title: Building an atlas of transposable elements reveals the extensive roles of young SINE in gene regulation, genetic diversity, and complex traits in pigs

abstract: Transposable elements (TEs) are an extensive source of genetic polymorphisms and play an indispensable role in chromatin architecture, transcriptional regulatory networks, and genomic evolution. The pig is an important source of animal protein and serves as a biomedical model for humans, yet the functional role of TEs in pigs and their contributions to complex traits are largely unknown. Here, we built a comprehensive catalog of TEs (n = 3,087,929) in pigs by a newly developed pipeline. Through integrating multi-omics data from 21 tissues, we found that SINEs with different ages were significantly associated with genomic regions with distinct functions across tissues. The majority of young SINEs were predominantly silenced by histone modifications, DNA methylation, and decreased accessibility. However, the expression of transcripts that were derived from the remaining active young SINEs exhibited strong tissue specificity through cross-examining 3,570 RNA-seq from 79 tissues and cell types. Furthermore, we detected 211,067 polymorphic SINEs (polySINEs) in 374 individuals genome-wide and found that they clearly recapitulated known patterns of population admixture in pigs. Out of them, 340 population-specific polySINEs were associated with local adaptation. Mapping these polySINEs to genome-wide associations of 97 complex traits in pigs, we found 54 candidate genes (e.g., ANK2 and VRTN) that might be mediated by TEs. Our findings highlight the important roles of young SINEs in functional genomics and provide a supplement for genotype-to-phenotype associations and modern breeding in pigs.


title: Pathogen prevalence modulates medication behavior in ant Formica fusca

abstract: Ants face unique challenges regarding pathogens, as the sociality which has allowed them to form large and complex colonies also raises the potential for transmission of disease within these colonies. To cope with the threat of pathogens, ants have developed a variety of behavioral and physiological strategies. One of these strategies is self-medication, in which animals use biologically active compounds to combat pathogens in a way which would be harmful in the absence of them. Formica fusca ants are to date the only species of ants proven to successfully self-medicate against an active infection caused by a fungal pathogen by supplementing their diet with food containing hydrogen peroxide. Here, we build on that research by investigating how the prevalence of disease in colonies of F. fusca affects the strength of the self-medication response. We exposed either half of the workers of each colony or all of them to a fungal pathogen and offered them different combinations of diets. We see that workers of F. fusca engage in self-medication behavior even if exposed to a low lethal dose of a pathogen, and that the strength of that response is affected by the prevalence of the disease in the colonies. We also saw that the infection status of the individual foragers did not significantly affect their decision to forage on either control food or medicinal food as uninfected workers were also foraging on hydrogen peroxide food, which opens up the possibility of kin medication in partially infected colonies. Our results further affirm the ability of ants to self-medicate against fungal pathogens, shed new light on plasticity of self-medication and raise new questions to be investigated on the role self-medication has in social immunity.

category: animal behavior and cognition


title: Comprehensive analysis of the human ESCRT-III-MIT domain interactome reveals new cofactors for cytokinetic abscission

abstract: The 12 related human ESCRT-III proteins form filaments that constrict membranes and mediate fission, including during cytokinetic abscission. The C-terminal tails of polymerized ESCRT-III subunits also bind proteins that contain Microtubule-Interacting and Trafficking (MIT) domains. MIT domains can interact with ESCRT-III tails in many different ways to create a complex binding code that recruits essential cofactors to sites of ESCRT activity. Here, we have comprehensively and quantitatively mapped the interactions between all known ESCRT-III tails and 19 pure recombinant human MIT domains. We measured 228 pairwise interactions, quantified 58 positive interactions, and discovered 16 previously unreported interactions. We also report the crystal structure of the SPASTIN MIT domain in complex with the IST1 C-terminal tail. Three MIT enzymes were studied in detail and shown to: 1) localize to cytokinetic midbody membrane bridges through interactions with their specific ESCRT-III binding partners (SPASTIN-IST1, KATNA1-CHMP3, and CAPN7-IST1), 2) function in abscission (SPASTIN, KATNA1, and CAPN7), and 3) function in the "NoCut" abscission checkpoint (SPASTIN and CAPN7). Our studies define the human MIT-ESCRT-III interactome, identify new factors and activities required for cytokinetic abscission and its regulation, and provide a platform for analyzing ESCRT-III and MIT cofactor interactions in all ESCRT-mediated processes.

category: biochemistry


title: Mitonuclear interactions produce extreme differences in response to redox stress

abstract: Incompatibilities between mitochondrial and nuclear genes can perturb respiration, biosynthesis, signalling and gene expression. Here we investigate whether mild mitonuclear incompatibilities alter response to redox stress induced by N-acetyl cysteine (NAC). We studied three Drosophila melanogaster lines with mitochondrial genomes either coevolved (WT) or mildly mismatched (BAR, COX) to an isogenic nuclear background. Responses to NAC varied substantially with mitonuclear genotype, sex, tissue and dose. NAC caused infertility and high mortality in some groups but not others. Using tissue-specific fluorespirometry, we show that NAC did not alter H2O2 flux but suppressed complex I-linked respiration in female flies, maintaining a reduced glutathione pool. High mortality in BAR females was associated with severe suppression of complex I-linked respiration, rising H2O2 flux in ovaries and oxidation of the glutathione pool. Our results suggest that redox stress is attenuated by suppression of complex-I linked respiration, to the point of death in some mitonuclear lines.


title: Continuous two-phase in vitro co-culture model of the enthesis

abstract: The enthesis is the interfacial tissue between ligament or tendon, and bone, which connects tissues of distinctly different mechanical properties. Although ligament and enthesis injury is commonplace, the development and healing mechanisms of these tissues are yet unclear. Current models for investigating these mechanisms are primarily in vivo animal models as in vitro models have been limited. In this study, an in vitro enthesis model was developed using a modified gel aspiration-ejection (GAE) method. Continuous two-phase aligned dense collagen (ADC) hydrogels with an overlapping interface were fabricated within 2 hours. The mechanical properties of acellular two-phase ADC confirmed the continuous nature of this model, as the mechanical properties showed no significant difference compared to single-phase ADC and maintained comparable structural and mechanical characteristics of immature ligaments and unmineralized bone. Human anterior cruciate ligament (ACL) fibroblasts and human spine vertebral osteoblasts were isolated from donor tissues and were seeded to form the enthesis model. These were cultured for 14 days, at which the viability and proliferation was observed to be 85 {+/-} 7.5% and 230 {+/-} 52%, respectively. Histological and immunofluorescence analyses at day 14 revealed extensive cell-driven matrix remodelling, and the seeded fibroblasts and osteoblasts maintained their phenotype within their compartments of the layered co-culture model. These results demonstrate the rapid fabrication of a two-phase co-culture system that can be utilized as an in vitro model to further understand the degenerative and regenerative mechanisms within the enthesis.

category: bioengineering


title: Sensitive Spatiotemporal Tracking of Spontaneous Metastasis in Deep Tissues via a Genetically-Encoded Magnetic Resonance Imaging Reporter

abstract: Metastasis remains a poorly understood aspect of cancer biology and the leading cause of cancer-related death, yet most preclinical cancer studies do not examine metastasis, focusing solely on the primary tumor. One major factor contributing to this paradox is a gap in available tools for accurate spatiotemporal measurements of metastatic spread in vivo. Our objective was to develop an imaging reporter system that offers sensitive three-dimensional detection of cancer cells at high resolutions in live mice. We utilized organic anion-transporting polypeptide lb3 (oatp1b3) as a magnetic resonance imaging (MRI) reporter gene to this end, and systematically optimized its framework for in vivo tracking of viable cancer cells in a spontaneous metastasis model. We were able to image metastasis on oatp1b3-MRI at the single lymph node level and continued to track its progression over time as cancer cells spread to multiple lymph nodes and different organ systems in single animals. While initial single lesions were successfully imaged in parallel via bioluminescence, later metastases were obscured by light scatter from the initial node. Importantly, we demonstrate and validate that 100-m isotropic resolution MR images could detect micrometastases in lung tissue estimated to contain fewer than 103 cancer cells. In summary, oatp1b3-MRI enables precise determination of lesion size and location over time and offers a path towards deep-tissue tracking of any oatp1b3-engineered cell type with combined high resolution, high sensitivity, 3D spatial information, and surrounding anatomical context.


title: An explainable unsupervised framework for alignment-free protein classification using sequence embeddings

abstract: Protein classification is a cornerstone of biology that relies heavily on alignment-based comparison of primary sequences. However, the systematic classification of large protein superfamilies is impeded by unique challenges in aligning divergent sequence datasets. We developed an alignment-free approach for sequence analysis and classification using embedding vectors generated from pre-trained protein language models that capture underlying protein structural-functional properties from unsupervised training on millions of biologically-observed sequences. We constructed embedding-based trees (with branch support) which depict hierarchical clustering of protein sequences and infer fast/slow evolving sites through interpretable sequence projections. Applied towards diverse protein superfamilies, embedding tree infers Casein Kinase 1 (CK1) as the basal protein kinase clade, identifies convergent functional motifs shared between divergent phosphatase folds, and infers evolutionary relationships between diverse radical S-Adenosyl-L-Methionine (SAM) enzyme families. Overall results indicate that embedding trees effectively capture global data structures, functioning as a general unsupervised approach for visualizing high-dimensional manifolds.

category: bioinformatics


title: sgcocaller and comapr: personalised haplotype assembly and comparative crossover map analysis using single gametes

abstract: Profiling gametes of an individual enables the construction of personalised haplotypes and meiotic crossover landscapes, now achievable at larger scale than ever through the availability of high-throughput single-cell sequencing technologies. However, high-throughput single-gamete data commonly have low depth of coverage per gamete, which challenges existing gametebased haplotype phasing methods. In addition, haplotyping a large number of single gametes from high-throughput singlecell DNA sequencing data and constructing meiotic crossover profiles using existing methods requires intensive processing. Here, we introduce efficient software tools for the essential tasks of generating personalised haplotypes and calling crossovers in gametes from single-gamete DNA sequencing data (sgcocaller), and constructing, visualising, and comparing individualised crossover landscapes from single gametes (comapr). With additional data pre-possessing, the tools can also be applied to bulk-sequenced samples. We demonstrate that sgcocaller is able to generate impeccable phasing results for high-coverage datasets, on which it is more accurate and stable than existing methods, and also performs well on low-coverage single-gamete sequencing datasets for which current methods fail. Our tools achieve highly accurate results with user-friendly installation, comprehensive documentation, efficient computation times and minimal memory usage.


