title: Reliability of Mouse Behavioural Tests of Anxiety: a Systematic Review and Meta-Analysis on the Effects of Anxiolytics.

abstract: Animal research on anxiety and anxiety disorders relies on valid animal models of anxiety. However, the validity of widely used rodent behavioural tests of anxiety has repeatedly been questioned, as they often fail to produce consistent results across independent replicate studies using different study populations or different anxiolytic compounds. In this study, we assessed the sensitivity of behavioural tests of anxiety in mice to detect anxiolytic effects of drugs prescribed to treat anxiety in humans. To this end, we conducted a pre-registered systematic review of studies reporting tests of anxiolytic compounds against a control treatment using common behavioural tests of anxiety in mice. PubMed and EMBASE were searched on August 21st 2019 for studies published in English and 814 papers were identified for inclusion. Risk of bias was assessed based on Syrcles risk of bias tool and the Camarades study quality checklist on a randomly selected subsample of 180 papers. Meta-analyses on effect sizes of treatments using standardized mean differences (Hedges g) showed that only two of 17 test measures reliably detected effects of anxiolytic compounds other than diazepam. Further, we report considerable variation in both direction and size of effects of most anxiolytics on most outcome variables, indicating poor replicability of test results. This was corroborated by high heterogeneity in most test measures. Finally, we found an overall high risk of bias. Our findings indicate a general lack of sensitivity of common behavioural tests of anxiety in mice to anxiolytic compounds and cast serious doubt on both construct and predictive validity of most of those tests. The use of animals to model human conditions can be justified only if the expected results are informative, reproducible, and translatable. In view of scientifically valid and ethically responsible research, we call for a revision of behavioural tests of anxiety in mice and the development of more predictive tests.


title: Recent SIV-Macaque Trials: A Reassessment of Immune Priming and Varying Infectability in Repeated Low-dose Challenge Studies

abstract:
Nowadays, most preclinical HIV treatment trials use a protocol of administering repeated low-dose challenges (RLCs) of simian immunodeficiency virus (SIV) to macaques. Statistical analyses of treatment efficacy under the RLC protocol need to consider two confounding hypotheses, both pertinent biologically to HIV: (1) the non-infecting challenges may immunize animals against SIV; and (2) the animals may vary in intrinsic infectability ("frailty"). To explore the two hypotheses, a previous study (Regoes 2012) assembled a database from 7 articles with SIV-macaque treatment trials. With two explicable exceptions, Regoes concluded that the control data did not support either confounding hypothesis. Recent SIV-macaque trials present opportunities to evaluate the conclusions robustness. Accordingly, the present article assembles from 24 articles an updated database containing net survival curves from both control and treatment arms in SIV-macaque treatment trials. Broad patterns of statistical significance (at p<0.05, uncorrected for multiple testing) made it difficult to dismiss the confounding hypotheses completely in the controls. Although statistical analysis has focused on defense against variable frailty, only one set of controls showed significant variable frailty, whereas many sets showed significant immunization. As trials progressed, changes in the probability of infection per challenge were significant in 8/28 trials (1/3 trials using oral challenges; 2/4 trials using vaginal challenges; and 5/21 trials using rectal challenges). The results suggest the possibility that vaginal challenges may immunize animals faster than rectal challenges, and they also bear on previous conclusions that repeated exposure to HIV without treatment may have no effect on infectability or may even reduce it.

Author SummaryMany preclinical trials of HIV treatments rely on repeatedly administering low-dose SIV challenges to macaques until infection occurs. The repeated low-dose protocol reuses macaques and is more sensitive to subtle therapeutic efficacies than a protocol administering a single large dose to each macaque. The animal reuse raises some pertinent biological questions, notably: (1) do macaques have intrinsically variable infectabilities? and (2) do the repeated SIV challenges immunize macaques against infection? A 2012 study collected a database of eight macaque trials, concluding that variable infectability and immunization were at most sporadic and readily explicable. I expanded the 2012 database to twenty-eight trials, discovering that the conclusions were not robust. Although only 1/28 SIV-macaque trials showed variable infectability, 7/28 showed immunization, with few ready explanations. Statistical analysis of SIV-macaque trials has focused on the confounding effects of variable infectability to the neglect of immunization, so the expanded database provides a rich empirical resource. The trials have general medical importance because they provide a model for analyzing animal trials of infectious disease therapies and other sparse trials, e.g., for breast cancer. My findings also indirectly suggest that repeated human exposure to HIV inconsistently immunizes and can foster either immune priming or tolerance.

category: microbiology


title: Construction of transcript regulation mechanism prediction models based on binding motif environment of transcription factor AoXlnR in Aspergillus oryzae

abstract:
Recent study revealed that there are thousands of genes that remain unaffected by increased AoXlnR expression, despite the presence of one or more AoXlnR-binding motifs in their promoter region. Given this knowledge, we designed this study to construct several predictive models for determining whether a gene can exhibit a differential response to changes in AoXlnR expression. These models were constructed using 3D DNA shape information determined using the sequence around the AoXlnR binding motifs with classification as functional or nonfunctional. These models were created using a support vector machine followed by the evaluations designed to determine whether these DNA shape-based models can correctly classify functional motifs in terms of area under the receiver operating characteristic curve. The results showed that the differential expression levels of genes located downstream of the AoXlnR motif are closely related to specific DNA shape information around the binding motifs. Furthermore, we found that the parameters contributing to differential expressions differed depending on the number of motifs in the promoter region by comparing the prediction models using regions with only one binding DNA motif and those with multiple binding DNA motifs.

Author SummaryDNA-binding transcription factors (TFs) play a central role in transcriptional regulation mechanisms, mainly through their specific binding to target sites on the genome and regulation of the expression of downstream genes. Therefore, a comprehensive analysis of the function of these TFs will lead to the understanding of various biological mechanisms. However, the functions of TFs in vivo are diverse and complicated, and the identified binding sites on the genome are not necessarily involved in the regulation of downstream gene expression. In this study, we investigated whether DNA structural information around the binding site of transcription factors can be used to predict the involvement of the binding site in the regulation of the expression of genes located downstream of the binding site. Specifically, we calculated the structural parameters based on the DNA shape around the DNA binding motif located upstream of the gene whose expression is directly regulated by the transcription factor AoXlnR from Aspergillus oryzae, and showed that the presence or absence of expression regulation can be predicted from the sequence information with high accuracy by machine learning incorporating these parameters.

category: genomics


title: Brain connectivity-based prediction of real-life creativity is mediated by semantic memory structure

abstract: Creative cognition relies on the ability to form remote associations between concepts, which allows to generate novel ideas or solve new problems. Such an ability is related to the organization of semantic memory; yet whether real-life creative behavior relies on semantic memory organization and its neural substrates remains unclear. Therefore, this study explored associations between brain functional connectivity patterns, network properties of individual semantic memory, and real-life creativity. We acquired multi-echo functional MRI data while participants underwent a semantic relatedness judgment task. These ratings were used to estimate their individual semantic memory networks, whose properties significantly predicted their real-life creativity. Using a connectome-based predictive modeling approach, we identified patterns of task-based functional connectivity that predicted creativity-related semantic memory network properties. Furthermore, these properties mediated the relationship between functional connectivity and real-life creativity. These results provide new insights into how brain connectivity supports the associative mechanisms of creativity.

category: neuroscience


title: 4D live-cell imaging of microgametogenesis in the human malaria parasite Plasmodium falciparum

abstract: Formation of gametes in the malaria parasite occurs in the midgut of the mosquito and is critical to onward parasite transmission. Transformation of the male gametocyte into microgametes, called microgametogenesis, is an explosive cellular event and one of the fastest eukaryotic DNA replication events known. The transformation of one microgametocyte into eight flagellated microgametes requires reorganisation of the parasite cytoskeleton, replication of the 22.9 Mb genome, axoneme formation and host erythrocyte egress, all of which occur simultaneously in <20 minutes. Whilst high-resolution imaging has been a powerful tool for defining stages of microgametogenesis, it has largely been limited to fixed parasite samples, given the speed of the process and parasite photosensitivity. Here, we have developed a live-cell fluorescence imaging workflow that captures the explosive dynamics of microgametogenesis in full. Using the most virulent human malaria parasite, Plasmodium falciparum, our live-cell approach combines three-dimensional imaging through time (4D imaging) and covers early microgametocyte development through to microgamete release. Combining live-cell stains for DNA, tubulin and the host erythrocyte membrane, 4D imaging enables definition of the positioning of newly replicated and segregated DNA. It also shows the microtubular cytoskeleton, location of newly formed basal bodies and elongation of axonemes, as well as behaviour of the erythrocyte membrane, including its specific perforation prior to microgamete egress. 4D imaging was additionally undertaken in the presence of known transmission-blocking inhibitors and the untested proteasomal inhibitor bortezomib. Here, for the first time we find that bortezomib inhibition results in a clear block of DNA replication, full axoneme nucleation and elongation. These data not only define a framework for understanding microgametogenesis in general but also suggest that the process is critically dependent on proteasomal activity, helping to identify potentially novel targets for transmission-blocking antimalarial drug development.


title: Precision Autism: Genomic Stratification of Disorders Making Up the Broad Spectrum May Demystify its "Epidemic Rates"

abstract: In the last decade, Autism has broadened and often shifted its diagnostics criter a, allowing several neuropsychiatric and neurological disorders of known etiology. This has resulted in a highly heterogeneous spectrum with apparent exponential rates in prevalence. I ask if it is possible to leverage existing genetic information about those disorders making up Autism today and use it to stratify this spectrum. To that end, I combine genes linked to Autism in the SFARI database and genomic information from the DisGeNet portal on 25 diseases, inclusive of non-neurological ones. I use the GTEx data on genes expression on 54 human tissues and ask if there are overlapping genes across those associated to these diseases and those from SFARI-Autism. I find a compact set of genes across all brain-disorders which express highly in tissues fundamental for somatic-sensory-motor function, self-regulation, memory, and cognition. Then, I offer a new stratification that provides a distance-based orderly clustering into possible Autism subtypes, amenable to design personalized targeted therapies within the framework of Precision Medicine. I conclude that viewing Autism through this physiological (Precision) lens, rather than viewing it exclusively from a psychological behavioral construct, may make it a more manageable condition and dispel the Autism epidemic myth.


