title: A within-host infection model to explore tolerance andresistance

abstract: How are some individuals surviving infections while others die? The answer lies in how infected individuals invest into controlling pathogen proliferation and mitigating damage, two strategies respectively called resistance and disease tolerance. Pathogen within-host dynamics (WHD), influenced by resistance, and its connection to host survival, determined by tolerance, decide the infection outcome. To grasp these intricate effects of resistance and tolerance, we used a deterministic theoretical model where pathogens interact with the immune system of a host. The model describes the positive and negative regulation of the immune response, consider the way damage accumulate during the infection and predicts WHD. When chronic, infections stabilize at a Set-Point Pathogen Load (SPPL). Our model predicts that this situation can be transient, the SPPL being then a predictor of life span which depends on initial condition (e.g. inoculum). When stable, the SPPL is rather diagnostic of non lethal chronic infections. In lethal infections, hosts die at a Pathogen Load Upon Death (PLUD) which is almost independent from the initial conditions. As the SPPL, the PLUD is affected by both resistance and tolerance but we demonstrate that it can be used in conjunction with mortality measurement to distinguish the effect of disease tolerance from that of resistance. We validate empirically this new approach, using Drosophila, melanogaster and the pathogen Providencia rettgeri.


title: Machine Learning Prediction of Non-Coding Variant Impact in Human Retinal Cis-Regulatory Elements

abstract:
PurposePrior studies demonstrate the significance of specific cis-regulatory variants in retinal disease, however determining the functional impact of regulatory variants remains a major challenge. In this study, we utilize a machine learning approach, trained on epigenomic data from the adult human retina, to systematically quantify the predicted impact of cis-regulatory variants.

MethodsWe used human retinal DNA accessibility data (ATAC-seq) to determine a set of 18.9k high-confidence putative cis-regulatory elements. 80% of these elements were used to train a machine learning model utilizing a gapped k-mer support vector machine-based approach. In silico saturation mutagenesis and variant scoring was applied to predict the functional impact of all potential single nucleotide variants within cis-regulatory elements. Impact scores were tested in a 20% hold-out dataset and compared to allele population frequency, phylogenetic conservation, transcription factor (TF) binding motifs, and existing massively parallel reporter assay (MPRA) data.

ResultsWe generated a model that distinguishes between human retinal regulatory elements and negative test sequences with 95% accuracy. Among a hold-out test set of 3.7k human retinal CREs, all possible single nucleotide variants (SNVs) were scored. Variants with negative impact scores correlated with reduced population allele frequency, higher phylogenetic conservation of the reference allele, disruption of predicted TF binding motifs, and massively-parallel reporter expression.

ConclusionsWe demonstrated the utility of human retinal epigenomic data to train a machine learning model for the purpose of predicting the impact of non-coding regulatory sequence variants. Our model accurately scored sequences and predicted putative transcription factor binding motifs. This approach has the potential to expedite the characterization of pathogenic non-coding sequence variants in the context of unexplained retinal disease.

category: genomics


title: Freestanding Hydrogel Lumens for Biological Assays

abstract: Lumen structures exist throughout the human body, and the vessels of the circulatory system are essential for carrying nutrients and oxygen and regulating inflammation. Vasodilation, the widening of the blood vessel lumen, is important to the immune response as it increases blood flow to a site of inflammation, raises local temperature, and enables optimal immune system function. A common method for studying vasodilation uses excised vessels from animals; major drawbacks include heterogeneity in vessel shape and size, time-consuming procedures, sacrificing animals, and differences between animal and human biology. We have developed a simple, userfriendly in vitro method to form freestanding cell-laden hydrogel rings from collagen and quantitatively measure the effects of vasodilators on ring size. The hydrogel rings are composed of collagen I and can be laden with human vascular smooth muscle cells, a major cellular and structural component of blood vessels, or lined with endothelial cells in the lumen. The methods presented include a 3D printed device (which is amenable to future fabrication by injection molding) and commercially available components (e.g., Teflon tubing or a syringe) to form hydrogel rings between 2.6-4.6 mm outer diameter and 0.79-1.0 mm inner diameter. Here we demonstrate a significant difference in ring area in the presence of a known vasodilator, fasudil (p<0.0001). Our method is easy to implement and provides a medium-throughput solution to generating vessel model structures for future investigations of the fundamental mechanisms of vasodilation (e.g., studying uncharacterized endogenous molecules that may have vasoactivity) and testing vasoactive drugs.

category: bioengineering


title: CandyCollect: At-home saliva sampling for respiratory pathogen capture

abstract: Streptococcus pyogenes is a major human-specific bacterial pathogen and a common cause of a wide range of symptoms from mild infection such as pharyngitis (commonly called strep throat) to lifethreatening invasive infection. Traditional methods for diagnosis include collecting a sample using a pharyngeal swab, which can cause discomfort and even discourage adults and children from seeking proper testing and treatment in the clinic. Saliva samples are an alternative to pharyngeal swabs. To improve the testing experience for strep throat, we developed a novel lollipop-inspired sampling platform (called CandyCollect) to capture bacteria in saliva. The device can be used in clinics or in the home and shipped back to a lab for analysis, integrating with telemedicine. CandyCollect is designed to capture bacteria on an oxygen plasma treated polystyrene surface embedded with flavoring substances to enhance the experience for children and inform the required time to complete the sampling process. In addition, the open channel structure prevents the tongue from scraping and removing the captured bacteria. Flavoring substances did not affect bacterial capture and the device has a shelf life of at least 2 months (with experiments ongoing to extend the shelf life). We performed a usability study with 17 participants who provided feedback on the device design and the dissolving time of the candy. This technology and advanced processing techniques, including polymerase chain reaction (PCR), will enable user-friendly and effective diagnosis of streptococcal pharyngitis.


title: CandyCollect: At-home saliva sampling for capture of respiratory pathogens


title: Ligand geometry dictates cellular and in vivo uptake of 3D DNA nanostructures

abstract: Fabrication of nanoscale DNA devices to generate 3D nano-objects with precise control of shape, size, and presentation of ligands has shown tremendous potential for therapeutic applications. The interactions between different topologies of 3D DNA nanostructures and the cell membranes are crucial for designing efficient tools for interfacing DNA devices with biological systems. The practical applications of these DNA nanocages are still limited in cellular and biological systems owing to the limited understanding of interactions of different surface topologies of DNA nanodevices with cell membranes. The correlation between the geometry of DNA nanostructures and their internalization efficiency remains elusive. We investigated the influence of the shape and size of 3D DNA nanostructure on their cellular internalization efficiency. We found that of different geometries designed, one particular geometry, i.e., the tetrahedral shape, is more favoured over other geometries for their cellular uptake in 2D and 3D cell models. This is also replicable for cellular processes like 3D cell invasion assays in 3D spheroid models and passing the epithelial barriers in in-vivo zebrafish model systems. Our work establishes ground rules for the rational designing of DNA nanodevices for their upcoming biological and biomedical applications.


title: Novel graph theoretic biological pathway network analytics methods for analyzing and discovering Alzheimer's disease related genes

abstract:
BackgroundAlzheimers disease (AD) is the most common form of dementia among older people. It is a complex disease and the genetics and environmental factors behind it are not conclusive yet. Traditional statistical analyses are inadequate to identify variants, genes, or pathways capable of explaining AD as a unit. In this context, pathway network analysis based on a set of curated AD-specific genes identified in the literature can elucidate biological mechanisms underneath AD. Through the network, we can infer influential pathways that can together explain AD. Consequently, we can target those pathways and corresponding genes for further analysis to develop new drugs, discover novel AD-related genes, combine multiple hypotheses, and so forth.

MethodsWe have developed a novel graph theoretic algorithm that can elucidate complex biology from a given set of disease-related genes. It constructs a weighted network of enriched pathways where similarity score between a pair of pathways is defined in a context-specific manner. To make the network robust, we employ topological overlap techniques on top of the raw similarity measure. We then provide the importance of each pathway with respect to the entire network, functional modules and importance of each pathway in a specific module, gene clusters, and so forth. We also provide a method to identify a set of novel genes that can further explain the disease-related genes and the disease itself.

ResultsWe have employed our algorithms onto a set of AD-specific genes. It identified three distinct functional modules that are related to metabolism, cancer, and infectious disease related pathways. These findings are matched with three recognized hypotheses in Alzheimers disease, e.g. "metabolism hypothesis," "cell cycle hypothesis," and "infectious disease hypothesis." By analyzing the curated genes common among those functional modules, we can attain more understanding about this fateful disease. We have also identified 24 novel AD-related genes of which at least 14 genes are known to be involved in AD.

ConclusionsWe developed a computational framework for analyzing biological pathways in a context-specific manner. It can be used in any sets of disease-related genes. We manifest its efficacy, reliability, and accuracy by employing a set of AD-specific genes.

category: bioinformatics


title: KIMGENS: A novel method to estimate kinship in organisms with mixed haploid diploid genetic systems robust to population structure

abstract:
MotivationKinship estimation is necessary for evaluating violations of assumptions or testing certain hypotheses in many population genomic studies. However, kinship estimators are usually designed for diploid systems and cannot be used in populations with mixed haploid diploid genetic systems. The only estimators for different ploidies require datasets free of population structure, limiting their usage.

ResultsWe present KIMGENS, an estimator for kinship estimation among individuals of various ploidies, that is robust to population structure. This estimator is based on the popular KING-robust estimator but uses diploid relatives of the individuals of interest as references of heterozygosity and extends its use to haploid-diploid and haploid pairs of individuals. We demonstrate that KIMGENS estimates kinship more accurately than previously developed estimators in simulated panmictic, structured and admixed populations, but has lower accuracy when the individual of interest is inbred. KIMGENS also outperforms other estimators in a honeybee dataset. Therefore, KIMGENS is a valuable addition to a population geneticists toolbox.

Availability and ImplementationKIMGENS and its association simulation tool are implemented and available open-source at https://github.com/YenWenWang/HapDipKinship.

