title: APRILE: Exploring the Molecular Mechanisms of Drug Side Effects with Explainable Graph Neural Networks

abstract: The majority of people over the age of 65 take two or more medications. While many individual drug side effects are known, polypharmacy side effects due to novel drug combinations poses great risk. Here, we present APRILE: an explainable artificial intelligence (XAI) framework that uses graph neural networks to explore the molecular mechanisms underlying polypharmacy side effects. Given a list of side effects and the pairs of drugs causing them, APRILE identifies a set of proteins (drug targets or non-targets) and associated Gene Ontology (GO) terms as mechanistic  explanations of associated side effects. Using APRILE, we generate such explanations for 843,318 (learned) and 93,966 (novel) side effect-drug pair events, spanning 861 side effects (472 diseases, 485 symptoms and 9 mental disorders) and 20 disease cate-gories. We show that our two new metrics--pharmacogenomic information utilization and protein-protein interaction information utilization--provide quantitative estimates of mechanism complexity. Explanations were significantly consistent with state of the art disease-gene associations for 232/239 (97%) side effects. Further, APRILE generated new insights into molecular mechanisms of four diverse categories of adverse drug reactions: infection, metabolic diseases, gastrointestinal diseases, and mental disorders, including paradoxical side effects. We demonstrate the viability of discovering polypharmacy side effect mechanisms by training an XAI framework on massive biomedical data. Consequently, it facilitates wider and more reliable use of AI in healthcare.

category: bioinformatics


title: Strainline: full-length de novo viral haplotype reconstruction from noisy long reads

abstract: Haplotype-resolved de novo assembly of highly diverse virus genomes is critical in prevention, control and treatment of viral diseases. Current methods either can handle only relatively accurate short read data, or collapse haplotype-specific variations into consensus sequence. Here, we present Strainline, a novel approach to assemble viral haplotypes from noisy long reads without a reference genome. As a crucial consequence, Strainline is the first approach to provide strain-resolved, full-length de novo assemblies of viral quasispecies from noisy third-generation sequencing data. Benchmarking experiments on both simulated and real datasets of varying complexity and diversity confirm this novelty, by demonstrating the superiority of Strainline in terms of relevant criteria in comparison with the state of the art.


title: phasebook: haplotype-aware de novo assembly of diploid genomes from long reads

abstract:
Haplotype-aware diploid genome assembly is crucial in genomics, precision medicine, and many other disciplines. Long-read sequencing technologies have greatly improved genome assembly thanks to advantages of read length. However, current long-read assemblers usually introduce disturbing biases or fail to capture the haplotype diversity of the diploid genome. Here, we present phasebook, a novel approach for reconstructing the haplotypes of diploid genomes from long reads de novo.

Benchmarking experiments demonstrate that our method outperforms other approaches in terms of haplotype coverage by large margins, while preserving competitive performance or even achieving advantages in terms of all other aspects relevant for genome assembly.


title: Sliding of HIV-1 reverse transcriptase over DNA creates a transient P pocket - Targeting P-pocket by fragment screening

abstract: HIV-1 reverse transcriptase (RT) slides over an RNA/DNA or dsDNA substrate while copying the viral RNA to a proviral DNA. We report a crystal structure of RT/dsDNA complex in which RT overstepped the primer 3-end of a dsDNA substrate and created a transient P-pocket at the priming site. We performed a high-throughput screening of 300 drug-like fragments by X-ray crystallography and identified binding of two to P-pocket, which is composed of structural elements from polymerase active site, primer grip, and template-primer that are resilient to drugresistance mutations. Analogs of a fragment were synthesized of which two showed noticeable RT inhibition. An engineered RT/DNA aptamer complex trapped the transient P-pocket in solution. Structures of the RT/DNA complex were determined with a fragment and a synthesized analog bound at P-pocket by single-particle cryo-EM. Identification of P-pocket and the devised structurebased platform provide an opportunity for designing new types of polymerase inhibitors.

