title: Identification of antibiotic resistance proteins via MiCId's augmented workflow. A mass spectrometry-based proteomics approach

abstract: Fast and accurate identifications of pathogenic bacteria along with their associated antibiotic resistance proteins are of paramount importance for patient treatments and public health. While mass spectrometry has become an important, technique for diagnostics of infectious disease, there is a need for mass spectrometry workflows offering this capability. To meet this need, we have augmented the previously published Microorganism Classification and Identification (MiCId) workflow for this capability. To evaluate the performance of the newly augmented MiCId workflow, we have used MS/MS datafiles from samples of 10 antibiotic resistance bacterial strains belonging to three different species: Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa. The evaluation results show that MiCIds workflow has a sensitivity value around 85% (with a lower bound at about 72%) and a precision greater than 95% in the identification of antibiotic resistance proteins. Using MS/MS datasets from samples of two bacterial clonal isolates, one being antibiotic-sensitive while the other (obtained from the same patient at different times) being multidrug-resistant, we applied MiCIds workflow to investigate possible mechanisms of antibiotic resistance in these pathogenic bacteria; the results showed that MiCIds conclusions are in agreement with the published study. Furthermore, we show that MiCIds workflow is fast. It pro-vides microorganismal identifications, protein identifications, sample biomass estimates, and antibiotic resistance protein identifications in 6-17 minutes per MS/MS sample using computing resources that are available in most desktop and laptop computers, making it a highly portable workflow. This study demonstrated that MiCIds workflow is fast, portable, and with high sensitivity and high precision, making it a valuable tool for rapid identifications of bacteria as well as detection of their antibiotic resistance proteins. The new version of MiCId (v.07.01.2021) is freely available for download at https://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads.html.

category: systems biology


title: A general model of the dynamics of genes with dual σ factor preference

abstract: Escherichia coli uses {sigma} factors to quickly control large gene cohorts during stress conditions. While most of its genes respond to a single {sigma} factor, approximately 5% of them have dual {sigma} factor preference. The most common are those responsive to both {sigma}70, which controls housekeeping genes, and {sigma}38, which activates genes during stationary growth and stresses. Using RNA-seq and flow-cytometry measurements, we show that  {sigma}70+38 genes are nearly as upregulated in stationary growth as  {sigma}38 genes. Moreover, we find a clear quantitative relationship between their promoter sequence and their response strength to changes in {sigma}38 levels. We then propose and validate a sequence dependent model of {sigma}70+38 genes, with dual sensitivity to {sigma}38 and {sigma}70, that is applicable in the exponential and stationary growth phases, as well in the transient period in between. We further propose a general model, applicable to other stresses and {sigma} factor combinations. Given this, promoters controlling {sigma}70+38 genes (and variants) could become important building blocks of synthetic circuits with predictable, sequence-dependent sensitivity to transitions between the exponential and stationary growth phases.


title: Sequence-dependent model of genes with dual σ factor preference


title: Multiple trajectory alignment reconstructs disease dynamics for discovery and clinical benefit

abstract: Biological processes are changes occurring concomitantly over time. Therefore, any comparison ignorant of temporal changes is greatly deficient. Even in longitudinal experimental designs, data is usually collected at fixed intervals, whereas process dynamics vary between individuals. We developed TimeAx, which brings time into the equation by building a comparative framework for capturing biological processes dynamics from  omic data. We used TimeAx to study influenza infection dynamics and Urothelial bladder cancer tumorigenesis, discovering molecular mechanisms that drive disease progression as well as promoting clinical symptoms, for short and long term biological processes. Specifically, we detected an "inflection point", where the tumor progresses into an advanced, pro-metastatic state. Overall, we present a powerful framework for studying high resolution temporal dynamics, providing improved molecular interoperability and clinical benefit.


title: Susceptibility monitoring and the molecular characterization of resistance of Spodoptera frugiperda (Lepidoptera: Noctuidae) to lambda-cyhalothrin and chlorpyrifos

abstract: Spodoptera frugiperda (J. E. Smith) is a serious and widespread agricultural pest with several records of resistance to different insecticides and Bt proteins, including the neurotoxic insecticides chlorpyrifos (organophosphate) and lambda-cyhalothrin (pyrethroid). In this study, we (i) characterized and monitored the susceptibility of field populations of S. frugiperda to chlorpyrifos (194 populations) and lambda-cyhalothrin (197 populations) collected from major maize-growing regions of Brazil from 2003 to 2016, and (ii) compared gene expression levels of chlorpyrifos- and lambda-cyhalothrin-resistant strains to a susceptible reference strain (Sf-ss) of S. frugiperda. Laboratory-guided assays to monitor larval susceptibility detected average survival ranging from 29.3% to 36.0% to chlorpyrifos, and 23.1% to 68.0% to lambda-cyhalothrin at diagnostic concentration, based on LC99 of the susceptible reference strain of each insecticide. The resistance ratio of the chlorpyrifos-resistant strain (Clo-rr) was 25.4-fold and of the lambda-cyhalothrin-resistant strain (Lam-rr) was 217-fold. Differential gene expression analyses between resistant vs susceptible strains identified 1,098 differentially expressed genes (DEGs) between Clo-rr and Sf-ss, and 303 DEGs between Lam-rr and Sf-ss. Functional analyses of the DEGs revealed the up-regulation of several detoxification enzymes, mainly cytochrome P450 belonging to the CYP3 and CYP6 clans. Genes associated with regulatory processes, such as the forkhead box O (FoxO) were also up-regulated. Our data points that the resistance mechanisms of Clo-rr and Lam-rr strains of S. frugiperda to chlorpyrifos and lambda-cyhalothrin are mainly mediated by enzyme detoxification.

category: zoology


title: Modulation of hippocampal network oscillation by PICK1-dependent cell surface expression of mGlu3 receptors

abstract: mGlu3 receptors control the sleep/wake architecture which plays a role in the glutamatergic pathophysiology of schizophrenia. Interestingly, mGlu3 receptors expression is decreased in the brain of schizophrenic patients. However, little is known about the molecular mechanisms regulating mGlu3 receptors at the cell membrane. Subcellular receptor localization is strongly dependent on proteinprotein interactions. Here we show that mGlu3 interacts with PICK1 and that their binding is important for receptor surface expression and function. Disruption of their interaction via an mGlu3 C-terminal mimicking peptide or an inhibitor of the PDZ domain of PICK1 altered the functional expression of mGlu3 receptors. Consequently, we investigated whether disruption of the mGlu3-PICK1 interaction affects hippocampal theta oscillations in vitro and in vivo. We found a decreased frequency of theta oscillations in organotypic hippocampal slices, similar to what previously observed in mGlu3 -/- mice. In addition, hippocampal theta power was reduced during REM sleep, NREM sleep and wake states after intra-ventricular administration of the mGlu3 C-terminal mimicking peptide. Targeting the mGlu3-PICK1 complex could thus be relevant to the pathophysiology of schizophrenia.

category: neuroscience


title: Body shape as a visual feature: evidence from spatially-global attentional modulation in human visual cortex

abstract: Feature-based attention modulates visual processing beyond the focus of spatial attention. Previous work has reported such spatially-global effects for low-level features such as color and orientation, as well as for faces. Here, using fMRI, we provide evidence for spatially-global attentional modulation for human bodies. Participants were cued to search for one of six object categories in two vertically-aligned images. Two additional, horizontally-aligned, images were simultaneously presented but were never task-relevant across three experimental sessions. Analyses time-locked to the objects presented in these task-irrelevant images revealed that responses evoked by body silhouettes were modulated by the participants top-down attentional set, becoming more body-selective when participants searched for bodies in the task-relevant images. These effects were observed both in univariate analyses of the body-selective cortex and in multivariate analyses of the object-selective visual cortex. Additional analyses showed that this modulation reflected response gain rather than a bias induced by the cues, and that it reflected enhancement of body responses rather than suppression of non-body responses. These findings provide evidence for a spatially-global attention mechanism for body shapes, supporting the rapid and parallel detection of conspecifics in our environment.


title: The output of interneurons in the primary visual cortex is best reflected by pre-synaptic activity, not somatic activity

abstract: Recent advances in 2-photon calcium-imaging in awake mice have made it possible to study the effect of different behavioural states on cortical circuitry. Many studies assume that somatic activity can be used as a measure for neuronal output. We set out to test the validity of this assumption by comparing somatic activity with the pre-synaptic activity of VIP (Vasoactive intestinal peptide)- and SST (Somatostatin)-positive interneurons in layer 2/3 of the primary visual cortex (V1). We used mice expressing genetically encoded calcium indicators in VIP/SST-interneurons across the whole cell (VIP/SST:GCaMP6f) or confined to pre-synapses (VIP/SST:SyGCaMP5). Mice were exposed to a full-field visual stimulation protocol consisting of 60-second-long presentations of moving Gabor gratings (0.04 cpd, 2 Hz) alternated by 30 seconds of grey screen. During imaging, mice were placed on an air-suspended Styrofoam ball, allowing them to run voluntarily. We compared neural activity during three 4-second time-windows: Before visual stimulation (-4 to 0 sec), during the initial onset (1 to 5 sec) and at the end of the stimulation (56 to 60 sec.). These were further compared while the mice were stationary and while they were voluntarily locomoting. Unlike VIP-somas, VIP-pre-synapses showed strong suppressive responses to the visual stimulus. Furthermore, VIP-somas were positively correlated with locomotion, whereas in VIP-synapses we observed a split between positive and negative correlations. In addition, a similar but weaker distinction was found between SST-somas and pre-synapses. The excitatory effect of locomotion in VIP-somas increased over the course of the visual stimulus but this property was only shared with the positively correlated VIP-pre-synapses. The remaining negatively correlated pre-synapses showed no relation to the overall activity of the Soma. Our results suggest that when making statements about the involvement of interneurons in V1 layer 2/3 circuitry it is crucial to measure from synaptic terminals as well as from somas.