ContactYen-Wen Wang Email: ywang883@wisc.edu


title: Expanding the pool of public controls for GWAS via a method for combining genotypes from arrays and sequencing

abstract: Genome-wide association studies (GWAS) have made impactful discoveries for complex diseases, often by amassing very large sample sizes. Yet, GWAS of many diseases remain underpowered, especially for non-European ancestries. One cost-effective approach to increase sample size is to combine existing case-only cohorts with public controls, but this approach is limited by the need for a large overlap in variants across genotyping arrays and the scarcity of non-European controls. We developed and validated a protocol, Genotyping Array-WGS Merge (GAWMerge), for combining genotypes from arrays and whole genome sequencing, ensuring complete variant overlap, and allowing for diverse samples like Trans-Omics for Precision Medicine to be used. Our protocol involves phasing, imputation, and filtering. We illustrated its ability to control type I error and recover known disease-associated signals across technologies, independent datasets, and ancestries in smoking-related cohorts. GAWMerge enables genetic studies to leverage existing cohorts to validly increase sample size and enhance discovery.


title: ZipHiC: a novel Bayesian framework to identify enriched interactions and experimental biases in Hi-C data

abstract: Several computational and statistical methods have been developed to analyse data generated through the 3C-based methods, especially the Hi-C. Most of existing methods do not account for dependency in Hi-C data. Here, we present ZipHiC, a novel statistical method to explore Hi-C data focusing on detection of enriched contacts. ZipHiC implements a Bayesian method based on a hidden Markov random field (HMRF) model and the Approximate Bayesian Computation (ABC) to detect interactions in two-dimensional space based on Hi-C contact frequency matrix. ZipHiC uses data on the sources of biases related to contact frequency matrix, allows borrowing information from neighbours using the Potts model and improves computation speed by using the ABC model. In addition to outperforming existing tools on both simulated and real data, our model also provides insights into different sources of biases that affects Hi-C data. We show that some datasets display higher biases from DNA accessibility or Transposable Elements content. Furthermore, approximately half of the detected significant interactions connect promoters with other parts of the genome indicating a functional biological role. Finally, we found that the micro-C datasets display higher biases from DNA accessibility compared to a similar Hi-C experiment, but this can be corrected by ZipHiC.


title: BioCompute Objects to communicate a viral detection pipeline with potential for use in a regulatory environment

abstract: The volume of nucleic acid sequence data has exploded in recent years, and with it, the challenge of finding and transforming relevant data into meaningful information. Processing the abundance of data can require a dynamic ecosystem of customized tools. As analysis pipelines become more complex, there is an increased difficulty in communicating analysis details in a way that is understandable yet of sufficient detail to make informed decisions about results or repeat the analysis. This may be of particular interest to institutions and private companies that need to communicate complex computations in a regulatory environment. To meet this need for standard reporting, the open source BioCompute framework was developed as a standardized mechanism for communicating the details of an analysis in a concise and organized way, and other tools and interfaces were subsequently developed according to the standard. The goal of BioCompute is to streamline the process of communicating computational analyses. Reports that conform to the BioCompute standard are called BioCompute Objects (BCOs). Here, a comprehensive suite of BCOs is presented, representing interconnected elements of a computation that is modeled after those that might be found in a regulatory submission, but which can be shared publicly. Because BCOs are human and machine readable, they can be displayed in customized ways to further improve their utility, and an example of a collapsible format is shown. The work presented here serves as a real world implementation that imitates actual submissions, providing concrete examples. As an example, a pipeline designed to identify viral contaminants in biological manufacturing, such as for vaccines, is developed and rigorously tested to establish a rate of false positive detection, and is described in a BCO report. That pipeline relies on a specially curated database for alignment, and a set of synthetic reads for testing, both of which are also descriptively packaged in their own BCOs. All of the sufficiently complex processes associated with this analysis are therefore represented as BCOs that can be cross-referenced, demonstrating the modularity of BCOs, their ability to organize tremendous complexity, and their use in a lifelike regulatory environment.


title: A Computational Approach in Identification of Putative Risk Genes in Parkinsons Disease

abstract:
This study focussed on identification of risk genes involved in PD through analysis of microarray data. The two methods were applied viz; WGCNA and DEGs Analysis to identify important genes that are downregulated or upregulated in PD. Both methods show high agreement with each other and also with the available biomedical literature available on this neurodegenerative disease. On the basis of their p-value, 20 significantly upregulated and 19 significantly downregulated genes were found to be playing role in the manifestation of motor and non motor symptoms of the disease, as interpreted from the enrichment analysis.

Gene expression dataset of Parkinsons Disease (PD) used in this study was obtained from the GeneExpression Omnibus namely GSE8397, GSE20164, and GSE20295 (Edgar, 2002). Among the important genes extracted, the top downregulated and upregulated genes were studied using enrichment analysis. Out of the 19 common downregulated genes, 10 were directly associated with neuron development and differentiation. Two of the genes, FGF13 and CDC42 were associated with multiple signalling pathways. The gene NSF was found to be enriched with GABAergic synapse, associated with the predominating inhibitory neurotransmitter in the mammalian CNS. The inhibitory synapses are thought to provide a brake to neural firing.

The upregulated genes DDIT4, HSPB1, NUPR1, GPNMB and CH13L1 were enriched with apoptotic signalling pathway while MT1M, MT1E, MT1F, MT1X were associated with mineral absorption pathways. Genes like CDC42 have already been reported to be potential diagnostic markers of PD in clinic (Chi et al., 2018).


title: Cross-border investigations on the prevalence and transmission dynamics of Cryptosporidium species in dairy cattle farms in western mainland Europe

abstract: Cryptosporidium is comprised an apicomplexan parasitic protist, which infects a wide range of hosts, causing cryptosporidiosis. In cattle farms, the incidence of cryptosporidiosis results in high mortality in calves leading to considerable economic loss in the livestock industry. Infected animals may also act as a major reservoir of Cryptosporidium spp., in particular C. parvum, the most common cause of cryptosporidiosis in calves. This poses a significant risk to other farms via breeding centres, to trading of livestock and to human health. This study, funded by the Interreg-2-seas programme, is a part of a global project aimed at strategies to tackle cryptosporidiosis. To reach this target, it was essential to determine whether prevalence was dependent on the studied countries or if the issue was borderless. Indeed, C. parvum occurrence was assessed across dairy farms in certain regions of Belgium, France and the Netherlands. At the same time, the animal-to-animal transmission of the circulating C. parvum subtypes was studied. To accomplish this, 1084 faecal samples, corresponding to 57 dairy-farms from all three countries, were analysed. Well-established protocols amplifying the 18S rDNA and gp60 genes fragments, followed by DNA sequencing, were used for the detection and subtyping C. parvum; the DNA sequences obtained were further characterised using a combination of bioinformatics and phylogenetics methods. Our results show 25.7%, 24.9% and 20.8% prevalence of Cryptosporidium spp. in Belgium, France and the Netherlands respectively. Overall, 93% of the farms were Cryptosporidium positive. The gp60 subtyping demonstrated a significant number of the C. parvum positives belonged to the IIa allelic family, which has been also detected in humans. Consequently, this study highlights how widespread is C. parvum in dairy farms and endorses cattle as a major carrier of zoonotic C. parvum subtypes, which subsequently pose a significant threat to human health.

category: microbiology


title: Hysteresis in PIF4 and ELF3 dynamics dominates warm daytime memory in Arabidopsis

abstract: Plants may experience large diurnal temperature fluctuations. Our knowledge of the molecular mechanisms of integration of these fluctuations and the resulting growth patterns is limited. Here we show that hypocotyl growth during the night responded not only to the current temperature but also to preceding daytime temperatures, revealing a memory of previous conditions. Daytime temperature affected the nuclear levels of PHYTOCHROME INTERACTING FACTOR 4 (PIF4) and LONG HYPOCOTYL 5 (HY5) during the next night. These jointly accounted for the observed growth kinetics, whereas memory of prior daytime temperature was impaired in the pif4 and hy5 mutants. PIF4 promoter activity largely accounted for the temperature dependent changes in PIF4 protein levels. Noteworthy, the decrease in PIF4 promoter activity triggered by cooling required a stronger temperature shift than the increase caused by warming. This hysteretic pattern required EARLY-FLOWERING 3 (ELF3). Warm temperatures promoted the formation of nuclear condensates of ELF3 in hypocotyl cells during the afternoon but not in the morning. These nuclear speckles showed poor sensitivity to subsequent cooling. We conclude that ELF3 achieves hysteresis and drives the PIF4 promoter into the same behaviour, enabling a memory of daytime temperature conditions.

category: plant biology


title: Driving singing behaviour in songbirds using multi-modal, multi-agent virtual reality

abstract: Interactive biorobotics provides unique experimental potential to study the mechanisms underlying social communication but is limited by our ability to build expressive robots that exhibit the complex behaviours of birds and small mammals. An alternative to physical robots is to use virtual reality (VR). Here, we designed and built a modular, audio-visual virtual reality environment that allows online, multi-modal, multi-agent interaction for social communication. We tested this system in songbirds, which provide an exceptionally powerful and tractable model system to study social communication. We show that zebra finches (Taeniopygia guttata) communicating through the VR environment exhibit normal call timing behaviour, males sing female directed song and both males and females display high-intensity courtship behaviours to their mates. These results suggest that the VR system provides a sufficiently natural environment to elicit normal social communication behaviour. Furthermore, we developed a fully unsupervised online song motif detector and used it to manipulate the virtual social environment of male zebra finches based on the number of motifs sung. Our VR setup represents a first step in taking automatic behaviour annotation into the online domain and allows for animal-computer interaction using higher level behaviours such as song. Our unsupervised acoustic analysis eliminates the need for annotated training data thus reducing labour investment and experimenter bias.

category: animal behavior and cognition


title: Machine learning applied to molecular identification of Acinetobacter baumannii Global Clone 1

abstract:
Since the emergence of clones with epidemic behavior, or "high-risk clones", uninterrupted investigations have been undertaken to understand the genetic and biological basis that led their widespread in nosocomial settings at a global scale. However, its complex genetic and ecological nature only allowed the identification of partial biomarkers with low specificity. The implication of our study is that we successfully applied machine learning algorithms to recognize genetic biomarkers for the identification of Acinetobacter baumannii Global Clone 1, one of the most widespread high-risk clones. Support Vector Machine model predicted U1 sequence with 367 nucleotides length as a specific biomarker for A. baumannii GC1 strains. U1 sequence matched AYE genome in ABAYE1552 locus between 558 and 924 coordinates that corresponds to a fragment of the moaCB gene which encodes a bifunctional protein that includes the molybdenum cofactor biosynthesis protein C and protein B. This region of the gene moaCB allows to differentiate between the A. baumannii GC1 and non-GC1 strains, becoming a suitable biomarker capable of being translated into clinical settings as a molecular typing method such as PCR. Our findings highlight that machine learning can be fruitfully useful even in complex gaps of knowledge of epidemic clones and signify a noteworthy contribution to the literature that could be used to identify challenging nosocomial biomarkers for other multidrug resistant pandemic clones.