category: biophysics


title: The first observation of osmotically neutral sodium accumulation in the myocardial interstitium

abstract: The aim of this study was the detection and quantification of the Na+ depositions in the extracellular matrix of myocardial tissue, which are suggested to be bound by negatively charged glycosaminoglycan (GAG) structures. The presented experimental results are based on high resolution X-ray fluorescence (XRF) spectromicroscopy technique used to perform a comparative analysis of sodium containment in intracellular and interstitial spaces of cardiac tissues taken from animals selected by low and high sodium intake rates. The experimental results obtained show that high sodium daily intake can result in a remarkable increase of sodium concentration in the myocardial interstitium.


title: Fatty acid binding proteins shape the cellular response to activation of the glucocorticoid receptor

abstract: Glucocorticoids are steroid hormones that are essential for life in mammals. Therapeutically, they are some of the most cost-effective drugs for the treatment of inflammatory diseases ranging from skin rashes to COVID-19, but their use is limited by adverse effects. Glucocorticoids exert their effects via the glucocorticoid receptor, a type I nuclear hormone receptor which modulates gene expression. The transcriptional activity of some related, but nuclear restricted, type II nuclear hormone receptors can be enhanced by a family of intracellular transport proteins, the fatty acid binding proteins (FABPs). We find that the transcriptional activity of the GR can be altered by a sub-set of FABP family members dependent on the GR-ligand. The ability of some FABPs to selectively promote or limit the transcriptional activity of the GR in a ligand-dependent manner could facilitate the discovery of drugs that narrow GR activity to only the desired subset of therapeutically relevant genes.

category: pharmacology and toxicology


title: Making BrainWaves: Portable Brain Technologies in Biology Education

abstract: Neuroscience is one of the fastest growing STEM fields, yet its presence in K-12 science education is very limited, partially due to the lack of accessible teaching materials and tools. Here, we describe a new high school neuroscience curriculum ("BrainWaves"), where students utilize recent advances in low-cost, portable Electroencephalography (EEG) technology to investigate their own brain activity. This semester-long curriculum is supported by science mentors and an educational application that guides students through the process of recording and analyzing their own brain activity. Evaluation data collected in 5 public New York City schools in 2018/19 indicate significant positive shifts in content knowledge and self-efficacy among students who participated in BrainWaves compared to students in other courses of the same teacher. The quantitative findings are supported by interviews, where students reported increased appreciation for neuroscience and college readiness and discussed the benefits of collaborating with scientists and using portable brain technology in classrooms.

category: scientific communication and education


title: Motif-centric phosphoproteomics to target kinase-mediated signaling pathways

abstract:
Identifying cellular phosphorylation pathways based on kinase-substrate relationships is a critical step to understanding the regulation of physiological functions in cells. Mass spectrometry-based phosphoproteomics workflows have made it possible to comprehensively collect information on individual phosphorylation sites in a variety of samples. However, there is still no generic approach to uncover phosphorylation networks based on kinase-substrate relationships in rare cell populations. Here, we describe a motif-centric phosphoproteomics approach combined with multiplexed isobaric labeling, in which in vitro kinase reaction is used to generate the targeted phosphopeptides, which are spiked into one of the isobaric channels to increase detectability. Proof-of-concept experiments demonstrate selective and comprehensive quantification of targeted phosphopeptides by using multiple kinases for motif-centric channels. Over 7,000 tyrosine phosphorylation sites were quantified from several tens of {micro}g of starting materials. This approach enables the quantification of multiple phosphorylation pathways under physiological or pathological regulation in a motif-centric manner.

MotivationSensitivity for detecting phosphopeptides with a particular phosphorylation motif is limited, especially for tyrosine phosphopeptides.

category: systems biology


title: The HAPPE plus Event-Related (HAPPE+ER) Software: A Standardized Processing Pipeline for Event-Related Potential Analyses

abstract: Event-Related Potential (ERP) designs are a common method for interrogating neurocognitive function with electroencephalography (EEG). However, the gold standard of preprocessing ERP data is manual-editing - a subjective, time-consuming processes. A number of automated pipelines have recently been created to address the need for standardization, automation, and quantification of EEG data processing; however, few are optimized for ERP analyses (especially in developmental or clinical populations). To fill this need, we propose and validate the HAPPE plus Event-Related (HAPPE+ER) software, a standardized and automated processing pipeline optimized for ERP analyses in EEG data. HAPPE+ER processes event- related potential data from raw files through a series of filtering, line noise reduction, bad channel detection, artifact rejection from continuous data, segmentation, and bad segment rejection methods. HAPPE+ER also includes post-processing reports of both data quality and pipeline quality metrics to facilitate the evaluation and reporting of data processing in a standardized manner. Finally, HAPPE+ER includes a post-processing script to facilitate generating ERP figures and measures for statistical analysis. We describe multiple approaches with both adult and developmental data to optimize and validate pipeline performance. HAPPE+ER software is freely available under the terms of GNU General Public License at https://github.com/PINE-Lab/HAPPE.