title: Micro-state-based neural decoding of speech categorization using Bayesian non-parametrics

abstract: Understanding the many-to-many mapping between patterns of functional brain connectivity and discrete behavioral responses is critical for speech-language processing. We present a microstate-based analysis of EEG recordings to characterize spatio-temporal dynamics of neural activities that underly rapid speech categorization decisions. We implemented a data driven approach using Bayesian non-parametrics to capture the mapping between EEG and the speed of listeners phoneme identification [i.e., response time (RT)] during speech labeling tasks. Based on our empirical analyses, we show task-relevant events such as resting-state, stimulus coding, auditory-perceptual object (category) formation, and response selection can be explained using patterns of micro-state dwell-time and are decodable as unique time segments during speech perception. State-dependent activities localize to a fronto-temporo-parietal circuit (superior temporal, supramarginal, inferior frontal gyri) exposing a core decision brain network (DN) underlying rapid speech categorization. Furthermore, RTs were inversely proportional to the frequency of state transitions, such that the rate of change between brain microstates was higher for trials with slower compared to faster RTs. Our findings imply that during rapid speech perception, higher uncertainty producing prolonged RTs (slower decision-making) is associated with staying in the DN longer compared lower RTs (faster decisions). We also show that listeners perceptual RTs are highly sensitive to individual differences. Our computational method opens a new avenue in segmentation and dynamic brain connectivity for modeling neuroimaging data and understanding task-related cognitive events.


title: Affinity Scores: An Individual-centric Fingerprinting Framework for Neuropsychiatric Disorders

abstract:
BackgroundPopulation-centric frameworks of biomarker identification for psychiatric disorders focus primarily on comparing averages between groups and assume that diagnostic groups are (1) mutually-exclusive, and (2) homogeneous. There is a paucity of individual-centric approaches capable of identifying individual-specific  fingerprints across multiple domains. To address this, we propose a novel framework, combining a range of biopsychosocial markers, including brain structure, cognition, and clinical markers, into higher-level  fingerprints, capable of capturing intra-illness heterogeneity and inter-illness overlap.

MethodsA multivariate framework was implemented to identify individualised patterns of brain structure, cognition and clinical markers based on affinity to other participants in the database. First, individual-level affinity scores defined each participants "neighbourhood" across each measure based on variable-specific hop sizes. Next, diagnostic verification and classification algorithms were implemented based on multivariate affinity score profiles. To perform affinity-based classification, data were divided into training and test samples, and 5-fold nested cross-validation was performed on the training data. Affinity-based classification was compared to weighted K-nearest neighbours (KNN) classification. K-means clustering was used to create clusters based on multivariate affinity score profiles. The framework was applied to the Australian Schizophrenia Research Bank (ASRB) dataset.

ResultsIndividualised affinity scores provided a  fingerprint of brain structure, cognition, and clinical markers, which described the affinity of an individual to the representative groups in the dataset Diagnostic verification capability was moderate to high depending on the choice of multivariate affinity metric. Affinity score-based classification achieved a high degree of accuracy in the training, nested cross-validation and prediction steps, and outperformed KNN classification in the training and test datasets.

ConclusionAffinity scores demonstrate utility in two keys ways: (1) Early and accurate diagnosis of neuropsychiatric disorders, whereby an individual can be grouped within a diagnostic category/ies that best matches their fingerprint, and (2) identification of biopsychosocial factors that most strongly characterise individuals/disorders, and which may be most amenable to intervention.


title: Stimulus-induced narrow-band gamma oscillations in humans can be recorded using open-hardware low-cost EEG amplifier

abstract: Stimulus-induced narrow-band gamma oscillations (30-70 Hz) in human electro - encephalograph (EEG) have been linked to attentional and memory mechanisms and are abnormal in mental health conditions such as autism, schizophrenia and Alzheimers Disease. This suggests that gamma oscillations could be valuable both as a research tool and an inexpensive, non-invasive biomarker for disease evaluation. However, since the absolute power in EEG decreases rapidly with increasing frequency following a "1/f" power law, and the gamma band includes line noise frequency, these oscillations are highly susceptible to instrument noise. Previous studies that recorded stimulus-induced gamma oscillations used expensive research-grade EEG amplifiers to address this issue. While low-cost EEG amplifiers have become popular in Brain Computer Interface applications that mainly rely on low-frequency oscillations (< 30 Hz) or steady-state-visually-evoked-potentials, whether they can also be used to measure stimulus-induced gamma oscillations is unknown. We recorded EEG signals using a low-cost, open-source amplifier (OpenBCI) and a traditional, research-grade amplifier (Brain Products GmbH) in male (N = 6) and female (N = 5) subjects (22-29 years) while they viewed full-screen static gratings that are known to induce gamma oscillations. OpenBCI recordings showed gamma response in almost all the subjects who showed a gamma response in Brain Products recordings, and the spectral and temporal profiles of these responses in alpha (8-13 Hz) and gamma bands were highly correlated between OpenBCI and Brain Products recordings. These results suggest that low-cost amplifiers can potentially be used in stimulus induced gamma response detection, making its research, and application in medicine more accessible.


title: Integrative Omics Analysis Reveals the Immunomodulatory Effects of the Parasitic Dinoflagellate Hematodinium on Crustacean Immunity

abstract:
Parasitic dinoflagellates in genus Hematodinium have caused substantial economic losses to multiple commercially valuable marine crustaceans around the world. In the present study, comprehensive omics approaches (miRNA transcriptomics, iTRAQ-based proteomics) were applied to investigate the host-parasite interaction between hemocytes from Portunus trituberculatus and Hematodinium perezi. The parasitic dinoflagellate remodeled the miRNome and proteome of hemocytes from challenged hosts, modulated the host immune response at both post-transcriptional and translational levels and caused post-transcriptional regulation to the host immune response. Multiple important cellular and humoral immune-related pathways (ex. Apoptosis, Endocytosis, ECM-receptor interaction, proPO activation pathway, Toll- like signaling pathway, Jak-STAT signaling pathway) were significantly affected by Hematodinium parasites. Through modulation of the host miRNome, the host immune responses of nodulation, proPO activation and antimicrobial peptides were significantly suppressed. Cellular homeostasis was imbalanced via post-transcriptional dysregulation of the phagosome, peroxisome, and lysosome pathways. Cellular structure and communication was seriously impacted by post-transcriptional downregulation of ECM-receptor interaction and focal adhesion pathways.

Author summaryThe parasitic dinoflagellate Hematodinium infects many economically important marine crustaceans. Recent efforts to better understand the life cycle and biology of the parasite have improved our understanding of the disease ecology. However, studies on the host-parasite interaction, especially how Hematodinium parasites evade the host immune response are lacking. To address this shortfall, we used miRNA transcriptomics and iTRAQ-based proteomic approaches to explore the immune responses of Portunus trituberculatus when challenged with Hematodinium perezi. Striking changes in the miRNome and proteome of hemocytes were observed, and the parasite exhibited multifaceted immunomodulatory effects and potential immune-evasion mechanisms in this crustacean host.

category: immunology


title: Nanoviricides platform technology based NV-CoV-2 polymer increases the half-life of Remdesivir in vivo

abstract:
So far, there are seven coronaviruses identified that infect humans and only 4 of them belong to the beta family of coronavirus (HCoV-HKU1, SARS-CoV-2, MERS-CoV and SARS-CoV). SARS family are known to cause severe respiratory disease in humans. In fact, SARS-CoV-2 infection caused a pandemic COVID-19 disease with high morbidity and mortality. Remdesivir (RDV) is the only antiviral drug so far approved for COVID-19 therapy by the FDA. However, the efficacy of RDV in vivo is limited due to its low stability in presence of plasma. This is the report of analysis of the non-clinical pharmacology study of NV-CoV-2 (Polymer) and NV-CoV-2-R (Polymer encapsulated Remdesivir) in both infected and uninfected rats with SARS-CoV-2.

Detection and quantification of NV-CoV-2-R in plasma samples was done by MS-HPLC chromatography analyses of precipitated plasma samples from rat subjects.

O_LINV-CoV-2-R show RDV peak in MS-HPLC chromatography, whereas only NV-CoV-2 does not show any RDV-Peak, as expected.
C_LIO_LINV-CoV-2 polymer encapsulation protects RDV in vivo from plasma-mediated catabolism.
C_LIO_LIBody weight measurements of the normal (uninfected) rats after administration of the test materials (NV-CoV-2, and NV-CoV-2-R) show no toxic effects on them.
C_LI

Our platform technology based NV-387-encapsulated-RDV (NV-CoV-2-R) drug has a dual effect on coronaviruses. First, NV-CoV-2 itself as an antiviral regimen. Secondly, RDV is protected from plasma-mediated degradation in transit, rendering altogether the safest and an efficient regimen against COVID-19.

category: pharmacology and toxicology


title: Suppressed prefrontal neuronal firing variability and impaired social representation in IRSp53-mutant mice

abstract: Social deficit is a major feature of neuropsychiatric disorders, including autism spectrum disorders, schizophrenia, and attention-deficit/hyperactivity disorder, but its neural mechanisms remain unclear. Here, we examined neuronal discharge characteristics in the medial prefrontal cortex (mPFC) of IRSp53-mutant mice, which show social deficits, during social approach. IRSp53-mutant excitatory mPFC neurons displayed an increase in baseline neuronal firing and decreases in variability and dynamic range of firing rates and burst firing during social and non-social target approaches compared to wild-type controls. As a consequence, their firing activity was less differential between social and non-social targets. In addition, there was a decrease in the proportion of excitatory mPFC neurons encoding social information but not that of those encoding non-social information. These results suggest that insufficient neuronal activity dynamics may underlie impaired cortical encoding of social information and social behaviors in IRSp53-mutant mice.


title: Proteomic analysis of liver tissue reveals Aeromonas hydrophila infection mediated modulation of host metabolic pathways in Labeo rohita

abstract:
Aeromonas hydrophila (Ah) is an opportunistic Gram-negative bacterium and a serious global pathogen causing Motile Aeromonas Septicaemia (MAS) in fish and many other vertebrates. The pathogenesis of aeromonas septicaemia is complex and involves multiple perturbed pathways. Molecular analysis of host tissues could be a powerful approach to identify mechanistic and diagnostic immune signatures of disease. We performed a deep proteomic analysis of Labeo rohita liver tissue to examine changes in the host proteome during Ah infection. A total of 2525 proteins were identified of which 158 were found differentially expressed during Ah infection. Functional analysis of significant proteins identified the dysregulation of several metabolic enzymes, antioxidative proteins, cytoskeletal proteins and immune related proteins. Proteomic analysis revealed the alterations in the cellular defence mechanisms including phagolysosomal killing and apoptosis during Ah infection. Our systemic approach revealed the protein dynamics in the host cells to explore the putative biological processes underlying the metabolic reprogramming of the host cells during Ah infection. Our findings paved the way for future research into the role of Toll-like receptors (Tlr3), C-type lectins (Clec4e) and metabolic enzymes in Ah pathogenesis leading towards host directed immunotherapies to tackle the Ah infection in fish.

