title: The CXCR6/CXCL16 axis links inflamm-aging to disease severity in COVID-19 patients

abstract: Advancing age and chronic health conditions, significant risk factors for severe COVID-19, are associated with a pro-inflammatory state, termed inflamm-aging. CXCR6+ T cells are known to traffic to the lung and have been reported to increase with age. The ligand of CXCR6, CXCL16, is constitutively expressed in the lung and upregulated during inflammatory responses and the CXCR6/CXCL16 axis is associated with severe lung disease and pneumonia. Genome-wide association studies have also recently identified 3p21.31, encompassing the CXCR6 gene, as a susceptibility locus for severe COVID-19. We assessed numbers T cells expressing the chemokine receptor CXCR6 and plasma levels of CXCL16, in control and COVID-19 patients. Results demonstrated that circulating CD8+CXCR6+ T cells were significantly elevated with advancing age, yet virtually absent in patients with severe COVID-19. Peripheral levels of CXCL16 were significantly upregulated in severe COVID-19 patients compared to either mild COVID-19 patients or SARS-CoV-2 negative controls. This study supports a significant role of the CXCR6/CXCL16 axis in the immunopathogenesis of severe COVID-19.


title: Towards a unifying framework for diversity and dissimilarity coefficients

abstract: Diversity and dissimilarity within and between species assemblages have now been studied for more than half a century by community ecologists in relation to their connections with ecosystem functioning. However, a generalized framework that puts diversity and dissimilarity coefficients under the same formal umbrella is still lacking. In this paper, we show that generalized means represent an effective tool to develop a unifying formulation for the construction of a large array of parametric diversity and dissimilarity measures. These measures include some of the classical diversity coefficients, such as the Shannon entropy, the Gini-Simpson index or the parametric diversity of Patil and Taillie, together with a large number of dissimilarity coefficients of the Bray-Curtis family and can be further extended to the measurement of functional and phylogenetic differences within and between plots.

category: ecology


title: Design, construction, and deployment of an affordable and long-lasting moored deep-water fish aggregation device

abstract: Fish aggregation devices (FADs) are used worldwide to enhance the efficiency of various fisheries. Devices consist of a floating or subsurface component designed to exploit natural fish behavior, using species attraction to structure (e.g., Sargassum spp.) to aggregate fish and increase capture success in open ocean environments. Concerns have arisen regarding the scale and management of FAD-associated fisheries, however, the efficiency of FADs to aggregate fish also introduces the possibility for FADs to be used as conservation tools to study pelagic species ecology. Building on two successful and several failed deployments of anchored deep-water (>500 m) subsurface (10 m) FADs over three years in The Bahamas, and observations from the subsequent FAD monitoring program, the objectives of the paper are to: 1) provide details and considerations for the design, construction, and deployment of an affordable and durable deep-water subsurface FAD that can be deployed using small boats; and 2) highlight the potential for a long-lasting moored FAD to be used as a sustainable and reliable scientific platform for pelagic species research and conservation, lending specifically to several research applications. This information will be useful for assessing the impacts that FADs and other anthropogenic marine infrastructure have on wild marine species, and their efficacy for conserving pelagic fish through increased encounters for study.


title: Assessing the impact of static and fluctuating ocean acidification on the behavior of Amphiprion percula

abstract: Coral reef organisms are exposed to both an increasing magnitude of pCO2, and natural fluctuations on a diel scale. For coral reef fishes, one of the most profound effects of ocean acidification is the impact on ecologically important behaviors. Previous behavioral research has primarily been conducted under static pCO2 conditions and have recently come under criticism. Recent studies have provided evidence that the negative impacts on behavior may be reduced under more environmentally realistic, fluctuating conditions. We investigated the impact of both present and future day, static (500 and 1000 atm) and diel fluctuating (500 {+/-} 200 and 1000 {+/-} 200 atm) pCO2 on the lateralization and chemosensory behavior of juvenile anemonefish, Amphiprion percula. Our static experimental comparisons support previous findings that under elevated pCO2, fish become un-lateralized and lose the ability to discriminate olfactory cues. Diel-fluctuating pCO2 may aid in mitigating the severity of some behavioral abnormalities such as the chemosensory response, where a preference for predator cues was significantly reduced under a future diel-fluctuating pCO2 regime. This research aids in ground truthing earlier findings and contributes to our growing knowledge of the role of fluctuating conditions.

category: animal behavior and cognition


title: The human brain's intrinsic network architecture is organized to represent diverse cognitive task information

abstract: A set of distributed cognitive control networks are known to contribute to diverse cognitive demands, yet it is unclear how these networks gain this domain-general capacity. We hypothesized that this capacity is largely due to the particular organization of the human brains intrinsic network architecture. Specifically, we tested the possibility that each brain regions domain generality is reflected in its level of global (hub-like) intrinsic connectivity, as well as its particular global connectivity pattern (connectivity fingerprint). Consistent with prior work, we found that cognitive control networks exhibited domain generality, as they represented diverse task context information covering sensory, motor response, and logic rule domains. Supporting our hypothesis, we found that the level of global intrinsic connectivity (estimated with resting-state fMRI) was correlated with domain generality during tasks. Further, using a novel information fingerprint mapping approach, we found that each cognitive control regions unique rule response profile (information fingerprint) could be predicted based on its unique intrinsic connectivity fingerprint and the information content in non-cognitive control regions. Together these results suggest that the human brains intrinsic network architecture supports its ability to represent diverse cognitive task information, largely via the location of multiple-demand regions within the brains global network organization.

category: neuroscience


title: Global connectivity fingerprints predict the domain generality of multiple-demand regions


title: Intelligence and academic performance: Is it all in your head?

abstract: Academic performance relies, in part, on intelligence; however, intelligence quotient (IQ) is limited in predicting academic success. Furthermore, while the search for the biological seat of intelligence predates neuroscience itself, its findings remain conflicting. Here, we assess the interplay between IQ, academic performance, and brain connectivity with behavioral and functional MRI data collected from undergraduate students as they completed an active learning or lecture-based semester-long university physics course. IQ (i.e., full-scale WAIS scores) increased significantly pre-to post-instruction, were associated with physics knowledge and reasoning measures, but were unrelated to overall course grade. IQ was related to brain connectivity during physics-related cognition, but connectivity did not mediate IQs association with task performance. These relations depended on students sex and instructional environment, providing evidence that physics classroom environment and pedagogy may have a gendered influence on students performance. Discussion focuses on opportunities to improve physics reasoning skills for all students.


title: Effects of Task Demands on Neural Correlates of Acoustic and Semantic Processing in Challenging Listening Conditions

abstract:
PurposeListeners shift their listening strategies to prioritize lower-level acoustic information and higher-level semantic information in challenging listening conditions. However, the neural mechanisms underlying different strategies are unclear. The current study examined the extent to which encoding of lower-level acoustic cues is modulated by task demand and relationships with the higher-level semantic processing.

MethodElectroencephalography (EEG) was acquired while participants listened to sentences in noise that contained either higher or lower probability final words. Task difficulty was modulated by time available to process responses. Cortical tracking of speech - neural correlates of acoustic temporal envelope processing - were estimated using temporal response functions (TRFs).

ResultsTask difficulty did not affect cortical tracking of temporal envelope of speech under challenging listening conditions. No correlations were observed between the cortical tracking of temporal envelope of speech and semantic processes, even after controlling for the effect of individualized signal-to-noise ratios.

ConclusionsCortical tracking of temporal envelope of speech and semantic processing are differentially influenced by task difficulty. While increased task demands modulated higher-level semantic processing, cortical tracking of temporal envelope of speech may be influenced by task difficulty primarily when the demand is manipulated in terms of acoustic properties of the stimulus, consistent with an emerging perspective in speech perception.


title: Defects in translation-dependent quality control pathways lead to convergent molecular and neurodevelopmental pathology

abstract: Translation-dependent quality control pathways such as no-go decay (NGD), non-stop decay (NSD) and nonsense-mediated decay (NMD) govern protein synthesis and proteostasis by resolving non-translating ribosomes and preventing the production of potentially toxic peptides derived from faulty and aberrant mRNAs. However, how translation is altered and the in vivo defects that arise in the absence of these pathways are poorly understood. Here, we show that the NGD/NSD factors Pelo and Hbs1l are critical for cerebellar neurogenesis but expendable for survival of these neurons after development. Analysis of mutant embryonic fibroblasts revealed translational pauses, alteration of signaling pathways, and translational reprogramming. Similar effects on signaling pathways, the translatome and cerebellar development were observed upon deletion of the NMD factor Upf2. These data reveal that these quality control pathways that function to mitigate errors at distinct steps in translation can evoke similar cellular responses.

category: cell biology


title: Diet composition, body condition and sexual size dimorphism of the common African toad (Amietophrynus regularis) in urban and agricultural landscape

abstract: Land use and land cover change (LULCC) are major drivers of global biodiversity loss. The conversion of natural habitats into human-modified landscapes poses novel and multifaceted environmental stressors to organisms, influencing their ecology, physiology, life history and fitness. Although the effects of LULCC have been studied extensively at the community level, there is scant information about its effect on population and individual characteristics. We assessed the diet composition, body condition, and sexual size dimorphism of the common African toad (Amietophrynus regularis) in urban and agricultural landscape. Diet composition was evaluated using gut content analysis, while body condition was measured using residual mass index. Overall, 935 prey items comprising six classes, at least 18 orders and 31 families were obtained from toads. This broad dietary niche suggested that Amietophrynus regularis is a generalist predator. The family Formicidae was the most consumed prey item, with a frequency of occurrence above 80% at both sites. We found no sex- or habitat-biased dietary partitioning in the toads. A statistically significant positive correlation existed between snout-vent-length (SVL) and diversity of prey items (Pearsons correlation r = 0.999, p [≤] 0.0001) for toads from farmland, which also had better body conditions. The toads showed female-biased sexual size dimorphism, but males had longer tibio-fibula, radio-ulna, foot, and distal fore limbs. This study is probably the first to assess the diet composition, body condition and sexual size dimorphism of Amietophrynus regularis simultaneously. The ecological, evolutionary and conservation implications of our findings are discussed.