category: neuroscience


title: Out of rhythm: Compromised precision of theta-gamma coupling impairs associative memory in old age

abstract:
Episodic memory declines with advancing adult age. This decline is particularly pronounced when associations between items and their contexts need to be formed. According to theories of neural communication, the precise coupling of gamma power to the phase of the theta rhythm supports associative memory formation. To investigate whether age differences in associative memory are related to compromised theta-gamma coupling, we took electroencephalographic (EEG) recordings during the encoding phase of an item-context association task. Fifty-eight younger and 55 older adults studied pictures of objects superimposed on background scenes. In a recognition test, objects were presented on old or new backgrounds, and participants responded if they had seen (1) the object and (2) the object-scene pair. Theta-gamma coupling supported pair memory formation in both age groups. Whereas pair memory was associated with coupling closer to the peak of the theta rhythm, item-only memory was associated with a deviation in phase angle relative to pair memory. Furthermore, a stable relation between coupling phase and pair memory performance demonstrated that coupling closer to the peak is beneficial for associative memory. Critically, older adults lower pair memory was accompanied by a shift in coupling phase relative to younger adults. In concert, the present results are consistent with the hypothesis that decrements in the precision with which gamma power is coupled to the theta phase underlie the decline of associative memory in normal cognitive aging.

Significance StatementAccording to prominent theories of neural communication, the precise coordination of oscillatory activity enables the formation of associative memories. We propose that normal cognitive aging impairs associative memory formation by compromising the precision of neural communication. We show that the coupling of high-frequency gamma power to low-frequency theta phase supports associative memory formation in both younger and older adults, with coupling closer to the theta peak benefitting memory performance. However, compared to younger adults, the coupling phase angle is shifted and more variable in older adults. We conclude that alterations in the precision of theta-gamma coupling contribute to adult age differences in associative memory.


title: Healthcare experience disrupts representational similarity between one's and others' pain in anterior insula

abstract: Medical students and professional healthcare providers often underestimate patients pain, an effect associated with decreased neural response of the anterior insula to pain information. However, the functional significance of these neural modulations is still debated. We recruited university medical students and emergency caregivers to test the role of healthcare experience on the behavioral/neural reactivity to others pain, emotions, and beliefs. We confirmed that healthcare experience decreased the sensitivity to others suffering, as measured by subjective ratings and insular response. This effect was independent from stimulus modality (pictures, texts), but specific for pain, as it did not generalize to emotions or beliefs. Critically, multivariate pattern analysis revealed that healthcare experience impacted specifically a component of the neural representation of others pain shared with that of first-hand nociception. This suggests a reduced likelihood of appraising others sufferance as ones own, and might offer a mechanistic explanation for pain underestimation in clinical settings.


title: A multimodal AI system for out-of-distribution generalization of seizure detection

abstract:
Epilepsy is one of the most common severe neurological disorders worldwide. The International League Against Epilepsy (ILAE) define epilepsy as a brain disorder that generates (1) two unprovoked seizures more than 24 hrs apart, or (2) one unprovoked seizure with at least 60% risk of recurrence over the next ten years. Complete remission has been defined as ten years seizure free with the last five years medication free. This requires a cost-effective ambulatory ultra-long term out-patient monitoring solution. The common practice of self-reporting is inaccurate. Applying artificial intelligence (AI) to scalp electroencephalogram (EEG) interpretation is becoming increasingly common, but other data modalities such as electrocardiograms (ECGs) are simpler to collect and often recorded simultaneously with EEG. Both recordings contain biomarkers in the detection of seizures.