IMPORTANCEBacterial disease is one of the most serious problems in aquaculture industry. Aeromonas hydrophila (Ah), a Gram-negative bacterium causes motile aeromonas septicaemia (MAS) in fish. Small molecules that target the metabolism of the host have recently emerged as potential treatment possibilities in infectious diseases. However, the ability to develop new therapies is hampered due to lack of knowledge about pathogenesis mechanisms and host-pathogen interactions. Molecular level analysis of host tissues could be helpful in finding mechanistic immunological markers of diseases. We examined alterations in the host proteome during Ah infection in Labeo rohita liver tissue to find cellular proteins and processes affected by Ah infection. Our systemic approach revealed protein dynamics underlying the host cells metabolic reprogramming during Ah infection. Our work is an important step towards leveraging host metabolism in targeting the disease by providing a bigger picture on proteome pathology correlation during Ah infection.


title: Sharing individualised template MRI data for MEG source reconstruction: a solution for open data while keeping subject confidentiality

abstract:
The increasing requirements for adoption of FAIR data management and sharing original research data from neuroimaging studies can be at odds with protecting the anonymity of the research participants due to the person-identifiable anatomical features in the data. We propose a solution to this dilemma for anatomical MRIs used in MEG source analysis. In MEG analysis, the channel-level data is reconstructed to the source-level using models derived from anatomical MRIs. Sharing data, therefore, requires sharing the anatomical MRI to replicate the analysis. The suggested solution is to replace the individual anatomical MRIs with individualised warped templates that can be used to carry out the MEG source analysis and that provide sufficient geometrical similarity to the original participants MRIs.

First, we demonstrate how the individualised template warping can be implemented with one of the leading open-source neuroimaging analysis toolboxes. Second, we compare results from four different MEG source reconstruction methods performed with an individualised warped template to those using the participants original MRI. While the source reconstruction results are not numerically identical, there is a high similarity between the results for single dipole fits, dynamic imaging of coherent sources beamforming, and atlas-based virtual channel beamforming. There is a moderate similarity between minimum-norm estimates, as anticipated due to this method being anatomically constrained and dependent on the exact morphological features of the cortical sheet.

We also compared the morphological features of the warped template to those of the original MRI. These showed a high similarity in grey matter volume and surface area, but a low similarity in the average cortical thickness and the mean folding index within cortical parcels.

Taken together, this demonstrates that the results obtained by MEG source reconstruction can be preserved with the warped templates, whereas the anatomical and morphological fingerprint is sufficiently altered to protect the anonymity of research participants. In cases where participants consent to sharing anatomical MRI data, it remains preferable to share the original defaced data with an appropriate data use agreement. In cases where participants did not consent to share their MRIs, the individualised warped MRI template offers a good compromise in sharing data for reuse while retaining anonymity for those research participants.


title: Awake ripples enhance emotional memory encoding in the human brain

abstract: Intracranial recordings from the human amygdala and the hippocampus during an emotional memory encoding and discrimination task reveal increased awake sharp-wave/ripples (aSWR) after encoding of emotional compared to neutral stimuli. Further, post-encoding aSWR-locked memory reinstatement in the amygdala and the hippocampus was predictive of later memory discrimination. These findings provide electrophysiological evidence that post-encoding aSWRs enhance memory for emotional events.


title: Hidden temporal structure of the ongoing task impacts detection strategy and is reflected in pupillary dynamics

abstract: Estimating temporal regularities in incoming sensory inputs supports optimal decisions in noisy environments. In particular, inferred temporal structure can ease the detection of likely target events. Here we postulated that timely urgency signals can adapt subjects decision-making to the ongoing task temporal structure, possibly through neuromodulatory tone. To test this hypothesis, we used an auditory change detection task in which targets followed a block-based temporal contingency, unbeknownst to participants. False alarm occurrences were driven by the distribution of target timings, indicating that participants adapted their behavior to the ongoing temporal structure. Task-evoked pupillary responses were larger for blocks with earliest target timings, and correlated with individual subjects behavioral adaptation. Individual pupil responses matched an urgency signal extracted from a decision model fitted to behavior. This work demonstrates that internal temporal expectation can be tracked through pupillary dynamics, suggesting a role of neuromodulatory systems in context-dependent modulation of decision variable dynamics.


title: Analysis of the computational strategy of a detailed laminar cortical microcircuit model for solving the image-change-detection task

abstract: The neocortex can be viewed as a tapestry consisting of variations of rather stereotypical local cortical microcircuits. Hence understanding how these microcircuits compute holds the key to understanding brain function. Intense research efforts over several decades have culminated in a detailed model of a generic cortical microcircuit in the primary visual cortex from the Allen Institute. We are presenting here methods and first results for understanding computational properties of this largescale data-based model. We show that it can solve a standard image-change-detection task almost as well as the living brain. Furthermore, we unravel the computational strategy of the model and elucidate the computational role of diverse subtypes of neurons. Altogether this work demonstrates the feasibility and scientific potential of a methodology based on close interaction of detailed data and large-scale computer modelling for understanding brain function.


title: Not so fast: Limited validity of deep convolutional neural networks as in silico models for human naturalistic face processing

abstract: Deep convolutional neural networks (DCNNs) trained for face identification can rival and even exceed human-level performance. The relationships between internal representations learned by DCNNs and those of the primate face processing system are not well understood, especially in naturalistic settings. We developed the largest naturalistic dynamic face stimulus set in human neuroimaging research (700+ naturalistic video clips of unfamiliar faces) to investigate this problem. DCNN representational geometries were weakly but significantly correlated with neural response geometries across the human face processing system. Intermediate layers better matched visual, face-selective cortices, and behavioral similarity judgments than the final fully-connected layers. Our results showed DCNNs captured only a small amount of the rich information in the neural representations during naturalistic face viewing. Future artificial neural networks trained with more ecological objective functions may help advance artificial intelligence toward the ultimate goal of mimicking human intelligence in naturalistic, real-world scenarios.


title: Modeling naturalistic face processing in humans with deep convolutional neural networks


title: Anatomical connectivity along the anterior-posterior axis of the human hippocampus: new insights using quantitative fibre-tracking.

abstract: The hippocampus supports multiple cognitive functions including episodic memory. Recent work has highlighted functional differences along the anterior-posterior axis of the human hippocampus but the neuroanatomical underpinnings of these differences remain unclear. We leveraged track-density imaging to systematically examine anatomical connectivity between the cortical mantle and the anterior-posterior axis of the in-vivo human hippocampus. We first identified the most highly connected cortical areas and detailed the degree to which they preferentially connect along the anterior-posterior axis of the hippocampus. Then, using a tractography pipeline specifically tailored to measure the location and density of streamline endpoints within the hippocampus, we characterised where, within the hippocampus, these cortical areas preferentially connect. Our results were striking in showing that different parts of the hippocampus preferentially connect with distinct cortical areas. Furthermore, we provide evidence that both gradients and circumscribed areas of dense extrinsic anatomical connectivity exist within the human hippocampus. These findings inform conceptual debates in the field by unveiling how specific regions along the anterior-posterior axis of the hippocampus are associated with different cortical inputs/outputs. Overall, our results represent a major advance in our ability to map the anatomical connectivity of the human hippocampus in-vivo and inform our understanding of the neural architecture of hippocampal dependent memory systems in the human brain. This detailed characterization of how specific portions of the hippocampus anatomically connect with cortical brain regions may promote a better understanding of its role in cognition and we emphasize the importance of considering the hippocampus as a heterogeneous structure.


title: Impaired oligodendrocyte maturation is an early feature in SCA3 disease pathogenesis

abstract:
Spinocerebellar ataxia type 3 (SCA3), the most common dominantly inherited ataxia, is a polyglutamine neurodegenerative disease for which there is no disease-modifying therapy. The polyglutamine-encoding CAG repeat expansion in the ATXN3 gene results in expression of a mutant form of the ATXN3 protein, a deubiquitinase that causes selective neurodegeneration despite being widely expressed. The mechanisms driving neurodegeneration in SCA3 are unclear. Research to date, however, has focused almost exclusively on neurons. Here, using equal male and female age-matched transgenic mice expressing full-length human mutant ATXN3, we identified early and robust transcriptional changes in selectively vulnerable brain regions that implicate oligodendrocytes in disease pathogenesis. We mapped transcriptional changes across early, mid, and late stages of disease in two selectively vulnerable brain regions, the cerebellum and brainstem. The most significant disease-associated module through weighted gene co-expression network analysis revealed dysfunction in SCA3 oligodendrocyte maturation. These results reflect a toxic gain of function mechanism, as ATXN3 knockout mice do not exhibit any impairments in oligodendrocyte maturation. Genetic crosses to reporter mice revealed a marked reduction in mature oligodendrocytes in SCA3-disease vulnerable brain regions and ultrastructural microscopy confirmed abnormalities in axonal myelination. Further study of isolated oligodendrocyte precursor cells from SCA3 mice established that this impairment in oligodendrocyte maturation is a cell autonomous process. We conclude that SCA3 is not simply a disease of neurons and the search for therapeutic strategies and disease biomarkers will need to account for non-neuronal involvement in SCA3 pathogenesis.