title: Personalized Perturbation Profiles Reveal Concordance between Autism Blood Transcriptome Datasets

abstract: The complex heterogeneity of Autism Spectrum Disorder (ASD) has made quantifying disease specific molecular changes a challenge. Blood based transcriptomic assays have been performed to isolate these molecular changes and provide biomarkers to aid in ASD diagnoses, etiological understanding, and potential treatment1-6. However, establishing concordance amongst these studies is made difficult in part by the variation in methods used to call putative biomarkers. Here we use personal perturbation profiles to establish concordance amongst these datasets and reveal a pool of 1,189 commonly perturbed genes and new insights into poorly characterized genes that are perturbed in ASD subjects. We find the resultant perturbed gene pools to include the following unnamed genes: C18orf25, C15orf39, C1orf109, C1orf43, C19orf12, C6orf106, C3orf58, C19orf53, C17orf80, C4orf33, C21orf2, C10orf2, C1orf162, C10orf25 and C10orf90. Investigation into these genes using differential correlation analysis and the text mining tool Chilibot reveal interesting connections to DNA damage, ubiquitination, R-loops, autophagy, and mitochondrial damage. Our results support evidence that these cellular events are relevant to ASD molecular mechanisms. The personalized perturbation profile analysis scheme, as described in this work, offers a promising way to establish concordance between seemingly discordant expression datasets and expose the relevance of new genes in disease.

category: bioinformatics


title: Machine learning to extract muscle fascicle length changes from dynamic ultrasound images in real-time

abstract:
Background and objectiveDynamic muscle fascicle length measurements through B-mode ultrasound have become popular for the non-invasive physiological insights they provide regarding musculoskeletal structure-function. However, current practices typically require time consuming post-processing to track muscle length changes from B-mode images. A real-time measurement tool would not only save processing time but would also help pave the way toward closed-loop applications based on feedback signals driven by in vivo muscle length change patterns. In this paper, we benchmark an approach that combines traditional machine learning (ML) models with B-mode ultrasound recordings to obtain muscle fascicle length changes in real-time. To gauge the utility of this framework for  in-the-loop applications, we evaluate accuracy of the extracted muscle length change signals against time-series derived from a standard, post-hoc automated tracking algorithm.

MethodsWe collected B-mode ultrasound data from the soleus muscle of six participants performing five defined ankle motion tasks: (a) seated, constrained ankle plantarflexion, (b) seated, free ankle dorsi/plantarflexion, (c) weight-bearing, calf raises (d) walking, and then a (e) mix. We trained machine learning (ML) models by pairing muscle fascicle lengths obtained from standardized automated tracking software (UltraTrack) with the respective B-mode ultrasound image input to the tracker, frame-by-frame. Then we conducted hyperparameter optimizations for five different ML models using a grid search to find the best performing parameters for a combination of high correlation and low RMSE between ML and UltraTrack processed muscle fascicle length trajectories. Finally, using the global best model/hyperparameter settings, we comprehensively evaluated training-testing outcomes within subject (i.e., train and test on same subject), cross subject (i.e., train on one subject, test on another) and within/direct cross task (i.e., train and test on same subject, but different task).

ResultsSupport vector machine (SVM) was the best performing model with an average r = 0.70 {+/-}0.34 and average RMSE = 2.86 {+/-}2.55 mm across all direct training conditions and average r = 0.65 {+/-}0.35 and average RMSE = 3.28 {+/-}2.64 mm when optimized for all cross-participant conditions. Comparisons between ML vs. UltraTrack (i.e., ground truth) tracked muscle fascicle length versus time data indicated that ML tracked images reliably capture the salient qualitative features in ground truth length change data, even when correlation values are on the lower end. Furthermore, in the direct training, calf raises condition, which is most comparable to previous studies validating automated tracking performance during isolated contractions on a dynamometer, our ML approach yielded 0.90 average correlation, in line with other accepted tracking methods in the field.

ConclusionsBy combining B-mode ultrasound and classical ML models, we demonstrate it is possible to achieve real-time tracking of human soleus muscle fascicles across a number of functionally relevant contractile conditions. This novel sensing modality paves the way for muscle physiology in-the-loop applications that could be used to modify gait via biofeedback or unlock novel wearable device control techniques that could enable restored or augmented locomotion performance.

category: physiology


title: AMMI and GGE biplot analysis of yield of different elite wheat lines under terminal heat stress and irrigated environment

abstract: Wheat crop in Nepal faces terminal heat stress which accelerates the gain filling rate and shortens the filling period which leads to reduced grain weight, size, number, quality that is yield loss. For minimization of this loss, genotypic selection of high yielding lines should be performed understanding the gene-environment interaction. With the view to obtain a high yielding line with stable performance across the environments an experiment was conducted using 18 elite wheat line and 2 check varieties in alpha lattice design (2 replication and 5 blocks per replication) in different environments viz. irrigated and terminal heat stressed environment. The analysis of variance revealed that genotype, environment and their interaction had highly significant effect on the yield. Furthermore, which-won-where model indicated specific adaptation of elite lines NL-1179, NL-1420, BL-4407, NL-1368 to irrigated environment and BL-4919 and NL-1350 to terminal heat-stressed environment. Similarly, Mean-versus-stability study indicated that elite line BL-4407, NL-1368, BL-4919, NL-1350 and NL-1420 had above average yield and higher stability whereas elite lines Gautam, NL-1412, NL-1376, NL-1387, NL-1404 and N-1381 had below average yield and lower stability. Also, ranking elite lines biplot, PCA1 explaining 73.6% and PCA2 explaining 26.4% of the interaction effect, showed the rank of elite line, NL-1420 > NL-1368> NL-1350 > other lines, close to ideal line. From these findings, NL-1420 with high yield and stability can be recommended across both the environment while NL-1179 is adapted specifically for irrigated and NL-1350 adapted specifically for terminal heat-stressed environment.

category: plant biology


title: Deciphering the transcriptomic regulation of heat stress responses in Nothofagus pumilio

abstract: Global warming is predicted to exert negative impacts on plant growth due to the damaging effect of high temperatures on plant physiology. Revealing the genetic architecture underlying the heat stress response is therefore crucial for the development of conservation strategies, and for breeding heat-resistant plant genotypes. Here we investigated the transcriptional changes induced by heat in Nothofagus pumilio, an emblematic tree species of the sub-Antarctic forests of South America. Through the performance of RNA-seq of leaves of plants exposed to 20{degrees}C (control) or 34{degrees}C (heat shock), we generated the first transcriptomic resource for the species. We also studied the changes in protein-coding transcripts expression in response to heat. We found 5,214 contigs differentially expressed between temperatures. The heat treatment resulted in a down-regulation of genes related to photosynthesis and carbon metabolism, whereas secondary metabolism, protein re-folding and response to stress were up-regulated. Moreover, several transcription factor families like WRKY or ERF were promoted by heat, alongside spliceosome machinery and hormone signaling pathways. Through a comparative analysis of gene regulation in response to heat in Arabidopsis thaliana, Populus tomentosa and N. pumilio we provide evidence of the existence of shared molecular features of heat stress responses across angiosperms, and identify genes of potential biotechnological application.


title: NOMIS: Quantifying morphometric deviation from normality over the lifetime in the adult human brain

abstract: We present NOMIS (https://github.com/medicslab/NOMIS), a comprehensive open MRI tool to assess morphometric deviation from normality in the adult human brain. Based on MR anatomical images from 6,909 cognitively healthy individuals aged 18-100 years, we modeled 1,344 measures computed using the open access FreeSurfer pipeline, considering account personal characteristics (age, sex, intracranial volume) and image quality (resolution, contrast-to-noise ratio and surface reconstruction defect holes), and providing expected values for any new individual. Then, for each measure, the NOMIS tool was built to generate Z-score effect sizes denoting the extent of deviation from the normative sample. Depending on the user need, NOMIS offers four versions of Z-score adjusted on different sets of variables. While all versions consider head size and image quality, they can also incorporate age and/or sex, thereby facilitating multi-site neuromorphometric research across adulthood.


title: NOMIS: Quantifying morphometric deviations from normality over the lifetime of the adult human brain


title: Hemagglutination Inhibition (HAI) Antibody Landscapes after Vaccination with diverse H7 hemagglutinin (HA) proteins

abstract:
BackgroundA systemic evaluation of the antigenic differences of the H7 influenza hemagglutinin (HA) proteins, especially for the viruses isolated after 2016, are limited. The purpose of this study was to investigate the antigenic differences of major H7 strains with an ultimate aim to discover H7 HA proteins that can elicit protective receptor-blocking antibodies against co-circulating H7 influenza strains.

MethodA panel of nine H7 influenza strains were selected from 3,633 H7 HA amino acid sequences identified over the past two decades (2000-2018). The sequences were expressed on the surface of virus like particles (VLPs) and used to vaccinate C57BL/6 mice. Serum samples were collected and tested for hemagglutination-inhibition (HAI) activity. The vaccinated mice were challenged with lethal dose of H7N9 virus, A/Anhui/1/2013.

ResultsVLPs expressing the H7 HA antigens elicited broadly reactive antibodies each of the selected H7 HAs, except the A/Turkey/Italy/589/2000 (Italy/00) H7 HA. A putative glycosylation due to an A169T substitution in antigenic site B was identified as a unique antigenic profile of Italy/00. Introduction of the putative glycosylation site (H7 HA-A169T) significantly altered the antigenic profile of HA of the A/Anhui/1/2013 (H7N9) strain.