Here, we propose a state-of-the-art performing AI system that combines EEG and ECG for seizure detection, tested on clinical data with early evidence demonstrating generalization across hospitals. The model was trained and validated on the publicly available Temple University Hospital (TUH) dataset. To evaluate performance in a clinical setting, we conducted nonpatient-specific inference-only tests on three out-of-distribution datasets, including EPILEPSIAE (30 patients) and the Royal Prince Alfred Hospital (RPAH) in Sydney, Australia (31 patients shortlisted by neurologists and 30 randomly selected). Across all datasets, our multimodal approach improves the area under the receiver operating characteristic curve (AUC-ROC) by an average margin of 6.71% and 14.42% for prior state-of-the-art approaches using EEG and ECG alone, respectively. Our models state-of-the-art performance and robustness to out-ofdistribution datasets can improve the accuracy and efficiency of epilepsy diagnoses.


title: Striatal role in everyday life and laboratory developed habits

abstract: The dorsolateral striatum plays a major role in stimulus-response habits that are learned in the experimental laboratory. Here, we use meta-analytic procedures to identify the neural circuits activated during the execution of stimulus-response behaviours acquired in everyday-life and those activated by habits acquired in the laboratory. In the case of everyday-life habits we dissociated motor and associative components. We found that motor-dominant stimulus-response associations developed outside the laboratory engaged posterior dorsal putamen, supplementary motor area (SMA) and cerebellum. Associative components were also represented in the posterior putamen. Meanwhile, newly learned habits relied more on the anterior putamen with activation expanding to caudate and nucleus accumbens. Importantly, common neural representations for both naturalistic and laboratory based habits were found in posterior left and anterior right putamen. Our findings suggest a common striatal substrate for behaviours with significant stimulus-response associations, independently of whether they were acquired in the laboratory or everyday-life.


title: Single-orientation Quantitative Susceptibility Mapping identifies the Ventral Intermediate Nucleus of the Thalamus

abstract:
IntroductionThe ventral intermediate nucleus (VIM) represents the primary target in the treatment of tremor. Accurate localization is extremely important given its proximity to other thalamic nuclei. We utilized single orientation quantitative susceptibility mapping (QSM) at 3T to directly visualize the VIM.

MethodsFour adult volunteers, one adult cadaver, and an essential tremor patient were scanned on a 3T MRI using a multi-echo gradient echo sequence. QSM images were generated using the improved sparse linear equation and least-squares (iLSQR) algorithm. Two adult subjects underwent multiple head orientation imaging for multi-orientation QSM reconstruction. The VIM was prospectively identified with direct visualization as well as indirect landmark-based localization.

ResultsThe bilateral VIM was consistently identified as a hypointense structure within the lateral thalamus, appearing similar on multi-orientation and single-orientation QSM, corresponding to the myelinated dentatorubrothalamic tract (DRTT). The indirect method resulted in a comparatively inferomedial localization, at times missing the VIM and DRTT.

ConclusionSingle-orientation QSM offers a clinically feasible, non-invasive imaging-based approach to directly localize the VIM.


title: Deep learning the arrow of time in brain activity: characterising brain-environment behavioural interactions in health and disease

abstract: The complex intrinsic and extrinsic forces from the body and environment push the brain into non-equilibrium. The arrow of time, central to thermodynamics in physics, is a hallmark of non-equilibrium and serves to distinguish between reversible and non-reversible dynamics in any system. Here, we use a deep learning Temporal Evolution NETwork (TENET) framework to discover the asymmetry in the flow of events,  arrow of time, in human brain signals, which provides a quantification of how the brain is driven by the interplay of the environment and internal processes. Specifically, we show in large-scale HCP neuroimaging data from a thousand participants that the levels of non-reversibility/non-equilibrium change across time and cognitive state with higher levels during tasks than when resting. The level of non-equilibrium also differentiates brain activity during the seven different cognitive tasks. Furthermore, using the large-scale UCLA neuroimaging dataset of 265 participants, we show that the TENET framework can distinguish with high specificity and sensitivity resting state in control and different neuropsychiatric diseases (schizophrenia, bipolar disorders and ADHD) with higher levels of non-equilibrium found in health. Overall, the present thermodynamics-based machine learning framework provides vital new insights into the fundamental tenets of brain dynamics for orchestrating the interactions between behaviour and brain in complex environments.