SIGNIFICANCE STATEMENTDespite advances in SCA3 disease understanding, much remains unknown about how the disease gene causes brain dysfunction ultimately leading to cell death. We completed a longitudinal transcriptomic analysis of vulnerable brain regions in SCA3 mice to define the earliest and most robust changes across disease progression. Through gene network analyses followed up with biochemical and histological studies in SCA3 mice, we provide evidence for severe dysfunction in oligodendrocyte maturation early in SCA3 pathogenesis. Our results advance understanding of SCA3 disease mechanisms, identify additional routes for therapeutic intervention, and may provide broader insight into polyglutamine diseases beyond SCA3.


title: Broadly-neutralizing antibodies that bind to the influenza hemagglutinin stalk domain enhance the effectiveness of neuraminidase inhibitors via Fc-mediated effector functions

abstract: The conserved hemagglutinin stalk domain is an attractive target for broadly effective antibody-based therapeutics and next generation universal influenza vaccines. Protection provided by hemagglutinin stalk binding antibodies is principally mediated through activation of immune effector cells. Titers of stalk-binding antibodies are highly variable on an individual level, and tend to increase with age as a result of increasing exposures to influenza virus. In our study, we show that stalk-binding antibodies cooperate with neuraminidase inhibitors to protect against influenza virus infection in an Fc-dependent manner. These data suggest that the effectiveness of neuraminidase inhibitors is likely influenced by an individuals titers of stalk-binding antibodies, and that neuraminidase inhibitors may enhance the effectiveness of future stalk-binding monoclonal antibody-based treatments.


title: Evaluating the contribution of aestivation to the persistence of malaria mosquitoes through the Sahelian dry season using stable isotopes

abstract:
Data suggests the malaria vector Anopheles coluzzii persists in the Sahel by dry-season aestivation though evidence is scant. We have marked Anopheles mosquitoes using deuterium (2H) to assess the contribution of aestivation to persistence of mosquitoes through the seven-month dry season. If local aestivation is the only way A. coluzzii persists, the frequency of marked mosquitoes should remain stable throughout, whereas finding no marked mosquitoes would be evidence against aestivation. Larval sites were spiked with 2H at the end of the 2017 wet season in two Sahelian villages in Mali. We monitored 2H-enriched populations until the onset of rains. By the end of the enrichment period, 33% of A. coluzzii mosquitoes were clearly marked. Expectedly, 2H levels in marked mosquitoes degraded over time, resulting in a partial overlap of the marked and non-marked 2H distributions. We utilized three methods to estimate the fraction of marked mosquitoes in the population. Seven months after enrichment, 7% of the population had 2H values above the highest pre-enrichment value. An excess of 21% exceeded the 3rd quartile of the pre-enrichment population. A finite mixed population model showed 2.5% represented a subpopulation of marked mosquitoes with elevated 2H, compatible with our predictions. We provide evidence that aestivation is a major persistence mechanism of A. coluzzii in the Sahel, contributing at least 20% of the adults at the onset of rains, suggesting A. coluzzii utilizes multiple persistence strategies enabling its populations rapid buildup, facilitating subsequent malaria resurgence. These may complicate vector control and malaria elimination campaigns.

Significance statementHere we estimated the contribution of aestivation to the persistence of mosquitoes through the seven-month long dry season, by marking a known fraction of the adult population through larval site 2H-spiking by the end of the wet season and assessing the change in this fraction through the dry season, until after the onset of the first rain of the subsequent wet season. In a mark-release-recapture study using stable isotopes, we provide compelling evidence that the primary Sahelian malaria vector Anopheles coluzzii aestivates on a population-scale, contributing at least 20% of the adults which reestablish the population of the subsequent wet season. The capacity to use multiple strategies of persistence in time and space might complicate vector control and elimination campaigns.

category: ecology


title: scCODE: an R package for personalized differentially expressed gene detection on single-cell RNA-sequencing data

abstract: Differential expression (DE) gene detection in single-cell RNA-seq (scRNA-seq) data is a key step to understand the biological question investigated. We find that DE methods together with gene filtering have profound impact on DE gene identification, and different datasets will benefit from personalized DE gene detection strategies. Existing tools dont take gene filtering into consideration, and couldnt evaluate DE performance on real datasets without prior knowledge of true results. Based on two new metrics, we propose scCODE (single cell Consensus Optimization of Differentially Expressed gene detection), an R package to automatically optimize DE gene detection for each experimental scRNA-seq dataset.

category: bioinformatics


title: VIVID: a web application for variant interpretation and visualisation in multidimensional analyses

abstract: Large-scale comparative genomics- and population genetic studies generate enormous amounts of polymorphism data in the form of DNA variants. Ultimately, the goal of many of these studies is to associate genetic variants to phenotypes or fitness. We introduce VIVID, an interactive, user-friendly web application that integrates a wide range of approaches for encoding genotypic to phenotypic information in any organism or disease, from an individual or population, in three-dimensional (3D) space. It allows mutation mapping and annotation, calculation of interactions and conservation scores, prediction of harmful effects, analysis of diversity and selection, and 3-dimensional (3D) visualisation of genotypic information encoded in Variant Call Format (VCF) on AlphaFold2 protein models. VIVID enables the rapid assessment of genes of interest in the study of adaptive evolution and the genetic load, and it helps prioritising targets for experimental validation. We demonstrate the utility of VIVID by exploring the evolutionary genetics of the parasitic protist Plasmodium falciparum, revealing geographic variation in the signature of balancing selection in potential targets of functional antibodies.


title: Mechanistic insights into global suppressors of protein folding defects

abstract:
BackgroundMost amino acid substitutions in a protein either lead to partial loss of function or are near neutral. Several studies have shown the existence of second-site mutations that can rescue defects caused by diverse loss of function mutations. Such global suppressor mutations are key drivers of protein evolution. However, the mechanisms responsible for such suppression remain poorly understood.

ResultsTo address this, we characterized multiple suppressor mutations both in isolation and in combination with inactive mutants. We examined five global suppressors of the bacterial toxin CcdB, the known M182T global suppressor of TEM-1 {beta}-lactamase, the N239Y global suppressor of p53-DBD and three suppressors of the SARS-CoV-2 spike Receptor Binding Domain. We observed that the suppressors were able to significantly enhance the thermodynamic stability parameters (Tm and Cm) of multiple inactive mutants. Stabilisation enhancement by the suppressor was much higher when present in the background of the inactive mutants than in the wild type (WT) background. We also observe that the inactive mutants showed higher unfolding and lower refolding rates relative to the WT, the suppressors alone and the inactive mutant-suppressor pairs. From in vitro binding studies, we concluded that in the background of the suppressors, the formerly inactive CcdB mutants now showed improved binding to GyrA14 for both native and refolded proteins. An estimation of the in vitro aggregation propensities of the mutants measured from thermal stress studies showed that the inactive mutants in the background of the suppressors had enhanced thermal tolerance relative to the inactive mutants alone. In the case of CcdB, where novel suppressors were isolated, we determined the crystal structures of three such suppressors to obtain insight into the specific molecular interactions responsible for the observed effects.

ConclusionsOur study demonstrates that global suppressors both alone, and in conjunction with inactive mutants, stabilise the protein both thermodynamically and kinetically in-vitro, predominantly through acceleration of the refolding rate parameters. When coupled to inactive mutants they promote increased in-vivo solubilities as well as regain-of-function phenotypes. While most individual suppressors result in small stability enhancements relative to wildtype, which can be combined to yield significant stability increases, thermodynamic stabilisation is neither necessary nor sufficient for suppressor action.

category: biophysics


title: Adhesion strength between cells regulate non-monotonic growth by a biomechanical feedback mechanism

abstract: We probe the interplay between intercellular interactions and pressure fluctuations associated with single cells in regulating cell proliferation using simulations of a minimal model for three-dimensional multicellular spheroid (MCS) growth. The emergent spatial variations in the cell division rate, that depends on the location of the cells within the MCS, is regulated by intercellular adhesion strength (fad). This in turn results in non-monotonic proliferation of cells in the MCS with varying adhesion strength, which accords well with experimental results. A biomechanical feedback mechanism coupling the fad and cell-dependent pressure fluctuations relative to a threshold value (pc) determines the onset of a dormant phase, and explains the non-monotonic proliferation response. Increasing fad from low values enhances cell proliferation because pressure on individual cells is smaller compared to pc. In contrast, at high fad, cells readily become dormant and cannot rearrange effectively, leading to arrested cell proliferation. Our work, which shows that proliferation is regulated by pressure-adhesion feedback loop, may be a general feature of tumor growth.


title: In silico drug discovery strategies identified ADMET properties of decoquinate RMB041 and its potential drug targets against Mycobacterium Tuberculosis

abstract: The highly adaptive cellular response of Mycobacterium tuberculosis to various antibiotics and the high costs for clinical trials, hampers the development of novel antimicrobial agents with improved efficacy and safety. Subsequently, in silico drug screening methods are more commonly being used for the discovery and development of drugs, and have been proven useful for predicting the pharmacokinetics, toxicities, and targets, of prospective new antimicrobial agents. In this investigation we used a reversed target fishing approach to determine potential hit targets and their possible interactions between M. tuberculosis and decoquinate RMB041, a propitious new antituberculosis compound. Two of the thirteen identified targets, Cyp130 and BlaI, were strongly proposed as optimal drug-targets for dormant M. tuberculosis, of which the first showed the highest comparative binding affinity to decoquinate RMB041. The metabolic pathways associated to the selected target proteins were compared to previously published molecular mechanisms of decoquinate RMB041 against M. tuberculosis, whereby we confirmed disrupted metabolism of proteins, cell wall components, and DNA. We also described the steps within these pathways that are inhibited and elaborated on decoquinate RMB041s activity against dormant M. tuberculosis. This compound has previously showed promising in vitro safety and good oral bioavailability, which were both supported by this in silico study. The pharmacokinetic properties and toxicity of this compound were predicted and investigated using the online tools pkCSM and SwissADME, and Discovery Studio software, which furthermore supports previous safety and bioavailability characteristics of decoquinate RMB041 for use as an antimycobacterial medication.


title: Prostaglandin PGE2 receptor EP4 regulates microglial phagocytosis and increases susceptibility to diet-induced obesity

abstract:
BackgroundIn rodents, susceptibility to diet-induced obesity requires microglial activation, but the molecular components of this pathway remain incompletely defined. Prostaglandin E2 (PGE2) levels increase in the mediobasal hypothalamus during high fat diet (HFD) feeding, and the PGE2 receptor EP4 regulates microglial activation state and phagocytic activity, suggesting a potential role for microglial EP4 signaling in obesity pathogenesis.