IMPORTANCEHigh-risk clones play a major role in the spread of resistance. The factors driving the emergence and the dissemination capacity of these clones are not well understood. The dissemination of A. baumannii strains belonging to high-risk GC1 is a global concern. Molecular methods have been used to type GC1 clones such as a particular deletion in intI1 that identify among islands in comM with a Tn6019 backbone. However, since some GC1 strains do not harbor the genomic island AbaR, and intI1 is very common in clinical samples, a more specific biomarker is necessary. The significance of our research is that we successfully applied machine learning methods to predict A. baumannii GC1. Our findings highlight that machine learning can be successfully applied not only to find high-risk clones putative biomarkers but also in disentangling genetic traits that could be used as therapeutic targets to reduce dissemination of lineages with epidemic behavior.


title: Integrative system biology analysis of barley transcriptome - hormonal signaling against biotic stress

abstract: Biotic stresses are environmental factors that cause a variety of crop diseases and damages. In contrast, crops trigger specific transduction signaling pathways that the hormones are the central players. Integrative OMICS for systems genetic engineering approach contributes in the understanding of molecular mechanisms. In this research, the system biology approaches were applied to discover particular molecular interactions between biotic stresses and hormonal signaling in barley. The meta-analysis of the data identified a total of 1232 and 304 differentially expressed genes (DEGs) respectively so that were significantly involved in defense processes and hormone signaling. A total of 24 TFs belonged to 15 conserved families and 6 TFs belonged to 6 conserved families were identified for biotic and hormonal data respectively, whereas NF-YC, GNAT, and whirly families were the most abundant groups. The functional analysis of the upstream regions for over-represented cis-acting elements revealed that were involved activation of transcription factors in response to pathogens and hormones. Based on the co-expression analysis, 6 and 7 distinct co-expression modules related to biotic stresses and hormonal signaling were respectively uncovered. The gene network analysis also identified novel hub genes such as TIM10, DRT101, ADG1, and TRA2 which may be involved in regulating defense responses to biotic stresses. In addition, many new genes with unknown function were obtained. Since this study represents a first preliminary curated system biology analysis of barley transcriptomic responses to biotic stresses and hormone treatments, introduces important candidate genes that may be beneficial to crop biotechnologists to accelerate genetic engineering programs.

category: systems biology


title: Language experience shapes music processing across 40 tonal, pitch-accented, and non-tonal languages

abstract: Tonal languages differ from other languages in their use of pitch (tones) to distinguish words. Some research suggests that the linguistic pitch expertise of tonal language speakers may generalize to improved discrimination of some aspects of musical pitch: tonal language speakers may therefore have music perception advantages over speakers of other languages. The evidence is mixed, however, as prior studies have studied small numbers of participants in only a few tonal languages and countries, making it challenging to disentangle the effects of linguistic experience from variability in music training experience, cultural differences, and so on. Here, we report an assessment of music perception skill in native speakers of 40 languages, with a preregistered exploratory-confirmatory design, including tonal (e.g., Mandarin, Vietnamese), pitch-accented (e.g., Japanese, Croatian), and non-tonal (e.g., Spanish, Hungarian) languages. Whether or not participants had taken music lessons, native speakers of tonal languages (confirmatory n = 20,102) had an improved ability to discriminate musical melodies. But this improvement came with a trade-off: relative to speakers of pitch-accented (confirmatory n = 9,694) or non-tonal languages (confirmatory n = 242,096), tonal speakers were worse at discriminating fine-scale pitch-tuning and worse at processing the musical beat. These results, which held across 5 tonal languages and were robust to geographic and demographic variation, demonstrate that linguistic experience shapes music perception ability, with implications for relations between music, language, and culture in the human mind.

category: neuroscience


title: Cables1 links Slit/Robo and Wnt/Frizzled signaling in commissural axon guidance

abstract: During neural circuit formation, axons navigate from one intermediate target to the next, until they find their final target. At intermediate targets, axons switch from being attracted to being repelled by changing the guidance receptors on the growth cone surface. For smooth navigation of the intermediate target and the continuation of their journey, the switch in receptor expression has to be orchestrated in a precisely timed manner. As an alternative to changes in expression, receptor function could be regulated by phosphorylation of receptors or components of signaling pathways. We identifed Cables1 as a linker between floor-plate exit of commissural axons regulated by Slit/Robo signaling and the rostral turn of post-crossing axons regulated by Wnt/Frizzled signaling. Cables1 localizes {beta}-Catenin phosphorylated at tyrosine 489 by Abelson kinase to the distal axon, which in turn is necessary for the correct navigation of post-crossing commissural axons in the developing chicken spinal cord.


title: Theta coordinates hippocampal-entorhinal ensembles during wake and rest

abstract:
Precisely timed interactions between hippocampal and cortical cells, during quiescent periods dominated by replay of CA1 cell sequences, are thought to support memory consolidation. However, the processes during encoding that lead to coordinated offline replay remain poorly understood. We found entrainment of deep-layer medial entorhinal cortex (dMEC) cells to CA1 cell assemblies dictated their later recruitment and synchronisation with hippocampal replay. These assembly-entrained cells participated preferentially in replay which included their CA1 assembly partner and in forward-projecting replay sequences. Finally, replay coordination of these dMEC cells showed a marked experience-dependent increase; becoming stronger as an animal became fluent with a novel spatial task. Together these findings suggest cell assemblies may support information propagation in hippocampo-cortical circuits and the establishment of long-term memories.

One-Sentence SummaryEntrainment of cortical cells to hippocampal cell assemblies dictates their later involvement in hippocampal replay


title: Triazolopyrimidines target aerobic respiration in Mycobacterium tuberculosis

abstract: We previously identified a series of triazolopyrimidines with anti-tubercular activity. We determined that Mycobacterium tuberculosis strains with mutations in a component of the cytochrome bc1 system (QcrB) were resistant to the series. A cytochrome bd oxidase deletion strain was also more sensitive to this series. We isolated resistant mutants, all of which had mutations in Rv1339. Compounds were active against intracellular bacteria but did not inhibit mitochondrial respiration in human HepG2 cells. These data are consistent with triazolopyrimidines acting via inhibition of M. tuberculosis QcrB.


title: Uncovering the Genetic Architecture of Broad Antisocial Behavior through a Genome-Wide Association Study Meta-analysis.

abstract: Despite the substantial heritability of antisocial behavior (ASB), specific genetic variants robustly associated with the trait have not been identified. The present study by the Broad Antisocial Behavior Consortium (BroadABC) meta-analyzed data from 28 discovery samples (N = 85,359) and five independent replication samples (N = 8,058) with genotypic data and broad measures of ASB. We identified the first significant genetic associations with broad ASB, involving common intronic variants in the forkhead box protein P2 (FOXP2) gene (lead SNP rs12536335, P = 6.32 x 10-10). Furthermore, we observed intronic variation in Foxp2 and one of its targets (Cntnap2) distinguishing a mouse model of pathological aggression (BALB/cJ strain) from controls (BALB/cByJ strain). The SNP-based heritability of ASB was 8.4% (s.e.= 1.2%). Polygenic-risk-score (PRS) analyses in independent samples revealed that the genetic risk for ASB was associated with several antisocial outcomes across the lifespan, including diagnosis of conduct disorder, official criminal convictions, and trajectories of antisocial development. We found substantial genetic correlations of ASB with mental health (depression rg{square}={square}0.63, insomnia rg = 0.47), physical health (overweight rg = 0.19, waist-to-hip ratio rg = 0.32), smoking (rg{square}={square}0.54), cognitive ability (intelligence rg= -0.40), educational attainment (years of schooling rg = -0.46) and reproductive traits (age at first birth rg={square}- 0.58, fathers age at death rg= -0.54). Our findings provide a starting point towards identifying critical biosocial risk mechanisms for the development of ASB.

category: genetics


title: Genetic and genomic architecture of species-specific cuticular hydrocarbon variation in parasitoid wasps

abstract: Cuticular hydrocarbons (CHCs) serve two fundamental functions in insects: protection against desiccation and chemical signaling. CHC profiles can consist of dozens of different compounds and are considered a prime example for a complex trait. How the interaction of genes shapes CHC profiles, which are essential for insect survival, adaptation, and reproductive success, is still poorly understood. Here we investigate the genetic and genomic basis of CHC biosynthesis and variation in parasitoid wasps of the genus Nasonia. Taking advantage of the wasps haplo-diploid sex determination and cross-species fertility, we mapped 91 quantitative trait loci (QTL) explaining variation of a total of 43 CHCs in F2 hybrid males from interspecific crosses between three Nasonia species. To identify candidate genes, we localized orthologs of CHC biosynthesis-related genes in the Nasonia genomes. By doing so, we discovered multiple genomic regions where the location of QTL coincides with the location of CHC biosynthesis-related candidate genes. Most conspicuously, on a region on chromosome 1 close to the centromere, multiple CHC biosynthesis-related candidate genes co-localize with several QTL explaining variation in methyl-branched alkanes. The genetic underpinnings behind this compound class are not well understood so far, despite their high potential for encoding chemical information as well as their prevalence in both Nasonia CHC profiles and many other Hymenoptera. Our study considerably extends our knowledge on the so far little-known genetic and genomic architecture governing biosynthesis and variation of this fundamental compound class, establishing a model for methyl-branched alkane genetics in the Hymenoptera in general.