ConclusionThis study identified key amino acid mutations that result in severe vaccine mismatches for future H7 epidemics. Future universal influenza vaccine candidates will need to focus on viral variants with these key mutations.

category: immunology


title: Dendritic cell CX3CR1 and macrophages F4/80 play a central role in between gut micro biome and inflammation in Arsenic induced mice

abstract: Microbiota plays a crucial role to protect the intestine contrary to the harmful foreign microorganisms and organize the immune system via numerous mechanisms, which include either direct or indirect environmental factors. The underlying mechanism arsenic (As) influenced immune system and regulates inflammation by altering gut microbiome in ileum remains unclear. However, chronic exposure to arsenic (at doses of 0.15 mg or 1.5 mg or 15 mg As2O3/ L in drinking water) significantly increased mRNA and protein levels of F4/80 and CX3CR1, concurrently, the increased levels of mRNA and protein IFN{gamma}, TNF, IL-18 and decreased levels of IL-10 were found in both 3 and 6 months exposure periods. High-throughput sequencing analysis revealed that gut microbiota at phylum; family and taxonomical levels were showed the abundance of gut microbiota. Evidentially, the ultra-structure of intestinal villi, microbes engulfed and immune cell migration were showed by the transmission electron microscopy. Chronic exposure to As influenced the inflammation by changing immune system and altered gut microbiota. In this study we conclude that chronic exposure to As breakdown the normal gut microbial community and increase the pathogenicity, the resultant risk pathogen direct contact with intestinal immune system and regulate the inflammation.

category: molecular biology


title: Adherent and suspension baby hamster kidney cells have a different cytoskeleton and surface receptor repertoire

abstract: Animal cell culture, with single cells growing in suspension, ideally in a chemically defined environment, is a mainstay of biopharmaceutical production. The synthetic environment lacks exogenous growth factors and usually requires a time-consuming adaptation process to select cell clones that proliferate in suspension to high cell numbers. The molecular mechanisms that facilitate the adaptation and that take place inside the cell are largely unknown. Especially for cell lines that are used for virus antigen production such as baby hamster kidney (BHK) cells, the restriction of virus growth through the evolution of undesired cell characteristics is highly unwanted. The comparison between adherently growing BHK cells and suspension cells with different susceptibility to foot-and-mouth disease virus revealed differences in the expression of cellular receptors such as integrins and heparan sulfates, and in the organization of the actin cytoskeleton. Transcriptome analyses and growth kinetics demonstrated the diversity of BHK cell clones and confirmed the importance of well-characterized parental cell clones and mindful screening to make sure that essential cellular features do not get lost during adaptation.


title: Ecological habitat partitioning and feeding specialisations of coastal minke whales (Balaenoptera acutorostrata) using a designated MPA in northeast Scotland

abstract: In the design of protected areas for cetaceans, spatial maps rarely take account of the life-history and behaviour of protected species relevant to their spatial ambit, which may be important when modelling population trends or assessing susceptibility to anthropogenic threats. In the present study, we examined the distribution and feeding behaviours of minke whales by age-class (adults versus juveniles) from long-term studies in the Moray Firth in northeast Scotland, where a Marine Protected Area (MPA) has recently been designated. Data were collected from dedicated boat surveys between 2000 and 2019, during which 657 encounters with 774 whales of confirmed age-class (444 juveniles and 330 adults) were recorded from 50,041 km of survey effort, resulting in 224 individual follows. Feeding/foraging whales were documented in 84% of the encounters. Adults and juveniles were occasionally seen together, but their distributions were not statistically correlated, and GIS revealed spatial separation by age-class[-]with juveniles preferring shallow, inshore waters with sandy-gravel sediments and adults preferring deeper, offshore waters with steep benthic slope. Whilst adult minkes employed a range of "active" prey-entrapment specialisations, showing seasonal flexibility in their targeted prey with interindividual variation, juveniles almost exclusively used "passive" (low energy) feeding methods, targeting low-density patches of inshore prey. These findings corroborate the need to incorporate demographic/behavioural data into spatial models when identifying priority areas for protected cetaceans and may be important to adaptive management objectives for the species in the Moray Firth MPA.


title: Generalizable prediction of stimulus-independent, task-unrelated thought from functional brain networks

abstract: Neural substrates of "mind wandering" have been widely reported, yet experiments have varied in their contexts and their definitions of this psychological phenomenon, limiting generalizability. We aimed to develop and test the generalizability, specificity, and clinical relevance of a functional brain network-based marker for a well-defined feature of mind wandering--stimulus-independent, task-unrelated thought (SITUT). Combining functional MRI (fMRI) with online experience sampling in healthy adults, we defined a connectome-wide model of inter-regional coupling--dominated by default-frontoparietal control subnetwork interactions--that predicted trial-by-trial SITUT fluctuations within novel individuals. Model predictions generalized in an independent sample of attention-deficit/hyperactivity disorder (ADHD) adults. In three additional resting-state fMRI studies (total n=1,115), including healthy and ADHD populations, we demonstrated further prediction of SITUT (at modest effect sizes) defined using multiple trait-level and in-scanner measures. Our findings suggest that SITUT is represented within a common pattern of brain network interactions across time scales, populations, and contexts.


title: Divergent Connectional Asymmetries of the Inferior Parietal Lobule Shape Hemispheric Specialization in Humans, Chimpanzees, and Macaque Monkeys

abstract: The inferior parietal lobule (IPL) is one of the most expanded cortical regions in humans relative to other primates. It is also among the most structurally and functionally asymmetric regions in the human cerebral cortex. Whether the structural and connectional asymmetries of IPL subdivisions differ across primate species and how this relates to functional asymmetries remain unclear. We identified IPL subregions that exhibited positive allometric in both hemispheres, scaling across rhesus macaque monkeys, chimpanzees, and humans. The patterns of IPL subregions asymmetry were similar in chimpanzees and humans, but no IPL asymmetries were evident in macaques. Among the comparative sample of primates, humans showed the most widespread asymmetric connections in the frontal, parietal, and temporal cortices, constituting leftward asymmetric networks that may provide an anatomical basis for language and tool use. Unique human asymmetric connectivity between the IPL and primary motor cortex might be related to handedness. These findings suggest that structural and connectional asymmetries may underlie hemispheric specialization of the human brain.


title: Connectional Asymmetry of the Inferior Parietal Lobule Shapes Hemispheric Specialization in Humans, Chimpanzees, and Rhesus Macaques


title: Whole Genome Selective Sweeps Analysis in Pakistani Kamori Goat

abstract: Natural and artificial selection fix certain genomic regions of reduce heterozygosity which is an initial process in breed development. Primary goal of the current study is to identify these genomic selection signatures under positive selection and harbor genes in Pakistani Kamori goat breed. High throughput whole genome pooled-seq of Kamori (n = 12) and Bezoar (n = 8) was carried out. Raw fastq files were undergone quality checks, trimming and mapping process against ARS1 reference followed by calling variant allele frequencies. Selection sweeps were identified by applying pooled heterozygosity (Hp) and Tajimas D (TD) on Kamori while regions under divergent selection between Kamori & Bezoar were observed by Fixation Index (FST) analysis. Genome sequencing yielded 619,031,812 reads of which, 616,624,284 were successfully mapped. Total 98,574 autosomal selection signals were detected; 32,838 from Hp and 32,868 from each FST & TD statistics. Annotation of the regions with threshold (-ZHp [≥] 5, TD [≤] -2.72 & FST [≤] 0.09) detected 60 candidate genes. The top hits harbor Chr.1, 6, 8 & 21 having genes associated with body weight (GLIS3, ASTE1), coat color (DOCK8, MIPOL1) & body height (SLC25A21). Other significant windows harbor milk production, wool production, immunity, adaptation and reproduction trait related genes. Current finding highlighted the under-selection genomic regions of Kamori breed and likely to be associated with its vested traits and further useful in breed improvement, and may be also propagated to other undefined goat breeds by adopting targeted breeding policies to improve the genetic potential of this valued species.

category: genomics


title: A behavioral paradigm for cortical control of a robotic arm by freely moving rats in a one-dimensional center-out reaching task

abstract: Controlling the trajectory of a neuroprosthetic device to reach multiple targets is a commonly used brain-machine interface (BMI) task in primates and has not been available for rodents yet. Here, we describe a novel experimental paradigm which enables this task for rats in one-dimensional space for reaching two distant targets depending on their limited cognitive and visual capabilities compared to primates. An online transform was used to convert the activity of a pair of primary motor cortex (M1) units into two robotic actions. The rats were shaped to adapt to the transform and direct the robotic actuator toward the selected target by modulating the activity of the M1 neurons. All three rats involved in the study were capable of achieving randomly selected targets with at least 78% accuracy. A total of 9 out of 16 pairs of units examined were eligible for exceeding this success criterion. Two out of three rats were capable of reversal learning, where the mapping between the activity of the unit pairs and the robotic actions were reversed. The present work is the first demonstration of trajectory-based control of a neuroprosthetic device by rodents to reach two distant targets using visual feedback. The paradigm introduced here may be used as a cost-effective platform for elucidating the information processing principles in the neural circuits related to neuroprosthetic control and for studying the performance of novel BMI technologies using freely moving rats.


title: A behavioral paradigm for cortical control of a robotic arm by freely moving rats in a one-dimensional two-target reaching task


title: Sea of Electrodes Array (SEA): Extremely Dense and High-Count Silicon-Based Electrode Array Technology for High-Resolution High-Bandwidth Interfacing with 3D Neural Structures

abstract: In this work, we propose a new silicon-based micro-fabrication technology to fabricate 3D high-density high-electrode-count neural micro-probe arrays scalable to thousands and even millions of individual electrodes with user-defined length, width, shape, and tip profile. This unique technology utilizes DRIE of ultra-high aspect-ratio holes in silicon and refilling them with multiple films to form thousands of individual needles with metal tips making up the "sea-of-electrodes" array (SEA). World-record density of 400 electrodes/mm2 in a 5184-needle array is achieved. The needles are ~0.5-1.2mm long, <20m wide at the base, and <1m at the tip. The silicon-based structure of these 3D array probes with sharp tips, makes them stiff enough and easily implantable in the brain to reach a targeted region without failing. Moreover, the high aspect ratio of these extremely fine needles reduces the tissue damage and improves the chronic stability. Functionality of the electrodes is investigated using acute in vivo recording in a rat barrel field cortex under isoflurane anesthesia.