title: sgcocaller and comapr: personalised haplotype assembly and comparative crossover map analysis using single-gamete sequencing data


title: Fine-Tuning Transformers For Genomic Tasks

abstract: Transformers are a type of neural network architecture that has been successfully used to achieve state-of-the-art performance in numerous natural language processing tasks. However, what about DNA, the language life written in the four-letter alphabet? In this paper, we review the current state of Transformers usage in genomics and molecular biology in general, introduce a collection of benchmark datasets for the classification of genomic sequences, and compare the performance of several model architectures on those benchmarks, including a BERT-like model for DNA sequences DNABERT as implemented in HuggingFace (armheb/DNA_bert_6 model). In particular, we explore the effect of pre-training on a large DNA corpus vs training from scratch (with randomized weights). The results presented here can be used for identification of functional elements in human and other genomes.


title: DNABERT-based explainable lncRNA identification in plant genome assemblies

abstract:
Long non-coding ribonucleic acids (lncRNAs) have been shown to play an important role in plant gene regulation, being involved in both epigenetic and transcript regulation. LncRNAs are transcripts longer than 200 nucleotides that are not translated into functional proteins but can be translated into small peptides. Machine learning and deep learning models have predominantly used transcriptome data with manually defined features to detect lncRNAs, however, they often underrepresent the abundance of lncRNAs and can be biased in their detection. Here we present a study using Natural Language Processing (NLP) models to identify plant lncRNAs from genomic sequences rather than transcriptomic data. The NLP models were trained to predict lncRNAs for seven model and crop species (Zea mays, Arabidopsis thaliana, Brassica napus, Brassica oleracea, Brassica rapa, Glycine max and Oryza sativa) using publicly available genomic references. We demonstrated that lncRNAs can be accurately predicted from genomic sequences, and that genome assembly quality affects the accuracy of lncRNA identification. Furthermore, we demonstrated that the NLP models are applicable for cross-species prediction as they could predict lncRNAs from a species not used to train the model, with an average of 61% accuracy. Finally, we show that the models can be interpreted using explainable artificial intelligence to identify motifs important for lncRNA prediction and that these motifs were frequently present flanking the lncRNA sequence.

HighlightsO_LIWe demonstrate for the first time the identification of lncRNAs from genomic sequences, instead of transcriptome sequences, allowing the identification of lowly expressed lncRNAs.
C_LIO_LIA deep learning model (natural language processing) was employed for the prediction of lncRNAs in two monocot and five dicot plant species.
C_LIO_LIWe used explainable machine learning to extract the genomic motifs associated with lncRNA identification, highlighting potentially conserved structures present in more than one plant species.
C_LI


title: Automated speech detection in eco-acoustic data enables privacy protection and human disturbance quantification

abstract:
Eco-acoustic monitoring is increasingly being used to map biodiversity across huge scales, yet little thought is given to the privacy concerns and potential scientific value of inadvertently recorded human speech. Automated speech detection is possible using Voice Activity Detection (VAD) models, but existing approaches have been developed for indoor or urban use cases, rather than diverse natural soundscapes. In this study we used a data augmentation approach to create ecoVAD, a convolutional neural network designed for robust voice detection in eco-acoustic data. We performed playback experiments using speech samples from a woman, man, and child in two ecosystems in Borsa, Norway, and showed that ecoVAD was able to accurately detect voices at distances of up to 20m - at which point the speech was unintelligible. We compared ecoVAD with two existing VAD models and found that ecoVAD consistently outperformed the state-of-the-art (mean F1 scores: ecoVAD, 0.917; pyannote, 0.890; WebRTC VAD, 0.876). Using long-term passive recordings from a popular hiking location in Bymarka, Norway, we found that the frequency of speech detections was linked closely to peak traffic hours (using bus timings) demonstrating how VAD models can be used to quantify human activity with a fine temporal resolution. Anonymising audio data effectively using VAD models will allow eco-acoustic monitoring to continue to deliver invaluable ecological insight at scale, whilst minimising the risk of data misuse. Furthermore, using speech detections as a fine scale measure of human disturbance opens new possibilities for studying subtle human-wildlife interactions on the vast scales made possible by eco-acoustic monitoring technology.

Author SummaryEco-acoustic monitoring (i.e., recording and analysing the sounds of an ecosystem) allows us to monitor biodiversity and ecological health on vast spatial and temporal scales. However, as networks of audio recorders are increasingly being deployed across the world by scientists and land managers, little thought has been given to the implications of inadvertently recorded human speech in these datasets. We developed a neural-network model to detect and remove speech from audio data, and showed it performed more accurately than existing state-of-the-art models when evaluated on eco-acoustic datasets. Furthermore, we showed frequency of voice detections could be used to monitor human pressure on an ecosystem. Our work paves the way for ethical and responsible processing of eco-acoustic data and provides a novel approach to studying human wildlife interactions on a large scale with high temporal resolution.


title: A deep learning model trained on only eight whole-slide images accurately segments tumors: wise data use versus big data

abstract: Computer-assisted pathology is one of the biggest challenges in the medicine of the future. However, artificial intelligence is struggling to gain acceptance in the broader medical community due to data security issues, lack of trust in the machine, and poor data availability. Here, we develop a tumor delineation algorithm with only eight whole slide images of ovarian cancer to demonstrate the feasibility of an artificial intelligence application created from only a few data, finely annotated and with optimal processing. We test the model on seventeen other slides from the same hospital. The predictions are similar to the ground truth annotations made by an expert pathologist, with a mean DICE score of 0.90 [0.85 - 0.93]. The results on slides from another hospital are consistent, suggesting that the model is generalizable and that its performance does not suffer from different data acquisition. This study demonstrates the feasibility of a contouring algorithm based on a reduced dataset well optimized, going against the commonly accepted idea that a phenomenal amount of data is paramount. This study paves the way for other medical applications, especially for rare pathologies with limited available data.


title: Cellular limitation of enzymatic capacity explains glutamine addiction in cancers

abstract: Metabolism within the tumor microenvironment, where a complex mixture of different cell types resides in a nutrient-deprived surrounding, is not fully understood due to difficulties in measuring metabolic fluxes and exchange of metabolites between different cell types in vivo. Genome-scale metabolic modeling enables estimation of such exchange fluxes as well as an opportunity to gain insight into the metabolic behavior of individual cell types. Here, we estimated the availability of nutrients and oxygen within the tumor microenvironment using concentration measurements from blood together with a metabolite diffusion model. In addition, we developed an approach to efficiently apply enzyme usage constraints in a comprehensive metabolic model of human cells. The combined modeling reproduced severe hypoxic conditions and the Warburg effect, and we found that limitations in enzymatic capacity contribute to cancer cells preferential use of glutamine as a substrate to the citric acid cycle. Furthermore, we investigated the common belief that some stromal cells are exploited by cancer cells to produce metabolites useful for the cancer cells. We identified a total of 233 potential metabolites that could support collaboration between cancer cells and cancer associated fibroblasts, but when limiting to metabolites previously identified to participate in such collaboration, no growth advantage was observed. Our work highlights the importance of enzymatic capacity limitations for cell behaviors and exemplifies the utility of enzyme constrained models for accurate prediction of metabolism in cells and tumor microenvironments.

category: cancer biology


title: Training induced improvements in knee extensor force accuracy are associated with reduced vastus lateralis motor unit firing variability

abstract:
BackgroundMuscle force output during sustained submaximal isometric contractions fluctuates around an average value and is known to be influenced by variation in motor unit (MU) firing rates. MU firing rate variability seemingly reduces following exercise training interventions, however, much less is known with respect to peripheral MU properties. We therefore investigated whether targeted force accuracy training could lead to improved muscle functional capacity and control, in addition to determining any alterations of individual MU features.

MethodsTen healthy participants (7 females, 3 males, 27{+/-}6 years, 170{+/-}8 cm, 69{+/-}16kg) underwent a 4-week supervised, unilateral, force accuracy training intervention. The coefficient of variation for force (FORCECoV) and sinusoidal wave force tracking accuracy (FORCESinu) were determined at 25% maximal voluntary contraction (MVC) pre- and post-training. Intramuscular electromyography was utilised to record individual MU potentials from the vastus lateralis (VL) muscles at 25% MVC during sustained contractions, pre- and post-training.

ResultsKnee extensor muscle strength remained unchanged following training, with no improvements in unilateral leg-balance. FORCECoV and FORCESinu significantly improved in only the trained knee extensors by ~13% (p=0.01) and ~30% (p<0.0001) respectively. MU firing rate variability significantly reduced in the trained VL by ~16% (n=8; p=0.001), with no further alterations to MU firing rate or neuromuscular junction transmission instability.