MethodMetabolic phenotyping, as assessed by body weight, energy expenditure, glucose, and insulin tolerance, was performed in microglia-specific EP4 knockout (MG-EP4 KO) mice and littermate controls on HFD. Morphological and gene expression analysis of microglia, and a histological survey of microglia-neuron interactions in the arcuate nucleus was performed. Phagocytosis was assessed using in vivo and in vitro pharmacological techniques.

ResultsMicroglial EP4 deletion markedly reduced weight gain and food intake in response to HFD feeding. In correspondence with this lean phenotype, insulin sensitivity was also improved in the HFD-fed MG-EP4 KO mice though glucose tolerance remained surprisingly unaffected. Mechanistically, EP4-deficient microglia showed an attenuated phagocytic state marked by reduced CD68 expression and fewer contacts with POMC neuron soma and processes. These cellular changes observed in the microglial EP4 knockout mice corresponded with an increased density of POMC neurites extending into the paraventricular nucleus.

ConclusionThese findings reveal that microglial EP4 signaling promotes body weight gain and insulin resistance during HFD feeding. Furthermore, the data suggest that curbing microglial phagocytic function may preserve POMC cytoarchitecture and PVN input to limit overconsumption during diet-induced obesity.

category: physiology


title: The evidence for anthocyanins in the betalain-pigmented genus Hylocereus is weak

abstract: Here we respond to Zhou et al., 2020 "Combined Transcriptome and Metabolome analysis of Pitaya fruit unveiled the mechanisms underlying Peel and pulp color formation" published in BMC Genomics. Given the evolutionary conserved anthocyanin biosynthesis pathway in betalain-pigmented species, we are open to the idea that species with both anthocyanins and betalains might exist. However, in absence of LC-MS/MS spectra, apparent lack of biological replicates, and no comparison to authentic standards, the findings of Zhou et al., 2020 are not a strong basis to propose the presence of anthocyanins in betalain-pigmented pitaya. In addition, our re-analysis of the datasets indicates the misidentification of important genes and the omission of key anthocyanin synthesis genes ANS and DFR. Finally, our re-analysis of the RNA-Seq dataset reveals no correlation between anthocyanin biosynthesis gene expression and pigment status.

category: plant biology


title: Towards a catalog of pome tree architecture genes: the draft 'd'Anjou' genome (Pyrus communis L.)

abstract: The rapid development of sequencing technologies has led to a deeper understanding of horticultural plant genomes. However, experimental evidence connecting genes to important agronomic traits is still lacking in most non-model organisms. For instance, the genetic mechanisms underlying plant architecture are poorly understood in pome fruit trees, creating a major hurdle in developing new cultivars with desirable architecture, such as dwarfing rootstocks in European pear (Pyrus communis). Further, the quality and content of genomes vary widely. Therefore, it can be challenging to curate a list of genes with high-confidence gene models across reference genomes. This is often an important first step towards identifying key genetic factors for important traits. Here we present a draft genome of P. communis  dAnjou and an improved assembly of the latest P. communis  Bartlett genome. To study gene families involved in tree architecture in European pear and other rosaceous species, we developed a workflow using a collection of bioinformatic tools towards curation of gene families of interest across genomes. This lays the groundwork for future functional studies in pear tree architecture. Importantly, our workflow can be easily adopted for other plant genomes and gene families of interest.


title: Trajectory of rich club properties in structural brain networks

abstract: Many organizational principles of structural brain networks are established before birth and undergo considerable developmental changes afterwards. These include the topologically central hub regions and a densely connected rich club. While several studies have mapped developmental trajectories of brain connectivity and brain network organization across childhood and adolescence, comparatively little is known about subsequent development over the course of the lifespan. Here, we present a cross-sectional analysis of structural brain network development in N = 8,066 participants aged 5 to 80 years. Across all brain regions, structural connectivity strength followed an  inverted-U-shaped trajectory with vertex in the early 30s. Connectivity strength of hub regions showed a similar trajectory and the identity of hub regions remained stable across all age groups. While connectivity strength declined with advancing age, the organization of hub regions into a rich club did not only remain intact but became more pronounced, presumingly through a selected sparing of relevant connections from age-related connectivity loss. The stability of rich club organization in the face of overall age-related decline is consistent with a "first come, last served" model of neurodevelopment, where the first principles to develop are the last to decline with age. Rich club organization has been shown to be highly beneficial for communicability and higher cognition. A resilient rich club might thus be protective of a functional loss in late adulthood and represent a neural reserve to sustain cognitive functioning in the aging brain.


title: kTMP: A New Non-invasive Magnetic Induction Method to Modulate Cortical Excitability.

abstract: We report a novel subthreshold non-invasive brain stimulation approach that we refer to as kilohertz transcranial magnetic perturbation, or kTMP. kTMP is a magnetic induction method that delivers kHz-frequency cortical E-fields and, through amplitude modulation of the kHz carrier frequency, may mimic E-fields at physiological frequencies. To evaluate the efficacy of kTMP, we used suprathreshold TMS to elicit motor-evoked potentials (MEP) in a peripheral muscle, comparing the amplitude of the MEPs before and after kTMP stimulation. In Experiment 1, we used non-modulated kTMP with an E-field amplitude of 2 V/m over motor cortex. Ten minutes of kTMP stimulation resulted in an increase in cortical excitability in a frequency-specific manner. We replicated this effect in Experiment 2 and found that amplitude-modulation at 20 Hz produced an additional boost in cortical excitability. The only percept associated with kTMP is a faint auditory tone, making kTMP ideal for double-blind experimentation.


title: The influence of somatosensory and auditory evoked potentials on concurrent transcranial-magnetic stimulation electroencephalography recordings

abstract:
BackgroundTranscranial magnetic stimulation (TMS) evoked potentials (TEPs) can be used to index cortical excitability. However, it remains unclear to what extent TEPs reflect somatosensory and auditory-evoked potentials which arise from the scalp sensation and click of the TMS coil, as opposed to transcranial stimulation of cortical circuits.

ObjectivesThe present study had two aims; a) to determine the extent to which sensory potentials contaminate TEPs using a spatially matched sham condition, and b) to determine whether sensory potentials reflect auditory or somatosensory potentials alone, or a combination of the two.

MethodsTwenty healthy participants received active or sham stimulation, with the latter consisting of the click of a sham coil combined with scalp electrical stimulation. Earplugs/headphones were used to suppress the TMS click noise. Two additional control conditions i) electrical stimulation alone and ii) auditory stimulation alone were included in a subset of 13 participants.

ResultsSignals from active and sham stimulation were correlated in spatial and temporal domains, especially >70ms post-stimulation. Relative to auditory or electrical stimulation alone, combined (sham) stimulation resulted in a) larger evoked responses b) stronger correlations with active stimulation and c) a signal that could not be explained by the linear sum of electrical and auditory stimulation alone.

ConclusionsSensory potentials can confound data interpretations of TEPs at timepoints >70ms post-TMS, while earlier timepoints appear reflective of cortical excitability. Furthermore, contamination of TEPs cannot be explained by auditory or somatosensory potentials alone, but instead reflects a non-linear interaction between both sources. Future studies may benefit from controlling for sensory contamination using sham conditions that are spatially matched to active TMS, and which consist of combined auditory and somatosensory stimulation.


title: Multiple adaptive solutions to face climatic constraints: novel insights in the debate over the role of convergence in local adaptation

abstract: The extent to which genomic convergence shapes locally adapted phenotypes in different species remains a fundamental question in evolutionary biology. To bring new insights to this debate we set up a framework which aimed to compare the adaptive trajectories of two domesticated mammal species co-distributed in diversified landscapes. We sequenced the genomes of 160 sheep and 161 goats extensively managed along environmental gradients, including temperature, rainfall, seasonality and altitude, to identify genes and biological processes shaping local adaptation. Allele frequencies at adaptive loci were rarely found to vary gradually along environmental gradients, but rather displayed a discontinuous shift at the extremities of environmental clines. Of the more than 430 adaptive genes identified, only 6 were orthologous between sheep and goats and those responded differently to environmental pressures, suggesting different adaptive mechanisms in these two closely related species. Such diversity of adaptive pathways may result from a high number of biological functions involved in adaptation to multiple eco-climatic gradients, and provides more arguments for the role of contingency and stochasticity in adaptation rather than repeatability.

category: evolutionary biology


title: Ecological changes have driven biotic exchanges across the Indian Ocean

abstract: The Indian Ocean has a complex geological history that has drawn the attention of naturalists for almost a century now. Due to its tectonic history, many geological elements and processes have been evoked to explain the exchange of species between landmasses. Here, we revisited previous studies on twenty-three taxa to investigate trends across time since the Gondwana breakup. We investigated these datasets by applying a time-calibrated Bayesian framework to them and reconstructing their ancestral ranges. We conclude that ecological transformations have presented opportunities for the establishment of migrants. The role of donating and receiving migrants has shifted several times according to these transformations. Time-specific trends show weak evidence for the stepping-stones commonly suggested as physical routes between landmasses. However, before its collision with Asia, India may have served as an intermediary for such exchanges.