title: Characterization of peptide-protein relationships in protein ambiguity groups via bipartite graphs

abstract: In bottom-up proteomics, proteins are enzymatically digested into peptides before measurement with mass spectrometry. The relationship between proteins and their corresponding peptides can be represented by bipartite graphs. We conduct a comprehensive analysis of bipartite graphs using quantified peptides from measured data sets as well as theoretical peptides from an in silico digestion of the corresponding complete taxonomic protein sequence databases. The aim of this study is to characterize and structure the different types of graphs that occur and to compare them between data sets. We observed a large influence of the accepted minimum peptide length during in silico digestion. When changing from theoretical peptides to measured ones, the graph structures are subject to two opposite effects. On the one hand, the graphs based on measured peptides are on average smaller and less complex compared to graphs using theoretical peptides. On the other hand, the proportion of protein nodes without unique peptides, which are a complicated case for protein inference and quantification, is considerably larger for measured data. Additionally, the proportion of graphs containing at least one protein node without unique peptides rises when going from database to quantitative level. The fraction of shared peptides and proteins without unique peptides as well as the complexity and size of the graphs highly depends on the data set and organism. Large differences between the structures of bipartite peptide-protein graphs have been observed between database and quantitative level as well as between analyzed species. In the analyzed measured data sets, the proportion of protein nodes without unique peptides ranged from 6.4% to 55.0%. This highlights the need for novel methods that can quantify proteins without unique peptides. The knowledge about the structure of the bipartite peptide-protein graphs gained in this study will be useful for the development of such algorithms.

category: bioinformatics


title: Patient-specific Boolean models of signaling networks guide personalized treatments

abstract:
Prostate cancer is the second most occurring cancer in men worldwide. To better understand the mechanisms of tumorigenesis and possible treatment responses, we developed a mathematical model of prostate cancer which considers the major signalling pathways known to be deregulated.

We personalised this Boolean model to molecular data to reflect the heterogeneity and specific response to perturbations of cancer patients. 488 prostate samples were used to build patient-specific models and compared to available clinical data. Additionally, eight prostate cell-line-specific models were built to validate our approach with dose-response data of several drugs.

The effects of single and combined drugs were tested in these models under different growth conditions. We identified 15 actionable points of interventions in one cell-line-specific model whose inactivation hinders tumorigenesis. To validate these results, we tested nine small molecule inhibitors of five of those putative targets and found a dose-dependent effect on four of them, notably those targeting HSP90 and PI3K. These results highlight the predictive power of our personalized Boolean models and illustrate how they can be used for precision oncology.

category: systems biology


title: Patient-derived gene and protein expression signatures of NGLY1 deficiency

abstract: N-Glycanase 1 (NGLY1) deficiency is a rare and complex genetic disorder. Although recent studies have shed light on the molecular underpinnings of NGLY1 deficiency, a systematic characterization of gene and protein expression changes in patient-derived cells has been lacking. Here, we performed RNA-sequencing and mass spectrometry to determine the transcriptomes and proteomes of 66 cell lines representing 4 different cell types derived from 14 NGLY1 deficient patients and 17 controls. While gene and protein expression levels agreed well with each other, expression differences were more pronounced at the protein level. Although NGLY1 protein levels were up to 9.5-fold downregulated in patients compared to parent controls, depending on the genotype, NGLY1 protein was still detectable in all patient-derived lymphoblastoid cell lines. Consistent with the role of NGLY1 as a regulator of the transcription factor Nrf1, we observed a cell type-independent downregulation of proteasomal genes in NGLY1 deficient cells. In contrast, genes involved in ribosomal mRNA processing were upregulated in multiple cell types. In addition, we observed cell type-specific effects. For example, genes and proteins involved in glutathione synthesis, such as the glutamate-cystein ligase subunits GCLC and GCLM, were downregulated specifically in lymphoblastoid cells. We provide a web application that enables access to all results generated in this study at https://apps.embl.de/ngly1browser. This resource will guide future studies of NGLY1 deficiency in directions that are most relevant to patients.


title: Muscarinic receptors mediate motivation via preparatory neural activity in humans

abstract: Motivation depends on dopamine, but might be modulated by acetylcholine which influences dopamine release in the striatum, and amplifies motivation in animal studies. A corresponding effect in humans would be important clinically, since anticholinergic drugs are frequently used in Parkinsons disease, a condition that can also disrupt motivation. Reward and dopamine make us more ready to respond, as indexed by reaction times (RT), and move faster, sometimes termed vigour. These effects may be controlled by preparatory processes that can be tracked using EEG. We measured vigour in a placebo-controlled, double-blinded study of trihexyphenidyl (THP), a muscarinic antagonist, with an incentivised eye movement task and EEG. Participants responded faster and with greater vigour when incentives were high, but THP blunted these motivation effects, suggesting that muscarinic receptors facilitate invigoration by reward. Preparatory EEG build-up (contingent negative variation; CNV) was strengthened by high incentives and by muscarinic blockade. The amplitude of preparatory activity predicted both vigour and RT, although over distinct scalp regions. Frontal activity predicted vigour, whereas a larger, earlier, central component predicted RT. Indeed the incentivisation of RT was partly mediated by the CNV, though vigour was not. Moreover, the CNV mediated the drugs effect on dampening incentives, suggesting that muscarinic receptors underlie the motivational influence on this preparatory activity. Taken together, these findings show that a muscarinic blocker used to treat Parkinsons disease impairs motivated action in healthy people, and that medial frontal preparatory neural activity mediates this for RT.


title: Cross-species comparison of human and rodent primary reward consumption under budget constraints

abstract: Optimal use of resources is of great importance for survival of all species. Previous studies have shown that rats optimize their allocation of a limited number of operant responses (akin to a finite budget) to trade for food rewards. Here, we propose a novel human cost-benefit decision paradigm translated from an economic task initially developed for rodents, to conduct a cross-species comparison of primary reward consumption under budget constraints. Participants had a limited budget of effortful button-presses to obtain the opportunity to drink milk rewards or watch erotic pictures. Like rodents, they adapted their choice allocation when the price (i.e. fixed-ratio requirement for reward) and the budget changed when purchasing milk rewards. However, this was not the case when purchasing the opportunity to watch erotic pictures: compared to the milk and to the rodent task, participants made more internally inconsistent, hence, irrational choices, despite otherwise identical task structures. We found non-linear changes in arousal as a function of reward selection that might underlie the irrationality in the picture task. Our study shows that the type of reward matters not only for capturing the convergence in human and non-human economic decision-making, but also for understanding the factors behind compromised economic rationality.


title: In situ cryo-electron tomography reveals local cellular machineries for axon branch development

abstract: Neurons are highly polarized cells forming an intricate network of dendrites and axons. They are shaped by the dynamic reorganization of cytoskeleton components and cellular organelles. Axon branching allows to form new paths and increases circuit complexity. However, our understanding of branch formation is sparse due to technical limitations. Using in situ cellular cryo-electron tomography on primary mouse neurons, we directly visualized the remodeling of organelles and cytoskeleton structures at axon branches. Strikingly, branched areas functioned as hotspots concentrating organelles to support dynamic activities. Unaligned actin filaments assembled at the base of premature branches and remained while filopodia diminished. Microtubules and ER co-migrated into preformed branches to support outgrowth together with accumulating compact ~500 nm mitochondria and locally clustered ribosomes. We obtained a roadmap of events and present the first direct evidence of local protein synthesis selectively taking place at axon branches, allowing to serve as unique control hubs for axon development and downstream neural network formation.


title: Modeling habitat suitability of vulnerable Mollucan Babirusa Babyrousa babyrussa in small island of Buru, Indonesia

abstract: Babirusa is a mammal belongs to Suidae family. This mammal belongs to Babyrousa genus is known endemic to Indonesia. Recently there are 3 species of Babyrousa, one species is Babyrousa babyrussa, listed as  Vulnerable on the IUCN Red List of Threatened Species. Babyrousa occurs in Indonesia on Sulawesi island, Togian, Sula islands, and Taliabu, Mangole and Buru islands in the Molucca regions. The Moluccan Babirusa is now restricted to upland forests and mountainous terrain. Then this study aims to assess the suitability of Buru island as habitat for Moluccan Babirusa. The suitability analysis was based on GIS analysis using 4 determinant environmental variables required by B. babyrussa species including NDVI, barren soil, elevation, and river network. The particular location was a Batabual landscape sizing 292.60 km2 located in the east parts of Buru island. Based on NDVI, less vegetation covers were observed in north and east parts of Batabual. In contrast, NDVI values were higher in the central, west, and south indicating that half of the landscape was covered by intact primary forest. Batabual has a hilly landscape surrounded by coastal areas with hilly areas were observed in the south and west. There were 2 river streams in the east parts. The analysis has divided the landscape into several parts based on the habitat suitability levels. About one third of the landscape located in north was considered less and not suitable for Babirusa. Some areas in west were also considered moderate to be inhabited by Babirusa considering a presence of hilly landscape that may limit the vertical distribution of Babirusa. Most suitable habitats were estimated in central parts of the landscape spanning to the south. South parts of the landscape were characterized by high NDVI values and forest covers then these areas were considered as suitable habitats for Babirusa. The size of this suitable habitat was estimated around 188.62 km2 or more than half of the size (64.46%) of Batabual landscape.

category: ecology


title: Transgenic expression of Nix converts genetic females into males and allows automated sex sorting in Aedes albopictus

abstract:
Aedes albopictus is a major vector of arboviruses. Better understanding of its sex determination is crucial for developing mosquito control tools, especially genetic sexing strains. In Aedes aegypti, Nix is the primary gene responsible for masculinization and Nix-expressing genetic females develop into fertile, albeit flightless, males. In Ae. albopictus, Nix has also been implicated in masculinization but its role remains to be further characterized.