title: The secreted tyrosine kinase VLK is essential for normal platelet activation and thrombus formation

abstract: Tyrosine phosphorylation of extracellular proteins is observed in cell cultures and in vivo, but little is known about the functional roles of tyrosine phosphorylation of extracellular proteins. Vertebrate Lonesome Kinase (VLK) is a broadly expressed secretory pathway tyrosine kinase present in platelet [a]-granules. It is released from platelets upon activation and phosphorylates substrates extracellularly. Its role in platelet function, however, has not been previously studied. In human platelets, we identified phosphorylated tyrosines mapped to luminal or extracellular domains of transmembrane and secreted proteins implicated in the regulation of platelet activation. To determine the role of VLK in extracellular tyrosine phosphorylation and platelet function, we generated mice with a megakaryocyte/platelet-specific deficiency of VLK. Platelets from these mice are normal in abundance and morphology, but have dramatic changes in function both in vitro and in vivo. Resting and thrombin-stimulated VLK-deficient platelets demonstrate a significant decrease of several tyrosine phosphobands. Functional testing of VLK-deficient platelets shows decreased PAR4- and collagen-mediated platelet aggregation, but normal responses to ADP. Dense granule and -granule release are reduced in these platelets. Furthermore, VLK-deficient platelets exhibit decreased PAR4-mediated Akt (S473) and Erk1/2(T202/Y204) phosphorylation, indicating altered proximal signaling. In vivo, mice lacking VLK in megakaryocytes/platelets demonstrate strongly reduced platelet accumulation and fibrin formation following laser-injury of cremaster arterioles compared to controls. These studies demonstrate that the secretory pathway tyrosine kinase VLK is critical for stimulus-dependent platelet activation and thrombus formation, providing the first evidence that a secreted protein kinase is required for normal platelet function.


title: Hox genes regulate asexual reproductive behavior and tissue segmentation in adult animals

abstract: Hox genes are highly conserved transcription factors renowned for their roles in the segmental patterning of the embryonic anterior-posterior (A/P) axis1. Emerging evidence for Hox gene expression and function in postnatally derived structures has fueled interest in their additional roles beyond embryogenesis2,3. We report novel functions for Hox genes in A/P adult tissue segmentation and transverse fission behavior underlying asexual reproduction in the planarian flatworm, Schmidtea mediterranea. Silencing of each of the planarian Hox family members identified 5 Hox genes required for asexual reproduction. Among these, silencing of hox3 genes resulted in supernumerary segments, while silencing of post2b eliminated segmentation altogether. The opposing roles of hox3 and post2b in segmentation are paralleled in their respective regulation of fission behavior. Silencing of hox3 increased the frequency of fission behavior initiation, while silencing of post2b eliminated fission behavior entirely. Furthermore, we identified a network of downstream effector genes mediating Hox gene regulation of asexual reproduction, thereby providing insight into their respective mechanisms of action. Our study establishes postembryonic roles for Hox genes in regulating the emergence of tissue segmentation and specific behaviors associated with asexual reproduction in adult animals.

category: developmental biology


title: TWO-SIGMA-G: A New Competitive Gene Set Testing Framework for scRNA-seq Data Accounting for Inter-Gene and Cell-Cell Correlation

abstract: We propose TWO-SIGMA-G, a competitive gene set test for scRNA-seq data. TWO-SIGMA-G uses a mixed-effects regression model based on our previously published TWO-SIGMA to test for differential expression at the gene-level. This regression-based model provides flexibility and rigor at the gene-level in (1) handling complex experimental designs, (2) accounting for the correlation between biological replicates, and (3) accommodating the distribution of scRNA-seq data to improve statistical inference. Moreover, TWO-SIGMA-G uses a novel approach to adjust for inter-gene-correlation (IGC) at the set-level to control the set-level false positive rate. Simulations demonstrate that TWO-SIGMA-G preserves type-I error and increases power in the presence of IGC compared to other methods. Application to two datasets identified HIV-associated Interferon pathways in xenograft mice and pathways associated with Alzheimers disease progression in humans.


title: Pose Estimation of Free-Flying Fruit Flies

abstract: Insect flight is a complex interdisciplinary phenomenon. Understanding its multiple aspects, such as flight control, sensory integration and genetics, often requires the analysis of large amounts of free flight kinematic data. Yet, one of the main bottlenecks in this field is automatically and accurately extracting such data from multi-view videos. Here, we present a model-based method for pose-estimation of free-flying fruit flies from multi-view high-speed videos. To obtain a faithful representation of the fly with minimum free parameters, our method uses a 3D model that mimics two new aspects of wing deformation: a non-fixed wing hinge and a twisting wing surface. The method is demonstrated for free and perturbed flight. Our method does not use prior assumptions on the kinematics apart from the continuity of one wing angle. Hence, this method can be readily adjusted for other insect species.


title: Implant- and anesthesia-related factors affecting threshold intensities for vagus nerve stimulation

abstract: Vagus nerve stimulation (VNS) is used as therapy in epilepsy and depression and is tested as a potential treatment for several chronic disorders. Typically, VNS is delivered at increasing stimulus intensity until a response is observed (threshold intensity). Factors that affect threshold intensities for engagement of different fiber types and concomitant physiological responses have not been studied. We determined neural and physiological responses to increasing stimulus intensities of VNS in anesthetized and awake animals, and examined the effect of implant- and anesthesia-related factors on threshold intensities in a rodent model of VNS. In acute and long-term cervical vagus nerve implants (53 and 14 rats, respectively) VNS was delivered under isoflurane, ketamine-xylazine, or awake at different intensities. Stimulus-evoked compound action potentials (eCAPs) were recorded, elicited physiological responses were registered, including changes heart rate (HR), breathing, and blood pressure (BP), and threshold intensities were determined. The intensity that elicits eCAPs ("neural threshold") is significantly lower than what elicits a physiological response ("physiological threshold", PT) (25 A {+/-}1.8 vs. 70 A {+/-}5.2, respectively; Mean {+/-}SEM). Changes in BP occur at the lowest stimulus intensities (80 A {+/-}7), followed by changes in HR (105 A {+/-}8.4) and finally in breathing (310 A {+/-}32.5). PT is lower with than without electrode insulation (60 A {+/-}12, vs. 700 A {+/-}123). PT and electrode impedance are correlated in long-term (r=0.47; p<0.001) but not in acute implants (r=-0.34; p NS); both PT and impedance increase with implant age (Pearson correlation r=0.44; p<0.001 and r=0.64; p<0.001, respectively). PT is lowest when animals are awake (210 A {+/-}33; Mean {+/-}SEM), followed by ketamine-xylazine (630 A {+/-}154), and isoflurane (1075 A {+/-}131). The sequence of physiological responses with increasing VNS intensity is similar in both anesthetized and awake states. Implant age, electrical impedance and the type of anesthesia affect VNS threshold and should be accounted for when determining stimulation dose.

category: bioengineering


title: Heterogeneity in PHGDH protein expression potentiates cancer cell dissemination and metastasis

abstract: Cancer metastasis requires the transient activation of cellular programs enabling dissemination and seeding in distant organs. Genetic, transcriptional and translational intra-tumor heterogeneity contributes to this dynamic process. Beyond this, metabolic intra-tumor heterogeneity has also been observed, yet its role for cancer progression remains largely elusive. Here, we discovered that intra-tumor heterogeneity in phosphoglycerate dehydrogenase (PHGDH) protein expression drives breast cancer cell dissemination and metastasis formation. Specifically, we observed intra-tumor heterogeneous PHGDH expression in primary breast tumors, with low PHGDH expression being indicative of metastasis in patients. In mice, Phgdh protein, but not mRNA, expression is low in circulating tumor cells and early metastatic lesions, leading to increased dissemination and metastasis formation. Mechanistically, low PHGDH protein expression induces an imbalance in glycolysis that can activate sialic acid synthesis. Consequently, cancer cells undergo a partial EMT and show increased p38 as well as SRC phosphorylation, which activate cellular programs of dissemination. In turn, inhibition of sialic acid synthesis through knock-out of cytidine monophosphate N-acetylneuraminic acid synthetase (CMAS) counteracts the increased cancer cell dissemination and metastasis induced by low PHGDH expression. In conclusion, we find that heterogeneity in PHGDH protein expression promotes cancer cell dissemination and metastasis formation.

category: cancer biology


title: Optimization of Ethanol-Assisted Aqueous Oil Extraction from a Cicadidae Sp

abstract: Edible insects have been considering as a rich resource of high-quality protein and lipid content and at the same time a low-cost nutritious resource acquiring the least expenditure during farming, breeding, rearing and harvesting. On the other hand, organic solvent consumptions in industrial areas need to be limited; being flammable by environmental hazards. That is why seeking for alternative non-toxic solvents is highly substantial. In this study ethanol-aqueous extraction method applied at three different levels to find the optimum yield of edible oil extracted of Homoptera Cicadidae Magicicada, a seasonal insect residing underground, which is consuming locally as a whole meal. These levels set using Design of expert software to variables as pH, ethanol-concentration and solvent/sample ratio and the maximum yield extracted respectively at 6, 50 and 5, by the yield of 19.5%, that is comparable to oil extracted by conventional hexane oil extraction method at 27%. Fatty acids profile of recent method and hexane extraction method analyzed using GC-MS method and the physicochemical properties of either alternative method investigated. The results were on the standard ranges. Fatty acid profile of HCM was for the most part consisted of oleic acid, following by palmitic and linoleic acid 66.5, 19.2 and 7.8 respectively in hexane extraction method and 66.3, 17.7 and 9.5 in ethanol aqueous extraction method. The Iodine Value of HCM oil was noticeably high which introduces a medicinal applicatory besides the rich amount of MUFAs and PUFAs essential oils that are well-known for their incredible health benefits.

category: pharmacology and toxicology


title: Dorsal color variation among subspecies of the "Oregon" Dark-eyed Junco complex

abstract: Initial descriptions of avian subspecies were based on expert opinions of geographic variation in phenotypes and are inherently subjective. Although best practices for subspecies delimitation continue to be debated, reassessing subspecies limits with current, quantitative methods is important toward refining and improving taxonomic treatments. Plumage coloration is the basis of many subspecies diagnoses, but is potentially problematic because of the historical lack of quantitative methods to quantify color. Recently developed methods, such as colorimetry, provide repeatable measurements of color variation that can be used to reassess subspecies limits. In this study, we reassess color variation among subspecies of the Oregon Dark-eyed Junco (Junco hyemalis [oreganus Group]) complex, in which differences in back and hood color were established as diagnostic characters. We measured back and hood brightness and hue in 206 museum specimens among five Oregon Dark-eyed Junco subspecies using a colorimeter. We then compared mean measurements among subspecies and conducted a discriminant function analysis to assess how well dorsal color predicted subspecies. Our data correctly classified only 67.9% of males and 82.5% of females to their presumed subspecies. Furthermore, no adjacent subspecies pairs passed the "75% rule" due to extensive overlap in plumage characters. Thus, back color alone is not as effective in diagnosing Oregon Dark-eyed Junco subspecies as originally described, suggesting a possible taxonomic revision. Specifically, similarity in phenotypic and genetic data suggests that some combination of thurberi, montanus, and shufeldti may be lumped to recognize broad, clinal variation in dorsal color alongside clinal variation in other phenotypes and extensive gene flow.

category: zoology


title: Large-scale analysis of interindividual variability in single and paired-pulse TMS data: results from the 'Big TMS Data Collaboration'

abstract:
ObjectiveInterindividual variability of single and paired-pulse TMS data has limited the clinical and experimental applicability of these methods. This study brought together over 60 TMS researchers to create the largest known sample of individual participant single and paired-pulse TMS data to date, enabling a more comprehensive evaluation of factors driving response variability.