ConclusionOur results suggest muscle force control and tracking accuracy is a trainable characteristic in the knee extensors, which is likely explained by the reduction in MU firing rate variability apparent in the trained limb only.

category: physiology


title: TEMPRANILLO homologs in apple regulate flowering time in the woodland strawberry Fragaria vesca

abstract: Many economically valuable fruit trees belong to the Rosaceae family. The long juvenile period of fruit trees makes their breeding costly and time-consuming. Therefore, flowering time regulation and shortening the juvenile phase have been a breeding priority for genetic improvement of fruit tree crops. TEMPRANILLO genes act as floral inhibitors in Arabidopsis and so, two orthologs of this gene were isolated here from apple (Malus domestica) and functionally analysed in Arabidopsis and woodland strawberry by being overexpressed in both model plants, and partially silenced in strawberry. The overexpression of MdTEM genes down-regulated FvFT1, FvGA3OX1, and FvGA3OX2 genes in strawberry. The overexpression lines exhibited delayed flowering, both in terms of days to flowering and the number of leaves at flowering. RNAi-mediated silencing of TEM resulted in early flowering plants. These plants flowered approximately five days earlier than wild type plants with a lower number of leaves. However, the overexpression of MdTEM genes could not functionally rescue the Arabidopsis mutants. According to the results, it can be concluded that MdTEM1 and MdTEM2 are orthologs of FvTEM gene, which play an important role in regulating the juvenile phase and flowering time through controlling FT and GA biosynthetic gene expression.

category: plant biology


title: Exotic alleles contribute to heat tolerance in wheat under field conditions

abstract: Global warming is one of the most significant threats to food security. With temperatures predicted to rise and extreme weather events becoming more common we must safeguard food production by developing crop varieties that are more tolerant to heat stress without compromising yield under favourable conditions. By evaluating 149 spring wheat lines in the field under yield potential and heat stressed conditions, we demonstrate how strategic integration of exotic material significantly increases yield under heat stress compared to elite lines, with no significant yield penalty under favourable conditions. Genome-wide association analysis revealed three marker trait associations, which together increase yield under heat stress by over 50% compared to lines without the advantageous alleles and was associated with approximately 2{degrees}C lower canopy temperature. We identified an Aegilops tauschii introgression underlying the most significant of these associations. By comparing overlapping recombination of this introgressed segment between lines, we identified a 1.49Mbp region of the introgression responsible for this association that increases yield under heat stress by 32.4%. The genes within this region were extracted from diverse Ae. tauschii genomes, revealing a novel Ae. tauschii MAPK gene, a SOC1 orthologue and a pair of type-B two-component response regulators. Incorporating these exotic alleles into breeding programmes could serve as a pre-emptive strategy to produce high yielding wheat cultivars that are resilient to the effects of future climate uncertainty with no yield penalty under favourable conditions.


title: CELLoGeNe - an Energy Landscape Framework for Logical Networks Controlling Cell Decisions

abstract: Experimental and computational efforts are constantly made to elucidate mechanisms controlling cell fate decisions during development and cell reprogramming. One powerful method is to consider cell commitment and reprogramming as movements in an energy landscape. Here, we develop CELLoGeNe (Computation of Energy Landscapes of Logical Gene Networks), which maps Boolean implementation of gene regulatory networks (GRNs) into energy landscapes. CELLoGeNe removes inadvertent symmetries in the energy landscapes normally arising from standard Boolean operators. Furthermore, CELLoGeNe provides a tool for visualising multi-dimensional energy landscapes and a platform to stochastically probe and analyse the shapes of the computed landscapes corresponding to the epigenetic landscapes for development and reprogramming. We demonstrate CELLoGeNe on a GRN governing maintenance and self-renewal of pluripotency, identifying attractors experimentally validated. We also apply CELLoGeNe on a network controlling reprogramming from mouse embryonic fibroblast (MEF) to induced pluripotent stem cells (iPSCs) where we identify potential roadblocks as attractors. CELLoGeNe is a general framework that can be applied to various biological systems offering a broad picture of intracellular dynamics otherwise inaccessible with existing methods.

category: systems biology


title: Alterations to parvalbumin-expressing interneuron function and associated network oscillations in the hippocampal - medial prefrontal cortex circuit during natural sleep in APPNL-G-F mice

abstract: In the early stages of Alzheimers disease (AD) the accumulation of the peptide amyloid-{beta} (A{beta}) damages synapses and disrupts neuronal activity, leading to the dysfunction of neuronal oscillations associated with cognitive function. This is thought to be largely due to impairments in CNS synaptic inhibition, particularly via parvalbumin (PV)-expressing interneurons that are pivotal contributors to several key oscillations. During non-rapid eye movement (NREM) sleep, communication between the hippocampus and medial prefrontal cortex (mPFC) facilitates the reorganisation of newly acquired hippocampal memories into the cortex for long-term consolidation, a process named systems consolidation. This occurs through the temporal coupling of the cortical slow wave oscillation (SWO), sleep spindles and hippocampal sharp-wave ripples (SWRs); oscillations generated, in part, through the action of PV-expressing interneurons. Disturbances to NREM sleep and impairments to these oscillations occur in preclinical AD and in mouse models of amyloidopathy, yet in-depth characterisation of how this circuit is affected is presently lacking. Therefore, using 16 month-old homozygous APPNL-G-F mice, we recorded the electrical activity of this circuit during natural sleep. Despite widespread A{beta} pathology, deficits in the SWO were not detected at this age, yet an increase in the amplitude of mPFC spindles and decrease in the power of hippocampal SWRs was identified. The former was associated with a decrease in the density of mPFC PV-expressing interneurons and the latter, was accompanied by an increase in the synchronisation of PV-expressing interneuron activity, as measured using two-photon Ca2+ imaging. Furthermore, although changes were detected in the local oscillations and networks, the temporal communication between prefrontal and hippocampal circuits was intact, potentially suggesting the early stages of circuit breakdown in response to pathological A{beta}.

category: neuroscience


title: M2 Receptors are required for spatiotemporal sequence learning in mouse primary visual cortex

abstract: Acetylcholine (ACh) is a neurotransmitter that plays a variety of roles in the central nervous system (CNS). It was previously shown that blocking muscarinic receptors with a non-selective antagonist prevents a form of experience-dependent plasticity termed "spatiotemporal sequence learning" in the mouse primary visual cortex (V1). Muscarinic signaling is a complex process involving the combined activities of five different G-protein coupled receptors, M1-M5, all of which are expressed in the murine brain but differ from each other functionally and in anatomical localization. Here we present electrophysiological evidence that M2, but not M1, receptors are required for spatiotemporal sequence learning in mouse V1. We show that M2 is highly expressed in the neuropil in V1, especially in thalamorecipient layer 4, and co-localizes to the soma in a subset of somatostatin expressing neurons in deep layers. We also show that expression of M2 receptors is higher in the monocular region of V1 than it is in the binocular region, but that the amount of experience-dependent sequence potentiation is similar in both regions. This work establishes a new functional role for M2-type receptors in processing temporal information and demonstrates that monocular circuits are modified by experience in a manner similar to binocular circuits.


title: The direction and timing of theta and alpha traveling waves modulate human memory processing

abstract: To support a range of behaviors, the brain must flexibly coordinate neural activity across widespread brain regions. One potential mechanism for this coordination is a traveling wave, in which a neural oscillation propagates across the brain while organizing the order and timing of activity across regions1,2. Although traveling waves are present across the brain in various species3-5, their potential functional relevance remained unknown. Here, using rare direct human brain recordings, we demonstrate two novel functional roles for traveling waves of theta- and alpha-band (2-13 Hz) oscillations in the cortex. First, traveling waves propagate in different directions during separate cognitive processes. In episodic memory, traveling waves tended to propagate in posterior-to-anterior and anterior-to-posterior directions, respectively, during encoding and retrieval. Second, traveling waves are informative about the timing of behavior, with the phase of ongoing traveling waves indicating when subjects would retrieve memories. Because traveling waves of oscillations correspond to local neuronal spiking, these patterns indicate that rhythmic pulses of activity move across the brain with different directions and timing for separate behaviors. More broadly, our results suggest a fundamental role for traveling waves and oscillations in dynamically coordinating neural connectivity, by flexibly organizing the timing and directionality of network interactions across the cortex to support cognition and behavior.


title: A robust core architecture of functional brain networks supports topological resilience and cognitive performance in aging

abstract: Aging is associated with gradual changes in cognition, yet some individuals exhibit protection against aging-related cognitive decline. The topological characteristics of brain networks that support protection against cognitive decline in aging are unknown. Here, we investigated whether the robustness of brain networks, queried via the delineation of the brains core network structure, supports superior cognitive performance in healthy aging individuals (n=320, ages 60-90). First, we decomposed each subjects functional brain networks using k-shell decomposition, finding that cognitive function is associated with more robust connectivity of core nodes, primarily within the frontoparietal control network (FPCN). Next, we find that the resilience of core brain network nodes, within the FPCN in particular, relates to cognition. Finally, we show that the degree of segregation in functional networks mediates relationships between network resilience and cognition. Together, these findings suggest that brain networks balance between robust core connectivity and segregation to facilitate high cognitive performance in aging.


title: Reduced Hippocampal-Cortical Connectivity During Memory Suppression Predicts the Ability to Forget Unwanted Memories

abstract: The ability to suppress unwelcome memories is important for productivity and well-being. Successful memory suppression is associated with hippocampal deactivations and a concomitant disruption of this regions functionality. Much of the previous neuroimaging literature exploring such suppression-related hippocampal modulations has focused on the regions negative coupling with the prefrontal cortex. In contrast, task-based changes in functional connectivity between the hippocampus and other brain regions have remained relatively underexplored. Here, we utilize psychophysiological interactions and seed connectome-based predictive modeling (seed-CPM) to investigate the relationship between the hippocampus and the rest of the brain as 134 participants attempted to suppress unwanted memories during the Think/No-Think task. The results show that during retrieval suppression, the right hippocampus exhibited decreased functional connectivity with visual cortical areas (bilateral intracalcarine cortex, right cuneal cortex, left lingual gyrus, right supracalcarine cortex, right occipital pole), left nucleus accumbens and the brain-stem that predicted superior forgetting of unwanted memories on later memory tests. Validation tests verified that prediction performance was not an artifact of head motion or prediction method and that the negative features remained consistent across different brain parcellations. These findings suggest that systemic memory suppression involves more than the modulation of hippocampal activity--it alters functional connectivity patterns between the hippocampus and visual cortex, leading to successful forgetting.