title: Activation of SGK1.1 up-regulates the M-current in the presence of epilepsy mutations

abstract: In the central nervous system, the M-current plays a critical role in regulating subthreshold electrical excitability of neurons, determining their firing properties and responsiveness to synaptic input. The M-channel is mainly formed by subunits Kv7.2 and Kv7.3 that co-assemble to form a heterotetrametric channel. Mutations in Kv7.2 and Kv7.3 are associated with hyperexcitability phenotypes including benign familial neonatal epilepsy (BFNE) and neonatal epileptic encephalopathy (NEE). SGK1.1, the neuronal isoform of the serum and glucocorticoids-regulated kinase 1 (SGK1), increases M-current density in neurons, leading to reduced excitability and protection against seizures. Herein, using two-electrode voltage clamp on Xenopus laevis oocytes, we demonstrate that SGK1.1 selectively activates heteromeric Kv7 subunit combinations underlying the M-current. Importantly, activated SGK1.1 is able to up-regulate M-channel activity in the presence of two different epilepsy mutations found in Kv7.2 subunit, R207W and A306T. In addition, proximity ligation assays in the N2a cell line allowed us to address the effect of these mutations on Kv7-SGK1.1-Nedd4 molecular associations, a proposed pathway underlying M-channel up-regulation by SGK1.1


title: Pupil Dilation and Response Slowing Distinguish Deliberate Explorative Choices in the Probabilistic Learning Task

abstract: This study examined whether pupil size and response time would distinguish directed exploration from random exploration and exploitation. Eighty-nine participants performed the two-choice probabilistic learning task while their pupil size and response time were continuously recorded. Using LMM analysis, we estimated differences in the pupil size and response time between the advantageous and disadvantageous choices as a function of learning success, i.e., whether or not a participant has learned the probabilistic contingency between choices and their outcomes. We proposed that before a true value of each choice became known to a decision-maker, both advantageous and disadvantageous choices represented a random exploration of the two options with an equally uncertain outcome, whereas the same choices after learning manifested exploitation and direct exploration strategies, respectively. We found that disadvantageous choices were associated with increases both in response time and pupil size, but only after the participants had learned the choice-reward contingencies. For the pupil size, this effect was strongly amplified for those disadvantageous choices that immediately followed gains as compared to losses in the preceding choice. Pupil size modulations were evident during the behavioral choice rather than during the pretrial baseline. These findings suggest that occasional disadvantageous choices, which violate the acquired internal utility model, represent directed exploration. This exploratory strategy shifts choice priorities in favor of information seeking and its autonomic and behavioral concomitants are mainly driven by the conflict between the behavioral plan of the intended exploratory choice and its strong alternative, which has already proven to be more rewarding.


title: Differences in spike generation instead of synaptic inputs determine the feature selectivity of two retinal cell types.

abstract: The output of spiking neurons depends both on their synaptic inputs and on their intrinsic properties. Retinal ganglion cells (RGCs), the spiking projection neurons of the retina, comprise over 40 different types in mice and other mammals, each tuned to different features of visual scenes. The circuits providing synaptic input to different RGC types to drive feature selectivity have been studied extensively, but there has been substantially less research aimed at understanding how the intrinsic properties of RGCs differ and how those differences impact feature selectivity. Here, we introduce an RGC type in the mouse, the Bursty Suppressed-by-Contrast (bSbC) RGC, whose contrast selectivity is shaped by its intrinsic properties. Surprisingly, when we compare the bSbC RGC to the OFF sustained alpha (OFFsA) RGC that receives similar synaptic input, we find that the two RGC types exhibit starkly different responses to an identical stimulus. We identified spike generation as the key intrinsic property behind this functional difference; the bSbC RGC undergoes depolarization block in conditions where the OFFsA RGC maintains a high spike rate. Pharmacological experiments, imaging, and compartment modeling demonstrate that these differences in spike generation are the result of differences in voltage-gated sodium channel conductances. Our results demonstrate that differences in intrinsic properties allow these two RGC types to detect and relay distinct features of an identical visual stimulus to the brain.


title: T cell receptor and IL-2 signaling strength control memory CD8+ T cell functional fitness via chromatin remodeling

abstract:
Cognate antigen signal controls CD8+ T cell priming, expansion size and effector versus memory cell fates, but it is not known if and how it modulates the functional features of memory CD8+ T cells. Here we show that the strength of T cell receptor (TCR) signaling determines the requirement for interleukin-2 (IL-2) signals to form a pool of memory CD8+ T cells that competitively re-expand upon secondary antigen encounter. Combining strong TCR and intact IL-2 signaling synergistically induces genome-wide chromatin accessibility in regions targeting a wide breadth of biological processes, consistent with their greater functional fitness. Chromatin accessibility in promoters of genes encoding for stem cell, cell cycle and calcium-related proteins correlated with faster intracellular calcium accumulation, initiation of cell cycle and more robust expansion. High-dimensional flow-cytometry analysis also highlights higher subset diversity and phenotypes. These results formally establish that epitope selection in vaccine design strongly impacts memory CD8+ T cell epigenetic programming and functions.

One Sentence SummaryThe strength of antigenic and interleukin 2 signals received by CD8+ T cells during vaccination epigenetically programs their ability to form functional memory.

category: immunology


title: Influence of DNA extraction kits on the fungal DNA metabarcoding for freshwater environmental DNA

abstract:
BackgroundEnvironmental DNA (eDNA) metabarcoding is a common technique for efficient biodiversity monitoring, especially of microbes. Recently, the usefulness of aquatic eDNA in monitoring the diversity of both terrestrial and aquatic fungi has been suggested. In eDNA studies, different experimental factors, such as DNA extraction kits or methods, can affect the subsequent analyses and the results of DNA metabarcoding. However, few methodological studies have been carried out on eDNA of fungi, and little is known about how experimental procedures can affect the results of biodiversity analysis. In this study, we focused on the effect of DNA extraction method on fungal DNA metabarcoding using freshwater samples obtained from rivers and lakes.

MethodsDNA was extracted from freshwater samples using the DNeasy PowerSoil kit, which is mainly used to extract microbial DNA from soil, and the DNeasy Blood & Tissue kit, which is commonly used for eDNA studies on animals. We then compared PCR inhibition and fungal DNA metabarcoding results; i.e., operational taxonomic unit (OTU) number and composition of the extracted samples.

ResultsNo PCR inhibition was detected in any of the samples, and no significant differences in the number of OTUs and OTU compositions were detected between the samples processed using different kits. These results indicate that both DNA extraction kits may provide similar diversity results for the river and lake samples evaluated in this study. Therefore, it may be possible to evaluate the diversity of fungi using a unified experimental method, even with samples obtained for diversity studies on other taxa such as those of animals.


title: Influence of DNA extraction kits on freshwater fungal DNA metabarcoding


title: A kinesin-1 variant reveals motor-induced microtubule damage in cells

abstract: Kinesins drive the transport of cellular cargoes as they walk along microtubule tracks, however, recent work has suggested that the physical act of kinesins walking along microtubules can stress the microtubule lattice. Here, we describe a kinesin-1 KIF5C mutant with an increased ability to generate defects in the microtubule lattice as compared to the wild-type motor. Expression of the mutant motor in cultured cells resulted in microtubule breakage and fragmentation, suggesting that kinesin-1 variants with increased damage activity would have been selected against during evolution. The increased ability to damage microtubules is not due to the altered motility properties of the mutant motor as expression of the kinesin-3 motor KIF1A, which has similar single-motor motility properties, also caused increased microtubule pausing, bending, and buckling but not breakage. In cells, motor-induced microtubule breakage could not be prevented by increased a-tubulin K40 acetylation, a post-translational modification known to increase microtubule flexibility. In vitro, lattice damage induced by wild-type KIF5C was repaired by soluble tubulin and resulted in increased rescues and microtubule growth whereas lattice damage induced by the KIF5C mutant resulted in larger repair sites that made the microtubule vulnerable to breakage and fragmentation when under mechanical stress. These results demonstrate that kinesin-1 motility causes defects in and damage to the microtubule lattice in cells. While cells have the capacity to repair lattice damage, conditions that exceed this capacity result in microtubule breakage and fragmentation and may contribute to human disease.

category: cell biology


title: Global distribution of mammal herbivore biomass reveals megafauna extinction patterns

abstract: Terrestrial mammalian herbivores strongly shape ecosystems and influence Earth system processes. Herbivorous mammals can alter vegetation structure, accelerate nutrient distribution, and modify carbon cycling. The Late Pleistocene megafauna extinctions triggered significant changes in ecosystems and climate, and current extinctions are having similarly pervasive consequences. A lack of global dynamic models of mammal populations limits our understanding of the ecological role of wild mammals and the consequences of their past and future extinctions. Here we present a global model of herbivore mammal populations defined by their ecological role based on a classification of all extant herbivores (n = 2599) in 24 functional groups. The eco-physiological model predicts present-day mammal biomass in natural conditions. Biomass hotspots occur in areas today dominated by humans, which account for 30% of biomass loss and limit future rewilding potentials. Large herbivore (body mass > 5 kg) biomass is higher in hot and wet areas with high evapotranspiration. Conversely, small herbivore biomass is more evenly distributed, particularly in colder climates. Thus, energy-water dependency is higher in large herbivores than smaller ones. Negative deviations from the biomass and water-energy relationship unveil past extinction patterns. Late Pleistocene extinctions may have triggered a collapse of biomass in Australia and South America and heavy losses in North America and northern Asia. The herbivore biomass estimates provide a quantitative benchmark for conservation and management actions. The herbivore model and the functional classification create new opportunities to integrate mammals into Earth system science.