Methods118 corresponding authors provided deidentified individual TMS data. Mixed-effects regression investigated a range of individual and study level variables for their contribution to variability in response to single and pp TMS data.

Results687 healthy participants TMS data was pooled across 35 studies. Target muscle, pulse waveform, neuronavigation use, and TMS machine significantly predicted an individuals single pulse TMS amplitude. Baseline MEP amplitude, M1 hemisphere, and biphasic AMT significantly predicted SICI response. Baseline MEP amplitude, test stimulus intensity, interstimulus interval, monophasic RMT, monophasic AMT, and biphasic RMT significantly predicted ICF response. Age, M1 hemisphere, and TMS machine significantly predicted motor threshold.

ConclusionsThis large-scale analysis has identified a number of factors influencing participants responses to single and paired pulse TMS. We provide specific recommendations to increase the standardisation of TMS methods within and across laboratories, thereby minimising interindividual variability in single and pp TMS data.

HighlightsO_LI687 healthy participants TMS data was pooled across 35 studies
C_LIO_LISignificant relationships between age and resting motor threshold
C_LIO_LISignificant relationships between baseline MEP amplitude and SICI/ICF
C_LI


title: Deconstruction of the retrosplenial granular cortex for social behavior in the mouse model of fragile X syndrome

abstract:
Deficits in fragile X mental retardation 1 protein lead to fragile X syndrome (FXS) with mental retardation and social activity disorder. Until now, the neuronal circuits that mediate the social impairments of FXS were mostly unclear. Accidently, we found fewer c-fos expression in RSG of KO than WT mice after social behavior test. Inactivation of RSG neurons decreased social novelty but not the sociability of naive mice. Interestingly, although the RSG neurons of KO mice had higher background activity, fewer social contact-related Ca2+ neurons were observed during social interaction test via one-photon Ca2+ imaging in freely-behaving mice. Strikingly, enhancing the activity of RSG neurons rescued the abnormal social novelty in KO mice. Further studies proved that the innervations from the subiculum and ACC to RSG contributes to the social behavior. Take together, we found that abnormal activity in the retrosplenial granular cortex (RSG) led to social novelty deficits in Fmr1-knockout (KO) mice. Moreover, selective manipulation of RSG neurons may be an effective strategy to treat the social deficits in FXS.

One Sentence SummaryDeletion of FMRP leads to lower social-related neuronal activity in the RSG; this causes social novelty deficits in Fmr1-KO mice.


title: The brain clock portal system: SCN-OVLT

abstract: Vascular portal systems are key structures, necessary for transporting products directly from the capillary bed of one region to the capillary bed of another region in high concentrations, without first returning to the heart. The only known portal systems in the brain is the hypophyseal-pituitary portal system, a structure necessary for survival and reproduction. Secretions from specific populations of hypothalamic neurons travel into fenestrated capillaries of the median eminence (ME) and thence drain into portal veins which break up into the secondary capillary plexus of the anterior pituitary. Neurons of the hypothalamic suprachiasmatic nucleus (SCN), locus of the brains master clock, also produces secretions deeply implicated in health and survival (Karatsoreos, 2019; Musiek & Holtzman, 2016). Here we describe a portal system connecting the SCN and organum vasculosum of the lamina terminalis (OVLT) - a circumventricular organ (CVO). CVOs lie around ventricles and lack a blood-brain barrier, enabling communication between the blood, brain, and cerebrospinal fluid. This "clock portal system" points to entirely new routes and targets for secreted signals, restructuring our understanding of brain communication pathways. Whether any of the remaining six CVOs in the mammalian brain bear portal systems is yet to be determined.


title: Training for object recognition with increasing spatial frequency: A comparison of deep learning with human vision.

abstract: The ontogenetic development of human vision, and the real-time neural processing of visual input, both exhibit a striking similarity - a sensitivity towards spatial frequencies that progress in a coarse-to-fine manner. During early human development, sensitivity for higher spatial frequencies increases with age. In adulthood, when humans receive new visual input, low spatial frequencies are typically processed first before subsequently guiding the processing of higher spatial frequencies. We investigated to what extent this coarse-to-fine progression might impact visual representations in artificial vision and compared this to adult human representations. We simulated the coarse-to-fine progression of image processing in deep convolutional neural networks (CNNs) by gradually increasing spatial frequency information during training. We compared CNN performance, after standard and coarse-to-fine training, with a wide range of datasets from behavioural and neuroimaging experiments. In contrast to humans, CNNs that are trained using the standard protocol are very insensitive to low spatial frequency information, showing very poor performance in being able to classify such object images. By training CNNs using our coarse-to-fine method, we improved the classification accuracy of CNNs from 0% to 32% on low-pass filtered images taken from the ImageNet dataset. When comparing differently trained networks on images containing full spatial frequency information, we saw no representational differences. Overall, this integration of computational, neural, and behavioural findings shows the relevance of the exposure to and processing of input with a variation in spatial frequency content for some aspects of high-level object representations.


title: Long-term monitoring reveals topographical features and vegetation explain winter habitat use of an Arctic rodent

abstract: Collapsing lemming cycles have been observed across the Arctic, presumably due to global warming creating less favorable winter conditions. The quality of wintering habitats, such as depth of snow cover, plays a key role in sustaining population dynamics of arctic lemmings. However, few studies so far investigated habitat use during the arctic winter. Here, we used a unique long-term time series to test whether lemmings are associated with topographical and vegetational habitat features for their winter refugi. We examined yearly numbers and distribution of 22,769 winter nests of the collared lemming Dicrostonyx groenlandicus from an ongoing long-term research on Traill Island, Northeast Greenland, collected between 1989 and 2019, and correlated this information with data on dominant vegetation types, elevation and slope. We specifically asked if lemming nests were more frequent at sites with preferred food plants such as Dryas octopetala x integrifolia and at sites with increased snow cover. We found that the number of lemming nests was highest in areas with a high proportion of Dryas heath, but also correlated with other vegetation types which suggest some flexibility in resource use of wintering lemmings. Conversely, they showed a distinct preference for sloped terrain, probably as it enhances the formation of deep snow drifts which increases the insulative characteristics of the snowpack and protection from predators. With global warming, prime lemming winter habitats may become scarce through alteration of snow physical properties, potentially resulting in negative consequence for the whole community of terrestrial vertebrates.


title: Direct and indirect effects of high temperatures on fledging success in a cooperatively breeding bird

abstract:
High temperatures and low rainfall consistently constrain reproduction in arid-zone bird species. Understanding the mechanisms underlying this pattern is critical for predicting how climate change will influence population persistence and to inform conservation and management. In this study, we analysed Southern Pied Babbler Turdoides nestling survival, daily growth rate and adult investment behaviour during the nestling period over three austral summer breeding seasons. High temperatures were associated with lower body mass, shorter tarsi, and reduced daily growth rates of nestlings. Piecewise structural equation modelling suggests that direct impacts of temperature had the strongest influence, followed by changes in provisioning rates by adults to older nestlings.

Adjustments to adult provisioning strategies did not compensate for direct negative effects of high air temperatures on nestling body mass, tarsus and wing length, or daily growth rates. Declining reproductive success during hot weather poses a potentially serious threat to population replacement and persistence as climate change progresses, even for currently common and widespread species. Significantly lower offspring survival as a result of climate warming will likely contribute to the collapse of animal communities well before temperatures regularly approach or exceed lethal tolerance limits. Detailed mechanistic data like these allow us to model the pathways by which high temperature causes nest failure. In turn, this could allow us to design targeted conservation action to effectively mitigate climate effects.


title: Ecological consequences of urbanization on a legume-rhizobia mutualism

abstract: Mutualisms are key determinants of community assembly and composition, but urbanization can alter the dynamics of these interactions and associated effects on ecosystem functions. Legume-rhizobia mutualisms are a model interaction to evaluate the ecological and ecosystem-level effects of urbanization, particularly urban-driven eutrophication and nitrogen (N) deposition. Here, we evaluated how urbanization affected the ecology of the mutualism between white clover (Trifolium repens) and its rhizobial symbiont (Rhizobium leguminosarum symbiovar trifolii) along an urbanization gradient. We found that the abundance of rhizobium nodules on white clover decreased with urbanization. White clover acquired N from mixed sources of N fixation and uptake from the soil for the majority of the urbanization gradient, but white clover primarily acquired N from the soil rather than N fixation by rhizobia at the urban and rural limits of the gradient. Importantly, we identified soil N as a critical nexus for urban-driven changes in the white clover-rhizobium mutualism. Taken together, our results demonstrate that urbanization alters the ecological consequences of a legume-rhizobium mutualism, with direct and indirect effects of the urban landscape on an ecologically-important mutualistic interaction.