In this work, we established Ae. albopictus transgenic lines ectopically expressing Nix. Several were composed exclusively of genetic females, with transgenic individuals being phenotypic and functional males due to the expression of the Nix transgene. Their reproductive fitness was marginally impaired, while their flight performance was similar to controls. Overall, our results show that Nix is sufficient for full masculinization in Ae. albopictus. Moreover, the transgene construct contains a fluorescence marker allowing efficient automated sex sorting. Consequently, such strains constitute valuable sexing strains for genetic control.

category: bioengineering


title: Pharmacokinetics and biodistribution of extracellular vesicles administered intravenously and intranasally to Macaca nemestrina

abstract: Extracellular vesicles (EVs) have great potential as novel drug carriers for the treatment of various diseases. These lipid bilayer vesicles are naturally abundant in mammalian tissues and circulation, can be loaded with therapeutic small molecule drugs, (si)RNA, proteins and CRISPR/Cas9, and may be engineered for retention by specific tissues. However, many questions remain on the optimal dosing, administration route, and pharmacokinetics of EVs. Previous studies have addressed biodistribution and pharmacokinetics in rodents, but little evidence is available from larger animals. Here, we investigated the pharmacokinetics and biodistribution of Expi293F-derived EVs labelled with a highly sensitive nanoluciferase reporter (palmGRET) in a non-human primate model (Macaca nemestrina), comparing intravenous (IV) and intranasal (IN) administration over a 125-fold dose range. We report that EVs administered IV had markedly longer circulation times in plasma than previously reported in mice, and were detectable in cerebrospinal fluid (CSF) after 30-60 minutes. Already after one minute following IV administration, we observed EV uptake by PBMCs, most notably B-cells. EVs were detected in liver and spleen within one hour of IV administration. None of the IN doses resulted in readily detectable EV levels in plasma, CSF, or organs, suggesting that IN delivery of EVs in large animals including humans may require reconsideration or pretreatment approaches. Furthermore, EV circulation times strongly decreased after repeated IV administration, possibly due to immune responses and with clear implications for xenogeneic EV-based therapeutics. We hope that our findings from this baseline study in macaques will help to inform future research and therapeutic development of EVs.

category: pharmacology and toxicology


title: Chemogenetic Inhibition of Corticostriatal Circuits Reduces Cued Reinstatement of Methamphetamine Seeking

abstract: Methamphetamine (meth) causes enduring changes within the medial prefrontal cortex (mPFC) and the nucleus accumbens (NA). Projections from the mPFC to the NA have a distinct dorsal-ventral distribution, with the prelimbic (PL) mPFC projecting to the NAcore, and the infralimbic (IL) mPFC projecting to the NAshell. Inhibition of these circuits has opposing effects on cocaine relapse. Inhibition of PL-NAcore reduces cued reinstatement of cocaine seeking and IL-NAshell inhibition reinstates cocaine seeking. Meth, however, exhibits a different profile, as pharmacological inhibition of either the PL or IL decrease cued reinstatement of meth-seeking. The potentially opposing roles of the PL-NAcore and IL-NAshell projections remain to be explored in the context of cued meth seeking. Here we used an intersectional viral vector approach that employs a retrograde delivery of Cre from the NA and Cre-dependent expression of DREADD in the mPFC, in both male and female rats to inhibit or activate these parallel pathways. Inhibition of the PL-NAcore circuit reduced cued reinstatement of meth seeking under short and long-access meth self-administration and after withdrawal with and without extinction. Inhibition of the IL-NAshell also decreased meth cued reinstatement. Activation of the parallel circuits was without an effect. These studies show that inhibition of the PL-NAcore or the IL-NAshell circuits can inhibit reinstated meth seeking. Thus, the neural circuitry mediating cued reinstatement of meth seeking is similar to cocaine in the dorsal, but not ventral, mPFC-NA circuit.


title: Developmental coupling of cerebral blood flow and fMRI fluctuations in youth

abstract:
To support brain development during youth, the brain must balance energy delivery and consumption. Previous studies in adults have demonstrated high coupling between cerebral blood flow and brain function as measured using functional neuroimaging, but how this relationship evolves over adolescence is unknown. To address this gap, we studied a sample of 831 children and adolescents (478 females, ages 8-22) from the Philadelphia Neurodevelopmental Cohort who were scanned at 3T with both arterial spin labeled (ASL) MRI and resting-state functional MRI (fMRI). Local coupling between cerebral blood flow (CBF, from ASL) and the amplitude of low frequency fluctuations (ALFF, from fMRI) was first quantified using locally weighted regressions on the cortical surface. We then used generalized additive models to evaluate how CBF-ALFF coupling was associated with age, sex, and executive function. Enrichment of effects within canonical functional networks was evaluated using spin-based permutation tests. Our analyses revealed tight CBF-ALFF coupling across the brain. Whole-brain CBF-ALFF coupling decreased with age, largely driven by coupling decreases in the inferior frontal cortex, precuneus, visual cortex, and temporoparietal cortex (pfdr <0.05). Females had stronger coupling in the frontoparietal network than males (pfdr <0.05). Better executive function was associated with decreased coupling in the somatomotor network (pfdr <0.05). Overall, we found that CBF-ALFF coupling evolves in development, differs by sex, and is associated with individual differences in executive function. Future studies will investigate relationships between maturational changes in CBF-ALFF coupling and the presence of psychiatric symptoms in youth.

SIGNIFICANCEThe functions of the human brain are metabolically expensive and reliant on coupling between cerebral blood flow and neural activity. Previous neuroimaging studies in adults demonstrate tight physiology-function coupling, but how this coupling evolves over development is unknown. Here, we examine the relationship between blood flow as measured by arterial spin labeling and the amplitude of low frequency fluctuations from resting-state magnetic resonance imaging across a large sample of youth. We demonstrate regionally specific changes in coupling over age and show that variations in coupling are related to biological sex and executive function. Our results highlight the importance of CBF-ALFF coupling throughout development; we discuss its potential as a future target for the study of neuropsychiatric diseases.


title: Sensory computations in the cuneate nucleus of macaques

abstract:
AO_SCPLOWBSTRACTC_SCPLOWTactile nerve fibers fall into a few classes that can be readily distinguished based on their spatiotemporal response properties. Because nerve fibers reflect local skin deformations, they individually carry ambiguous signals about object features. In contrast, cortical neurons exhibit heterogeneous response properties that reflect computations applied to convergent input from multiple classes of afferents, which confer to them a selectivity for behaviorally relevant features of objects. The conventional view is that these complex response properties arise within the cortex itself, implying that sensory signals are not processed to any significant extent in the two intervening structures - the cuneate nucleus (CN) and the thalamus. To test this hypothesis, we recorded the responses evoked in CN to a battery of stimuli that have been extensively used to characterize tactile coding in both the periphery and cortex, including skin indentations, vibrations, random dot patterns, and scanned edges. We found that CN responses are more similar to their cortical counterparts than they are to their inputs: CN neurons receive input from multiple classes of nerve fibers, they have spatially complex receptive fields, and they exhibit selectivity for object features. Contrary to consensus, then, CN plays a key role in processing tactile information.

SO_SCPLOWIGNIFICANCEC_SCPLOWPerception is the outcome of the sequential processing of sensory signals at multiple stages along the neuraxis. The conventional view is that tactile signals are processed predominantly in the cerebral cortex. We tested this view by investigating the response properties of neurons in the cuneate nucleus (CN), the first potential stage of processing along the primary touch neuraxis. We found that CN responses more nearly resemble those of cortical neurons than they do those of nerve fibers: CN neurons have spatially complex receptive fields reflecting convergent input from multiple classes of nerve fibers and exhibit a selectivity for object features, absent in the nerve. We conclude that CN plays a key, early role in the processing of tactile information.


title: Single voxel autocorrelation uncovers gradients of temporal dynamics in the hippocampus and entorhinal cortex during rest and navigation

abstract: During navigation, information at multiple scales needs to be integrated. Single- unit recordings in rodents suggest that gradients of temporal dynamics in the hippocampus and entorhinal cortex support this integration. In humans, gradients of representation are observed, such that granularity of information represented increases along the long axis of the hippocampus. The neural underpinnings of this gradient in humans, however, are still unknown. Current research is limited by coarse fMRI analysis techniques that obscure the activity of individual voxels, preventing investigation of how moment-to-moment changes in brain signal are organized and how they are related to behavior. Here, we measured the signal stability of single voxels over time to uncover previously unappreciated gradients of temporal dynamics in the hippocampus and entorhinal cortex. Using our novel, single voxel autocorrelation technique, we show a medial-lateral hippocampal gradient, as well as a continuous autocorrelation gradient along the anterolateral- posteromedial entorhinal extent. Importantly, we show that autocorrelation in the anterior-medial hippocampus was modulated by navigational difficulty, providing the first evidence that changes in signal stability in single voxels are relevant for behavior. This work opens the door for future research on how temporal gradients within these structures support the integration of information for goal- directed behavior.


title: Insights from spatial measures of intolerance to identify pathogenic variants in developmental and epileptic encephalopathies

abstract: Developmental and epileptic encephalopathies (DEEs) are a group of epilepsies with early onset and severe symptoms that sometimes lead to death. While a number of genes have been successfully implicated, it remains challenging to identify causative mutations within these genes from the background variation present in all individuals due to disease heterogeneity. Our ability to detect likely pathogenic variants has continued to improve as in silico predictors of deleteriousness have advanced. We investigate their use in prioritising likely pathogenic variants in epileptic encephalopathy patient whole exome sequences and show that the inclusion of structure-based predictors of intolerance improve upon previous attempts to demonstrate enrichment within epilepsy genes.