category: ecology


title: Multi-hallmark long noncoding RNA maps reveal non-small cell lung cancer vulnerabilities

abstract: Long noncoding RNAs (lncRNAs) are widely dysregulated in cancer, yet their functional roles in cellular disease hallmarks remain unclear. Here we employ pooled CRISPR deletion to perturb all 831 lncRNAs in KRAS-mutant non-small cell lung cancer (NSCLC), and measure their contribution to proliferation, chemoresistance and migration across two cell backgrounds. Integrative analysis of this data outperforms conventional "dropout" screens in identifying cancer genes, while prioritising disease-relevant lncRNAs with pleiotropic and background-independent roles. Altogether 60 high-confidence oncogenic lncRNAs are active in NSCLC, the majority identified here for the first time, and which tend to be amplified and overexpressed in tumours. A follow-up antisense oligonucleotide (ASO) screen shortlisted two candidates, Cancer Hallmarks in Lung LncRNA (CHiLL 1&2), whose knockdown consistently suppressed cancer hallmarks in a variety of 2D and 3D tumour models. Molecular phenotyping reveals that CHiLL 1&2 control cellular-level phenotypes via distinct transcriptional networks converging on common oncogenic pathways. In summary, this work reveals a multi-dimensional functional lncRNA landscape underlying NSCLC that contains potential therapeutic vulnerabilities.


title: Escherichia coli strains from patients with inflammatory bowel diseases have disease-specific genomic adaptations

abstract:
ObjectiveEscherichia coli is over-abundant in the gut microbiome of patients with IBD, yet most studies have focused on the adherent-invasive E. coli pathotype. Here, we aimed to identify IBD-specific or phenotype-specific genomic functions of diverse E. coli lineages.

DesignWe investigated E. coli from patients with UC, CD and a pouch and healthy subjects. The majority of E. coli genomes were reconstructed directly from metagenomic samples, including publicly available and newly sequenced fecal metagenomes. Clinical metadata and biomarkers were collected. Functional analysis at the gene and mutation level and genome replication rates of E. coli strains were performed, and correlated with IBD phenotypes and biomarkers.

ResultsOverall, 530 E. coli genomes were analysed. A specific E. coli lineage (B2) was more prevalent in UC compared to other IBD phenotypes. Genomic metabolic capacities varied across E. coli lineages and IBD phenotypes. Specifically, sialidases involved in host mucin utilization, were exclusively present in a single lineage and were depleted in patients with a pouch. In contrast, enzymes that hydrolyze inulin were enriched in patients with a pouch. E. coli from patients with UC were twice as likely to encode the genotoxic molecule colibactin than strains from patients with CD or pouch. Strikingly, patients with a pouch showed the highest E. coli growth rates, even in the presence of antibiotics. Fecal calprotectin did not correlate with the relative abundance of E. coli. Finally, we identified multiple IBD-specific loss-of function mutations in E. coli genes encoding for bacterial cell envelope and secretion components.

ConclusionThis study presents E. coli as a commensal species better adapted to the overly-active mucosal immune milieu in IBD, that may benefit from intestinal inflammation, rather than causing it. The evidence given here suggests adaptive evolution toward attenuated virulence in some E. coli strains, coupled with a rapid growth despite the presence of antibiotics.


title: Untwisted α-synuclein Filaments formed in the Presence of Lipid Vesicles

abstract: Accumulation of filamentous aggregates of -synuclein is a pathological hallmark of several neurodegenerative diseases including Parkinsons disease (PD). Interaction between -synuclein and lipids has been shown to play a critical role in aggregation of -synuclein. Most structural studies have, however, been focused on -synuclein filaments formed in the absence of lipids. Here, we report structural investigation of -synuclein filaments assembled under the quiescent conditions in the presence of anionic lipid vesicles using electron microscopy (EM) including cryo-EM. Our transmission electron microscopy (TEM) analyses reveal that -synuclein forms curly protofilaments at an early stage of aggregation. The flexible protofilaments were then converted to long filaments after a longer incubation of 30 days. More detailed structural analyses using cryo-EM reveal that the long filaments adopt untwisted structures with different diameters, which have not been observed in previous -synuclein filaments formed in vitro. The untwisted filaments are rather similar to straight filaments with no observable twist that are extracted from patients with dementia with Lewy bodies. Our structural studies highlight the conformational diversity of -synuclein filaments, requiring additional structural investigation of not only more ex vivo -synuclein filaments, but also in vitro -synuclein filaments formed in the presence of diverse co-factors to better understand the molecular basis of diverse molecular conformations of -synuclein filaments.

category: biochemistry


title: Pseudomonas aeruginosa cytochrome P450 CYP168A1 is a fatty acid hydroxylase that metabolizes arachidonic acid to the vasodilator 19-HETE

abstract: Pseudomonas aeruginosa is a gram-negative opportunistic human pathogen that is highly prevalent in individuals with cystic fibrosis (CF). A major problem in treating CF patients infected with P. aeruginosa is the development of antibiotic resistance. Therefore, the identification of novel P. aeruginosa antibiotic drug targets is of the upmost urgency. The genome of P. aeruginosa contains four putative cytochrome P450 enzymes (CYPs) of unknown function that have never before been characterized. Analogous to some of the CYPs from M. tuberculosis, the P. aeruginosa CYPs may be important for growth and colonization of the CF patients lung. In this study, we cloned, expressed, and characterized CYP168A1 from P. aeruginosa and identified it as a sub-terminal fatty acid hydroxylase. Spectral binding data and computational modeling of substrates and inhibitors suggest that CYP168A1 has a large, expansive active site preferring long chain fatty acids and large hydrophobic inhibitors. Furthermore, metabolism experiments confirm that the enzyme is capable of hydroxylating arachidonic acid, an important inflammatory signaling molecule present in abundance in the CF lung, to 19-hydroxyeicosatetraenoic acid (19-HETE; Km = 41.1 {micro}M, Vmax = 222 pmol/min/nmol P450), a potent vasoconstrictor which may play a role in the pathogens ability to colonize the mammalian lung. Metabolism of arachidonic acid is subject to substrate inhibition and is also inhibited by the presence of ketoconazole. This study points to the discovery of a new potential drug target that may be of utility in treating drug resistant P. aeruginosa.


title: Nuclear import and chaperoning of monomeric histones H3 and H4 is mediated by Imp5, NASP and the HAT1 complex

abstract:
Core histones package chromosomal DNA and regulate genomic transactions, with their import and deposition involving a dedicated repertoire of molecular chaperones. Histones H3 and H4 have been predominantly characterised as obligate heterodimers, however, recent findings have alluded to the existence of a significant pool of monomeric histone H3 in the nucleoplasm. Using a combination of in vitro and in vivo experiments, here we show that monomeric H3 and H4 use an Importin 5 (Imp5) dependent pathway for their nuclear import, distinct from Importin 4 (Imp4) previously described for H3-H4 dimers. Using mutants that disrupt the histone fold, we show monomeric H3 loses its interaction with Imp4, but retains interactions with Imp5 and the chaperone NASP. H4 monomeric mutants similarly bind Imp5 and not Imp4, however, they lose interaction with NASP, retaining their interaction with the HAT1-RBBP7 complex instead. In vitro experiments revealed that Imp5 and NASP are mutually exclusive in their binding, suggesting a facilitated hand-off mechanism. Furthermore, new H3 accumulates rapidly in a NASP-bound complex after nuclear translocation. NASP can assemble into three distinct co-chaperoning complexes, including a novel complex containing NASP, H3 and the putative ubiquitin ligase UBR7, a NASP-H3-H4-RBBP7 subcomplex and the previously characterised NASP-H3-H4-ASF1-HAT1-RBBP7 multi-chaperoning complex. Here we propose an alternative import pathway and folding mechanism for monomeric H3 and H4 that involves Imp5, rather than Imp4, and hands off to nuclear chaperones NASP, RBBP7 and HAT1.

Graphical Abstract

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title: Structural identification of individual helical amyloid filaments by integration of cryo-electron microscopy-derived maps in comparative morphometric atomic force microscopy image analysis

abstract: The presence of amyloid fibrils is a hallmark of more than 50 human disorders, including neurodegenerative diseases and systemic amyloidoses. A key unresolved challenge in understanding the involvement of amyloid in disease is to explain the relationship between individual structural polymorphs of amyloid fibrils, in potentially mixed populations, and the specific pathologies with which they are associated. Although cryo-electron microscopy (cryo-EM) and solid-state nuclear magnetic resonance (ssNMR) spectroscopy methods have been successfully employed in recent years to determine the structures of amyloid fibrils with high resolution detail, they rely on ensemble averaging of fibril structures in the entire sample or significant subpopulations. Here, we report a method for structural identification of individual fibril structures imaged by atomic force microscopy (AFM) by integration of high-resolution maps of amyloid fibrils determined by cryo-EM in comparative AFM image analysis. This approach was demonstrated using the hitherto structurally unresolved amyloid fibrils formed in vitro from a fragment of tau (297-391), termed  dGAE. Our approach established unequivocally that dGAE amyloid fibrils bear no structural relationship to heparin-induced tau fibrils formed in vitro. Furthermore, our comparative analysis resulted in the prediction that dGAE fibrils are closely related structurally to the paired helical filaments (PHFs) isolated from Alzheimers disease (AD) brain tissue characterised by cryo-EM. These results show the utility of individual particle structural analysis using AFM, provide a workflow of how cryo-EM data can be incorporated into AFM image analysis and facilitate an integrated structural analysis of amyloid polymorphism.

category: biophysics


title: Exit from quiescence couples epithelial stress amplification to fluidization

abstract: Cellular quiescence is a state of reversible cell cycle arrest that is associated with tissue dormancy. Timely regulated entry into and exit from quiescence is important for processes such as tissue homeostasis, tissue repair, stem cell maintenance, developmental processes and immunity. Here we show that quiescent human keratinocyte monolayers contain an actinomyosin-based system that facilitates global viscoelastic flow upon serum-stimulated exit from quiescence. Mechanistically, serum exposure causes rapid amplification of pre-existing contractile sites leading to a burst in monolayer stress that subsequently drives monolayer fluidization. The stress magnitude after quiescence exit correlates with quiescence depth, and a critical stress level must be reached to overcome the cell sheet displacement barrier. The study shows that static quiescent cell monolayers are mechanically poised for motility and identifies global stress amplification as a mechanism for tissue fluidization.


