance rather than the core mechanism of spatial attention.

category: neuroscience


title: ALS-linked KIF5A ΔExon27 mutant causes neuronal toxicity through gain of function

abstract: Mutations in the human kinesin family member 5A (KIF5A) gene were recently identified as a genetic cause of amyotrophic lateral sclerosis (ALS). Several KIF5A ALS variants cause exon 27 skipping and produce motor proteins with an altered C-terminal tail (referred to as {Delta}Exon27). However, the underlying pathogenic mechanism is still unknown. In this study, we performed a comprehensive analysis of {Delta}Exon27 at the single-molecule, cellular, and organism levels. Our results show that {Delta}Exon27 is prone to form cytoplasmic aggregates and is neurotoxic. The mutation relieves motor autoinhibition and increases motor self-association, leading to drastically enhanced processivity on microtubules. Finally, ectopic expression of {Delta}Exon27 in Drosophila melanogaster causes wing defects, motor impairment, paralysis and premature death. Our results suggest gain of function as an underlying disease mechanism in KIF5A-associated ALS.


title: The neural code for 'face cells' is not face specific

abstract: 1 Face cells are visual neurons that selectively respond more to faces than other objects. Clustered together in inferotemporal cortex, they are thought to form a network of modules specialized in face processing by encoding face-specific features. Here we reveal that their category selectivity is instead captured by domain-general attributes. Analyzing neural responses in and around macaque face patches to hundreds of objects, we discovered graded tuning for non-face objects that was more predictive of face preference than was tuning for faces themselves. The relationship between category-level face selectivity and image-level non-face tuning was not predicted by color and simple shape properties, but by domain-general information encoded in deep neural networks trained on object classification. These findings contradict the long-standing assumption that face cells owe their category selectivity to face-specific features, challenging the prevailing idea that visual processing is carried out by discrete modules, each specialized in a semantically distinct domain.


title: Sensory Tetanization to Induce LTP-Like Plasticity: A Review and Reassessment of the Approach

abstract: Great interest has been given to developing non-invasive approaches for studying cortical plasticity in humans. High frequency presentation of auditory and visual stimuli, or sensory tetanization, can induce LTP-like changes in cortical activity. However, contrasting effects across studies suggest that sensory tetanization may be unreliable. We review these contrasting effects, conduct our own study of auditory and visual tetanization, and conduct a meta-analysis to determine the average effect of sensory tetanization across studies. We measured auditory-evoked amplitude changes in a group of younger and older adults following tetanization to 1 kHz and 4 kHz tone bursts and following a slow-presentation control. We also measured visual-evoked amplitude changes following tetanization to horizontal and vertical sign gradients. Auditory and visual response amplitudes decreased following tetanization, consistent with some studies but contrasting with others finding amplitude increases (i.e. LTP-Like). Older adults exhibited more modest auditory-evoked amplitude decreases, but visual-evoked amplitude decreases like those of younger adults. Changes in response amplitude were not specific to tetanized stimuli. Importantly, slow presentation of auditory tone-bursts produced changes in response amplitude that were like those observed following tetanization. The meta-analysis incorporating our results with studies employing similar tetanization techniques revealed that the overall effect across studies and labs is not significant, suggesting sensory tetanization does not produce reliable changes in cortical responses. We discuss our findings with respect to other inconsistent findings across the literature concerning stimulus specificity and age effects and conclude that sensory tetanization is an unreliable method for inducing human cortical plasticity in vivo.


title: Goal-specific brain MRI harmonization

abstract: There is significant interest in pooling magnetic resonance image (MRI) data from multiple datasets to enable mega-analysis. Harmonization is typically performed to reduce heterogeneity when pooling MRI data across datasets. Most MRI harmonization algorithms do not explicitly consider downstream application performance during harmonization. However, the choice of downstream application might influence what might be considered as study-specific confounds. Therefore, ignoring downstream applications during harmonization might potentially limit downstream performance. Here we propose a goal-specific harmonization framework that utilizes downstream application performance to regularize the harmonization procedure. Our framework can be integrated with a wide variety of harmonization models based on deep neural networks, such as the recently proposed conditional variational autoencoder (cVAE) harmonization model. Three datasets from three different continents with a total of 2787 participants and 10085 anatomical T1 scans were used for evaluation. We found that cVAE removed more dataset differences than the widely used ComBat model, but at the expense of removing desirable biological information as measured by downstream prediction of mini mental state examination (MMSE) scores and clinical diagnoses. On the other hand, our goal-specific cVAE (gcVAE) was able to remove as much dataset differences as cVAE, while improving downstream cross-sectional prediction of MMSE scores and clinical diagnoses.