title: Epigenetic machinery is functionally conserved in cephalopods

abstract: Epigenetic regulatory mechanisms are divergent across the animal kingdom, yet little is known about the epigenome in non-model organisms. Unique features of cephalopods make them attractive for investigating behavioral, sensory, developmental and regenerative processes, but using molecular approaches in such studies is hindered by the lack of knowledge about genome organization and gene regulation in these animals. We combined bioinformatic and molecular analysis of Octopus bimaculoides to identify gene expression signatures for 12 adult tissues and a hatchling, and investigate the presence and pattern of DNA methylation and histone methylation marks across tissues. This revealed a dynamic gene expression profile encoding several epigenetic regulators, including DNA methylation maintenance factors that were highly conserved and functional in cephalopods, as shown by detection of 5-methyl-cytosine in multiple tissues of octopus, squid and bobtail squid. WGBS of octopus brain and RRBS from a hatchling revealed that less than 10% of CpGs are methylated, highlighting a non-random distribution in the genome of all tissues, with enrichment in the bodies of a subset of 14,000 genes and absence from transposons. Each DNA methylation pattern encompassed genes with distinct functions and, strikingly, many of these genes showed similar expression levels across tissues. In contrast to the static pattern of DNA methylation, the histone marks H3K27me3, H3K9me3 and H3K4me3 were detected at different levels in diverse cephalopod tissues. This suggests the methylome and histone code cooperate to regulate tissue specific gene expression in a way that may be unique to cephalopods.

category: genomics


title: ZARP: An automated workflow for processing of RNA-seq data

abstract:
RNA sequencing (RNA-seq) is a crucial technique for many scientific studies and multiple models, and software packages have been developed for the processing and analysis of such data. Given the plethora of available tools, choosing the most appropriate ones is a time-consuming process that requires an in-depth understanding of the data, as well as of the principles and parameters of each tool. In addition, packages designed for individual tasks are developed in different programming languages and have dependencies of various degrees of complexity, which renders their installation and execution challenging for users with limited computational expertise. The use of workflow languages and execution engines with support for virtualization and encapsulation options such as containers and Conda environments facilitates these tasks considerably. Computational workflows defined in those languages can be reliably shared with the scientific community, enhancing reusability, while improving reproducibility of results by making individual analysis steps more transparent.

Here we present ZARP, a general purpose RNA-seq analysis workflow which builds on state-of-the-art software in the field to facilitate the analysis of RNA-seq data sets. ZARP is developed in the Snakemake workflow language using best software development practices. It can run locally or in a cluster environment, generating extensive reports not only of the data but also of the options utilized. It is built using modern technologies with the ultimate goal to reduce the hands-on time for bioinformaticians and non-expert users. ZARP is available under a permissive Open Source license and open to contributions by the scientific community.

Contactmihaela.zavolan@unibas.ch, alexander.kanitz@unibas.ch


title: PURC v2.0: a program for improved sequence inference for polyploid phylogenetics and other manifestations of the multiple-copy problem

abstract: Inferring the true biological sequences from amplicon mixtures remains a difficult bioinformatic problem. The traditional approach is to cluster sequencing reads by similarity thresholds and treat the consensus sequence of each cluster as an "operational taxonomic unit" (OTU). Recently, this approach has been improved upon by model-based methods that correct PCR and sequencing errors in order to infer "amplicon sequence variants" (ASVs). To date, ASV approaches have been used primarily in metagenomics, but they are also useful for identifying allelic or paralogous variants and for determining homeologs in polyploid organisms. To facilitate the usage of ASV methods among polyploidy researchers, we incorporated ASV inference alongside OTU clustering in PURC v2.0, a major update to PURC (Pipeline for Untangling Reticulate Complexes). In addition to preserving original PURC functions, PURC v2.0 allows users to process PacBio CCS/HiFi reads through DADA2 to generate and annotate ASVs for multiplexed data, with outputs including separate alignments for each locus ready for phylogenetic inference. In addition, PURC v2.0 features faster demultiplexing than the original version and has been updated to be compatible with Python 3. In this chapter we present results indicating that PURC v2.0 (using the ASV approach) is more likely to infer the correct biological sequences in comparison to the earlier OTU-based PURC, and describe how to prepare sequencing data, run PURC v2.0 under several different modes, and interpret the output. We expect that PURC v2.0 will provide biologists with a method for generating multi-locus "moderate data" datasets that are large enough to be phylogenetically informative and small enough for manual curation.


title: Semi-supervised single-cell cross-modality translation using Polarbear

abstract: The emergence of single-cell co-assays enables us to learn to translate between single-cell modalities, potentially offering valuable insights from datasets where only one modality is available. However, the sparsity of single-cell measurements and the limited number of cells measured in typical co-assay datasets impedes the power of cross-modality translation. Here, we propose Polarbear, a semi-supervised translation framework to predict cross-modality profiles that is trained using a combination of co-assay data and traditional "single-assay" data. Polarbear uses single-assay and co-assay data to train an autoencoder for each modality and then uses just the co-assay data to train a translator between the embedded representations learned by the autoencoders. With this approach, Polarbear is able to translate between modalities with improved accuracy relative to state-of-the-art translation techniques. As an added benefit of the training procedure, we show that Polarbear also produces a matching of cells across modalities.


title: SubcellulaRVis: an app to visualize subcellular compartment enrichment

abstract:
High-throughput  omics methods result in lists of differentially regulated or expressed genes or proteins, whose function is generally studied through statistical methods such as enrichment analyses. One aspect of protein regulation is subcellular localization, which is crucial for their correct processing and function and can change in response to various cellular stimuli. Enrichment of proteins for subcellular compartments is often based on Gene Ontology Cellular Compartment annotations. Results of enrichment are typically visualized using bar-charts, however enrichment analyses can result in a long list of significant annotations which are highly specific, preventing researchers from gaining a broad understanding of the subcellular compartments their proteins of interest may be located in. Schematic visualization of known subcellular locations has become increasingly available for single proteins via the UniProt and COMPARTMENTS platforms. However, it is not currently available for a list of proteins (e.g. from the same experiment) or for visualizing the results of enrichment analyses.

To generate an easy-to-interpret visualization of protein subcellular localization after enrichment we developed the SubcellulaRVis web app, which visualizes the enrichment of subcellular locations of gene lists in an easy and impactful manner. SubcellulaRVis projects the results of enrichment analysis on a graphical representation of a eukaryotic cell. Implemented as a web app and an R package, this tool is user-friendly, provides exportable results in different formats, and can be used for gene lists derived from multiple organisms.

Here, we show the power of SubcellulaRVis to assign proteins to the correct subcellular compartment using gene list enriched in previously published spatial proteomics datasets. We envision SubcellulaRVis will be useful for cell biologists with limited bioinformatics expertise wanting to perform precise and quick enrichment analysis and immediate visualization of gene lists.

Author SummaryCells contain intracellular compartments, such as membrane-bound organelles and the nucleus, and are surrounded by a plasma membrane. Proteins can be found in different cellular compartments; depending on the subcellular compartment they are localized to, they can be differentially regulated or perform location-specific functions. High-throughput  omics experiments result in a list of proteins or genes of interest; one way in which their functional role can be understood is through their subcellular localization, as deduced through statistical enrichment for Gene Ontology Cellular Component (GOCC) annotations or similar. We have designed a bioinformatic tool, named SubcellulaRVis, that compellingly visualizes the results of protein localization after enrichment and simplifies the results for a quick interpretation. We demonstrate that SubcellulaRVis precisely describes the subcellular localization of gene lists whose locations have been previously ascertained in publications. SubcellulaRVis can be accessed via the web or as a stand-alone app. SubcellulaRVis will be useful for experimental biologists with limited bioinformatics expertise analyzing data related to cellular signalling, protein (re)localization and regulation, and location-specific functional modules within the cell.


title: TIS transformer: Re-annotation of the human proteome using deep learning

abstract: The precise detection of translation initiation sites is essential for proteome delineation. In turn, the accurate mapping of the proteome is fundamental in advancing our understanding of biological systems and cellular mechanisms. We propose TIS Transformer, a deep learning model for the determination of translation start sites, based on information embedded in processed transcript nucleotide sequences. Through the application of deep learning techniques first designed for natural language processing tasks, we have developed an approach that achieves state-of-the-art performances on the prediction of translation initiation sites. TIS Transformer utilizes the FAVOR+ algorithm for attention calculation, enabling processing of full transcript sequences by the model. Analysis of input importance revealed TIS Transformers ability to detect key features of translation, such as translation stop sites and reading frames. Furthermore, we demonstrate TIS Transformers ability to detect multiple peptides on a transcript, and peptides encoded by short Open Reading Frames (sORFs), either alongside a canonical coding sequence or in long non-coding RNAs. Using a cross-validation scheme, we apply TIS Transformer to re-annotate the full human transcriptome.


title: Deciphering a hexameric protein complex with Angstrom optical resolution

abstract:
Cryogenic optical localization in three dimensions (COLD) was recently shown to resolve up to four binding sites on a single protein. However, because COLD relies on intensity fluctuations that result from the blinking behavior of fluorophores, it is limited to cases, where individual emitters show different brightness. This significantly lowers the measurement yield. To extend the number of resolved sites as well as the measurement yield, we employ partial labeling and combine it with polarization encoding in order to identify single fluorophores during their stochastic blinking. We then use a particle classification scheme to identify and resolve heterogenous subsets and combine them to reconstruct the three-dimensional arrangement of large molecular complexes. We showcase this method (polarCOLD) by resolving the trimer arrangement of proliferating cell nuclear antigen (PCNA) and the hexamer geometry of Caseinolytic Peptidase B (ClpB) of Thermus thermophilus in its quaternary structure, both with Angstrom resolution. The combination of polarCOLD and single-particle cryogenic electron microscopy (cryoEM) promises to provide crucial insight into intrinsic, environmental and dynamic heterogeneities of biomolecular structures. Furthermore, our approach is fully compatible with fluorescent protein labeling and can, thus, be used in a wide range of studies in cell and membrane biology.