title: Mechanical coupling of supracellular stress amplification and tissue fluidization during exit from quiescence


title: Interspecific divergence of circadian properties in duckweed plants

abstract:
O_LIThe circadian clock system is widely conserved in plants; however, divergence in circadian rhythm properties is poorly understood. We conducted a comparative analysis of the circadian properties of closely related duckweed species.
C_LIO_LIUsing a particle bombardment method, a circadian bioluminescent reporter was introduced into duckweed plants. We measured bioluminescence circadian rhythms of eight species of the genus Lemna and seven species of the genus Wolffiella at various temperatures (20, 25, and 30 {degrees}C) and light conditions (constant light or constant dark). Wolffiella species inhabit relatively warm areas and lack some tissues/organs found in Lemna species.
C_LIO_LILemna species tended to show robust bioluminescence circadian rhythms under all conditions, while Wolffiella species showed lower rhythm stability, especially at higher temperatures. For Lemna, two species (L. valdiviana and L. minuta) forming a clade showed relatively lower circadian stability. For Wolffiella, two species (W. hyalina and W. repanda) forming a clade showed extremely long period lengths.
C_LIO_LIThe circadian properties of species primarily reflect their phylogenetic positions. The relationships between geographical and morphological factors and circadian properties are also suggested.
C_LI


title: OsMADS58 stabilizes gene regulatory circuits during rice stamen development

abstract: Rice (Oryza sativa) OsMADS58 is a C-class MADS box protein, and characterization of a transposon insertion mutant osmads58 suggested that OsMADS58 plays a role in stamen development. However, as no null mutation has been obtained, its role has remained unclear. Here, we report that the CRISPR knockout mutant osmads58 exhibits complex altered phenotypes, including anomalous diploid germ cell differentiation, aberrant meiosis, and delayed tapetum degeneration. This CRISPR mutant line exhibited stronger changes in expression of OsMADS58 target genes compared with the osmads58 dSpm (transposon insertion) line, along with changes in multiple pathways related to early stamen development. Notably, transcriptional regulatory circuits in young panicles covering the stamen at stages 4-6 were substantially altered in the CRISPR line compared to the dSpm line. These findings strongly suggest that the pleiotropic effects of OsMADS58 on stamen development derive from a potential role in stabilizing gene regulatory circuits during early stamen development. Thus, this work opens new avenues for viewing and deciphering the regulatory mechanisms of early stamen development from a network perspective.


title: Modelling altered signalling of G-protein coupled receptors in inflamed environment to advance drug design

abstract: We previously reported the successful design, synthesis and testing of the prototype opioid painkiller NFEPP that does not elicit adverse side effects. Uniquely, this design was based on mathematical modelling of extracellular interactions between G-protein coupled receptors (GPCRs) and ligands, recognizing that GPCRs function differently under pathological versus healthy conditions. We now present a novel stochastic model of GPCR function that includes intracellular dissociation of G-protein subunits and modulation of plasma membrane calcium channels associated with parameters of inflamed and healthy tissue (pH, radicals). The model is validated against in vitro experimental data for NFEPP and fentanyl ligands at different pH values. We found markedly reduced calcium channel inhibition induced by NFEPP at normal pH compared to lower pH, in contrast to the effect of fentanyl, and enhanced constitutive G-protein activation but lower probability of ligand binding with increasing radical concentrations. By means of molecular dynamics simulations, we also assessed qualitative changes of reaction rates due to additional disulfide bridges inside the GPCR binding pocket. The results suggest that, compared to radicals, low pH is a more important determinant of overall GPCR function in an inflamed environment. Future drug design efforts should take this into account.


title: Feature blindness: a challenge for understanding and modelling visual object recognition

abstract:
Humans rely heavily on the shape of objects to recognise them. Recently, it has been argued that Convolutional Neural Networks (CNNs) can also show a shape-bias, provided their learning environment contains this bias. This has led to the proposal that CNNs provide good mechanistic models of shape-bias and, more generally, human visual processing. However, it is also possible that humans and CNNs show a shape-bias for very different reasons, namely, shape-bias in humans may be a consequence of architectural and cognitive constraints whereas CNNs show a shape-bias as a consequence of learning the statistics of the environment. We investigated this question by exploring shape-bias in humans and CNNs when they learn in a novel environment. We observed that, in this new environment, humans (i) focused on shape and overlooked many non-shape features, even when non-shape features were more diagnostic, (ii) learned based on only one out of multiple predictive features, and (iii) failed to learn when global features, such as shape, were absent. This behaviour contrasted with the predictions of a statistical inference model with no priors, showing the strong role that shape-bias plays in human feature selection. It also contrasted with CNNs that (i) preferred to categorise objects based on non-shape features, and (ii) increased reliance on these non-shape features as they became more predictive. This was the case even when the CNN was pre-trained to have a shape-bias and the convolutional backbone was frozen. These results suggest that shape-bias has a different source in humans and CNNs: while learning in CNNs is driven by the statistical properties of the environment, humans are highly constrained by their previous biases, which suggests that cognitive constraints play a key role in how humans learn to recognise novel objects.

Author summaryAny object consists of hundreds of visual features that can be used to recognise it. How do humans select which feature to use? Do we always choose features that are best at predicting the object? In a series of experiments using carefully designed stimuli, we find that humans frequently ignore many features that are clearly visible and highly predictive. This behaviour is statistically inefficient and we show that it contrasts with statistical inference models such as state-of-the-art neural networks. Unlike humans, these models learn to rely on the most predictive feature when trained on the same data. We argue that the reason underlying human behaviour may be a bias to look for features that are less hungry for cognitive resources and generalise better to novel instances. Models that incorporate cognitive constraints may not only allow us to better understand human vision but also help us develop machine learning models that are more robust to changes in incidental features of objects.


title: The miR-124-AMPAR pathway connects polygenic risks with behavioral changes shared between schizophrenia and bipolar disorder

abstract: Schizophrenia (SZ) and bipolar disorder (BP) are highly heritable major psychiatric disorders that share a substantial portion of genetic risk as well as their clinical manifestations. This raises a fundamental question of whether, and how, common neurobiological pathways translate their shared polygenic risks into shared clinical manifestations. The present study shows the miR-124-AMPAR pathway as a key common neurobiological mediator that connects polygenic risks with behavioral changes shared between these two psychotic disorders. We discovered upregulation of miR-124 in biopsied neuronal cells and postmortem prefrontal cortex from both SZ and BP patients, implying its role not only as a biomarker, but also as a pathophysiological mediator. Intriguingly, the upregulation is associated with the polygenic risks shared between these two disorders. Seeking mechanistic dissection, we generated a mouse model that upregulates miR-124 in the medial prefrontal cortex, which includes brain regions homologous to sub-regions of the human prefrontal cortex. We demonstrated that upregulation of miR-124 increases GRIA2-lacking calcium permeable-AMPARs and perturbs AMPAR-mediated excitatory synaptic transmission, leading to deficits in the behavioral dimensions shared between SZ and BP.


title: Periodic and Aperiodic Neural Activity Displays Age-Dependent Changes Across Early-to-Middle Childhood

abstract: The neurodevelopmental period spanning early-to-middle childhood represents a time of significant growth and reorganisation throughout the cortex. Such changes are critical for the emergence and maturation of a range of social and cognitive processes. Here, we utilised both eyes open and eyes closed resting-state electroencephalography (EEG) to examine maturational changes in both oscillatory (i.e., periodic) and non-oscillatory (aperiodic,  1/f-like) activity in a large cohort of participants ranging from 4-to-12 years of age (N=139, average age=9.41 years, SD=1.95). The EEG signal was parameterised into aperiodic and periodic components, and linear regression models were used to evaluate if chronological age could predict aperiodic exponent and offset, as well as well as peak frequency and power within the alpha and beta ranges. Exponent and offset were found to both decrease with age, while aperiodic-adjusted alpha peak frequency increased with age; however, there was no association between age and peak frequency for the beta band. Age was also unrelated to aperiodic-adjusted spectral power within either the alpha or beta bands, despite both frequency ranges being correlated with the aperiodic signal. Overall, these results highlight the capacity for both periodic and aperiodic features of the EEG to elucidate age-related functional changes within the developing brain.


title: On the prediction of human intelligence from neuroimaging: A systematic review of methods and reporting

abstract: Human intelligence is one of the main objects of study in cognitive neuroscience. Reviews and meta-analyses have proved to be fundamental to establish and cement neuroscientific theories on intelligence. The prediction of intelligence using in vivo neuroimaging data and machine learning has become a widely accepted and replicated result. Here, we present a systematic review of this growing area of research, based on studies that employ structural, functional, and/or diffusion MRI to predict human intelligence in cognitively normal subjects using machine-learning. We performed a systematic assessment of methodological and reporting quality, using the PROBAST and TRIPOD assessment forms and 30 studies identified through a systematic search. We observed that fMRI is the most employed modality, resting-state functional connectivity (RSFC) is the most studied predictor, and the Human Connectome Project is the most employed dataset. A meta-analysis revealed a significant difference between the performance obtained in the prediction of general and fluid intelligence from fMRI data, confirming that the quality of measurement moderates this association. The expected performance of studies predicting general intelligence from fMRI was estimated to be r = 0.42 (CI95% = [0.35, 0.50]) while for studies predicting fluid intelligence obtained from a single test, expected performance was estimated as r = 0.15 (CI95% = [0.13, 0.17]). We further enumerate some virtues and pitfalls we identified in the methods for the assessment of intelligence and machine learning. The lack of treatment of confounder variables, including kinship, and small sample sizes were two common occurrences in the literature which increased risk of bias. Reporting quality was fair across studies, although reporting of results and discussion could be vastly improved. We conclude that the current literature on the prediction of intelligence from neuroimaging data is reaching maturity. Performance has been reliably demonstrated, although extending findings to new populations is imperative. Current results could be used by future works to foment new theories on the biological basis of intelligence differences.