title: State-dependent activity dynamics of hypothalamic stress effector neurons

abstract: The stress response necessitates an immediate boost in vital physiological functions from their homeostatic operation to elevated emergency response. However, neural mechanisms underlying this state-dependent change remain largely unknown. Using a combination of in vivo and ex vivo electrophysiology with computational modeling, we report that corticotropin releasing hormone (CRH) neurons in the paraventricular nucleus of the hypothalamus (PVN), the effector neurons of hormonal stress response, rapidly transition between distinct activity states through recurrent inhibition. Specifically, in vivo optrode recording shows that under non-stress conditions, CRHPVN neurons often fire with rhythmic brief bursts (RB), which, somewhat counterintuitively, constrains firing rate due to long ([~]2 s) inter-burst intervals. Stressful stimuli rapidly switch RB to continuous single spiking (SS), permitting a large increase in firing rate. A spiking network model shows that recurrent inhibition can control this activity-state switch, and more broadly the gain of spiking responses to excitatory inputs. In biological CRHPVN neurons ex vivo, the injection of whole-cell currents derived from our computational model recreates the in vivo-like switch between RB and SS, providing a direct evidence that physiologically relevant network inputs enable state-dependent computation in single neurons. Together, we present a novel mechanism for state-dependent activity dynamics in CRHPVN neurons.


title: Behavioral decomposition reveals rich encoding structure employed across neocortex

abstract: AO_SCPLOWBSTRACTC_SCPLOWThe Cortical population code is pervaded by activity patterns evoked by movement, but how such signals relate to the natural actions of unrestrained animals remains largely unknown, particularly in sensory areas. To address this we compared high-density neural recordings across four cortical regions (visual, auditory, somatosensory, motor) in relation to sensory modulation, posture, movement, and ethograms of freely foraging rats. Momentary actions, such as rearing or turning, were represented ubiquitously and could be decoded from all sampled structures. However, more elementary and continuous features, such as pose and movement, followed region-specific organization, with neurons in visual and auditory cortices preferentially encoding mutually distinct head-orienting features in world-referenced coordinates, and somatosensory and motor cortices principally encoding the trunk and head in egocentric coordinates. The tuning properties of synaptically coupled cells also exhibited connection patterns suggestive of different uses of behavioral information within and between regions. Together, our results speak for detailed, multi-level encoding of animal behavior subserving its dynamic employment in local cortical computations.


title: Principled clustering of functional signals reveals gradients in processing both within the anterior hippocampus and across its long axis

abstract:
A particularly elusive puzzle concerning the hippocampus is how the structural differences along its long, anteroposterior axis might beget meaningful functional differences, particularly in terms of the granularity of information processing. One measure posits to quantify this granularity by calculating the average statistical independence of the BOLD signal across neighboring voxels, or inter-voxel similarity (IVS), and has shown the anterior hippocampus to process coarser-grained information than that in the posterior hippocampus. This model of the hippocampus, however, conflicts with a number of task-oriented findings, many of which have varied in their fMRI acquisition parameters and hippocampal parcellation methods. In order to reconcile these findings, we measured IVS across two separate resting-state fMRI acquisitions and compared the results across many of the most widely used parcellation methods in a large young-adult sample (Acquisition 1, N = 253; Acquisition 2, N = 183). Finding conflicting results across acquisitions and parcellations, we reasoned that a principled, data-driven approach to hippocampal parcellation is necessary. To this end, we implemented a group masked independent components analysis (mICA) to identify functional subunits of the hippocampus, most notably separating the anterior hippocampus into separate anterior-medial, anterior-lateral, and posteroanterior-lateral components. Measuring IVS across these components revealed a decrease in IVS along the medial-lateral axis of the anterior hippocampus but an increase from anterior to posterior. We conclude that representational granularity may not change linearly or unidirectionally across the hippocampus, and that moving the study of the hippocampus towards reproducibility requires grounding it in a functionally informed approach.

Significance StatementProcessing information along hierarchical scales of granularity is critical for many of the feats of cognition considered most human. Recently, the changes in structure, cortical connectivity, and apparent functional properties across parcels of the hippocampal long axis have been hypothesized to underlie this hierarchical gradient in information processing. We show here, however, that the choice of parcellation method itself drastically affects the perceived granularity across the hippocampus, and that a principled, functionally informed approach to parcellation reveals gradients both within the anterior hippocampus and in non-linear form across the long axis. These results point to the issue of parcellation as a critical one in the study of the hippocampus and reorient interpretation of existing results.


title: Distinct features of the cortical N1 response to balance perturbation are associated with balance and cognitive impairments in Parkinson's disease

abstract: Mechanisms underlying associations between balance and cognitive impairments in older adults with and without Parkinsons disease (PD) are poorly understood. Balance disturbances evoke a cortical N1 response that is associated with both balance and cognitive abilities in unimpaired populations. We hypothesized that the N1 response reflects a neural mechanism that is shared between balance and cognitive function, and would therefore be associated with both balance and cognitive impairments in PD. Although N1 responses did not differ at the group level they showed distinct associations with balance and cognitive function in the PD vs. control (noPD) groups. In noPD, higher N1 amplitudes were correlated with lower cognitive set shifting ability and lower balance confidence. However, in PD, higher N1 amplitudes were correlated with lower overall cognitive function, while earlier and narrower N1 peaks were correlated with more severe PD and balance impairments. Our results show that balance and cognitive impairments are dissociable and associated with distinct features of the N1 response, suggesting that the N1 response reflects coordination of distinct mechanisms for balance and cognitive function. Identifying coordinated but dissociable mechanisms underlying balance and cognitive processes may reveal potential targets for rehabilitation of comorbid balance and cognitive impairments.


title: Unbiased stereologic estimates of dopaminergic and GABAergic neurons in the A10, A9, and A8 subpopulations in the young male Macaque

abstract:
The ventral midbrain is the primary source of dopamine- (DA) expressing neurons in most species. GABA-ergic and glutamatergic cell populations are intermixed among DA-expressing cells and purported to regulate both local and long-range dopamine neuron activity. Most work has been conducted in rodent models, however due to evolutionary expansion of the ventral midbrain in primates, the increased size and complexity of DA subpopulations warrants further investigation. Here, we quantified the number of DA neurons, and their GABA-ergic complement in classic DA cell groups A10 (midline ventral tegmental area nuclei [VTA] and parabrachial pigmented nucleus [PBP]), A9 (substantia nigra, pars compacta [SNc]) and A8 (retrorubral field [RRF]) in the macaque. Because the PBP is a disproportionately expanded feature of the A10 group, and has unique connectional features in monkeys, we analyzed A10 data by dividing it into  classic midline nuclei and the PBP. Unbiased stereology revealed total putative DA neuron counts to be 210,238 +/- 17,127 (A10 = 110,319 +/- 9,649, A9= 87,399 +/-7,751 and A8=12,520 +/- 827). Putative GABAergic neurons were fewer overall, and evenly dispersed across the DA subpopulations (GAD67= 71,215 +/- 5,663; A10=16,836 +/- 2,743; A9=24,855 +/- 3,144 and A8=12,633 +/- 3,557). Calculating the GAD67/TH ratio for each subpopulation revealed differential balances of these two cell types across the DA subpopulations. The A8 subpopulation had the highest complement of GAD67-positive neurons compared to TH-positive neurons (1:1), suggesting a potentially high capacity for GABAergic inhibition of DA output in this region.

HIGHLIGHTSO_LIThe A10 subpopulation expands laterally and caudally in nonhuman primates
C_LIO_LIThe A10, A9, and A8 subpopulations comprise 52%, 42% and 6% of DA neurons
C_LIO_LIGABAergic neurons are more evenly dispersed
C_LIO_LIThe A8 subpopulation has the highest ratio of GABA: DA neurons
C_LI


title: Selective integration of diverse taste inputs within a single taste modality

abstract: Each sensory system contains a diverse repertoire of sensory cells. In the gustatory system, individual taste modalities contain sensory cells that reside in different locations or express different combinations of taste receptors. These different input channels may converge onto common downstream circuits and drive the same behaviors, or they may activate separate pathways to regulate distinct behaviors. To distinguish between these models in Drosophila, we first characterized a repertoire of behaviors induced by optogenetic activation of sugar- or bitter-sensing neurons. We then activated subsets of bitter-sensing neurons within specific organs. Different subsets elicited a broad and highly overlapping set of behaviors, suggesting that they converge onto common downstream pathways, but we also observed behavioral differences that argue for selective convergence. Transsynaptic tracing experiments provided a neuronal substrate for these results, revealing that bitter neuron subsets connect to overlapping downstream regions with biased connectivity. We characterized one type of second-order bitter neuron that integrates multiple types of bitter input and regulates a subset of bitter-induced behaviors. These results suggest that different bitter inputs are selectively integrated early in the circuit, enabling the pooling of sensory information, and the circuit then diverges into multiple pathways that may have different behavioral roles.


title: Functionally competent CD4+ T cells express high levels of T-bet in Plasmodium chabaudi infected young mice

abstract: The immune system plays an important role in the elimination of Plasmodium parasites that cause malaria, which affect children the most worldwide. Immunity to malaria, especially in young children is poorly understood due to the absence of a developmentally-equivalent rodent model to study the pathogenesis of disease. We have developed a mouse model using 15-day old mice (pups) of malaria infection in neonatal mice. Using C57BL/6 pups, we determined that P. chabaudi infection decreases the growth rate of young mice compared to controls, and results in 60% mortality, and neurological damage not present in adults, as indicated by a battery of behavioral assays. When all splenic cells were stimulated in vitro stimulation, cells from pups proliferated faster than adult cells, but purified CD4 T cells were slower. Upon infection with Plasmodium parasites, both adult and pup CD4+ T cells were activated and differentiated to an effector T cell (Teff) phenotype; however, pup CD4+ Teff were less differentiated than adult Teff. Pup CD4+ T cells also produced more IL-2 than cells from adult B6 mice, and TNF- was increased in parasite-specific BALB/c pup T cells. Interestingly, there were more pup CD4+T-bethi Teff after infection suggestive of increased Th1 commitment, potentially contributing to cerebral symptoms.