title: Spike-in normalization for single-cell RNA-seq reveals dynamic global transcriptional activity mediating anti-cancer drug response

abstract: The transcriptional plasticity of cancer cells promotes intercellular heterogeneity in response to anti-cancer drugs and facilitates the generation of subpopulation surviving cells. Characterizing single-cell transcriptional heterogeneity after drug treatments can provide mechanistic insights into drug efficacy. Here we used single-cell RNA-seq to examine transcriptomic profiles of cancer cells treated with paclitaxel, celecoxib, and the combination of the two drugs. By normalizing the expression of endogenous genes to spike-in molecules, we found that celluar mRNA abundance shows dynamic regulation after drug treatment. Using a random forest model, we identified gene signatures classifying single cells into three states: transcriptional repression, amplification, and control-like. Treatment with paclitaxel or celecoxib alone generally repressed gene transcription across single cells. Interestingly, the drug combination resulted in transcriptional amplification and hyperactivation of mitochondrial oxidative phosphorylation pathway linking to enhanced cell killing efficiency. Finally, we identified a regulatory module enriched with metabolism and inflammation-related genes activated in a subpopulation of paclitaxel-treated cells, the expression of which predicted paclitaxel efficacy across cancer cell lines and in vivo patient samples. Our study highlights the dynamic global transcriptional activity driving single-cell heterogeneity during drug response and emphasizes the importance of adding spike-in molecules to study gene expression regulation using single-cell RNA-seq.


title: Novel bisubstrate inhibitors for protein N-terminal acetyltransferase D

abstract: Protein N-terminal acetyltransferase D (NatD, NAA40) that specifically acetylates the alpha-N-terminus of histone H4 and H2A has been implicated in various diseases, but no inhibitor has been reported for this important enzyme. Based on the acetyl transfer mechanism of NatD, we designed and prepared a series of highly potent NatD bisubstrate inhibitors by covalently linking coenzyme A to different peptide substrates via an acetyl or propionyl spacer. The most potent bisubstrate inhibitor displayed an apparent Ki value of 1.0 nM. Biochemical studies indicated that bisubstrate inhibitor is competitive to the peptide substrate and noncompetitive to the cofactor, suggesting NatD undergoes an ordered Bi-Bi mechanism. We also demonstrated that these inhibitors are highly specific towards NatD, displaying about 1,000-fold selectivity over other closely related acetyltransferases. High-resolution crystal structures of NatD bound to two of these inhibitors revealed the molecular basis for their selectivity and inhibition mechanism, providing a rational path for future inhibitor development.

category: biochemistry


title: Nuclear cholesterol is required for transcriptional repression by BASP1

abstract:
Lipids are present within the cell nucleus where they engage with factors involved in gene regulation. Cholesterol associates with chromatin in vivo and stimulates nucleosome packing in-vitro, but its effects on specific transcriptional responses are not clear. Here we show that the lipidated WT1 transcriptional corepressor, BASP1, interacts with cholesterol in the cell nucleus through a conserved cholesterol interaction motif. We demonstrate that BASP1 directly recruits cholesterol to the promoter region of WT1 target genes. Mutation of BASP1 to ablate its interaction with cholesterol or the treatment of cells with drugs that block cholesterol biosynthesis inhibit the transcriptional repressor function of BASP1. We find that the BASP1-cholesterol interaction is required for BASP1-dependent chromatin remodelling and the direction of transcription programs that control cell differentiation. Our study uncovers a mechanism for gene-specific targeting of cholesterol where it is required to mediate transcriptional repression.

SignificanceCholesterol is present within the cell nucleus where it associates with chromatin but to date, a direct role for cholesterol in nuclear processes has not been identified. We demonstrate that the transcriptional repressor BASP1 directly interacts with cholesterol within the cell nucleus through a consensus cholesterol interaction motif. BASP1 recruits cholesterol to the promoter region of target genes where it is required to mediate chromatin remodelling and transcriptional repression. Our work demonstrates that nuclear cholesterol plays a direct role in transcriptional regulation.


title: Profile hidden Markov model sequence analysis can help remove putative pseudogenes from DNA barcoding and metabarcoding datasets

abstract:
BackgroundPseudogenes are non-functional copies of protein coding genes that typically follow a different molecular evolutionary path as compared to functional genes. The inclusion of pseudogene sequences in DNA barcoding and metabarcoding analysis can lead to misleading results. None of the most widely used bioinformatic pipelines used to process marker gene (metabarcode) high throughput sequencing data specifically accounts for the presence of pseudogenes in protein-coding marker genes. The purpose of this study is to develop a method to screen for obvious pseudogenes in large COI metabarcode datasets. We do this by: 1) describing gene and pseudogene characteristics from a simulated DNA barcode dataset, 2) show the impact of two different pseudogene removal methods on mock metabarcode datasets with simulated pseudogenes, and 3) incorporate a pseudogene filtering step in a bioinformatic pipeline that can be used to process Illumina paired-end COI metabarcode sequences. Open reading frame length and sequence bit scores from hidden Markov model (HMM) profile were used to detect pseudogenes.

ResultsOur simulations showed that it was more difficult to identify pseudogenes from shorter amplicon sequences such as those typically used in metabarcoding ([~]300 bp) compared with full length DNA barcodes that are used in construction of barcode libraries ([~] 650 bp). It was also more difficult to identify pseudogenes in datasets where there is a high percentage of pseudogene sequences. We show that existing bioinformatic pipelines used to process metabarcode sequences already remove some apparent pseudogenes, especially in the rare sequence removal step, but the addition of a pseudogene filtering step can remove more.

ConclusionsThe combination of open reading frame length and hidden Markov model profile analysis can be used to effectively screen out obvious pseudogenes from large datasets. There is more to learn from COI pseudogenes such as their frequency in DNA barcode and metabarcoding studies, their taxonomic distribution, and evolution. Thus, we encourage the submission of verified COI pseudogenes to public databases to facilitate future studies.


title: Reproducibility of protein X-ray diffuse scattering and potential utility for modeling atomic displacement parameters

abstract: Protein structure and dynamics can be probed using X-ray crystallography. Whereas the Bragg peaks are only sensitive to the average unit-cell electron density, the signal between the Bragg peaks -- diffuse scattering -- is sensitive to spatial correlations in electron-density variations. Although diffuse scattering contains valuable information about protein dynamics, the diffuse signal is more difficult to isolate from the background compared to the Bragg signal, and the reproducibility of diffuse signal is not yet well understood. We present a systematic study of the reproducibility of diffuse scattering from isocyanide hydratase (ICH) in three different protein forms. Both replicate diffuse datasets and datasets obtained from different mutants were similar in pairwise comparisons (Pearson correlation coefficient (CC) [≥]0.8). The data were processed in a manner inspired by previously published methods using custom software with modular design, enabling us to perform an analysis of various data processing choices to determine how to obtain the highest quality data as assessed using unbiased measures of symmetry and reproducibility. The diffuse data then were used to characterize atomic mobility using a liquid-like motions (LLM) model. This characterization was able to discriminate between distinct anisotropic atomic displacement parameter (ADP) models arising from different anisotropic scaling choices that agreed comparably with the Bragg data. Our results emphasize the importance of data reproducibility as a model-free measure of diffuse data quality, illustrate the ability of LLM analysis of diffuse scattering to select among alternative ADP models, and offer insights into the design of successful diffuse scattering experiments.

category: biophysics


title: Programmable Viscoelasticity in Protein-RNA Condensates with Disordered Sticker-Spacer Polypeptides

abstract: Liquid-liquid phase separation of multivalent proteins and RNAs drives the formation of biomolecular condensates that facilitate membrane-free compartmentalization of subcellular processes. With recent advances, it is becoming increasingly clear that biomolecular condensates are network fluids with time-dependent material properties. Here, employing microrheology with optical tweezers, we reveal molecular determinants that govern the viscoelastic behavior of condensates formed by multivalent Arg/Gly-rich sticker-spacer polypeptides and RNA. These condensates behave as Maxwell fluids with an elastically-dominant rheological response at shorter timescales and a liquid-like behavior at longer timescales. The viscous and elastic regimes of these condensates can be tuned by the polypeptide and RNA sequences as well as their mixture compositions. Our results establish a quantitative link between the sequence- and structure-encoded biomolecular interactions at the microscopic scale and the rheological properties of the resulting condensates at the mesoscale, enabling a route to systematically probe and rationally engineer biomolecular condensates with programmable mechanics.


title: Global analysis of protein arginine methylation

abstract:
Quantitative information about the levels and dynamics of post-translational modifications (PTMs) is critical for an understanding of cellular functions. Protein arginine methylation (ArgMet) is an important subclass of PTMs and is involved in a plethora of (patho)physiological processes. However, due to the lack of methods for global analysis of ArgMet, the link between ArgMet levels, dynamics and (patho)physiology remains largely unknown. We utilized the high sensitivity and robustness of Nuclear Magnetic Resonance (NMR) spectroscopy to develop a general method for the quantification of global protein ArgMet. Our NMR-based approach enables the detection of protein ArgMet in purified proteins, cells, organoids, and mouse tissues. We demonstrate that the process of ArgMet is a highly prevalent PTM and can be modulated by small-molecule inhibitors and metabolites and changes in cancer and during ageing. Thus, our approach enables to address a wide range of biological questions related to ArgMet in health and disease.

Graphical Abstract

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category: systems biology


title: BAG3 regulation of Rab35 mediates the ESCRT/endolysosome pathway and tau clearance

abstract:
BackgroundDeclining proteostasis with aging contributes to increased susceptibility to neurodegenerative diseases, including Alzheimers disease (AD). Emerging studies implicate impairment of the endosome-lysosome pathway as a significant factor in the pathogenesis of these diseases. Our lab was the first to demonstrate that BAG3 regulates phosphorylated tau clearance. However, we did not fully define how BAG3 regulates endogenous tau proteostasis, especially in the early stages of disease progression.

MethodsMass spectrometric analyses were performed to identify neuronal BAG3 interactors. Multiple biochemical assays were used to investigate the BAG3-HSP70-TBC1D10B-Rab35-Hrs regulatory networks. Live-cell imaging was used to study the dynamic of endosomal pathway. Immunohistochemistry and immunoblotting were performed in human AD brains and BAG3 overexpressed P301S tau transgenic mice.