Significance statementFluorescence super-resolution microscopy has witnessed many clever innovations in the last two decades. Here, we advance the frontiers of this field of research by combining partial labeling and 2D image classification schemes with polarization-encoded single-molecule localization at liquid helium temperature to reach Angstrom resolution in three dimensions. We demonstrate the performance of the method by applying it to trimer and hexamer protein complexes. Our approach holds great promise for examining membrane protein structural assemblies and conformations in challenging native environments. The methodology closes the gap between electron and optical microscopy and offers an ideal ground for correlating the two modalities at the single-particle level. Indeed, correlative light and electron microscopy is an emerging technique that will provide new insight into cell biology.


title: Double mutant of chymotrypsin inhibitor 2 stabilized through increased conformational entropy

abstract: The conformational heterogeneity of a folded protein can affect both its function but also stability and folding. We recently discovered and characterized a stabilized double mutant (L49I/I57V) of the protein CI2 and showed that state-of-the-art prediction methods could not predict the increased stability relative to the wild-type protein. Here we have examined whether changed native state dynamics, and resulting entropy changes, can explain the stability changes in the double mutant protein, as well as the two single mutant forms. We have combined NMR relaxation measurements of the ps-ns dynamics of amide groups in the backbone and the methyl groups in the side-chains with molecular dynamics simulations to quantify the native state dynamics. The NMR experiments reveal that the mutations have different effects on the conformational flexibility of CI2: A reduction in conformational dynamics (and entropy) of the native state of L49I variant correlates with its decreased stability, while increased dynamics of the I57V and L49I/I57V variants correlates with their increased stability. These findings suggest that explicitly accounting for changes in native state entropy might be needed to improve the predictions of the effect of mutations on protein stability.


title: Characterization of plasma circulating small extracellular vesicles in patients with metastatic solid tumors and newly diagnosed brain metastasis.

abstract:
PurposeNearly 40% of the advanced cancer patients will present brain metastases during the course of their disease, with a 2-year life expectancy of less than 10%. Immune system impairment, including the modulation of both STAT3 and PD-L1, is one of the hallmarks of brain metastases. Liquid biopsy could offer several advantages in brain metastases management, such as the possibility of non-invasive dynamic monitoring. Extracellular vesicles (EVs) have been recently proposed as novel biomarkers especially useful in liquid biopsy due to their secretion in biofluids and their role in cell communication during tumor progression.

Materials and MethodsThe main aim of this work was to characterize the size and protein cargo of plasma circulating EVs in patients with solid tumors and their correlation with newly diagnosed brain metastases, in addition to their association with other relevant clinical variables.

ResultsWe analyzed circulating EVs in the plasma of 123 patients: 42 patients with brain metastases, 50 without brain metastases and 31 healthy controls. Patients with newly diagnosed brain metastases had a lower number of circulating EVs in the plasma and a higher protein concentration in small EVs (sEVs) compared to patients without brain metastases and healthy controls. Interestingly, melanoma patients with brain metastases presented decreased STAT3 activation and increased PD-L1 levels in circulating sEVs compared to patients without central nervous system metastases.

ConclusionsDecreased STAT3 activation and increased PD-L1 in plasma circulating sEVs identify melanoma patients with brain metastasis.

Statement of translational relevanceBrain metastases are critical for outcomes and quality of life in almost 50% of oncological patients, generally associated with a poor short-term prognosis. Early or preventive diagnosis of this complication represents an unmet need. There is a necessity of discovering new biomarkers that could aid to predict disease outcome.

In this study, we analyzed plasma circulating extracellular vesicles (EVs) from a cohort of 92 patients with different solid tumors (lung, breast, kidney cancer and melanoma) and found that newly diagnosed patients with brain metastases presented lower number of circulating particles and a higher protein concentration in small extracellular vesicles (sEVs) compared to patients without brain metastases and healthy controls. Out of all groups analyzed, melanoma patients with brain metastases presented decreased STAT3 activation and increased PD-L1 levels in circulating sEVs compared to patients without central nervous system metastases.

The data presented in this work suggest that circulating sEVs may represent the immunosuppressive status of newly diagnosed brain metastases characterized by the reduced phospho-STAT3 (pSTAT3) and increased PD-L1, although the origin of these molecules found in circulating sEVs remains to be uncovered.

category: cancer biology


title: BOXR1030, an anti-GPC3 CAR with exogenous GOT2 expression, shows enhanced T cell metabolism and improved antitumor activity

abstract:
PurposeThe solid tumor microenvironment (TME) drives T cell dysfunction and inhibits the effectiveness of immunotherapies such as chimeric antigen receptor-based T cell (CAR T) cells. Early data has shown that modulation of T cell metabolism can improve intratumoral T cell function in preclinical models.

Experimental DesignWe evaluated GPC3 expression in human normal and tumor tissue specimens. We developed and evaluated BOXR1030, a novel CAR T therapeutic co-expressing glypican-3 (GPC3)-targeted CAR and exogenous glutamic-oxaloacetic transaminase 2 (GOT2) in terms of CAR T cell function both in vitro and in vivo.

ResultsExpression of tumor antigen GPC3 was observed by immunohistochemical staining in tumor biopsies from hepatocellular carcinoma, liposarcoma, squamous lung cancer, and Merkel cell carcinoma patients. Compared to control GPC3 CAR alone, BOXR1030 (GPC3-targeted CAR T cell that co-expressed GOT2) demonstrated superior in vivo efficacy in aggressive solid tumor xenograft models, and showed favorable attributes in vitro including an enhanced cytokine production profile, a less-differentiated T cell phenotype with lower expression of stress and exhaustion markers, an enhanced metabolic profile and increased proliferation in TME-like conditions.

ConclusionsTogether, these results demonstrated that co-expression of GOT2 can substantially improve the overall antitumor activity of CAR T cells by inducing broad changes in cellular function and phenotype. These data show that BOXR1030 is an attractive approach to targeting select solid tumors. To this end, BOXR1030 will be explored in the clinic to assess safety, dose- finding, and preliminary efficacy (NCT05120271).


title: High diversity of pimpline parasitoid wasps (Hymenoptera, Ichneumonidae, Pimplinae) from the lowermost Eocene Fur Formation

abstract: With an estimated 100,000 extant species, Darwin wasps (Ichneumonidae) are more specious than all vertebrates together. However, only 288 fossil species have been described to date, with hundreds more awaiting formal description in palaeontological collections. One of the largest gaps in our knowledge concerns the ~12 million years between the K-PG mass extinction and the late Ypresian, from which only two species have been formally described, including Pimpla stigmatica Henriksen from the Danish Fur Formation (~55 Ma). Ie here redescribe and reclassify this species in the genus Epitheronia Gupta, n. comb., and describe nine new species from this fossil locality that are consistent with a placement in Pimplinae: Crusopimpla collina n. sp., C. elongata n. sp., C. minuta n. sp., C. rettigi n. sp., C. violina n. sp., Theronia? furensis n. sp., T. nigriscutum n. sp., Xanthopimpla ciboisae n. sp., and X. crescendae n. sp. The diagnosis of the genus Crusopimpla Kopylov, Spasojevic & Klopfstein is amend in the light of the new species. By comparing the preserved colouration between and within specimens of different species, we draw conclusions about the taxonomic usefulness of colour patterns observed in Fur Formation ichneumonids. The number of described species of pimpline parasitoid wasps from Fur is very high when compared to any other fossil deposit, but low with respect to numbers of extant species. Further study and excavation of Fur ichneumonids will certainly reveal an even higher diversity.

category: paleontology


title: Cytotoxicity mechanisms and composition of the glyphosate formulated herbicide RangerPro

abstract: Understanding the nature of co-formulants and toxic effects of major glyphosate-based herbicide (GBH) formulations is considered a research priority. Indeed, the toxicity of the co-formulants present in GBHs have been widely discussed and the European Union recently banned the co-formulant polyoxyethylene tallow amine (POEA). We provide a foundation for the development of new environmental epidemiological studies by reporting the presence of the most commonly used POEA, known as POE-15 tallow amine, in the widely used US GBH RangerPro. In order to understand if POE-15 tallow amine is present in RangerPro at a concentration at which it can exert toxic effects, we also tested the cytotoxicity of this GBH compared to glyphosate and POE-15 tallow amine in the human epithelial cell line Caco-2, a representative of the human intestinal epithelium, and the first to be exposed from the human diet to glyphosate herbicides. The lethal concentration 50 for each of these substances was 125 g/ml, 17200 g/ml, and 5.7 g/ml, for RangerPro, glyphosate and POE-15, respectively. The Caco-2 cell cytotoxicity assay indicated that RangerPro is more cytotoxic than glyphosate, suggesting that its toxicity can be due to the presence of the POE-15 surfactant. RangerPro and POE-15 tallow amine but not glyphosate exerted cell necrotic effects, but did not induce oxidative stress. We show that RangerPro contains POE-15 tallow amine at a concentration at which it could exert toxic effects, which offers a starting point for conducting surveys of co-formulant exposure in human populations.


title: Differential replay for reward and punishment paths predicts approach and avoidance

abstract: Planning is thought to involve neural replay, where states relevant to a task goal are rapidly reactivated in sequence. It remains unclear if, during planning, replay of a path relates to an actual prospective choice. Here, using magnetoencephalography (MEG), we studied participants while they planned to either approach or avoid an uncertain environment that contained paths leading to reward and to punishment. We show significant planning-related forward sequential replay with state-to-state transitions in the range of 20 to 90 ms. Replay of rewarding paths was boosted prior to a decision to avoid, and attenuated prior to a decision to approach. Crucially, a trial-by-trial bias in replaying punishing paths predicted an irrational choice to approach when a prospective environment was more risky, an effect that was particularly marked in more anxious participants. The findings reveal a coupling between the content of forwards replay and rational choice behaviour, such that replay prioritises an online representation of potential reward.