category: immunology


title: The Structure-Selective Endonucleases GEN1 and MUS81 are Functionally Complementary in Safeguarding the Genome of Proliferating B Lymphocytes

abstract: During the development of humoral immunity, activated B lymphocytes undergo vigorous proliferative, transcriptional, metabolic, and DNA remodeling activities; hence, their genomes are constantly exposed to an onslaught of genotoxic agents and processes. Recombination-dependent DNA transactions that preserve the integrity of the genome and of the DNA replication process generates Holliday junctions that must be eliminated for the accurate segregation of sister chromatids and faithful propagation of genomic material. To investigate the role of two Holliday junction resolvases, GEN1 and MUS81, in B cell biology, we established B-cell conditional knockout mouse models and found that targeted deletion of GEN1 and MUS81 in early B cell precursors halts their development and maturation while selective loss of the resolvases in mature B cells inhibits the generation of robust germinal centers. Upon activation, these double-null mature B lymphocytes fail to proliferate and survive while exhibiting transcriptional signatures of p53 signaling, apoptosis, and type I interferon response. Metaphase spreads of these resolvase-deficient cells showed severe and diverse chromosomal abnormalities, including a preponderance of chromosome breaks, consistent with a defect in resolving DNA recombination intermediates. These observations underscore the essential roles of GEN1 and MUS81 in safeguarding the genome to ensure the proper development and maintenance of B lymphocytes.


title: Targeting fatty acid beta-oxidation impairs monocyte differentiation and prolongs heart allograft survival

abstract: AO_SCPLOWBSTRACTC_SCPLOWMonocytes play an important role in the regulation of alloimmune responses after heart transplantation (HTx). Recent studies have highlighted the importance of immunometabolism in the differentiation and function of myeloid cells. While the importance of glucose metabolism in monocyte differentiation and function has been reported, a role for fatty acid {beta}-oxidation (FAO) has not been explored. Heterotopic HTx was performed using hearts from Balb/c donor mice implanted into C57Bl/6 recipient mice and treated with etomoxir (eto), an irreversible inhibitor of carnitine palmitoyltransferase 1 (Cpt1), a rate-limiting step of FAO, or vehicle control. FAO inhibition prolonged HTx survival, reduced early T cell infiltration/ activation and reduced dendritic cell (DC) and macrophage infiltration to heart allografts of eto-treated HTx recipients. ELISPOT demonstrated eto-treated HTx were less reactive to activated donor antigen presenting cells. FAO inhibition reduced monocyte-to-DC and monocyte-to-macrophage differentiation in vitro and in vivo. Further, FAO inhibition did not alter the survival of heart allografts when transplanted into Ccr2-deficient recipients, suggesting the effects of FAO inhibition on reduced immune cell infiltration and increased heart allograft survival were dependent on monocyte mobilization. Finally, we confirmed the importance of FAO on monocyte differentiation in vivo using conditional deletion of Cpt1a. Our findings demonstrate that targeting FAO attenuates alloimmunity after HTx, in part through impairing monocyte differentiation.


title: FoxP3 can fold into two distinct dimerization states with divergent functional implications for T cell homeostasis

abstract: FoxP3 is an essential transcription factor (TF) for immunologic homeostasis, but how it utilizes the common forkhead DNA-binding domain (DBD) to perform its unique function remains poorly understood. We here demonstrate that, unlike other known forkhead TFs, FoxP3 forms a head-to-head dimer using a unique linker (Runx1-binding region, RBR) preceding the forkhead domain. Head-to-head dimerization confers distinct DNA-binding specificity and creates a docking site for the cofactor Runx1. RBR is also important for proper folding of the forkhead domain, as truncation of RBR induces domain-swap dimerization of forkhead, which was previously considered the physiological form of FoxP3. Rather, swap-dimerization impairs FoxP3 function, as demonstrated with the disease-causing mutation R337Q, while a swap-suppressive mutation largely rescues R337Q-mediated functional impairment. Altogether, our findings suggest that FoxP3 can fold into two distinct dimerization states: head-to-head dimerization representing functional specialization of an ancient DBD and swap-dimerization with impaired functions.


title: Functional Specialization of Specific DC Subsets in the Synovial Fluid of JIA Patients

abstract: Dendritic cells (DC) are crucial for initiating and shaping immune responses. So far, little is known about heterogeneity and functional specialization of human DC subsets in (local) inflammatory conditions. We profiled conventional (c)DC1, cDC2 and monocytes based on phenotype, transcriptome and function from a local inflammatory site, namely synovial fluid (SF) from patients suffering from a chronic inflammatory condition, Juvenile Idiopathic Arthritis (JIA). cDC1, a relatively small dendritic cell subset in blood, are strongly enriched in SF. SF cDC1 showed a quiescent immune signature without a clear inflammatory profile low expression of PRR, chemokine, and cytokine receptors, and poor induction of T cell proliferation and cytokine production, but selective production of IFN{lambda} upon polyinosinic:polycytidylic acid exposure. In stark contrast, cDC2 and monocytes from the same environment, showed a pro-inflammatory transcriptional profile, high levels of (spontaneous) pro-inflammatory cytokine production, and strong induction of T cell proliferation and cytokine production, including IL-17. Although the cDC2 and monocytes showed an overlapping transcriptional core profile, there were clear differences in the transcriptional landscape and functional features, indicating that these cell types retain their lineage identity in chronic inflammatory conditions. In conclusion, our findings suggest that at the site of inflammation, there is specific functional programming of human DC subsets, especially cDC2. In contrast, the enriched subset of cDC1 remains relatively quiescent and seemingly unchanged under inflammatory conditions, pointing to a more regulatory role.


title: Identification and characterization of the HERV-K (HML-8) group of human endogenous retroviruses in the genome

abstract:
Human endogenous retroviruses (HERV) could vertically transmit in a Mendelian fashion and stable maintenance in the human genome which are estimated to comprise about 8%. HERVs affect human physiology and pathology based on the effect of the provirus-encoded protein or LTR elements. The characterization of the genomic distribution is an essential step to understanding the relationship between endogenous retrovirus expression and diseases. However, the poorly characterization of HML-8 hinders a detailed understanding of the expression regulation of this family in human health and its actual impact on host genomes. In the light of this, the definition of a precise and updated HERV-K HML-8 genomic map is urgently needed. Here we report a comprehensive analysis of HERV-K HML-8 sequences presence and distribution within the human genome, with a detailed description of the different structural and phylogenetic aspects characterizing the group. A total of 40 proviruses and 5 solo LTR elements were characterized with a detailed description of provirus structure, integration time, potentially regulated genes, transcription factor binding sites, and primer binding site feature. The integration time results showed that the HML-8 elements found in the human genome have been integrated in the primate lineage between 23.5 and 52 million years ago (mya). Overall, the results have finally clarified the composition of HML-8, providing an exhaustive background for subsequent functional studies.

Highlights[tpltrtarr] A comprehensive characterization of the HERV-K (HML-8) in human genome.
[tpltrtarr]There is an apparent preference of HML-8 into intergenic regions and introns.
[tpltrtarr]There are two distinct clusters for the env region of the HML-8 elements.
[tpltrtarr]The average time of HML-8 integration in human is 37.1 mya.

category: microbiology


title: MraZ is a transcriptional inhibitor of cell division in Bacillus subtilis

abstract: The bacterial division and cell wall (dcw) cluster is a highly conserved region of the genome which encodes several essential cell division factors including the central divisome protein FtsZ. Understanding the regulation of this region is key to our overall understanding of the division process. mraZ is found at the 5 end of the dcw cluster and previous studies have described MraZ as a sequence-specific DNA binding protein. In this article, we investigate MraZ to elucidate its role in Bacillus subtilis. Through our investigation, we demonstrate that increased levels of MraZ result in lethal filamentation due to repression of its own operon (mraZ-mraW-ftsL-pbpB). We observe rescue of filamentation upon decoupling ftsL expression, but not other genes in the operon, from MraZ control. Furthermore, through timelapse microscopy we were able to identify that overexpression of mraZ, results in de-condensation of the FtsZ ring (Z-ring). This is likely due to depletion of FtsL, and thus, we believe the precise role of FtsL is likely in Z-ring maturation and promotion of subsequent treadmilling. Our data suggests that regulation of the mra operon may be an alternative way for cells to quickly arrest cytokinesis potentially during entry into stationary phase and in the event of DNA replication arrest.


title: Lineages derived from Cryptococcus neoformans type strain H99 support a link between the capacity to be pleomorphic and virulence

abstract:
The pathogenic yeast Cryptococcus neoformans causes nearly 200,000 deaths annually in immunocompromised individuals. Cryptococcus cells can undergo substantial morphological change during mammalian infection, including increased capsule and cell size, the release of shed capsule, and the production of titan (> 10 m), micro (< 2 m) and irregular cells. We examined phenotypic variation under conditions designed to simulate in vivo stress in a collection of nine lineages derived from the C. neoformans type strain H99. These lineages are highly genetically similar but have a range of virulence levels. Strains from hypervirulent lineages had a larger average capsule size, greater variation in cell size, and an increased production of micro cells and shed capsule. We tested whether disruption of SGF29, which encodes a component of the SAGA histone acetylation complex that has previously been implicated in the hypervirulence of some lineages, might also have a role in the production of morphological variants. Deletion of SGF29 in a lineage with intermediate virulence substantially increased its production of micro cells and released capsule, consistent with a switch to hypervirulence. We further examined SGF29 in a set of 52 clinical isolates and found loss-of-function mutations were significantly correlated with patient death. Expansion of a TA repeat in the second intron of SGF29 was positively correlated with cell and capsule size, suggesting it may also affect Sgf29 function. This study extends the evidence for a link between pleomorphism and virulence in Cryptococcus, with a likely role for epigenetic mechanisms mediated by SAGA-induced histone acetylation.