ResultsThe primary group of neuronal BAG3 interactors identified are involved in the endocytic pathway. Among them were key regulators of small GTPases, such as the Rab35 GTPase activating protein, TBC1D10B. We demonstrated that a BAG3-HSP70-TBC1D10B complex attenuates the ability of TBC1D10B to inactivate Rab35. Thus, BAG3 interacts with TBC1D10B to support the activation of Rab35 and recruitment of Hrs, initiating ESCRT-mediated endosomal tau clearance. Further, TBC1D10B shows significantly less co-localization with BAG3 in AD brains than in age-matched controls. Overexpression of BAG3 in P301S tau transgenic mice increased the co-localization of phospho-tau with the ESCRT III protein CHMP2B and reduced the levels of the mutant human tau.

ConclusionWe identified a novel BAG3-TBC1D10B-Rab35 regulatory axis that modulates ESCRT-dependent protein degradation machinery and tau clearance. Dysregulation of BAG3 could contribute to the pathogenesis of AD.


title: BAG3 regulation of Rab35 mediates the Endosomal Sorting Complexes Required for Transport /endolysosome pathway and tau clearance


title: Nigrostriatal Dopamine Signals Sequence-Specific Action-Outcome Prediction Errors

abstract: Dopamine has been suggested to encode cue-reward prediction errors during Pavlovian conditioning. While this theory has been widely applied to reinforcement learning concerning instrumental actions, whether dopamine represents action-outcome prediction errors and how it controls sequential behavior remain largely unknown. Here, by training mice to perform optogenetic intracranial self-stimulation, we examined how self-initiated goal-directed behavior influences nigrostriatal dopamine transmission during single as well as sequential instrumental actions. We found that dopamine release evoked by direct optogenetic stimulation was dramatically reduced when delivered as the consequence of the animals own action, relative to non-contingent passive stimulation. This action-induced dopamine suppression was specific to the reinforced action, temporally restricted to counteract the expected outcome, and exhibited sequence-selectivity consistent with hierarchical control of sequential behavior. Together these findings demonstrate that nigrostriatal dopamine signals sequence-specific prediction errors in action-outcome associations, with fundamental implications for reinforcement learning and instrumental behavior in health and disease.


title: Basis profile curve identification to understand electrical stimulation effects in human brain networks

abstract:
Brain networks can be explored by delivering brief pulses of electrical current in one area while measuring voltage responses in other areas. We propose a convergent paradigm to study brain dynamics, focusing on a single brain site to observe the average effect of stimulating each of many other brain sites. Viewed in this manner, visually-apparent motifs in the temporal response shape emerge from adjacent stimulation sites. This work constructs and illustrates a data-driven approach to determine characteristic spatiotemporal structure in these response shapes, summarized by a set of unique "basis profile curves" (BPCs). Each BPC may be mapped back to underlying anatomy in a natural way, quantifying projection strength from each stimulation site using simple metrics. Our technique is demonstrated for an array of implanted brain surface electrodes in a human patient. This framework enables straightforward interpretation of single-pulse brain stimulation data, and can be applied generically to explore the diverse milieu of interactions that comprise the connectome.

Author summaryWe present a new machine learning framework to probe how brain regions interact using single-pulse electrical stimulation. Unlike previous studies, this approach does not assume a form for how one brain area will respond to stimulation in another area, but rather discovers the shape of the response in time from the data. We call the set of characteristic discovered response shapes "basis profile curves" (BPCs), and show how these can be mapped back onto the brain quantitatively. An illustrative example is included from one of our human patients to characterize inputs to the parahippocampal gyrus. A code package is downloadable from https://purl.stanford.edu/rc201dv0636 so the reader may explore the technique for own data, or study sample data provided to reproduce the illustrative case presented in the manuscript.


title: Adenosine metabolized from extracellular ATP promotes type 2 immunity through triggering A2BAR signaling on intestinal epithelial cells

abstract: Multicellular intestinal nematode parasites can cross the epithelial barrier potentially causing tissue damage and release of danger associated molecular patterns (DAMPs) that may promote type 2 responses and host protective immunity. We investigated whether adenosine specifically binding the A2B adenosine receptor (A2BAR) on epithelial cells played an important role in driving intestinal immunity. Specific blockade of epithelial cell A2BAR inhibited the host protective memory response to the enteric helminth, Heligmosomoides polygyrus bakeri, including disruption of granuloma development at the host:parasite interface during the transient tissue dwelling larval stage. Memory T cell development was blocked during the primary response and transcriptional analyses revealed profound impairment of A2BAR signaling in epithelial cells and reduced type 2 markers by 24 hours after inoculation. Extracellular ATP was visualized by 24 hours after inoculation and shown in CD39 deficient mice to be critical for the adenosine production mediating initiation of type 2 immunity.


title: Comparison of endogenously expressed fluorescent protein fusions behaviour for protein quality control and cellular aging research

abstract: The yeast Hsp104 protein disaggregase is often used as a reporter for misfolded or damaged protein aggregates and protein quality control and ageing research. Observing endogenously expressed Hsp104 fusions with fluorescent proteins is a popular approach to follow post stress protein aggregation, inclusion formation and disaggregation. Overall, such protein fusions used in molecular and microbiology research are often sparsely characterised. To address this issue, we performed a comparative assessment of Hsp104 fluorescent fusions function and behaviour. We provide experimental evidence that molecular behaviour may not only be altered by introducing a fluorescent protein tag but also varies depending on the fluorophore within the fusion. Although our findings are especially applicable to protein quality control and ageing research in yeast, similar effects and points may play a role in other eukaryotic systems.


title: DNA metabarcoding reveals adaptive seasonal variation of individual trophic traits in a critically endangered fish

abstract: Dietary studies are critical for understanding foraging strategies and have important applications in conservation and habitat management. We applied a robust metabarcoding protocol to characterize the diet of the critically endangered freshwater fish Zingel asper and conducted modelling and simulation analyses to characterize and identify some of the drivers of individual trophic trait variation in this species. We found that intra-specific competition and ontogeny had minor effects on the trophic niche of Z. asper. Instead, our results suggest that the majority of trophic niche variation was driven by seasonal variation in ecological opportunity (in our case, the seasonal variation in the availability of preferred prey types). Overall, our results are in line with the optimal foraging theory and suggest that Z. asper is specialized on a few ephemeropteran prey species (Baetis fuscatus and Ecdyonurus) but adapts its foraging by becoming more opportunistic as its favoured prey seasonally decline. Despite the now widespread usage of metabarcoding, very few studies have attempted to study inter- and intra-populational individual trophic traits variation with metabarcoding data. This study illustrates how metabarcoding data obtained from feces can be combined with modelling and simulation approaches to test hypotheses in the conventional analytic framework of trophic analysis.

category: ecology


title: Undersampling correction methods to control γ-dependence for comparing β-diversity between regions

abstract: Measures of {beta}-diversity are known to be highly constrained by the variation in {gamma}-diversity across regions (i.e., {gamma}-dependence), making it challenging to infer underlying ecological processes. Undersampling correction methods have attempted to estimate the actual {beta}-diversity in order to minimize the effects of {gamma}-dependence arising from the problem of incomplete sampling. However, no study has systematically tested their effectiveness in removing {gamma}-dependence, and examined how well undersampling-corrected {beta}-metrics reflect true {beta}-diversity patterns that respond to ecological gradients. Here, we conduct these tests by comparing two undersampling correction methods with the widely used individual-based null model approach, using both empirical data and simulated communities along a known ecological gradient across a wide range of {gamma}-diversity and sample sizes. We found that undersampling correction methods using diversity accumulation curves were generally more effective than the null model approach in removing {gamma}-dependence. In particular, the undersampling-corrected {beta}-Shannon diversity index was most independent on {gamma}-diversity and was the most reflective of the true {beta}-diversity pattern along the ecological gradient. Moreover, the null model-corrected Jaccard-Chao index removed {gamma}-dependence more effectively than either approach alone. Our validation of undersampling correction methods as effective tools for accommodating {gamma}-dependence greatly facilitates the comparison of {beta}-diversity across regions.


title: Soil causes gut microbiota to flourish and total serum IgE levels to decrease in mice

abstract: Traditional farm environments induce protection from allergic diseases. In this study, farm environmental factors were classified into three categories, environmental microbes, soil, and organic matter. To explore the impact of soil and environmental microorganisms on gut microbiota and immune function, mice were fed sterilized soil, soil microbes (in lieu of environmental microbes), or non-sterilized soil. Metagenomic sequencing results showed the intake of sterile soil i.e. inhaling a small amount of soil microbes in the air increased gut microbial diversity and the abundance of type III secretion system (T3SS) genes, and decreased serum immune globulin E (IgE) levels induced by 2-4-dinitrofluorobenzene(DNFB). The intake of soil microbes increased the abundance of genes involved in the metabolism of short chain fatty acids and amino acid biosynthesis. Meanwhile, the intake of soil increased gut microbial diversity, the abundance of T3SS genes and related infectious elements, and genes associated with the metabolism of short chain fatty acids and amino acid biosynthesis, and decreased serum IgE levels. Therefore, soil may be useful as a potential "prebiotic" promoting the reproduction and growth of some intestinal microorganisms that harbor bacterial secretion system genes, especially those of T3SS, whose abundance was positively and significantly correlated with innate immune function of mice.


title: Integrating Sample Similarities into Latent Class Analysis: A Tree-Structured Shrinkage Approach

abstract: SO_SCPLOWUMMARYC_SCPLOWThis paper is concerned with using multivariate binary observations to estimate the probabilities of unobserved classes with scientific meanings. We focus on the setting where additional information about sample similarities is available and represented by a rooted weighted tree. Every leaf in the given tree contains multiple samples. Shorter distances over the tree between the leaves indicate a priori higher similarity in class probability vectors. We propose a novel data integrative extension to classical latent class models (LCMs) with tree-structured shrinkage. The proposed approach enables 1) borrowing of information across leaves, 2) estimating data-driven leaf groups with distinct vectors of class probabilities, and 3) individual-level probabilistic class assignment given the observed multivariate binary measurements. We derive and implement a scalable posterior inference algorithm in a variational Bayes framework. Extensive simulations show more accurate estimation of class probabilities than alternatives that suboptimally use the additional sample similarity information. A zoonotic infectious disease application is used to illustrate the proposed approach. The paper concludes by a brief discussion on model limitations and extensions.