title: Slow fluctuations in ongoing brain activity decrease in amplitude with ageing yet their impact on task-related evoked responses is dissociable from behaviour

abstract: In humans, ageing is characterized by decreased brain signal variability and increased behavioural variability. To understand how reduced brain variability segregates with increased behavioural variability, we investigated the association between reaction time variability, evoked brain responses and ongoing brain signal dynamics, in young (N = 36) and older adults (N = 39). We studied the electroencephalogram (EEG) and pupil size fluctuations to characterize the cortical and arousal responses elicited by a cued go/no-go task. Evoked responses were strongly modulated by slow (< 2 Hz) fluctuations of the ongoing signals, which presented reduced power in the older participants. Although variability of the evoked responses was lower in the older participants, once we adjusted for the effect of the ongoing signal fluctuations, evoked responses were equally variable in both groups. Moreover, the modulation of the evoked responses caused by the ongoing signal fluctuations had no impact on reaction time, thereby explaining why although ongoing brain signal variability is decreased in older individuals, behavioural variability is not. Finally, we showed that adjusting for the effect of the ongoing signal was critical to unmask the link between neural responses and behaviour.


title: An insight into new glycotherapeutic in glial inflammation: Understanding the role of glycosylation from acute to chronic phase of inflammation

abstract: Glycosylation plays a critical role during inflammation and glial scar formation upon spinal cord injury (SCI) disease progression. Astrocytes and microglia are involved in this cascade to modulate the inflammation and tissue remodelling from acute to chronic phases. Therefore, understating the glycan changes in these glial cells is paramount. Herein a lectin microarray was undertaken using a cytokine-driven inflammatory MGC model, revealing considerable differential glycosylation from the acute to the chronic phase in a cytokine-combination generated inflamed MGC model. It was found that several N- and O-linked glycans associated with glia during SCI were differentially regulated. Pearsons correlation hierarchical clustering showed that groups were separated into several clusters, illustrating the heterogenicity among the control, cytokine combination, and LPS treated groups and the day on which treatment was given. Control and LPS treatments were observed to be in dense clusters. This was further confirmed with lectin immunostaining in which GalNAc, GlcNAc, mannose, fucose and sialic acid-binding residues were detected in astrocytes and microglia. However, this modification (upregulation of sialic acid expression) was inhibited by the sialyltransferase inhibitor which indeed modulates the mitochondrial functions. The present study is the first functional investigation of glycosylation modulation in a MGC (MGC) model which elucidates the role of the glycome in neuroinflammation and identified potential therapeutic targets for future glycol-therapeutics in neuroinflammation


title: Effortless integration of probabilistic visual input

abstract: Current theories of perception suggest that the brain represents features of the world as probability distributions, but can such uncertain foundations provide the basis for everyday vision? Perceiving objects and scenes requires knowing not just how features (e.g., colors) are distributed but also where they are and which other features they are combined with. Using a Bayesian computational model, we recover probabilistic representations used by human observers to search for odd stimuli among distractors. Importantly, we found that the brain integrates information between feature dimensions and spatial locations, leading to more precise representations compared to when information integration is not possible. We also uncover representational asymmetries and biases, showing their spatial organization and arguing against simplified "summary statistics" accounts. Our results confirm that probabilistically encoded visual features are bound with other features and to particular locations, proving how probabilistic representations can be a foundation for higher-level vision.


title: Probabilistic representations as building blocks for higher-level vision


title: A non-transcriptional function of Yap orchestrates the DNA replication program

abstract:
In multicellular eukaryotic organisms, the initiation of DNA replication occurs asynchronously throughout S-phase according to a regulated replication timing program. Here, using Xenopus egg extracts, we showed that Yap (Yes-associated protein 1), a downstream effector of the Hippo signaling pathway, is required for the control of DNA replication dynamics. We found that Yap is recruited to chromatin at the start of DNA replication and that Yap depletion accelerates DNA replication dynamics by increasing the number of activated replication origins. Furthermore, we identified Rif1, a major regulator of the DNA replication timing program, as a novel Yap binding protein. In Xenopus embryos, using a Trim-Away approach during cleavage stages devoid of transcription, we found that both Yap and Rif1 depletion trigger an acceleration of cell divisions, suggesting a shorter S-phase by alterations of the replication program. Finally, our data show that Rif1 knockdown leads to defects in the partitioning of early versus late replication foci in retinal stem cells, as we previously showed for Yap. Altogether, our findings unveil a non-transcriptional role for Yap in regulating replication dynamics. We propose that Yap and Rif1 function as breaks to control the DNA replication program in early embryos and post-embryonic stem cells.

HighlightsO_LIYap is recruited to chromatin during DNA replication dependent on pre-replicative complex assembly.
C_LIO_LIYap controls DNA replication dynamics by limiting origin firing.
C_LIO_LIThe replication timing regulatory factor 1, Rif1, is a novel Yap binding-partner.
C_LIO_LIBoth Yap and Rif1 regulate the length of the first embryonic cell cycles.
C_LIO_LILike Yap, Rif1 controls retinal stem cell DNA replication timing.
C_LI

category: developmental biology


title: DeepProjection: Rapid and structure-specific projections of tissue sheets embedded in 3D microscopy stacks using deep learning

abstract: The efficient extraction of local high-resolution content from massive amounts of imaging data remains a serious and unsolved problem in studies of complex biological tissues. Here we present DeepProjection, a trainable projection algorithm based on deep learning. This algorithm rapidly and robustly extracts image content contained in curved manifolds from time-lapse recorded 3D image stacks by binary masking of background content, stack by stack. The masks calculated for a given movie, when predicted, e.g., on fluorescent cell boundaries on one channel, can subsequently be applied to project other fluorescent channels from the same manifold. We apply DeepProjection to follow the dynamic movements of 2D-tissue sheets in embryonic development. We show that we can selectively project the amnioserosa cell sheet during dorsal closure in Drosophila melanogaster embryos and the periderm layer in the elongating zebrafish embryo while masking highly fluorescent out-of-plane artifacts.


title: Multitrophic higher-order interactions modulate species persistence

abstract: There is growing recognition that interactions between species pairs are modified in a multispecies context by the density of a third species. However, how these higher-order interactions (HOIs) affect species persistence remains poorly understood. To explore the effect of HOIs steaming from multiple trophic layers on plant persistence, we experimentally built a mutualistic system containing three plants and three pollinators species with two contrasting network structures. For both structures, we first estimated the statistically supported HOIs on plant species, in addition to the pairwise interactions among plants and plant-pollinators. Following a structuralist approach, we then assessed the effects of the supported HOIs on the persistence probability of each of the three competing plant species and their combinations. HOIs produced substantial effects on the strength and sign of per capita interactions between plant species to such an extent that predictions of species persistence differ from a non-HOIs scenario. Changes in network structure due to removing a plant-pollinator link further modulated the species persistence probabilities by reorganizing per capita interaction strengths of both pairwise interactions and HOIs. Our study provides empirical evidence of the joint importance of HOIs and network structure for determining the probability of species to persist within diverse communities.


title: Evolution of enzyme levels in metabolic pathways: A theoretical approach. Part 2

abstract: Metabolism is essential for cell function and adaptation. Because of their central role in metabolism, kinetic parameters and enzyme concentrations are under constant selective pressure to adapt the fluxes of the metabolic networks to the needs of the organism. In the line of various studies dealing with enzyme evolution, we recently developed a model of evolution of enzyme concentrations under selection for increased flux, considered as a proxy of fitness (Coton et al. 2021). Taking into account two realistic cellular constraints, competition for resources and co-regulations, we determined the evolutionary equilibria and the ranges of neutral variations of enzyme concentrations. In this article, we give more generality to this model, by considering that the enzymes of a pathway can belong to different groups of co-regulation. We determined the equilibria and showed that the constraints modify the adaptive landscape by limiting the number of independent dimensions. We also showed that any trade-off between enzyme concentration is sufficient to limit the flux and to relax selection for increasing other enzyme concentrations. Even though the model is based on simplifying assumptions, the complexity of the relationship between enzyme concentrations prevents the analysis of selective neutrality.


title: Histidine-rich protein 2: a new pathogenic factor of Plasmodium falciparum malaria

abstract: Plasmodium falciparum causes serious malaria symptoms; when this protozoan parasite infects human erythrocytes, it produces and secretes large amounts of histidine-rich protein 2 (PfHRP2) into human blood. Thus, PfHRP2 is a well-known diagnostic marker for malaria infection. Here, however, we also identified PfHRP2 as a pathogenic factor produced by P. falciparum. PfHRP2 showed cell penetration and cytotoxicity against various human cells. In particular, PfHRP2 showed significant cytotoxicity over 5 days at the same concentration as in P. falciparum-infected patients blood (90-100 nM). This result is consistent with the mortality rate of P. falciparum malaria, which increases rapidly in untreated cases for 3-7 days. In addition, the cell penetration and cytotoxicity of PfHRP2 increased 2.5- and 2.6-fold, respectively, in the absence of serum, which suggests that low serum protein concentrations (occurring during malnutrition, for example) increase the risk of adverse effects from PfHRP2 (consistent with malnutrition increasing the lethality of malaria infection). We also showed that PfHRP2 bound to Ca2+ ions, localized to intracellular lysosomes, increased lysosomal Ca2+ levels, and inhibited the basal level of autophagy by inhibiting autolysosome formation. Furthermore, the Ca2+-dependent cytotoxicity of PfHRP2 was suppressed by the metal ion chelator ethylenediaminetetraacetic acid (EDTA). In summary, our findings suggest that PfHRP2 acts as a pathogenic factor in P. falciparum-infected patients and is associated with the exacerbation of malaria. Furthermore, EDTA is a promising candidate as a therapeutic agent for the suppression of PfHRP2 pathogenicity. Overall, this study provides new insights into P. falciparum malaria pathogenesis and treatment.

category: biochemistry