IMPORTANCECryptococcosis is a devastating cause of death and disease worldwide. During infection, Cryptococcus cells can undergo substantial changes to their size and shape. In this study, we used a collection C. neoformans strains that are highly genetically similar but possess differing levels of virulence to investigate how morphological variation aligns with virulence. We found hypervirulent strains on average had larger capsules and greater variation in cell size, and also produced more micro cells and shed capsule. These hypervirulent strains possessed a mutation in SGF29, which encodes a component of the SAGA complex involved in epigenetic regulation. Analysis of the SGF29 gene in a set of clinical isolates found strains with loss-of-function mutations were associated with higher patient death rates. The capacity to vary appears to be linked with virulence in Cryptococcus, and this can occur in the absence of genetic variation via epigenetic mechanisms.


title: HiFi Metagenomic Sequencing Enables Assembly of Accurate and Complete Genomes from Human Gut Microbiota

abstract: Advances in metagenomic assembly have led to the discovery of genomes belonging to unculturable microorganisms. Metagenome-assembled genomes (MAGs) often suffer from discontinuity and chimerism. Recently, nanopore metagenomic sequencing assembled 20 complete MAGs (cMAGs) from 13 human fecal samples, but with low nucleotide accuracy. Here, we report 102 cMAGs obtained by high-accuracy long-read (HiFi) metagenomic sequencing of five human fecal samples, whose initial circular contigs were filtered for authentic prokaryotic genomes using our bioinformatics workflow. Nucleotide accuracy of the final cMAGs was similar to that of Illumina sequencing. The cMAGs could exceed 6 Mbp and included complete genomes of diverse taxa, including entirely unculturable RF39 and TANB77 orders, whose genomes have not been characterized yet. Moreover, cMAGs revealed that regions hard to assemble by short-read sequencing comprised mostly genomic islands and rRNAs. HiFi metagenomic sequencing will facilitate cataloging accurate and complete genomes of human gut microbiota, including unculturable species.


title: Examination of rickettsial host range for shuttle vectors based on dnaA and parA genes from the pRM plasmid of Rickettsia monacensis

abstract:
The genus Rickettsia encompasses a diverse group of obligate intracellular bacteria that are highly virulent disease agents of mankind as well as symbionts of arthropods. Native plasmids of Rickettsia amblyommatis (AaR/SC) have been used as models to construct shuttle vectors for genetic manipulation of several Rickettsia species. Here we report on the isolation of the complete plasmid (pRM658B) from Rickettsia monacensis (IrR/Munich) mutant Rmona658B and the construction of shuttle vectors based on pRM. To identify regions essential for replication, we made vectors containing the dnaA and parA genes of pRM with varying portions of the region surrounding these genes and a selection-reporter cassette conferring resistance to spectinomycin and expression of green fluorescent protein. Rickettsia amblyommatis (AaR/SC), R. monacensis (IrR/Munich), Rickettsia bellii (RML 369-C), Rickettsia parkeri (Tates Hell), and Rickettsia montanensis (M5/6) were successfully transformed with shuttle vectors containing pRM parA and dnaA. PCR assays targeting pRM regions not included in the vectors revealed that native pRM was retained in R. monacensis transformants. Determination of native pRM copy number using a plasmid-encoded gene (RM_p5) in comparison to chromosomal encoded gltA indicated reduced copy numbers in R. monacensis transformants. In transformed R. monacensis, native pRM and shuttle vectors with homologous parA and dnaA formed native plasmid-shuttle vector complexes. These studies provide insight on the maintenance of plasmids and shuttle vectors in rickettsiae.

IMPORTANCEO_LIThis paper describes a new series of plasmid shuttle vectors for the transformation of rickettsiae.
C_LIO_LIShuttle vectors based on parA and dnaA sequences of the plasmid pRM can be used to transform diverse rickettsia as well as its native host Rickettsia monacensis.
C_LIO_LIOur results provide insight into the maintenance of rickettsial-based shuttle vectors in rickettsiae.
C_LI


title: Generating Functional Cells Through Enhanced Interspecies Chimerism with Human Pluripotent Stem Cells

abstract: Obtaining functional human cells through interspecies chimerism with human pluripotent stem cells (hPSCs) remains unsuccessful due to its extreamly low efficiency. Here, we show that hPSCs failed to differentiate and contribute teratoma in presence of mouse PSCs (mPSCs). While, MYCN, a pro-growth factor dramatically promotes hPSC contribution in teratoma co-formation by hPSCs/mPSCs. MYCN combined with BCL2 (M/B) greatly enhanced conventional hPSCs to integrate into preimplantation embryos of different species, such as mice, rabbits and pigs and substrantially contributed to mouse post-implantation chimera in embryonic and extra-embyonic tissues. Strikingly, M/B-hPSCs injected into preimplantation Flk-1+/- mouse embryos show further enhanced chimerism that allows obtaining live human CD34+ blood progenitor cells from chimeras through cell sorting. The chimera derived human CD34+ cells further gave rise to various subtype blood cells in typical colony forming unit(CFU) assay. Thus, we proof the concept to obtain functional human cells through enchanced interspecies chimerism with hPSCs.

category: cell biology


title: Functional LINC complex maintains epigenetic landscape and decondenses DNA in mature muscles

abstract: The Linker of Nucleoskeleton and Cytoskeleton (LINC) complex transduces nuclear mechanical inputs suggested to control chromatin epigenetics. We analyzed the epigenetic landscape and genomic binding profile of HP1 and Polycomb transcription repressors, and of RNA-Pol II in Drosophila fully differentiated larval muscles lacking functional LINC complex. Our findings suggest a significant increase in chromatin repression promoted by enhanced binding of Polycomb and concomitant reduction of RNA-Pol II binding in the LINC mutant muscles. Consistently these mutants exhibited elevated levels of epigenetic repressive marks, tri-methylated H3K9 and H3K27, and reduced chromatin activation by H3K9 acetylation. These changes correlated with enhanced condensation of the DNA observed in the LINC mutant myonuclei. Importantly, we find larger repressive chromatin clusters marked by H3K27me3-GFP in live LINC mutant larval muscles. We suggest that the LINC complex is required for the stabilization of chromatin epigenetic landscape in non-dividing muscle fibers, possibly by inhibiting DNA condensation and restricting repressive cluster formation.


title: The GTPase Activity of the Double FYVE Domain Containing Protein 1 (DFCP1) Regulates Lipid Droplet Metabolism.

abstract: Lipid droplets (LDs) are transient lipid storage organelles that can be readily tapped to resupply cells with energy or lipid building blocks, and therefore play a central role in cellular metabolism. However, the molecular factors and underlying mechanisms that regulate the growth and degradation of LDs are poorly understood. It has emerged that LD metabolism is sensitive to the autophagy- and LD-associated protein Double FYVE Domain Containing Protein 1 (DFCP1), however, little is known about DFCP1s roles in autophagy and LD metabolism. Here, we show that DFCP1 contains a novel GTPase domain that regulates LD size by controlling the assembly of DFCP1 onto LDs in response to changes in nutrient availability. Specifically, we show that DFCP1 accumulation on LDs is independent of PI3P-binding, but requires a combination of the ER-binding domain and a unique GTPase domain. This novel GTPase domain possesses a low basal GTP turnover rate and has the ability to dimerize. Furthermore, mutations in the DFCP1 that either impact GTP hydrolysis or dimerization, result in changes in the accumulation of DFCP1 on LDs, as well as in changes in LD density and size. Importantly, the magnitude of these changes depends on the nutritional status of the cell. Collectively, our findings indicate that DFCP1 is a GTP-dependent metabolic sensor capable of modulating cellular storage of free fatty acids.


title: Ceramide-Rich Microdomains Facilitate Nuclear Envelope Budding during the Biogenesis of LTB4-containing Exosomes

abstract: Neutrophils migrating towards chemoattractant gradients amplify their recruitment range by releasing the secondary chemoattractant leukotriene B4 (LTB4)1,2. We previously demonstrated that LTB4 and its synthesizing enzymes, the 5-lipoxygenase (5-LO), 5-LO activating protein (FLAP), and leukotriene A4 hydrolase (LTA4H), are packaged and released in exosomes3. We now report that the biogenesis of the LTB4-containing exosomes is initiated at the nuclear envelope (NE) of activated neutrophils. We show that the neutral sphingomyelinase 1 (nSMase1)-mediated generation of ceramide enriched lipid-ordered microdomains initiates the clustering of the LTB4-synthesizing enzymes on the NE. We isolated and analyzed exosomes from activated neutrophils and established that the FLAP/5-LO-positive exosome population is distinct from that of the CD63-positive exosome population. Furthermore, we observed a strong co-localization between ALIX and FLAP at the periphery of nuclei and within cytosolic vesicles. We propose that the initiation of NE curvature and bud formation is mediated by nSMase1-dependent ceramide generation, which leads to FLAP and ALIX recruitment. Together, these observations elucidate the mechanism for LTB4 secretion and identify a novel pathway for exosome generation.


title: Eukaryotic plankton community assembly and influencing factors between continental shelf and slope sites in the northern South China Sea

abstract:
Eukaryotic plankton are pivotal members of marine ecosystems playing crucial roles in food webs and biogeochemical cycles. However, understanding the patterns and drivers of their community assembly remains a grand challenge. A study was conducted in the northern South China Sea (SCS) to address this issue. Here, 49 samples were collected and size-fractionated from discrete depths at continental shelf and continental slope in the northern South China Sea over a diel cycle. From high throughput sequencing of the 18S rDNA gene V4 region, 2,463 operational taxonomic units (OTUs) were retrieved. Alveolata and Opisthokonta overwhelmingly dominated the assemblages in relative abundance (44.76%, 31.08%) and species richness (59%, 12%). Biodiversity was higher in the slope than the shelf and increased with depth. Temperature and salinity were found as the major deterministic drivers of taxon composition. Community structure was influenced by multiple factors in the importance order of: environmental factors (temperature + salinity) > spatial factor > water depth > sampling time. Furthermore, the neutral model explained more variations in the smaller-sized (0.22-3m) community (24%) than larger-sized (3-200 m) community (16%) but generally explained less variations than did deterministic processes. Additionally, our data indicated that the larger plankton might be more environmentally filtered and less plastic whereas the smaller plankton had stronger dispersal ability. This study provides novel insights into differential contributions of the deterministic process and stochastic process and complexities of assembly mechanisms in shaping the community assembly of micro-nano and pico-eukaryotic biospheres in a subtropical ocean.