title: Molecular surveillance of zoonotic bacterial pathogens in farm dwelling peridomestic rodents across the upper Midwest, USA

abstract: The effective control of rodent populations on farms is a critical component of food- safety, as rodents are reservoirs and vectors for many foodborne pathogens in addition to several zoonotic pathogens. The functional role of rodents in the amplification and transmission of pathogens is likely underappreciated. Clear links have been identified between rodents and outbreaks of pathogens throughout Europe and Asia, however, comparatively little research has been devoted to studying this rodent-agricultural interface in the USA, particularly across the Midwest. Here, we address this existing knowledge gap by characterizing the metagenomic communities of rodent pests collected from Minnesota and Wisconsin food animal farms. We leveraged the Oxford Nanopore MinION sequencer to provide a rapid real-time survey of the putative zoonotic food- borne and other human pathogens. Rodents (mice and rats) were live trapped from three dairy and mixed animal farms. Tissues and fecal samples were collected from all rodents. DNA extraction was performed on 90 rodent colons along with 2 shrew colons included as outgroups in the study. Full-length 16S amplicon sequencing was performed with the MinION. Our data suggests the presence of putative foodborne pathogens including Salmonella spp., Campylobacter spp., Staphylococcus aureus, and Clostridium spp., along with many important mastitis pathogens. A critically important observation is that we discovered these pathogens within all five species of rodents (Microtus pennsylvanicus, Mus musculus, Peromyscus leucopus, Peromyscus maniculatus, and Rattus norvegicus) and shrew (Blarina brevicauda) in varying abundances. Interestingly, we observed a higher abundance of enteric pathogens (e.g. Salmonella) in shrew feces compared to the rodents analyzed in our study, however more data is required to establish that connection. Knowledge gained from our research efforts will directly inform and improve upon farm-level biosecurity efforts and public health interventions to reduce future outbreaks of foodborne and zoonotic disease.


title: Exploratory extracellular vesicle-bound miRNA profiling to identify candidate biomarkers of chronic alcohol drinking in non-human primates

abstract:
BackgroundLong-term alcohol drinking is associated with numerous health complications including susceptibility to infection, cancer, and organ damage. However, due to the complex nature of human drinking behavior, it is challenging to determine whether alcohol use should be considered a risk factor during diagnosis and treatment. We lack reliable biomarkers of alcohol use that could be used to determine drinking behavior prior to signs of overt organ damage. Recently, extracellular vesicle-bound microRNA (EV-miRNA) have been discovered to be consistent biomarkers of conditions including cancer and liver disease.

MethodsIn this study, we profiled the plasma EV-miRNA content by miRNA-Seq from 80 non-human primates after 12 months of voluntary ethanol drinking.

ResultsWe identified a list of up- and downregulated EV-miRNA candidate biomarkers of both heavy drinking as well as those positively correlated with ethanol dose. We further overexpressed these candidate miRNA in control primary peripheral immune cells to assess potential functional mechanisms of these EV-miRNA. We identified that overexpression of miR-155, miR-154, miR-34c, miR-450a, and miR-204 led to increased inflammatory TNF or IL-6 production in PBMC after stimulation.

ConclusionThis exploratory study identified several EV-miRNA that could serve as biomarkers of long-term alcohol drinking as well as provided a mechanism for alcohol-induced peripheral inflammation.

category: molecular biology


title: Ethanol pre-exposure enhances alcohol-seeking behavior at cellular level by chemoattraction and exhibits bleb-driven cellular stress response in uniform ethanol concentration

abstract: This study investigates the effect of ethanol and its pre-exposure on cell migration. Here, fibroblast cells were first pre-treated with ethanol, and their migratory behavior was tested in both chemotaxis and chemokinesis setup. 1% ethanol was taken as a potential chemotactic agent. The study reveals that in presence of ethanol gradient cells display migration towards ethanol, and pre-exposure further augments this migratory behavior by altering their chemotactic responsiveness. In uniform ethanol concentration, cells first undergo three staged adaptations to the new environment: shrinking, blebbing, and recovery, where cells use bleb-driven cell protection machinery to adapt. Thus, migration is initially stalled. But once the cells resume locomotion, no significant difference in migratory parameters is observed. Overall, this study establishes ethanol as a chemoattractant for fibroblasts, with cells showing enhanced alcohol-seeking behavior upon pre-exposure. Such behavior is reminiscent of seeking and tolerance exhibited by alcohol-dependent addictive behavior in higher organisms including humans.

category: cell biology


title: Inferring the intrinsic mutational fitness landscape of influenza-like evolving antigens from temporally ordered sequence data

abstract: There still are no effective long-term protective vaccines against viruses that continuously evolve under immune pressure such as seasonal influenza, which has caused, and can cause, devastating epidemics in the human population. For finding such a broadly protective immunization strategy it is useful to know how easily the virus can escape via mutation from specific antibody responses. This information is encoded in the fitness landscape of the viral proteins (i.e., knowledge of the viral fitness as a function of sequence). Here we present a computational method to infer the intrinsic mutational fitness landscape of influenza-like evolving antigens from yearly sequence data. We test inference performance with computer-generated sequence data that are based on stochastic simulations mimicking basic features of immune-driven viral evolution. Although the numerically simulated model does create a phylogeny based on the allowed mutations, the inference scheme does not use this information. This provides a contrast to other methods that rely on reconstruction of phylogenetic trees. Our method just needs a sufficient number of samples over multiple years. With our method we are able to infer single-as well as pairwise mutational fitness effects from the simulated sequence time series for short antigenic proteins. Our fitness inference approach may have potential future use for design of immunization protocols by identifying intrinsically vulnerable immune target combinations on antigens that evolve under immune-driven selection. This approach may in the future be applied to influenza and other novel viruses such as SARS-CoV-2, which evolves and, like influenza, might continue to escape the natural and vaccine-mediated immune pressures.

category: evolutionary biology


title: An atlas of healthy and injured cell states and niches in the human kidney

abstract: Understanding kidney disease relies upon defining the complexity of cell types and states, their associated molecular profiles, and interactions within tissue neighborhoods. We have applied multiple single-cell or -nucleus assays (>400,000 nuclei/cells) and spatial imaging technologies to a broad spectrum of healthy reference (n = 42) and disease (n = 42) kidneys. This has provided a high resolution cellular atlas of 100 cell types that include rare and novel cell populations. The multi-omic approach provides detailed transcriptomic profiles, epigenomic regulatory factors, and spatial localizations for major cell types spanning the entire kidney. We further identify and define cellular states altered in kidney injury, encompassing cycling, adaptive or maladaptive repair, transitioning and degenerative states affecting several segments. Molecular signatures of these states permitted their localization within injury neighborhoods using spatial transcriptomics, and large-scale 3D imaging analysis of [~]1.2 million neighborhoods provided linkages to active immune responses. These analyses further defined biological pathways relevant to injury niches, including signatures underlying the transition from reference to predicted maladaptive states that were associated with a decline in kidney function during chronic kidney disease. This human kidney cell atlas, including injury cell states and neighborhoods, will be a valuable resource for future studies.


title: Single cell analysis of endometriosis reveals a coordinated transcriptional program driving immunotolerance and angiogenesis across eutopic and ectopic tissues.

abstract: Endometriosis is characterized by growth of endometrial-like tissue outside of the uterus affecting many women in their reproductive age, causing years of pelvic pain and potential infertility. Its pathophysiology remains largely unknown, limiting diagnosis and treatment. We characterized peritoneal and ovarian lesions at single-cell transcriptome resolution and compared to matched eutopic endometrium, control endometrium, and organoids derived from these tissues, generating data on over 100,000 cells across 12 individuals. We spatially localized many of the cell types using imaging mass cytometry. We identify a perivascular mural cell unique to the peritoneal lesions with dual roles in angiogenesis promotion and immune cell trafficking. We define an immunotolerant peritoneal niche, fundamental differences in eutopic endometrium and between lesions microenvironments, and a novel progenitor-like epithelial cell subpopulation. Altogether, this study provides a holistic view of the endometriosis microenvironment representing the first comprehensive cell atlas of the disease, essential information for advancing therapeutics and diagnostics.


title: Long term conservation of DNA at ambient temperature. Implications for DNA data storage

abstract: DNA conservation is central to many applications. This leads to an ever-increasing number of samples which are more and more difficult and costly to store or transport. A way to alleviate this problem is to develop procedures for storing samples at room temperature while maintaining their stability. A variety of commercial systems have been proposed but they fail to completely protect DNA from deleterious factors, mainly water. On the other side, Imagene company has developed a procedure for long-term conservation of biospecimen at room temperature based on the confinement of the samples under an anhydrous and anoxic atmosphere maintained inside hermetic capsules. The procedure has been validated by us and others for purified RNA, and DNA in buffy coat or white blood cells lysates, but a precise determination of purified DNA stability is still lacking. We used the Arrhenius law to determine the DNA degradation rate at room temperature. We found that extrapolation to 25 {degrees}C gave a degradation rate constant equivalent to about 1 cut/century/100 000 nucleotides, a stability several orders of magnitude larger than the current commercialized processes. Such a stability is fundamental for many applications such as the preservation of very large DNA molecules (particularly interesting in the context of genome sequencing) or oligonucleotides for DNA data storage. Capsules are also well suited for this latter application because of their high capacity. One can calculate that the 64 zettabytes of data produced in 2020 could be stored, standalone, for centuries, in about 20 kg of capsules.

category: biochemistry


title: Surface electric fields increase human osteoclast resorption through improved wettability on carbonate-incorporated apatite

abstract: Osteoclast-mediated bioresorption can be of an efficient means of incorporating the dissolution of biomaterials in the bone remodeling process. Because of compositionally and structurally close resemblance of biomaterials with the natural mineral phases of the bone matrix, synthetic carbonate-substituted hydroxyapatite (CA) is considered as an ideal clinical biomaterial. The present study therefore investigated the effects of electrical polarization on the surface characteristics and interactions with human osteoclasts of hydroxyapatite (HA) and CA. Electrical polarization was found to improve the surface wettability of these materials by increasing the surface free energy, and this effect was maintained for one month. Analyses of human osteoclast cultures established that CA subjected to a polarization treatment accelerated osteoclast resorption but did not affect the early differentiation phase or the adherent morphology of the osteoclasts as evaluated by staining. These data suggest that the surface characteristics of the CA promoted osteoclast resorption. The results of this work are expected to contribute to the design of cell-mediated biomaterials that can be resorbed by osteoclasts after fulfilling their primary function as a scaffold for bone regeneration.


title: Prediction of DNA from context using neural networks

abstract:
One way to better understand the structure in DNA is by learning to predict the sequence. Here, we train a model to predict the missing base at any given position, given its left and right flanking contexts.