title: Cortico-Subcortical Interactions in Overlapping Communities of Edge Functional Connectivity

abstract: Both cortical and subcortical regions can be functionally organized into networks. Regions of the basal ganglia are extensively interconnected with the cortex via reciprocal connections that relay and modulate cortical function. Here we employ an edge-centric approach, which computes co-fluctuations among region pairs in a network to investigate the role and interaction of subcortical regions with cortical systems. By clustering edges into communities, we show that cortical systems and subcortical regions couple via multiple edge communities, with hippocampus and amygdala having a distinct pattern from striatum and thalamus. We show that the edge community structure of cortical networks is highly similar to one obtained from cortical nodes when the subcortex is present in the network. Additionally, we show that the edge community profile of both cortical and subcortical nodes can be estimates solely from cortico-subcortical interactions. Finally, we used a motif analysis focusing on edge community triads where a subcortical region coupled to two cortical regions and found that two community triads where one community couples the subcortex to the cortex were overrepresented. In summary, our results show organized coupling of the subcortex to the cortex that may play a role in cortical organization of primary sensorimotor/attention and heteromodal systems and puts forth the motif analysis of edge community triads as a promising method for investigation of communication patterns in networks.


title: Identification of novel therapeutic targets for polyglutamine toxicity disorders that target mitochondrial fragmentation

abstract:
Huntingtons disease (HD) is one of at least nine polyglutamine toxicity disorders caused by a trinucleotide CAG repeat expansion, all of which lead to age-onset neurodegeneration. Mitochondrial dynamics and function are disrupted in HD and other polyglutamine toxicity disorders. While multiple studies have found beneficial effects from decreasing mitochondrial fragmentation in HD models by disrupting the mitochondrial fission protein DRP1, disrupting DRP1 can also have detrimental consequences in wild-type animals and HD models. In this work, we examine the effect of decreasing mitochondrial fragmentation in a neuronal C. elegans model of polyglutamine toxicity called Neur-67Q. We find that Neur-67Q worms have deficits in mitochondrial morphology in GABAergic neurons and decreased mitochondrial function. Disruption of drp-1 eliminates differences in mitochondrial morphology and rescues deficits in both movement and longevity in Neur-67Q worms. In testing twenty-four RNA interference (RNAi) clones that decrease mitochondrial fragmentation, we identified eleven clones that increase movement and extend lifespan in Neur-67Q worms. Overall, we show that decreasing mitochondrial fragmentation may be an effective approach to treat polyglutamine toxicity disorders and identify multiple novel genetic targets that circumvent the potential negative side effects of disrupting the primary mitochondrial fission gene drp-1.

Significance StatementPolyglutamine toxicity disorders are caused by a trinucleotide CAG repeat expansion that leads to neurodegeneration. Both mitochondrial dynamics and function are disrupted in these disorders. In this work we use a simple genetic model organism, the worm C. elegans, to define the role of mitochondrial morphology in polyglutamine toxicity disorders. We show that CAG repeat expansion is sufficient to disrupt mitochondrial morphology and that genetic strategies that decrease mitochondrial fragmentation are beneficial in a neuronal model of polyglutamine toxicity. This work identifies multiple novel genes that are protective in worm models of polyglutamine toxicity, which may serve as potential therapeutic targets for Huntingtons disease and other polyglutamine toxicity disorders.


title: Cellular adhesion is a controlling factor in neutrophil extracellular trap formation induced by antineutrophil cytoplasmic antibodies

abstract: Anti-neutrophil cytoplasmic antibody (ANCA) associated vasculitis (AAV) is a life-threatening condition characterized by improper activation of neutrophils and release of neutrophil extracellular traps (NETs) in small vessels. This study aimed to explain the role of NETs in AAV pathogenesis by investigating a link between neutrophil adhesion and NET release. We leveraged an imaging flow cytometry-based assay and three-dimensional culture to demonstrate that neutrophil adhesion is essential for ANCA induced NET formation. We confirmed this requirement for cell adhesion using standard microscopy on ultra-low attachment hydrogel surfaces and demonstrate that this depends on the focal adhesion kinase pathway as determined using inhibitors for multiple targets in this process. ANCA increased expression of {beta}2 integrins on neutrophils, and we confirmed that these integrins were required for NET formation using blocking antibodies. Finally, inhibitors for oxidative burst prevented NET formation, and this oxidative burst was mediated by the focal adhesion pathway. Overall, our findings reveal a central role for neutrophil attachment in NET formation in response to ANCA, helping to explain the restricted localization pattern of vessel damage, and suggesting that targeting neutrophil adhesion factors may be beneficial in preventing pathological damage from NETs during AAV.


title: S-phase induced RNAs initiate formation of DNA replication origins

abstract: The mechanistic events leading to alterations of DNA replication in normal and diseased cells remain unknown. The present study uncovers the role of a new class of non-coding RNAs induced in early S-phase, able to activate and repress replication origins formation. The discovery of a RNA-mediated mechanism governing the replication of c-MYC locus offers novel strategies to control DNA replication by modulating transcriptional activity, and pave the way for future clinical applications to treat cancer and genetic disorders.

category: molecular biology


title: Characterising the vegetation-rainfall relationship in the Northeast Himalaya, India

abstract: Ecosystems are complex systems and are characterised by positive and negative feedbacks between the abiotic and biotic components. The response of an ecosystem to its environment can be determined by examining state diagrams, which are plots of the state variable as a function of the environmental driver. For instance, tree cover as a function of rainfall is widely used to characterise vegetation patterns. Previous studies have shown that tree cover shows bimodal distributions for intermediate rainfall regimes in Africa and South America. In this study, we construct a vegetation state diagram - by plotting vegetation cover as a function of mean annual rainfall - for Northeast India, which is part of the Eastern Himalaya and the Indo-Burma biodiversity hotspot. We use remotely sensed satellite data of Enhanced Vegetation Index (EVI) as a proxy for vegetation cover. We obtain Mean Annual Precipitation (MAP) from the CHIRPS data (Climate Hazards Group InfraRed Precipitation with Station data). We find that EVI increases monotonically as a function of MAP in the range 1000-2000 mm, after which it plateaus. The 1000 to 2000 mm MAP corresponds to the vegetation transitional zone (1200-3700 m), whereas >2000 MAP region covers the greater extent of the tropical forest (<1200 m) of NEI. In other words, we find no evidence for bimodality in tree cover or vegetation states at coarser scales in North Eastern India. Our characterisation of the state diagram for vegetation in northeast India is important to understand response to ongoing change in rainfall patterns.


title: Valuation of carbon services produced by wild animals finances conservation

abstract: Filling the global biodiversity financing gap will require significant investments from financial markets, which demand credible valuations of ecosystem services and natural capital. However, current valuation approaches discourage investment in conservation because their results cannot be verified using market-determined prices. Here, we bridge the gap between finance and conservation by valuing only wild animals carbon services for which market prices exist. By projecting the future path of carbon service production using a spatially-explicit demographic model, we place a credible value on the carbon-capture services produced by African forest elephants. If elephants were protected, their services would be worth $35.9 billion (24.3-41.2) and store 377 MtC (318-388) across tropical Africa. Our methodology can also place lower bounds on the social cost of nature degradation. Poaching would result in $10-14 billion of lost carbon services. Our methodology enables the integration of animal services into global financial markets with major implications for conservation, local socio-economies, and conservation.


title: Evolutionary trade-offs between heat and cold tolerance limit responses to fluctuating climates

abstract:
The evolutionary potential of species to cope with short-term temperature fluctuations during reproduction is critical to predicting responses to future climate change. Despite this, vertebrate research has focused on reproduction under high or low temperatures in relatively stable temperate climates. Here, we characterize the genetic basis of reproductive thermal tolerance to temperature fluctuations in the ostrich that lives in tropical and sub-tropical Africa. Both heat and cold tolerance are under selection and heritable, indicating that evolutionary responses to mean temperature change are possible. However, a negative, genetic correlation between heat and cold tolerance limits the potential for adaptation to fluctuating temperatures. Genetic constraints between heat and cold tolerance appears a crucial, yet underappreciated, factor influencing responses to climate change.

One-sentence summaryReproductive success in fluctuating climates is constrained by a negative genetic correlation between heat and cold tolerance

category: evolutionary biology


title: Intensive Single Cell Analysis Reveals Immune Cell Diversity among Healthy Individuals

abstract: It is believed that immune responses are different between individuals and at different times. In addition, personal health histories and unique environmental conditions should collectively determine the present state of immune cells. However, the cellular and molecular system mechanisms underlying such heterogeneity remain largely elusive. In this study, we conducted a systematic time-lapse single-cell analysis, using 171 single-cell libraries and 30 mass cytometry datasets intensively for seven healthy individuals. We found substantial diversity in immune cell populations and their gene expression patterns between different individuals. These patterns showed daily fluctuations even within the same individual spending a usual life. Similar diversities were also observed for the T cell receptor and B cell receptor repertoires. Detailed immune cell profiles at healthy statuses should give an essential background information to understand their immune responses, when the individual is exposed to various environmental conditions. To demonstrate this idea, we conducted the similar analysis for the same individuals on the vaccination of Influenza and SARS-CoV-2, since the date and the dose of the antigens are well-defined in these cases. In fact, we found that the distinct responses to vaccines between individuals, althougth key responses are common. Single cell immune cell profile data should make fundamental data resource to understand variable immune responses, which are unique to each individual.