ImportanceEukaryotic plankton are essential to the biogeochemical processes in the ocean. Understanding the plankton community and influence factors is rapidly increasing with the advances in high-throughput sequencing in recent years, especially the microbe. Our study documented the biodiversity and drivers of community assembly of eukaryotic plankton in the subtropic northern SCS. We found the community structure was influenced by multiple factors and the deterministic process was more important than the stochastic process in the assembly of the eukaryotic plankton communities. Temperture is the most important factors in deterministic factors rather the nutrients which were previously thought important in shaping the eukaryotic plankton community in this oceanic province. Furthermore, we found smaller-sized miceukaryotic plankton are less environment filtered and more plastic than the larger-sized plankton. This insight revealed the differential contributions of the deterministic process and stochastic process and complexities of assembly mechanisms in shaping the community of eukaryotic biospheres.

category: ecology


title: Controversy over the decline of arthropods: a matter of temporal baseline?

abstract: Recently, a number of studies have reported somewhat contradictory patterns of temporal trends in arthropod abundance, from decline to increase. Arthropods often exhibit non-monotonous abundance variations over time, making it important to account for temporal coverage in interpretation of abundance trends, which is often overlooked in statistical analysis. Combining four recently analysed datasets that led to contrasting outcomes, we first show that temporal abundance variations of arthropods are non-monotonous. Using simulations, we show non-monotony is likely to bias estimated linear abundance trends. Finally, analysing empirical data, we show that heterogeneity in estimated abundance trends is significantly related to the variation in temporal baseline of analysed time series. Once differences in baseline years, habitats and continents are accounted for, we do not find any statistical difference in estimated linear abundance trends among the four datasets. We also show that short time series produce more stochastic abundance trends than long series, making the dearth of old and long-term time series a strong limitation in the assessment of temporal trends in arthropod abundance. The lack of time series with a baseline year anterior to global change acceleration is likely to lead to an underestimation of global change effects on biodiversity.


title: Modelling the spread of resistance to Varroa in Australian feral honeybee populations

abstract:
Australia is the only country where Western honeybees, Apis mellifera, are not infested with the mite Varroa destructor. Hence, a collapse in the feral honeybee population, brought about by an incursion and spread of V. destructor, would have serious consequences for Australian horticulture given its dependence on managed and feral honeybees for pollination. Managing Varroa in commercial colonies is well understood and can be achieved, although at significant bee-health costs, by using miticides. Protecting the feral population in the event of a Varroa incursion is much more difficult, but nevertheless imperative. One way to mitigate against collapse of the feral population is to seed it with Varroa-resistant queens, so as to accelerate the spread of resistance. We developed a simulation model of the spread of Varroa-resistance in feral honeybee populations following the introduction of Varroa-resistant queens into the managed population.

We show that, compared with a do-nothing scenario, seeding the managed honeybee population with Varroa-resistant queens was only effective in decreasing the length of time for the feral honeybee population to recover when the size of the managed resistant population was large compared to the size of the feral population. This situation may be achievable in some urban areas where numbers of managed colonies are high and habitat for feral colonies is limited.

category: evolutionary biology


title: Single-cell analysis reveals a pathogenic cellular module associated with early allograft dysfunction after liver transplantation

abstract: Liver transplantation (LT) is the standard therapy for patients with end-stage liver disease. Although LT technology has markedly progressed in recent decades, early allograft dysfunction (EAD) exacerbates the current organ shortage and impacts the prognosis of recipients. However, understanding of cellular characteristics and molecular events contributing to EAD is limited. Here, a large single-cell transcriptomic atlas of transplanted livers collected from four patients is constructed, including 58,243 cells, which are classified into 14 cell types and 29 corresponding subtypes with known markers, including liver parenchymal cells and non-parenchymal cells with different cell states. Compared to the pre-LT livers, graft remodeling is noted in the post-LT livers, with marked changes in several immune cells in either cell ratios or cell states. More importantly, an EAD-associated pathogenic cellular module is identified, consisting of mucosal-associated invariant T (MAIT) cells, granzyme B (GZMB)+ granzyme K (GZMK)+ natural killer (NK) cells, and S100A12+ neutrophils, all of which are elevated in EAD patient after LT. This cellular module is also verified in two independent datasets. Collectively, these results reveal the cellular characteristics of transplanted livers and the EAD-associated pathogenic cellular module at the single-cell level, offering new insights into the EAD occurrence after LT.

category: genomics


title: Whole-genome sequencing of Bantu-speakers from Angola and Mozambique reveals complex dispersal patterns and interactions throughout sub-Saharan Africa

abstract: As the continent of origin for our species, Africa harbours the highest levels of diversity anywhere on Earth. This trove of diversity provides rich opportunities to discover unknown genomic variation and explore how human populations have moved and interacted on the continent over thousands of years. However, many regions of Africa remain under-sampled. Here we present the first collection of whole-genomes from Angola and Mozambique, enabling the construction of a high-quality reference variation catalogue including three million novel SNPs. Leveraging the power and flexibility of whole-genome sequencing data, we model the development and continuity of Bantu-population structure through time, widespread admixture involving source populations from these regions across sub-Saharan Africa, and the heterogeneous population histories of Western and Eastern Bantu-speakers. In contrast to depictions of the Bantu expansion as a single, continuous macro-event, we recover evidence of admixture among distinct Bantu-speaking groups in South-Eastern Africa and bring together concordant patterns from linguistics and archaeology to paint a more complex picture of Iron Age migrations into the region. Moreover, we generate reference panels that better represents the complete diversity of African populations involved in the Atlantic slave trade, improving imputation accuracy in African Americans and Brazilians over the 1000 Genomes Project. This study fills important gaps in the current record of global genetic diversity and informs on the most significant demographic events in the recent history of Africa. We anticipate that our collection of genomes will form the foundation for future genomic healthcare initiatives involving under-represented communities in Angola and Mozambique.


title: DBFE: Distribution-based feature extraction from copy number and structural variants in whole-genome data

abstract:
MotivationWhole-genome sequencing has revolutionized biosciences by providing tools for constructing complete DNA sequences of individuals. With entire genomes at hand, scientists can pinpoint DNA fragments responsible for different cancers and predict patient responses to cancer treatments. However, the sheer volume of whole-genome data makes it difficult to encode the characteristics of genomic variants as features for machine learning algorithms.

ResultsWe present three feature extraction methods that facilitate classifier learning from distributions of genomic variants. The proposed approaches use binning, clustering, and kernel density estimation to produce features that discriminate between two groups of patients. Experiments on genomes of 219 ovarian, 61 lung, and 929 breast cancer patients show that the proposed approaches automatically identify genomic biomarkers associated with cancer subtypes and clinical response to oncological treatment. Finally, we show that the extracted features can be used alongside unsupervised learning methods to analyze genomic samples.

AvailabilityThe source code of the presented algorithms and reproducible experimental scripts are available on Github at https://github.com/MNMdiagnostics/dbfe

Contactmaciej.piernik@cs.put.poznan.pl


title: The genome of tropically adapted Brahman cattle (Bos taurus indicus) reveals novel genome variation in production animals

abstract: Recent advances in sequencing technology have revolutionised access to large scale genomic data that can be assembled into a platinum quality genome. Here we present a high quality genome assembly with less than 300 gaps of a Brahman cow (B. taurus indicus). The assembly was generated using 195GB of PacBio and 169GB of Oxford Nanopore Technologies sequence data. The high quality genome assembly allows us to identify substantial GC content variation that is positively associated with gene rich islands, and negatively associated with genetic variation in the form of structural variants. In addition, 92371 structural variants that are segregating in the brahman population were identified. Gene ontology analysis revealed that genes with varying copy numbers were enriched for gene ontology terms related to immune function. This analysis has revealed the complex structure of the mammalian genome of an outbred species, and identifies the ability of long read data from diploid species can be used to not only assemble a high quality genome, but also discover novel genetic variation within that genome.


title: rG4-seq 2.0: enhanced transcriptome-wide RNA G-quadruplex structure sequencing for low RNA input samples

abstract: RNA G-quadruplexes (rG4s) are non-canonical structural motifs that have diverse functional and regulatory roles such as transcription termination, alternative splicing, mRNA localization and stabilization and translational process. We recently developed RNA G-quadruplex structure sequencing (rG4-seq) technique and discovered many rG4s in both eukaryotic and prokaryotic transcriptomes. However, rG4-seq suffers from complicated gel purification step and limited PCR product yield and thus requires a high RNA input amount, limiting its applications for physiologically or clinically relevant studies. In this study, we have developed rG4-seq 2.0 by introducing a new ssDNA adapter containing deoxyuridine in the library preparation to enhance the library quality with no gel purification step, less PCR amplification cycles and higher yield of PCR products. We demonstrate that rG4-seq 2.0 produced high quality cDNA libraries that supported reliable and reproducible rG4 identification at varying RNA inputs (as low as 10 ng amount of RNA). rG4-seq 2.0 also improved the rG4-seq calling outcome and nucleotide bias in rG4 detection persistent in rG4-seq 1.0. Our new method can improve the identification and study of rG4s in low abundance transcripts, and our findings can provide insights to optimize cDNA library preparation in other related methods.