Our best-performing model is a neural network that obtains an accuracy close to 54% on the human genome, which is 2% points better than modelling the data using a Markov model. In likelihood-ratio tests, we show that the neural network is significantly better than any of the alternative models by a large margin. We report on where the accuracy is obtained, observing first that the performance appears to be uniform over the chromosomes. The models perform best in repetitive sequences, as expected, although they are far from random performance in the more difficult coding sections, the proportions being ~ 70:40%. Exploring further the sources of the accuracy, Fourier transforming the predictions reveals weak but clear periodic signals. In the human genome the characteristic periods hint at connections to nucleosome positioning. To understand this we find similar periodic signals in GC/AT content in the human genome, which to the best of our knowledge have not been reported before.

On other large genomes similarly high accuracy is found, while lower predictive accuracy is observed on smaller genomes. Only in mouse did we see periodic signals in the same range as in human, though weaker and of different type. Interestingly, applying a model trained on the mouse genome to the human genome results in a performance far below that of the human model, except in the difficult coding regions.

Despite the clear outcomes of the likelihood ratio tests, there is currently a limited superiority of the neural network methods over the Markov model. We expect, however, that there is great potential for better modelling DNA using different neural network architectures.


title: Predictive modeling reveals that higher-order cooperativity drives transcriptional repression in a synthetic developmental enhancer

abstract: A challenge in quantitative biology is to predict output patterns of gene expression from knowledge of input transcription factor patterns and from the arrangement of binding sites for these transcription factors on regulatory DNA. We tested whether widespread thermodynamic models could be used to infer parameters describing simple regulatory architectures that inform parameter-free predictions of more complex enhancers in the context of transcriptional repression by Runt in the early fruit 2y embryo. By modulating the number and placement of Runt binding sites within an enhancer, and quantifying the resulting transcriptional activity using live imaging, we discovered that thermodynamic models call for higher-order cooperativity between multiple molecular players. This higher-order cooperativity capture the combinatorial complexity underlying eukaryotic transcriptional regulation and cannot be determined from simpler regulatory architectures, highlighting the challenges in reaching a predictive understanding of transcriptional regulation in eukaryotes and calling for approaches that quantitatively dissect their molecular nature.

category: biophysics


title: The complete genome of carbapenem-resistant Escherichia coli ST410 harbored blaNDM-5 isolated from reservoir water in Singapore.

abstract:
ObjectiveEscherichia coli ST410 with blaNDM-5 has been increasingly detected as multidrug resistance pathogens globally, even though there are very few reports of infections caused by blaNDM-5 producing E. coli in Singapore[1]. And significantly limit sequencing information of blaNDM-5 carried E. coli strain from Singapore. In 2018, our group obtained a carbapenem resistance E. coli ST410 strain SrichA-1 isolated from reservoir water in Singapore, determined to harbor the NDM-5 gene. (BioSample Accession: SAMN18579051).

MethodsThe susceptibility test to antimicrobials was performed with microdilution minimum inhibitory concentration (MIC) test and interpreted according to the Clinical And Laboratory Standards Institute (CLSI) -M100 standards. The genomic DNA of this strain was extracted and send for Whole-genome sequencing(WGS) with the Illumina platform. The WGS analysis was processed with the Center for Genomic Epidemiology (CGE, DTU) server.

ResultsDuring the minimum inhibitory concentration (MIC) test, SrichA-1 has shown strong resistance to all the beta-lactams, including cephalosporin and carbapenem, which can not be inhibited by the clavulanic acid. Further whole genome sequencing analysis has shown that the strain harboring five beta-lactamase genes covers all class A to D, including the carbapenemase genes as blaNDM-5.

ConclusionHere, we reported the complete chromosome sequence of this isolate as well as the sequence of a cycler plasmid. The pSGNDM-5 plasmid was furtherly identified to carry four beta-lactamase genes, including blaNDM-5, blaCTX-M-15, blaTEM-1B, blaOXA-1, while a blaCMY-2 was detected to be located on the chromosome.

category: pathology


title: Synaptotagmin 1 oligomerization via the juxtamembrane linker regulates spontaneous and evoked neurotransmitter release

abstract: Synaptotagmin-1 (syt1) is a Ca2+ sensor that regulates synaptic vesicle exocytosis. Cell-based experiments suggest that syt1 functions as a multimer, however biochemical and electron microscopy studies have yielded contradictory findings regarding putative self-association. Here, we performed dynamic light scattering on syt1 in solution, followed by electron microscopy, and used atomic force microscopy to study syt1 self-association on supported lipid bilayers under aqueous conditions. Ring-like multimers were clearly observed. Multimerization was enhanced by Ca2+ and required anionic phospholipids. Large ring-like structures ([~]180 nm) were reduced to smaller rings ([~]30 nm) upon neutralization of a cluster of juxtamembrane lysine residues; further substitution of residues in the second C2-domain completely abolished self-association. When expressed in neurons, syt1 mutants with graded reductions in self-association activity exhibited concomitant reductions in: a) clamping spontaneous release, and b) triggering and synchronizing evoked release. Thus, the juxtamembrane linker of syt1 plays a crucial role in exocytosis by mediating multimerization.


title: Functional connectomics spanning multiple areas of mouse visual cortex

abstract: The value of an integrated approach for understanding the neocortex by combining functional characterization of single neuron activity with the underlying circuit architecture has been understood since the dawn of modern neuroscience. However, in practice, anatomical connectivity and physiology have been studied mostly separately. Following in the footsteps of previous studies that have combined physiology and anatomy in the same tissue, here we present a unique functional connectomics dataset that contains calcium imaging of an estimated 75,000 neurons from primary visual cortex (VISp) and three higher visual areas (VISrl, VISal and VISlm), that were recorded while a mouse viewed natural movies and parametric stimuli. The functional data were co-registered with electron microscopy (EM) data of the same volume which were automatically segmented, reconstructing more than 200,000 cells (neuronal and non-neuronal) and 524 million synapses. Subsequent proofreading of some neurons in this volume yielded reconstructions that include complete dendritic trees as well the local and inter-areal axonal projections. The largest proofread excitatory axon reached a length of 19 mm and formed 1893 synapses, while the largest inhibitory axon formed 10081 synapses. Here we release this dataset as an open access resource to the scientific community including a set of analysis tools that allows easy data access, both programmatically and through a web user interface.


title: The timescale and magnitude of aperiodic activity decreases with cortical depth in humans, macaques and mice

abstract: Cortical dynamics obey a 1/f power law, exhibiting an exponential decay of spectral power with increasing frequency. The slope and offset of this 1/f decay reflect the timescale and magnitude of aperiodic neural activity, respectively. These properties are tightly linked to cellular and circuit mechanisms (e.g. excitation:inhibition balance and firing rates) as well as cognitive processes (e.g. perception, memory, and state). However, the physiology underlying the 1/f power law in cortical dynamics is not well understood. Here, we compared laminar recordings from human, macaque and mouse cortex to evaluate how 1/f aperiodic dynamics vary across cortical layers and species. We report that 1/f slope is steepest in superficial layers and flattest in deep layers in each species. Additionally, the magnitude of this 1/f decay is greatest in superficial cortex and decreases with depth. We could account for both of these findings with a simple model in which superficial cortical transmembrane currents had longer time constants and greater densities than those in deeper layers. Together, our results provide novel insight into the organization of cortical dynamics, suggesting that the amplitude and time constant of local currents control circuit processing as a function of laminar depth. This may represent a general mechanism to facilitate appropriate integration of fast sensory inputs (infragranular) with slow feedback-type inputs (supragranular) across cortical areas and species.


title: The timescale and magnitude of 1/f aperiodic activity decreases with cortical depth in humans, macaques and mice


title: Emotional context sculpts action goal representations in the lateral frontal pole

abstract:
Emotional states provide an ever-present source of contextual information that should inform behavioral goals. Despite the ubiquity of emotional signals in our environment, the neural mechanisms underlying their influence on goal-directed action remains unclear. Prior work suggests that the lateral frontal pole (FPl) is uniquely positioned to integrate affective information into cognitive control representations. We used pattern similarity analysis to examine the content of representations in FPl and interconnected mid-lateral prefrontal and amygdala circuitry. Healthy participants (n=37; n=21 females) were scanned while undergoing an event-related Affective Go/No-Go task, which requires goal-oriented action selection during emotional processing. We found that FPl contained conjunctive emotion-action goal representations that were related to successful cognitive control during emotional processing. These representations differed from conjunctive emotion-action goal representations found in the basolateral amygdala. While robust action goal representations were present in mid-lateral prefrontal cortex, they were not modulated by emotional valence. Finally, converging results from functional connectivity and multivoxel pattern analyses indicated that FPls emotional valence signals likely originated from interconnected subgenual ACC (BA25), which was in turn functionally coupled with the amygdala. Thus, our results identify a key pathway by which internal emotional states influence goal-directed behavior.