title: The Effects of Prenatal Nicotine and THC E-Cigarette Exposure on Motor Development in Rats

abstract: In the United States, nicotine and cannabis are the most common licit and illicit drugs used among pregnant women. Importantly, nicotine and cannabis are now being combined for consumption via e-cigarettes, an increasingly popular route of administration. Both nicotine and tetrahydrocannabinol (THC), the primary psychoactive component of cannabis, cross the placenta barrier. However, the consequences of prenatal cannabis use are not well understood, and less is known about potential combination effects when consumed with nicotine, especially via e-cigarettes. The present study used a rodent model to examine how prenatal e-cigarette exposure to nicotine, THC, and the combination impacts motor development among offspring. Pregnant Sprague-Dawley rats were exposed to nicotine (36 mg/mL), THC (100 mg/mL), the combination, or vehicle via e-cigarette inhalation from gestational days (GD) 5-20. One sex pair per litter was tested on an early sensorimotor development task (postnatal days [PD] 12-20) and a parallel bar motor coordination task (PD 30-32). Combined prenatal exposure to nicotine and THC delayed sensorimotor development, even though neither drug produced impairments on their own. In contrast, prenatal exposure to either nicotine or THC impaired motor coordination, whereas combined exposure exacerbated these effects, particularly among females. These data illustrate that prenatal exposure to either nicotine or THC may alter motor development, and that the combination may produce more severe effects. These findings have important implications for pregnant women as we better understand the teratogenic effects of these drugs consumed via e-cigarettes.


title: Novel torin1-sensitive phosphorylation sites on the metabolic regulator AMPK revealed by label-free mass spectrometry

abstract: AMPK and mTORC1 are nutrient-sensitive protein kinases that form a fundamental negative feedback loop that governs cell growth and proliferation. AMPK is an {beta}{gamma} heterotrimer that is directly phosphorylated by mTORC1 on 2S345 to suppress AMPK activity and promote cell proliferation under nutrient stress conditions. Using mass spectrometry, we generated precise phosphorylation profiles of all 12 AMPK complexes expressed in proliferating human cells. Of the 18 phosphorylation sites detected, seven were sensitive to pharmacological mTORC1 inhibition, including four in the AMPK {gamma}2 isoform NH2-terminal domain and 2S377 which is located in the nucleotide-sensing motif. In particular, {beta}1S182 and {beta}2S184 were found to be mTORC1 substrates in vitro and near-maximally or substantially phosphorylated under cellular growth conditions. {beta}S182 phosphorylation was elevated in 1-containing complexes, relative to 2, an effect partly attributable to the non-conserved -subunit serine/threonine-rich loop. While mutation of {beta}1S182 to a non-phosphorylatable Ala had no effect on basal and ligand-stimulated AMPK activity, {beta}2-S184A mutation increased nuclear AMPK activity and enhanced cell proliferation under nutrient stress. We conclude that mTORC1 governs the nuclear activity of AMPK to regulate transcription factors involved in metabolism and cell survival during nutrient shortage.


title: A quantitative comparison of human embryonic and induced stem cell proteomes

abstract: Human induced pluripotent stem cells (hiPSCs) have great potential to be used as alternatives to embryonic stem cells (hESCs) in regenerative medicine and disease modelling. However, a clear overview of their differences at the protein level is still incomplete. In this study we characterise the proteomes of hiPSC and hESC lines, where we find that they express a similar set of proteins but show consistent quantitative differences that can be masked by the normalisation methods. hiPSCs have a higher protein content, with over 1,500 proteins showing over two-fold increased expression. They also display proteomic differences in their mitochondria, with increased expression of mitochondrial transporters and metabolic proteins as well as mitochondrial translation machinery. The hiPSCs also show higher expression of important amino acid transporters, secreted proteins, and growth factors with potential to affect neighbouring cells, coupled with a systematic reduction in the expression levels of H1 histone variants. We conclude that despite hiPSCs and hESCs being highly similar cell types, they show important differences in protein expression that may be relevant for their use in clinical research.


title: Identifying the oncogenic potential of gene fusions exploiting miRNAs

abstract:
BackgroundIt is estimated that oncogenic gene fusions cause about 20% of human cancer morbidity. Identifying potentially oncogenic gene fusions may improve affected patients diagnosis and treatment. Previous approaches to this issue included exploiting specific gene-related information, such as gene function and regulation. Here we propose a model that profits from the previous findings and includes the microRNAs in the oncogenic assessment. We present a classifier called ChimerDriver for the classification of gene fusions as oncogenic or not oncogenic. ChimerDriver is based on a specifically designed neural network and trained on genetic and post-transcriptional information to obtain a reliable classification.

Results and discussionThe designed neural network integrates information related to transcription factors, gene ontologies, microRNAs and other detailed information related to the functions of the genes involved in the fusion and the gene fusion structure. As a result, the performances on the test set reached 0.83 f1-score and 96% recall. The comparison with state-of-the-art tools returned comparable or higher results. Moreover, ChimerDriver performed well in a real-world case where 21 out of 24 validated gene fusion samples were detected by the gene fusion detection tool Starfusion.

ConclusionsChimerDriver integrated transcriptional and post-transcriptional information in an ad-hoc designed neural network to effectively discriminate oncogenic gene fusions from passenger ones.


title: Repurposed nystatin to inhibit SARS-CoV-2 and mutants in the GI tract

abstract: The SARS-CoV-2 infections are considered as respiratory system diseases, mostly. In COVID-19, it might also be the infection of gastrointestinal (GI) tract too, especially at patients in severe clinical condition. SARS-CoV-2 can destroy the intestinal barrier, capable to spread into internal organs via blood and/or lymphatic circulation, and to cause serious damage there. Infected GI tract of COVID-19 patients is ideal environment for the coronavirus infection, replication and as virus reservoir might be the major source of pandemic reinfections, too. The process of virus budding is dependent on the host cell lipid rafts containing membrane-sterols, mainly cholesterol. The viral envelope may be challenged by polyene antibiotics, such as nystatin, which has strong affinity to sterols. Nystatin may block the establishment of the virus-host cell connection, too. In this study, the nystatin was investigated, as antiviral agent to SARS-CoV-2. We demonstrated by tests in Vero E6 cell based cytopathic assay, nystatin blocked the replication of SARS-CoV-2 in concentration 62.5 g/ml (IC50) at Wuhan and British mutant strains. No efficient SARS-CoV-2 antiviral agent is known so far to alleviate pandemic, to disinfect GI tract, where vaccines might have limited effect, only. Nystatin might be the first one with emergency use authorization, either, as a safe and efficient non-systemic antiviral drug, with well-established use, since decades.

category: pharmacology and toxicology


title: Oral Lisinopril Raises Tissue Levels of ACE2, the SARS-CoV-2 Receptor, in Healthy Male and Female Mice

abstract:
Angiotensin-converting enzyme 2 (ACE2) is the established cellular receptor for SARS-CoV-2. However, it is unclear whether ACE1 inhibitors (e.g., lisinopril) or angiotensin receptor blockers (e.g., losartan) alter tissue ACE2 expression. This study sought to determine whether lisinopril or losartan, as monotherapies or in combination, change tissue levels of ACE2 in healthy male and female mice.

Mice received lisinopril (10 mg/kg/day), losartan (10 mg/kg/day), or both for 21 days via drinking water. A control group received water without drug. ACE2 protein index (ACE2 protein / total protein) was determined on small intestine, lung, kidney, and brain. Oral lisinopril increased ACE2 protein index across all tissues (p < 0.0001 vs control). In contrast, the combination of lisinopril plus losartan did not increase ACE2 levels in any tissue (p = 0.89 vs control) and even decreased tissue expression of the Ace2 gene (p < 0.001 vs control). Tissue ACE2 remained elevated in mice 21 days after cessation of lisinopril (p = 0.02). Across both cohorts, plasma ACE2 did not correlate with ACE2 protein index in any tissue. A sex difference was observed: kidney ACE2 levels were higher in males than females (p < 0.0001).

Oral lisinopril increases ACE2, the cellular receptor for SARS-CoV-2, in tissues that are relevant to the transmission and pathogenesis of COVID-19. Remarkably, the addition of losartan prevented lisinopril-induced increases in ACE2 across tissues. These results suggest that ACE inhibitors and angiotensin receptor blockers interact to determine tissue levels of ACE2.


title: The anterior insular cortex associates temporally discontiguous stimuli during threat learning

abstract: Learning about potential threats in the environment is indispensable for survival. Deficits in threat learning constitute a key dimension of multiple brain disorders, which include posttraumatic stress disorder and anxiety disorder. While human brain imaging studies have highlighted a reliable engagement of the anterior insular cortex (AIC) in threat learning, its precise role remains elusive partly due to the lack of animal studies that can address causality and mechanistic questions. Filling in this gap, the present mouse study proposes a novel AIC-mediated mechanism underlying the association of temporally discontiguous stimuli during threat learning. We identified that activity of AIC layer 5 (L5) pyramidal neurons is required for associating temporally discontiguous stimuli, specifically during a time interval between them. Notably, the AIC is not required for associating temporally contiguous stimuli during threat learning. The AIC not only sends the essential information, via its L5 pyramidal neurons, to the basolateral amygdala (BLA) during the time interval, but also receives from the BLA. We also identified a modulatory role of AIC dopamine D1 receptor (D1R)-mediated dopamine signaling in associating temporally discontiguous stimuli during the time interval.


title: Preparation of ingestible antibodies to neutralize the binding of SarsCoV2 RBD (receptor binding domain) to human ACE2 Receptor

abstract:
COVID19 continues to be a serious threat to human health and mortality. There is dire need for new solutions to combat this pandemic especially for those individuals who are not vaccinated or unable to be vaccinated and continue to be exposed to the SARSCoV2. In addition, the emergence of new more transmissible variants such as delta pose additional threat from this virus.

To explore another solution for prevention and treatment of COVID 19, we have produced chicken egg derived IgY antibodies against the Receptor binding domain (RBD) of SARSCoV2 spike protein which is involved in binding to human cell ACE2 receptors. The - RBD IgY effectively neutralize the binding of RBD to ACE2 and prevent pseudovirus entry in a PRNT assay. Importantly our anti-RBD IgY also neutralize the binding of Sars CoV2 delta variant RBD to ACE2. Given that chicken egg derived IgY are safe and permissible for human consumption, we plan to develop these ingestible antibodies for prevention of viral entry in the oropharyngeal and digestive tract in humans as passive immunotherapy.