title: Mycorrhizal fungi stabilize bacterial growth and diversity in water-limited soils

abstract: Drought disrupts soil microbial activity and many biogeochemical processes. Although mycorrhizal fungi are known to impact plant functions and nutrient cycling during drought, their effects on drought-exposed soil microbial communities are not well resolved. We used H218O quantitative stable isotope probing (qSIP) to investigate microbial response to water limitation in the hyphospheres of two distinct mycorrhizal lineages (Rhizophagus irregularis and Serendipita bescii) grown with the bioenergy model grass Panicum hallii. In the absence of mycorrhizal inocula, water limitation resulted in significantly lower bacterial growth rates and lower diversity in the actively growing bacterial community. Water limitation also decoupled growth from CO2 efflux, resulting in a threefold lower growth efficiency. In contrast, both mycorrhizal lineages appeared to protect bacterial communities exposed to water limitation: bacterial growth rates, growth efficiency, and the diversity of the active bacterial community were similar in water-replete and water-limited soils inoculated with either fungus. Several of the bacterial taxa that responded positively to mycorrhizal inocula in water-limited soil belong to lineages that are considered drought-susceptible. Together, these results indicate that mycorrhizal-bacterial interactions can stabilize bacterial communities in water-limited environments. As drought frequency and severity increase, these synergistic relationships may support ecosystem resilience to moisture stress.

category: ecology


title: A molecular dynamic investigation of Human Rhinovirus 3C Protease Drug Target: Insights towards the design of potential Inhibitors

abstract:
The 3C protease is distinguished from most proteases due to the presence of cysteine nucleophile that plays an essential role in viral replication. This peculiar structure encompassed with its role in viral replication has promoted 3C protease as an interesting target for therapeutic agents in the treatment of diseases caused by human rhinovirus (HRV). Herein we present a comprehensive molecular dynamics study of the comparison of two potent inhibitors, sg85 and rupintrivir complexed with HRV-3C protease. The binding free energy studies revealed a higher binding affinity for sg85 -58.853 kcal/mol than for rupintrivir -54.0873 kcal/mol and this was found to be in correlation with the experimental data. The energy decomposition analysis showed that, residues Leu 127, Thr 142, Ser 144, Gly 145, Tyr 146, Cys 147, His 161, Val 162, Gly 163, Gly 164, Asn 165, Phe 170 largely contributed to the binding of sg85, whereas His 40, Leu 127 and Gly 163 impacted the binding of rupintrivir. It further showed that His 40, Glu 71, Leu 127, Cys 147 Gly 163 and Gyl 164 are crucial residues that play a key role in ligand-enzyme binding; amongst these residues are residues of the conserved active site (His 40, Glu 71 and Cys 147). These findings provide a comprehensive understanding of the dynamics and structural features and will serve as guidance in the design and development of potent novel inhibitors of HRV.

Graphical Abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY


title: Characterization of Hydrophobic Interactions of SARS-CoV-2 and MERS-CoV Spike Protein Fusion Peptides Using Single Molecule Force Measurements

abstract:
We address the challenge of understanding how hydrophobic interactions are encoded by fusion peptide sequences within coronavirus (CoV) spike proteins. Within the fusion peptides of SARS-CoV-2 and MERS-CoV, a largely conserved peptide sequence called FP1 (SFIEDLLFNK and SAIEDLLFDK in SARS-2 and MERS, respectively) has been proposed to play a key role in encoding hydrophobic interactions that drive viral-host cell membrane fusion. While a non-polar triad (LLF) is common to both FP1 sequences, and thought to dominate the encoding of hydrophobic interactions, FP1 from SARS and MERS differ in two residues (Phe 2 versus Ala 2 and Asn 9 versus Asp 9, respectively). Here we explore if single molecule force measurements can quantify hydrophobic interactions encoded by FP1 sequences, and then ask if sequence variations between FP1 from SARS and MERS lead to significant differences in hydrophobic interactions. We find that both SARS-2 and MERS wild-type FP1 generate measurable hydrophobic interactions at the single molecule level, but that SARS-2 FP1 encodes a substantially stronger hydrophobic interaction than its MERS counterpart (1.91 {+/-} 0.03 nN versus 0.68 {+/-} 0.03 nN, respectively). By performing force measurements with FP1 sequences with single amino acid substitutions, we determine that a single residue mutation (Phe 2 versus Ala 2) causes the almost threefold difference in the hydrophobic interaction strength generated by the FP1 of SARS-2 versus MERS, despite the presence of LLF in both sequences. Infrared spectroscopy and circular dichroism measurements support the proposal that the outsized influence of Phe 2 versus Ala 2 on the hydrophobic interaction arises from variation in the secondary structure adopted by FP1. Overall, these insights reveal how single residue diversity in viral fusion peptides, including FP1 of SARS-CoV-2 and MERS-CoV, can lead to substantial changes in intermolecular interactions proposed to play a key role in viral fusion, and hint at strategies for regulating hydrophobic interactions of peptides in a range of contexts.

SIGNIFICANCEFusion of coronaviruses (CoVs) and host cells is mediated by the insertion of the fusion peptide (FP) of the viral spike protein into the host cell membrane. Hydrophobic interactions between FPs with their host cell membranes regulate the viral membrane fusion process and are key to determining infection ability. However, it is not fully understood how the amino acid sequences in FPs mediate hydrophobic interactions. We use single-molecule force measurements to characterize hydrophobic interactions of FPs from SARS-CoV-2 and MERS-CoV. Our findings provide insight into the mechanisms by which the amino acid composition of FPs encodes hydrophobic interactions and their implications for fusion activity critical to the spread of infection.