Significance statementOptimal functioning in everyday life requires behavioral regulation that flexibly adapts to dynamically changing emotional states. However, precisely how emotional states influence goal-directed action remains unclear. Unveiling the neural architecture that supports emotion-goal integration is critical for our understanding of disorders such as psychopathy, which is characterized by deficits in incorporating emotional cues into goals, as well as mood and anxiety disorders, which are characterized by impaired goal-based emotion regulation. Our study identifies a key circuit through which emotional states influence goal-directed behavior. This circuitry comprised the lateral frontal pole (FPl), which represented integrated emotion-goal information, as well as interconnected amygdala and subgenual ACC, which conveyed emotional signals to FPl.


title: Evaluating the Effect of Semantic Congruency and Valence on Multisensory Integration

abstract: Previous studies demonstrate that semantics, the higher level meaning of multi-modal stimuli, can impact multisensory integration. Valence, an affective response to images, has not yet been tested in non-priming response time (RT) or temporal order judgement (TOJ) tasks. This study aims to investigate both semantic congruency and valence of non-speech audiovisual stimuli on multisensory integration via RT and TOJ tasks (assessing processing speed (RT), point of subjective simultaneity (PSS), and time-window when multisensory stimuli are likely to be perceived as simultaneous (Temporal Binding Window; TBW)). Forty participants (mean age: 26.25; females=17) were recruited from Prolific Academic resulting in 37 complete datasets. Both congruence and valence have a significant main effect on RT (congruent and high valence decrease RT) as well as an interaction effect (congruent/high valence condition being significantly faster than all others). For TOJ, images high in valence require visual stimuli to be presented significantly earlier than auditory stimuli in order for the audio and visual stimuli to be perceived as simultaneous. Further, a significant interaction effect of congruence and valence on the PSS revealed that the congruent/high valence condition was significantly earlier than all other conditions. A subsequent analysis shows there is a positive correlation between the TBW width (b-values) and RT (as the TBW widens, the RT increases) for the categories that differed most from 0 in their PSS (Congruent/High and Incongruent/Low). This study provides new evidence that supports previous research on semantic congruency and presents a novel incorporation of valence into behavioural responses.


title: Early Life Adversity in Male Mice Sculpts Reward Circuits.

abstract: Early life adversity (ELA) comprises a wide variety of negative experiences during early life and has been linked to cognitive impairments, reduced experiences of pleasure (anhedonia), and other long-term consequences implying that ELA impacts the reward circuitry. In this study, we focused on the projections from the dorsal raphe (DR) to the ventral tegmental area (VTA) and on to the nucleus accumbens (NAcc), an important pathway within the reward circuit. We hypothesized that ELA alters connectivity within the DR-VTA- NAcc pathway, manifested behaviorally as anhedonia in adulthood. We used the limited bedding and nesting model to induce ELA in mice and measured reward-related behaviors in adulthood using the three-chamber social interaction and sucrose preference tests. High resolution ex vivo diffusion tensor imaging (DTI) was acquired and processed for regional DTI metrics, including tractography to assess circuit organization. We found brain-wide changes in radial diffusivity (RD) and altered connectivity of the reward circuit in the ELA group. DR-VTA-NAcc circuit tractography and axial diffusivity (AD) along this tract exhibited dispersed organization where AD was increased in the VTA segment. Behaviorally, ELA elicited an anhedonic phenotype in adulthood with decreased direct social approach and time spent with peer but no overt differences in sucrose preference test. Our findings suggest that reward circuits, assessed using DTI, are altered following ELA and that these changes may drive enduring reward deficits.


title: TREM2 interacts with TDP-43 and mediates microglial neuroprotection against TDP-43-related neurodegeneration

abstract: Triggering receptor expressed on myeloid cell 2 (TREM2) is a surface receptor that, in the central nervous system, is exclusively expressed on microglia. TREM2 variants have been linked to increased risk for neurodegenerative diseases, but the functional effects of microglial TREM2 remain largely unknown. To this end, we investigated TAR-DNA binding protein 43 kDa (TDP-43)-related neurodegenerative disease via viral-mediated expression of human TDP-43 protein (hTDP-43) in neonatal and adult mice or inducible expression of hTDP43 with defective nuclear localization signals in transgenic mice. We found that TREM2 deficiency impaired microglia phagocytic clearance of pathological TDP-43, and enhanced neuronal damage and motor function impairments. Mass cytometry analysis revealed that hTDP-43 induced a TREM2-dependent subpopulation of microglia with high CD11c expression and higher phagocytic ability. Using mass spectrometry and surface plasmon resonance analysis, we further demonstrated an interaction between TDP-43 and TREM2, in vitro and in vivo, in hTDP-43-expressing transgenic mouse brains. We computationally identified the region within hTDP-43 that interacts with TREM2 and observed the potential interaction in ALS patient tissues. Our data reveal the novel interaction between TREM2 and TDP-43, highlighting that TDP-43 is a possible ligand for microglial TREM2 and the interaction mediates neuroprotection of microglial TREM2 in TDP-43-related neurodegeneration.


title: Multi-tier mechanics control stromal adaptations in swelling lymph nodes

abstract: Lymph nodes (LNs) comprise two main structural elements: Fibroblastic reticular cells (FRCs) that form dedicated niches for immune cell interaction and capsular fibroblasts that build a shell around the organ. While LNs are fairly stable in size during homeostatic conditions, immunological challenge causes more than 10-fold increase in size within only a few days. How a solid organ can accommodate such extreme volumetric changes is poorly understood. Here, we characterize the biomechanics of LN swelling on the cellular and organ scale. We identify lymphocyte trapping by influx and proliferation as drivers of an outward pressure force, causing FRCs and their associated conduits to stretch. After an initial phase of relaxation, FRCs sense the resulting strain via cell matrix adhesions, which coordinates local growth and remodeling of the stromal network. While the expanded FRC network adopts its typical configuration, a massive fibrotic reaction of the organ capsule sets in and counters further organ expansion. Thus, different fibroblast populations mechanically control LN swelling in a multi-tier fashion.

category: immunology


title: Systems analysis of immune responses to attenuated P. falciparum malaria sporozoite vaccination reveals excessive inflammatory signatures correlating with impaired immunity

abstract: Immunization with radiation-attenuated sporozoites (RAS) can confer sterilizing protection against malaria, although the mechanisms behind this protection are incompletely understood. We performed a systems biology analysis of samples from the Immunization by Mosquito with Radiation Attenuated Sporozoites IMRAS) trial, which comprised P. falciparum RAS-immunized (PfRAS), malaria-naive participants whose protection from malaria infection was subsequently assessed by controlled human malaria infection (CHMI). Blood samples collected after initial PfRAS immunization were analyzed to compare immune responses between protected and non-protected volunteers leveraging integrative analysis of whole blood RNA-seq, high parameter flow cytometry, and single cell CITEseq of PBMCs. This analysis revealed differences in early innate immune responses indicating divergent paths associated with protection. In particular, elevated levels of inflammatory responses early after the initial immunization were detrimental for the development of protective adaptive immunity. Specifically, non-classical monocytes and early type I interferon responses induced within 1 day of PfRAS vaccination correlated with impaired immunity. Non-protected individuals also showed an increase in Th2 polarized T cell responses whereas we observed a trend towards increased Th1 and T-bet+ CD8 T cell responses in protected individuals. Temporal differences in genes associated with natural killer cells suggest an important role in immune regulation by these cells. These findings give insight into the immune responses that confer protection against malaria and may guide further malaria vaccine development.


title: PLB-985 neutrophil-like cells release antifungal extracellular vesicles against the human-pathogenic fungus Aspergillus fumigatus

abstract:
Fungal infections remain a major global concern. Emerging fungal pathogens and increasing rates of resistance mean that additional research efforts and resources must be allocated to advancing our understanding of fungal pathogenesis and developing new therapeutic interventions. Neutrophilic granulocytes are a major cell type involved in protection against the important fungal pathogen Aspergillus fumigatus, where they employ numerous defense mechanisms, including production of antimicrobial extracellular vesicles. A major draw-back to work with neutrophils is the lack of a suitable cell line system for the study of fungal pathogenesis. To address this problem, we assessed the feasibility of using differentiated PLB-985 neutrophil-like cells as an in vitro model to study A. fumigatus infection. We find that dimethylformamide-differentiated PLB-985 cells provide a useful recapitulation of many aspects of A. fumigatus interactions with primary human polymorphonuclear leukocytes. We show that differentiated PLB-985 cells phagocytose fungal conidia and acidify conidia-containing phagolysosomes similar to primary neutrophils, release neutrophil extracellular traps, and also produce antifungal extracellular vesicles in response to infection. In addition, we provide an improved method for the isolation of extracellular vesicles produced during infection by employing a size-exclusion chromatography-based approach. Advanced LC-MS/MS proteomics revealed an enrichment of extracellular vesicle marker proteins and a decrease of cytoplasmic proteins in extracellular vesicles isolated using this improved method. Ultimately, we find that differentiated PLB-985 cells can serve as a genetically tractable model to study many aspects of A. fumigatus pathogenesis.