title: Stepwise Oxidations Play Key Roles in the Structural and Functional Regulations of DJ-1

abstract: DJ-1 is known to play neuroprotective roles by eliminating reactive oxygen species (ROS) as an antioxidant protein. However, the molecular mechanism of DJ-1 function has not been well elucidated. This study explored the structural and functional changes of DJ-1 in response to oxidative stress. We found that Cys46 is also reactive cysteine residue in DJ-1, which was identified employing an NPSB-B chemical probe that selectively reacts with redox sensitive cysteine sulfhydryl. Peroxidatic Cys46 readily formed an intra-disulfide bond with resolving Cys53, which was identified with nanoUPLC-ESI-q-TOF tandem mass spectrometry (MS/MS) employing DBond algorithm under the non-reducing condition. We also found that Cys46-Cys53 disulfide crosslinking affects the oxidative state of the third Cys106, which shows the crosstalk among three cysteine residues of DJ-1. Furthermore, we demonstrated that DJ-1 C46A mutant, not forming Cys46-Cys53 intra-disulfide bond, lost structural stability of DJ-1 employing hydrogen/deuterium exchange-mass spectrometry (HDX-MS) analysis. All three Cys mutants lost antioxidant activities in SN4741 cell, a dopaminergic neuronal cell, unlike wild type DJ-1. These findings suggest that DJ-1 regulates its structure and activities by concerted oxidative modifications of three cysteine residues. These studies broaden the understanding of regulatory mechanisms of DJ-1 that operate under oxidative conditions.


title: Haploflow: Strain-resolved de novo assembly of viral genomes

abstract: In viral infections often multiple related viral strains are present, due to coinfection or within-host evolution. We describe Haploflow, a de Bruijn graph-based assembler for de novo genome assembly of viral strains from mixed sequence samples using a novel flow algorithm. We assessed Haploflow across multiple benchmark data sets of increasing complexity, showing that Haploflow is faster and more accurate than viral haplotype assemblers and generic metagenome assemblers not aiming to reconstruct strains. Haplotype reconstructed high-quality strain-resolved assemblies from clinical HCMV samples and SARS-CoV-2 genomes from wastewater metagenomes identical to genomes from clinical isolates.


title: martini: an R package for genome-wide association studies using SNP networks

abstract: Systems biology shows that genes related to the same phenotype are often functionally related. We can take advantage of this to discover new genes that affect a phenotype. However, the natural unit of analysis in genome-wide association studies (GWAS) is not the gene, but the single nucleotide polymorphism, or SNP. We introduce martini, an R package to build SNP co-function networks and use them to conduct GWAS. In SNP networks, two SNPs are connected if there is evidence they jointly contribute to the same biological function. By leveraging such information in GWAS, we search SNPs that are not only strongly associated with a phenotype, but also functionally related. This, in turn, boosts discovery and interpretability. Martini builds such networks using three sources of information: genomic position, gene annotations, and gene-gene interactions. The resulting SNP networks involve hundreds of thousands of nodes and millions of edges, making their exploration computationally intensive. Martini implements two network-guided biomarker discovery algorithms based on graph cuts that can handle such large networks: SConES and SigMod. They both seek a small subset of SNPs with high association scores with the phenotype of interest and densely interconnected in the network. Both algorithms use parameters that control the relative importance of the SNPs association scores, the number of SNPs selected, and their interconnection. Martini includes a cross-validation procedure to set these parameters automatically. Lastly, martini includes tools to visualize the selected SNPs network and association properties. Martini is available on GitHub (hclimente/martini) and Bioconductor (martini).


title: Improved DNA-versus-Protein Homology Search for Protein Fossils

abstract: Protein fossils, i.e. noncoding DNA descended from coding DNA, arise frequently from transposable elements (TEs), decayed genes, and viral integrations. They can reveal, and mislead about, evolutionary history and relationships. They have been detected by comparing DNA to protein sequences, but current methods are not optimized for this task. We describe a powerful DNA-protein homology search method. We use a 64x21 substitution matrix, which is fitted to sequence data, automatically learning the genetic code. We detect subtly homologous regions by considering alternative possible alignments between them, and calculate significance (probability of occurring by chance between random sequences). Our method detects TE protein fossils much more sensitively than blastx, and > 10x faster. Of the ~7 major categories of eukaryotic TE, three have not been found in mammals: we find two of them in the human genome, polinton and DIRS/Ngaro. This method increases our power to find ancient fossils, and perhaps to detect non-standard genetic codes. The alternative-alignments and significance paradigm is not specific to DNA-protein comparison, and could benefit homology search generally.


title: Identification of candidate biomarkers and therapeutic agents for heart failure by bioinformatics analysis

abstract: Heart failure (HF) is a heterogeneous clinical syndrome and affects millions of people all over the world. HF occurs when the cardiac overload and injury, which is a worldwide complaint. The aim of this study was to screen and verify hub genes involved in developmental HF as well as to explore active drug molecules. The expression profiling by high throughput sequencing of GSE141910 dataset was downloaded from the Gene Expression Omnibus (GEO) database, which contained 366 samples, including 200 heart failure samples and 166 non heart failure samples. The raw data was integrated to find differentially expressed genes (DEGs) and were further analyzed with bioinformatics analysis. Gene ontology (GO) and REACTOME enrichment analyses were performed via ToppGene; protein-protein interaction (PPI) networks of the DEGs was constructed based on data from the HiPPIE interactome database; modules analysis was performed; target gene - miRNA regulatory network and target gene - TF regulatory network were constructed and analyzed; hub genes were validated; molecular docking studies was performed. A total of 881 DEGs, including 442 up regulated genes and 439 down regulated genes were observed. Most of the DEGs were significantly enriched in biological adhesion, extracellular matrix, signaling receptor binding, secretion, intrinsic component of plasma membrane, signaling receptor activity, extracellular matrix organization and neutrophil degranulation. The top hub genes ESR1, PYHIN1, PPP2R2B, LCK, TP63, PCLAF, CFTR, TK1, ECT2 and FKBP5 were identified from the PPI network. Module analysis revealed that HF was associated with adaptive immune system and neutrophil degranulation. The target genes, miRNAs and TFs were identified from the target gene - miRNA regulatory network and target gene - TF regulatory network. Furthermore, receiver operating characteristic (ROC) curve analysis and RT-PCR analysis revealed that ESR1, PYHIN1, PPP2R2B, LCK, TP63, PCLAF, CFTR, TK1, ECT2 and FKBP5 might serve as prognostic, diagnostic biomarkers and therapeutic target for HF. The predicted targets of these active molecules were then confirmed. The current investigation identified a series of key genes and pathways that might be involved in the progression of HF, providing a new understanding of the underlying molecular mechanisms of HF.


title: Modeling Protein Association from Homogeneous to Mixed Environments: A Reaction-Diffusion Dynamics Approach

abstract: Protein-protein association in vivo occur in a crowded and complex environment. Theoretical models based on hard-core repulsion predict stabilization of the product under crowded conditions. Soft interactions, on the contrary, can either stabilize or destabilize the product formation. Here we modeled protein association in presence of crowders of varying size, shape, interaction potential and used different mixing parameters for constituent crowders to study the influence on the association reaction. It was found that size a more dominant factor in crowder-induced stabilization than the shape. Furthermore, in a mixture of crowders having different sizes but identical interaction potential, the change of free energy is additive of the free energy changes produced by individual crowders. However, the free energy change is not additive if two crowders of same size interact via different interaction potentials. These findings provide a systematic understanding of crowding influences in heterogeneous medium.


title: rtcisE2F drives liver TIC self-renewal and metastasis via m6A-modulated mRNA stability of E2F6 and E2F3

abstract:
BackgroundLiver tumor initiating cells (TICs) harbor self-renewal and differentiation capacities, and well contribute to liver tumorigenesis, metastasis and heterogeneity. However, the molecular mechanisms of liver TIC self-renewal are unclear. N6-methyladenosine is the most abundant modification of RNA molecules, and is involved in RNA stability and translation, but the molecular mechanisms of m6A regulation remain largely unknown.

MethodscircRNA expression was detected by in situ hybridization, fluorescence in situ hybridization, quantitative real-time PCR and Northern blot. Target gene expression was examined by microarray analyses, quantitative real-time PCR and Western blot. CRISPR, CRISPR interference (CRISPRi) and short-hairpin RNA (shRNA) were used for circRNA/target gene knockout and knockdown. Liver TICs were enriched through sphere formation and FACS using CD133 as a marker, and liver TIC activity was assessed by tumor propagation, sphere formation, tumor-initiating, and transwell assays. Quantitative real-time PCR and Northern blot were used to determine mRNA stability. RNA-protein interactions were examined by RNA pulldown, RNA immunoprecipitation, Tagged RNA affinity purification (TRAP) and electrophoretic mobility shift assays (EMSA).

ResultsHere, we identified a functional rt-circRNA, termed rtcisE2F, that is highly expressed in liver cancer and liver TICs. rtcisE2F plays essential roles in the self-renewal and activities of liver TICs. rtcisE2F targets E2F6 and E2F3 mRNAs, attenuates mRNA turnover, and increases E2F6/E2F3 expression. Mechanistically, rtcisE2F functions as a scaffold of m6A reader IGF2BP2 and E2F6/E2F3 mRNA, promotes the association of E2F6/E2F3 mRNAs with IGF2BP2, and then inhibits their association with another m6A reader, YTHDF2. IGF2BP2 inhibits E2F6/E2F3 mRNA decay, whereas YTHDF2 promotes E2F6/E2F3 mRNA decay. By switching m6A readers, rtcisE2F enhances E2F6/E2F3 mRNA stability. E2F6 and E2F3 are both required for liver TIC self-renewal and Wnt/{beta}-catenin activation, and inhibition of these pathways is a potential strategy for preventing liver tumorigenesis and metastasis.

ConclusionThis work identified rtcisE2F as a key modulator in liver cancer and liver TICs, providing evidence for the biological function of rt-circRNA and unveiling a new regulatory layer for liver TIC self-renewal. rtcisE2F is involved in E2F6/E2F3 stability by switching their binding to the m6A readers IGF2BP2 and YTHDF2, providing a competitive mechanism between RNA molecules and m6A readers. Both E2F6 and E2F3 are required for liver TIC self-renewal and serve as therapeutic targets for liver TIC elimination.