title: Sen1 is a master regulator of transcription-driven conflicts

abstract: Cellular homeostasis requires the coordination of several machineries concurrently engaged on the DNA. Wide-spread transcription can interfere with other processes and transcription-replication conflicts (TRCs) threaten genome stability. The conserved Sen1 helicase terminates non-coding transcription, but also interacts with the replisome and reportedly resolves genotoxic R-loops. Sen1 prevents genomic instability but how this relates to its molecular functions remains unclear. We generated high-resolution, genome-wide maps of transcription-dependent conflicts and R-loops using a Sen1 mutant that has lost interaction with the replisome but is termination proficient. We show that Sen1 removes RNA polymerase II at TRCs within genes and the rDNA, but also at sites of transcription-transcription conflicts under physiological conditions, thus qualifying as a "master regulator of conflicts". We demonstrate that genomic stability is only affected by Sen1 mutation when, in addition to its role at the replisome, termination of non-coding transcription or R-loop removal are additionally compromised.


title: A historically balanced locus under recent directional selection in responding to changed nitrogen conditions during modern maize breeding

abstract: Understanding the patterns of selection during plant evolution and recent crop improvement processes is the central topic in plant breeding and genetics. As an essential macronutrient for plant growth and development, nitrogen (N) is a key factor in affecting plant adaptation and crop improvement. The widespread adoption of less expensive industrial N fixation has dramatically reshaped plant morphology by favoring compact maize plants to tolerant crowding stress. The associated genetic changes, however, have not been systematically studied. Here, we investigated maize inbred lines developed before and after the 1960s -- the time point when inorganic N fertilizer started to be widely used for maize production. We identified a strong selective sweep exhibiting pronounced genomic differentiation between Old-Era (pre-1960s) and New-Era (post-1960s) inbred lines. Further study revealed population genetics statistics in the sweep exhibited patterns consistent with historical balancing selection. This balanced genomic interval is associated with a number of morphological, physiological, and metabolite traits related to vegetative N responses. A cluster of three glutamate receptor-like (GLR) genes is located within the region targeted by selection. Functional characterizations suggested differences in transcriptional activity of the GLR genes between the haplotypes carried by Old-Era and New-Era inbred lines likely play an essential role in mediating distinct N responses. The identification of both targets of selection and changes in the regulation of N responsive genes between maize lines developed in different eras sheds light on the N sensing and regulation pathways and paves the way to developing N resilient crops.


title: Investigating carbohydrate-rich feed supplements and the feeding preferences of European starlings (Sturnus vulgaris)

abstract: In the current ecological and ornithological environment in the continental United States, the European starling (Sturnus vulgaris) is one of the most common exotic bird species. After being introduced on the East Coast of the United States, the species spread rapidly across regions and ecosystems, significantly affecting the greater ecology of the nation and often disturbing local species populations. To better understand the behavior and preferences of this species, a study was devised to test the field responses of a population of European starlings in Lyon County, Kansas over a total period of 144 hours (during 48 individual observation periods) to assess and yield knowledge pertaining to their behavior and feeding patterns within a suburban environment. For this experiment, four feed alternatives (i.e., one control and three experimental) were prepared to test the impact of the utilization of carbohydrate-rich feed supplements on the degree to which the starlings would frequent a feeding location. The different feed offered to the local starlings would consist of either 300g of conventional bird feed, 200g of conventional bird feed and 100g of the supplement, 100g of conventional bird feed and 200g of the supplement, or 300g of the supplement, with the conventional bird seed acting as the control. The data suggest that the differences observed with relation to the feed alternatives were negligible, as demonstrated by the starlings preference for the different supplement concentrations (according to their feeding frequency for the four alternatives).


title: Ontogeny of learning and visual discrimination in zebrafish

abstract: With the exception of humans, early cognitive development has been thoroughly investigated only in precocial species, well developed at birth and with a broad behavioural and cognitive repertoire. We investigated another highly altricial species, the zebrafish, Danio rerio, whose embryonic development is very rapid: 72 hours. The nervous system of hatchlings is poorly developed, and their cognitive capacities are largely unknown. Larvae trained at 8 days post-fertilisation rapidly learned to associate a visual pattern with a food reward, showing significant performance at 10 days post-fertilisation. We exploited this capacity to study hatchlings discrimination learning capacities. Larval zebrafish rapidly and accurately learned colour and shape discriminations. They also discriminated a figure from its mirror image and from its 90{degrees}-rotated version, although with lower performance. Our study revealed impressive similarities in learning and visual discrimination capacities between newborn and adult zebrafish despite their enormous differences in brain size and degree of development.


title: Arginine-rich C9ORF72 ALS proteins stall ribosomes in a manner distinct from a canonical ribosome-associated quality control substrate

abstract: Hexanucleotide expansion mutations in C9ORF72 are a cause of familial amyotrophic lateral sclerosis. We previously reported that long arginine-rich dipeptide repeats (DPR), mimicking abnormal proteins expressed from the hexanucleotide expansion, caused translation stalling when expressed in cell culture models. Whether this stalling provides a mechanism of pathogenicity remains to be determined. Here we explored the molecular features of DPR-induced stalling and examined whether known regulatory mechanisms of ribosome quality control (RQC) are involved to sense and resolve the stalls. We demonstrate that arginine-containing DPRs lead to stalling in a length dependent manner, with lengths longer than 40 repeats invoking severe translation arrest. Mutational screening of 40xGly-Xxx DPRs shows that stalling is most pronounced where Xxx are positively charged amino acids (Arg or Lys). Through a genome-wide knockout screen we find that genes regulating stalling on polyadenosine mRNA coding for poly-Lys, a canonical RQC substrate, respond differently to the readthrough of arginine-rich DPRs. Indeed, we find evidence that DPR-mediated stalling has no natural regulatory responses even though the stalls may be sensed, as evidenced by an upregulation of RQC gene expression. These findings therefore implicate arginine-rich DPR-mediated stalled ribosomes as posing a particular danger to cellular health and viability.


title: In-shoe plantar pressure depends on walking speed and type of weight-bearing activity in people with diabetes at high risk of ulceration

abstract:
BackgroundIn evaluating the biomechanical properties of therapeutic footwear, most often in-shoe plantar pressure is obtained during mid-gait steps at self-selected speed in a laboratory setting. However, this may not represent plantar pressures or indicate the cumulative stress experienced in daily life, where people adopt different walking speeds and weight-bearing activities.

Research questionIn people with diabetes at high risk of ulceration, 1) what is the effect of walking speed on plantar pressure measures, and 2) what is the difference in plantar pressure measures between walking at self-selected speed and other weight-bearing activities?

MethodsIn a cross-sectional study, we included 59 feet of 30 participants (5 females, mean age: 63.8 (SD 9.2) years). We assessed in-shoe plantar pressure with the Pedar-X system during three standardized walking speeds (0.8, 0.6 and 0.4 m/s) and eight types of activities versus walking at self-selected speed (3 components of the Timed Up and Go test (TUG), standing, accelerating, decelerating, stair ascending and descending and standing). Peak plantar pressure (PPP) and pressure-time integral (PTI) were determined for the hallux, metatarsal 1, metatarsal 2-3 and metatarsal 4-5. For statistical comparisons we used linear mixed models (<0.05) with Holm-Bonferroni correction.

ResultsWith increasing walking speed, PPP increased and PTI decreased for all regions (p[≤]0.001). Standing, decelerating, stair ascending and TUG showed lower PPP than walking at self-selected speed for most regions (p[≤]0.004), whereas accelerating and stair descending showed similar PPP. Stair ascending and descending showed higher PTI than walking at self-selected speed (p[≤]0.002), standing showed lower PTI (p[≤]0.001), while the other activities showed similar PTI for most regions.

SignificanceTo best evaluate the biomechanical properties of therapeutic footwear, and to assess cumulative plantar tissue stress of people with diabetes at high risk of ulceration, plantar pressures during different walking speeds and activities of daily living should be considered.


title: A Sulfonated Thermoresponsive Injectable Gel for Sequential Release of Therapeutic Proteins to Protect Cardiac Function After a Myocardial Infarction

abstract: Myocardial infarction causes cardiomyocyte death and persistent inflammatory responses, which generates adverse pathological remodeling. Delivering therapeutic proteins from injectable materials in a controlled release manner may present an effective biomedical approach for treating this disease. A thermoresponsive injectable gel composed of chitosan, conjugated with poly(N-isopropylacrylamide) and sulfonate groups, was developed for spatiotemporal protein delivery to protect cardiac function after a myocardial infarction. The thermoresponsive gel delivered VEGF, IL-10 and PDGF in a sequential and sustained manner in vitro. An acute myocardial infarction mouse model was used to evaluate polymer biocompatibility and to determine therapeutic effects from the delivery system on cardiac function. Immunohistochemistry showed biocompatibility of the hydrogel, while the controlled delivery of the proteins reduced macrophage infiltration and increased vascularization. Echocardiography showed an improvement in ejection fraction and fractional shortening after injecting the thermal gel and proteins. A factorial design of experiments study was implemented to optimize the delivery system for the best combination and doses of proteins for further increasing stable vascularization and reducing inflammation using a subcutaneous injection mouse model. The results showed that VEGF, IL-10, and FGF-2 demonstrated significant contributions towards promoting long-term vascularization, while PDGFs effect was minimal.


title: A Systematic Approach for Explaining Time and Frequency Features Extracted by CNNs from Raw EEG Data

abstract: In recent years, the use of convolutional neural networks (CNNs) for raw electroencephalography (EEG) analysis has grown increasingly common. However, relative to earlier machine learning and deep learning methods with manually extracted features, CNNs for raw EEG analysis present unique problems for explainability. As such, a growing group of methods have been developed that provide insight into the spectral features learned by CNNs. However, spectral power is not the only important form of information within EEG, and the capacity to understand the roles of specific multispectral waveforms identified by CNNs could be very helpful. In this study, we present a novel model visualization-based approach that adapts the traditional CNN architecture to increase interpretability and combines that inherent interpretability with a systematic evaluation of the model via a series of novel explainability methods. Our approach evaluates the importance of spectrally distinct first-layer clusters of filters before examining the contributions of identified waveforms and spectra to cluster importance. We evaluate our approach within the context of automated sleep stage classification and find that, for the most part, our explainability results are highly consistent with clinical guidelines. Our approach is the first to systematically evaluate both waveform and spectral feature importance in CNNs trained on EEG data.