IMPORTANCEPolymorphonuclear leukocytes are an important defense against human fungal pathogens, yet our model systems to study this group of cells remains very limited in scope. In this study, we established that differentiated PLB-985 cells can serve as a model to recapitulate several important aspects of human polymorphonuclear leukocyte interactions with the important human fungal pathogen Aspergillus fumigatus. The proposed addition of a cultured neutrophil-like cell line to the experimental toolbox to study fungal pathogenesis will allow for a more mechanistic description of neutrophil antifungal biology. In addition, the easier handling of the cell line compared to primary human neutrophils allowed us to use PLB-985 cells to provide an improved method for isolation of neutrophil-derived extracellular vesicles using size-exclusion chromatography. Together, these results provide significant tools and a baseline knowledge for the future study of neutrophil-derived extracellular vesicles in the laboratory.


title: PLB-985 neutrophil-like cells as a model to study Aspergillus fumigatus pathogenesis


title: Full-length, single-cell RNA-sequencing of human bone marrow subpopulations reveals hidden complexity

abstract:
Bone marrow progenitor cell differentiation has frequently been used as a model for studying cellular plasticity and cell-fate decisions. Recent analysis at the level of single-cells has expanded knowledge of the transcriptional landscape of human hematopoietic cell lineages. Using single-molecule real-time (SMRT) full-length RNA sequencing, we have previously shown that human bone marrow lineage-negative (Lin-neg) cell populations contain a surprisingly diverse set of mRNA isoforms. Here, we report from single cell, full-length RNA sequencing that this diversity is also reflected at the single-cell level. From fresh human bone marrow unselected and lineage-negative progenitor cells were isolated by droplet-based single-cell selection (10xGenomics). The single cell-derived mRNAs were analyzed by full-length SMRT and short-read sequencing. In both samples we detected an average of 8000 different genes using short-read sequencing. Differential expression analysis arranged the single-cells of the total bone marrow into only four clusters whereas the Lin-neg population was much more diverse with nine clusters. mRNA isoform analysis of the single-cell populations using full-length sequencing revealed that Lin-neg cells contain on average 24% more novel splice variants than the total bone marrow cells. Interestingly, among the most frequent genes expressing novel isoforms were members of the spliceosome, e.g. HNRNPs, DEAD box helicases and SRSFs. Mapping the isoforms from all genes to the cell type clusters revealed that total bone marrow cells express novel isoforms only in a small subset of clusters. On the other hand, lineage-negative progenitor cells expressing novel isoforms were present in nearly all subpopulations. In conclusion, on a single-cell level lineage-negative cells express a higher diversity of genes and more alternatively spliced novel isoforms suggesting that cells in this subpopulation are poised for different fates.

Graphical abstract

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title: A systematic review and meta-analysis of the potential non-human animal reservoirs and arthropod vectors of the Mayaro virus

abstract:
Improving our understanding of Mayaro virus (MAYV) ecology is critical to guide surveillance and risk assessment. We conducted a PRISMA-adherent systematic review of the published and grey literature to identify potential arthropod vectors and non-human animal reservoirs of MAYV. We searched PubMed, Embase, Web of Science, SciELO and grey-literature sources including PAHO databases and dissertation repositories. Studies were included if they assessed MAYV virological/immunological measured occurrence in field-caught, domestic, or sentinel animals or in field-caught arthropods. We conducted an animal seroprevalence meta-analysis using a random effects model. We compiled granular georeferenced maps of non-human MAYV occurrence and graded the quality of the studies using a customized framework. Overall, 57 studies were eligible out of 1523 screened, published between the years 1961 and 2020. Seventeen studies reported MAYV positivity in wild mammals, birds, or reptiles and five studies reported MAYV positivity in domestic animals. MAYV positivity was reported in 12 orders of wild-caught vertebrates, most frequently in the orders Charadriiformes and Primate. Sixteen studies detected MAYV in wild-caught mosquito genera including Haemagogus, Aedes, Culex, Psorophora, Coquillettidia, and Sabethes. Vertebrate animals or arthropods with MAYV were detected in Brazil, Panama, Peru, French Guiana, Colombia, Trinidad, Venezuela, Argentina, and Paraguay. Among non-human vertebrates, the Primate order had the highest pooled prevalence (PP) at 13.1% (95% CI: 4.3-25.1%). From the three most studied primate genera we found the highest prevalence was in Alouatta (PP: 32.2%, 95% CI: 0.0-79.2%), followed by Callithrix (PP: 17.8%, 95% CI: 8.6-28.5%), and Cebus/Sapajus (PP: 3.7%, 95% CI: 0.0-11.1%). We further found that MAYV occurs in a wide range of vectors beyond Haemagogus spp. The quality of evidence behind these findings was variable and prompts calls for standardization of reporting of arbovirus occurrence. These findings support further risk emergence prediction, guide field surveillance efforts, and prompt further in-vivo studies to better define the ecological drivers of MAYV maintenance and potential for emergence.

Author SummaryMayaro virus (MAYV) is an emerging tropical public health threat in the Americas. We conducted a georeferenced, quality-graded systematic review to evaluate the current evidence regarding MAYV occurrence in non-human vertebrates and arthropods. Overall, 57 studies were eligible out of 1523 screened, published between the years 1961 and 2020. Seventeen studies reported MAYV positivity in wild mammals, birds, or reptiles and five studies reported MAYV positivity in domestic animals. MAYV positivity was reported in 12 orders of wild-caught vertebrates, most frequently in the orders Charadriiformes and Primate. Our systematic review identified 12 orders of wild-caught vertebrates and seven mosquito genera with evidence of MAYV occurrence. Primates had the highest pooled MAYV prevalence according to a seroprevalence meta-analysis. The graded quality of evidence behind these findings was variable and prompts calls for standardization of reporting of MAYV and perhaps other emerging arbovirus occurrence in animals and vectors. This study provides important information for public health authorities and disease ecologists concerned with the growing threat of MAYV in Latin America. Our analysis provides a foundation for future laboratory and field studies focused on the MAYV transmission cycle.


title: Evolutionary dynamics of asexual hypermutators adapting to a novel environment

abstract:
How microbes adapt to a novel environment is a central question in evolutionary biology. While adaptive evolution must be fueled by beneficial mutations, whether higher mutation rates facilitate the rate of adaptive evolution remains unclear. To address this question, we cultured Escherichia coli hypermutating populations, in which a defective methyl-directed mismatch repair pathway causes a 140-fold increase in single-nucleotide mutation rates. In parallel with wild-type E. coli, populations were cultured in tubes containing Luria-Bertani broth, a complex medium known to promote the evolution of subpopulation structure. After 900 days of evolution, in three transfer schemes with different population-size bottlenecks, hypermutators always exhibited similar levels of improved fitness as controls. Fluctuation tests revealed that the mutation rates of hypermutator lines converged evolutionarily on those of wild-type populations, which may have contributed to the absence of fitness differences. Further genome-sequence analysis revealed that, although hypermutator populations have higher rates of genomic evolution, this largely reflects the effects of genetic draft under strong linkage. Despite these linkage effects, the evolved populations exhibit parallelism in fixed mutations, including those potentially related to biofilm formation, transcription regulation, and mutation-rate evolution. Together, these results generally negate the presumed relationship between high mutation rates and high adaptive speed of evolution, providing insight into how clonal adaptation occurs in novel environments.

Significance statementWhile mutations are critical source for the adaptation in a new environment, whether or not the elevated mutation rates can empirically lead to the elevated adaptation rates remains unclear, especially when the environment is more heterogenous. To answer this question, we evolved E. coli populations with different starting mutation rates in a complex medium for 900 days and then examined their fitness and genome profiles. In the populations that have a higher starting mutation rate, despite faster genome evolution, their fitness improvement is not significantly faster. Our results reveal that the effect of elevated mutation rates is only very limited, and the mutations accumulated in hypermutators are largely due to linkage effect.


title: Estimating dispersal using close kin dyads: The KINDISPERSE R package

abstract: Investigating dispersal in animal populations can be difficult, particularly for taxa that are hard to directly observe such as those that are small or rare. A promising solution may come from new approaches that use genome-wide sequence data to detect close kin dyads and estimate dispersal parameters from the distribution of these dyads. These methods have so far only been applied to mosquito populations. However, they should have broad applicability to a range of taxa, although no assessment has yet been made on their performance under different dispersal conditions and study designs. Here we develop an R package and Shiny app, O_SCPLOWKINDISPERSEC_SCPLOW, that can be used to estimate dispersal parameters from the spatial distribution of close kin. KO_SCPLOWINDISPERSEC_SCPLOW can handle study designs that target different life stages and allows for a range of dispersal kernel shapes and organismal life histories; we provide implementation examples for a vertebrate (Antechinus) and an invertebrate (Aedes). We use simulations run in O_SCPLOWKINDISPERSEC_SCPLOW to compare the performance of two published close kin methodologies, showing that one method produces unbiased estimates whereas the other produces downward-biased estimates. We also use O_SCPLOWKINDISPERSEC_SCPLOW simulations to investigate how study design affects dispersal estimates, and we provide guidelines for the size and shape of sample sites as well as the number of close kin needed for accurate estimates. O_SCPLOWKINDISPERSEC_SCPLOW is easily adaptable for application to a variety of research contexts ranging from invasive pests to threatened species where non-invasive DNA sampling can be used to detect close kin.

category: genetics


title: The swine spatiotemporal H3K27ac spectrum provides novel resources for exploring gene regulation related to complex traits and fundamental biological process

abstract: The limited knowledge of genomic non-coding and regulatory regions has limited our ability to decipher the genetic mechanisms underlying complex traits in pigs. In this study, we characterize the spatiotemporal landscape of putative enhancers and promoters and their target genes by combining H3K27ac targeted ChIP-Seq and RNA-Seq in fetal (day 74-75 pc) and adult (day 132-150 pn) tissues (brain, liver, heart, muscle and small intestine) sampled from Asian aboriginal Bamaxiang and European highly selected Large White pigs of both sexes. We identify 101,290 H3K27ac peaks marking 18,521 promoters and 82,769 enhancers, including peaks that are active across all tissues and developmental stages could indicate safe harbors for exogenous gene insertion, and tissue and developmental-stage specific peaks that regulate genes pathways matching tissue and developmental stage specific physiological functions. We found H3K27ac and DNA methylation in the promoter region of the XIST gene may involve in X chromosome inactivation, and demonstrate utility of the present resource to reveal regulatory patterns of known causal genes and to prioritize candidate causal variants for complex traits in pigs. We have developed a web browser to improve the accessibility of the results (http://39.108.231.116/browser/?genome=susScr11).


title: Outcome-selective reinstatement is partially context-dependent, and associated with c-Fos activation in the posterior dorsomedial striatum

abstract:
Research from human and animal studies has found that responding that has been successfully reduced following treatment can return upon exposure to certain contexts. An individual in recovery from alcohol use disorder, for example, might relapse to drinking upon visiting their favourite bar. However, most of these data have been derived from experiments involving a single (active) response, and the context-dependence of returned responding in situations involving choice between multiple actions and outcomes is less well-understood. We thus investigated how outcome-selective reinstatement - a procedure involving choice between multiple actions - was affected by altering the physical context in rats. In Experiment 1, rats were trained over 6 days to press a left lever for one food outcome (pellets or sucrose) and a right lever for the other outcome. Then, rats received an extinction session in either the same context (A) as lever press training, or in a different context (B). Rats were tested immediately (5 minutes) after extinction in Context A or B such that there were four groups in total: AAA, ABB, ABA, and AAB. Reinstatement testing consisted of one food outcome being delivered  freely (i.e. unearned by lever pressing and unsignalled by cues) to the food magazine every 4 minutes in the following order: Sucrose, Pellet, Pellet, Sucrose. Selective reinstatement was considered intact if pellet delivery increased pressing selectively on the pellet lever, and sucrose delivery selectively increased pressing on the sucrose lever. This result (Reinstated > Nonreinstated) was observed for rats in group AAA and ABB, but not rats in groups ABA and AAB. Experiment 2 was conducted identically, except that rats received two extinction sessions over two days and tested one day later. This time, all groups demonstrated intact outcome-selective reinstatement regardless of context. Analysis of c-Fos expression in several brain regions revealed that only c-Fos expression in the posterior dorsomedial striatum (pDMS) was related to intact reinstatement performance. Overall, these results suggest that outcome-selective reinstatement is predominantly context-independent, and that intact reinstatement is related to neuronal activity in the pDMS.

HighlightsO_LIOutcome-selective reinstatement is predominantly context-independent
C_LIO_LIOutcome-selective reinstatement is entirely context-independent after multiple extinction sessions
C_LIO_LIOutcome-selective reinstatement increases c-Fos expression in dorsomedial striatum
C_LIO_LIc-Fos expression in orbitofrontal cortex and dorsal hippocampus is unaffected by selective reinstatement.
C_LI

category: animal behavior and cognition


title: Outcome-selective reinstatement is predominantly context-independent, and associated with c-Fos activation in the posterior dorsomedial striatum


title: Hormonal contraceptives alter amphetamine place preference and responsivity in the intact female rat.

abstract: Hormonal contraceptives (HCs) are commonly used among reproductive aged women and alter the physiological state of the user by interfering with endogenous hormone concentrations and their actions on the reproductive tract. As hormones such as estradiol and progesterone modulate the incidence of substance abuse disorders in women, it is important to consider the influence HCs have on the female brain and behavior. This experiment explores how female sex steroid hormonal states associated with the rat estrous cycle, and modulating those states with HCs, influences measures of drug preference and responsivity. First, rats underwent food-light Pavlovian conditioning to measure conditioned orienting, a known predictor of amphetamine (AMP) place preference. Then, rats were conditioned and tested for AMP place preference with either an HC-implant or during estrous cycle stages associated with different ovarian hormone levels (i.e., proestrus (P) or metestrus/diestrus (M/D) while recording ultrasonic vocalizations (USVs) as an index of hedonic responsivity. Because of dopamines (DA) role in modulation of AMP actions, DA cell activity and availability were examined using tyrosine hydroxylase and FOS immunohistochemistry after final AMP challenge. Conditioned orienting did not differ between cycling and HC-implanted. P rats emitted more USVs during conditioning, showed higher AMP place preference throughout testing, and had higher DA cell activity in the substantia nigra compared to M/D and HC-implanted rats. Sex steroid hormone serum concentration and uterine horn thickness predicted some but not all of these measures. This experiment suggests ovarian hormones affect drug preference and responsivity, while providing novel insight into how hormone-altering contraceptives may reduce these measures.


title: Using Bayesian Inference to Estimate Plausible Muscle Forces in Musculoskeletal Models

abstract:
BackgroundMusculoskeletal modeling is currently a preferred method for estimating the muscle forces that underlie observed movements. However, these estimates are sensitive to a variety of assumptions and uncertainties, which creates difficulty when trying to interpret the muscle forces from musculoskeletal simulations. Here, we describe an approach that uses Bayesian inference to identify plausible ranges of muscle forces for a simple motion while representing uncertainty in the measurement of the motion and the objective function used to solve the muscle redundancy problem.

MethodsWe generated a reference elbow flexion-extension motion by simulating a set of muscle excitation signals derived from the computed muscle control tool built into OpenSim. We then used a Markov Chain Monte Carlo (MCMC) algorithm to sample from a posterior probability distribution of muscle excitations that would result in the reference elbow motion trajectory. We constructed a prior over the excitation parameters which down-weighted regions of the parameter space with greater muscle excitations. We used muscle excitations to find the corresponding kinematics using OpenSim, where the error in position and velocity trajectories (likelihood function) was combined with the sum of the cubed muscle excitations integrated over time (prior function) to compute the posterior probability density.

ResultsWe evaluated the muscle forces that resulted from the set of excitations that were visited in the MCMC chain (five parallel chains, 450,000 iterations per chain, runtime = 71 hours). The estimated muscle forces compared favorably with the reference motion from computed muscle control, while the elbow angle and velocity from MCMC matched closely with the reference with an average RMSE for angle and velocity equal to 0.008{degrees} and 0.18{degrees}/s, respectively. However, our rank plot analysis and potential scale reduction statistics, which we used to evaluate convergence of the algorithm, indicated that the parallel chains did not fully mix.

ConclusionsWhile the results from this process are a promising step towards characterizing uncertainty in muscle force estimation, the computational time required to search the solution space with, and the lack of MCMC convergence indicates that further developments in MCMC algorithms are necessary for this process to become feasible for larger-scale models.


title: InDeep : 3D fully convolutional neural networks to assist in silico drug design on protein-protein interactions

abstract:
AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSMotivationC_ST_ABSProtein-protein interactions (PPIs) are key elements in numerous biological pathways and the subject of a growing number of drug discovery projects including against infectious diseases. Designing drugs on PPI targets remains a difficult task and requires extensive efforts to qualify a given interaction as an eligible target. To this end, besides the evident need to determine the role of PPIs in disease-associated pathways and their experimental characterization as therapeutics targets, prediction of their capacity to be bound by other protein partners or modulated by future drugs is of primary importance.

ResultsWe present InDeep, a tool for predicting functional binding sites within proteins that could either host protein epitopes or future drugs. Leveraging deep learning on a curated data set of PPIs, this tool can proceed to enhanced functional binding site predictions either on experimental structures or along molecular dynamics trajectories. The benchmark of InDeep demonstrates that our tool outperforms state of the art ligandable binding sites predictors when assessing PPI targets but also conventional targets. This offers new opportunities to assist drug design projects on PPIs by identifying pertinent binding pockets at or in the vicinity of PPI interfaces.

AvailabilityThe tool is available on GitHub3 along with a PyMol plugin for visualization. Predictions of InDeep can be consulted at iPPI-DB4


title: EffectorP 3.0: prediction of apoplastic and cytoplasmic effectors in fungi and oomycetes

abstract: Many fungi and oomycete species are devasting plant pathogens. These eukaryotic filamentous pathogens secrete effector proteins to facilitate plant infection. Fungi and oomycete pathogens have diverse infection strategies and their effectors generally do not share sequence homology. However, they occupy similar host environments, either the plant apoplast or plant cytoplasm, and may therefore share some unifying properties based on the requirements of these host compartments. Here we exploit these biological signals and present the first classifier (EffectorP 3.0) that uses two machine learning models: one trained on apoplastic effectors and one trained on cytoplasmic effectors. EffectorP 3.0 accurately predicts known apoplastic and cytoplasmic effectors in fungal and oomycete secretomes with low estimated false positive rates of 3% and 8%, respectively. Cytoplasmic effectors have a higher proportion of positively charged amino acids, whereas apoplastic effectors are enriched for cysteine residues. The combination of fungal and oomycete effectors in training leads to a higher number of predicted cytoplasmic effectors in biotrophic fungi. EffectorP 3.0 expands predicted effector repertoires beyond small, cysteine-rich secreted proteins in fungi and RxLR-motif containing secreted proteins in oomycetes. We show that signal peptide prediction is essential for accurate effector prediction, as EffectorP 3.0 recognizes a cytoplasmic signal also in intracellular, non-secreted proteins. EffectorP 3.0 is available at http://effectorp.csiro.au.


title: Automated Reconstruction of Whole-Embryo Cell Lineages by Learning from Sparse Annotations

abstract: We present a method for automated nucleus identification and tracking in time-lapse microscopy recordings of entire developing embryos. Our method combines deep learning and global optimization to enable complete lineage reconstruction from sparse point annotations, and uses parallelization to process multi-terabyte light-sheet recordings, which we demonstrate on three common model organisms: mouse, zebrafish, Drosophila. On the most difficult dataset (mouse), our method correctly reconstructs 75.8% of cell lineages spanning 1 hour, compared to 31.8% for the previous state of the art, thus enabling biologists to determine where and when cell fate decisions are made in developing embryos, tissues, and organs.