title: Single nucleus transcriptomic analysis of human dorsal root ganglion neurons

abstract: Somatosensory neurons with cell bodies in the dorsal root ganglia (DRG) project to the skin, muscles, bones, and viscera to detect touch and temperature as well as to mediate proprioception and many types of interoception. In addition, the somatosensory system conveys the clinically relevant noxious sensations of pain and itch. Here we used single nuclear transcriptomics to characterize the classes of human DRG neurons that detect these diverse types of stimuli. Notably, multiple types of human DRG neurons have transcriptomic features that resemble their mouse counterparts although expression of genes considered important for sensory function often differed between species. More unexpectedly, we demonstrated that several classes of mouse neurons have no direct equivalents in humans and human specific cell-types were also identified. This dataset should serve as a valuable resource for the community, for example as means of focusing translational efforts on molecules with conserved expression across species.


title: Single-domain antibodies for targeting, detection and in vivo imaging of human CD4+ cells

abstract:
The advancement of new immunotherapies necessitates appropriate probes to monitor the presence and distribution of distinct immune cell populations. Considering the key role of CD4+ T cells in regulating immunological processes, we generated novel single-domain antibodies (nanobodies, Nbs) that specifically recognize human CD4. After in depth analysis of their binding properties, recognized epitopes, and effects on T cell proliferation, activation and cytokine release, we selected CD4 Nbs that did not interfere with crucial T cell processes in vitro and converted them into immune tracers for non-invasive molecular imaging.

By optical imaging, we demonstrate the ability of a high-affinity CD4-Nb to specifically visualize CD4+ cells in vivo using a xenograft model. Furthermore, time-resolved immune positron emission tomography (immunoPET) of a human CD4 knock-in mouse model showed rapid accumulation of 64Cu-radiolabeled CD4-Nb in CD4+ T cell-rich tissues. We propose that the CD4 Nbs presented here could serve as versatile probes for stratifying patients and monitoring individual immune responses during personalized immunotherapy in both cancer and inflammatory diseases.

category: immunology


title: Controlling Staphylococcus aureus by 2-phenol (2-MAMP) in a co-culture moderates the biofilm and virulence of Pseudomonas aeruginosa

abstract: Staphylococcus aureus and Pseudomonas aeruginosa are the most encountered organisms in a polymicrobial chronic wound infection. Production of multiple virulence factors by this duo delays wound healing process. Notably, P. aeruginosa displays enhanced virulence in the presence of S. aureus by a peptidoglycan sensing mechanism. Thus, novel therapies are imperative to address polymicrobial infections effectively. Previously, it has been suggested that targeting S. aureus might be a possible approach to reduce the severity of P. aeruginosa in a polymicrobial infection. In this aspect, we have used 2-[(Methylamino)methyl]phenol (2-MAMP), our previously reported QS inhibitor to target S. aureus and phenotypically determine the virulence factors of P. aeruginosa under this condition. Analysis of major virulence factors of Pseudomonas viz. biofilm, pyocyanin and pyoveridine showed a significant reduction. The competitive index (CI) and relative increase ratio (RIR) were determined to understand the organisms interaction in co-culture. Results indicated competitiveness among the strains and on increasing ratios of S. aureus cells, co-existence was noticed. Further, as a sensible approach antibiotic - antivirulence drug combinations were tested on co-culture. Significant improvement in the growth inhibition was observed. Our preliminary results presented here would enable further research to address polymicrobial infection in a novel way.

category: microbiology


title: Economic costs of biological invasions in the United States

abstract: The United States has thousands of invasive species, representing a sizable, but unknown burden to the national economy. Given the potential economic repercussions of invasive species, quantifying these costs is of paramount importance both for national economies and invasion management. Here, we used a novel global database of invasion costs (InvaCost) to quantify the overall costs of invasive species in the United States across spatiotemporal, taxonomic, and socioeconomic scales. From 1960 to 2020, reported invasion costs totaled $4.52 trillion (USD 2017). Considering only observed, highly reliable costs, this total cost reached $1.22 trillion with an average annual cost of $19.94 billion/year. These costs increased from $2.00 billion annually between 1960-1969 to $21.08 billion annually between 2010-2020. Most costs (73%) were related to resource damages and losses ($896.22 billion), as opposed to management expenditures ($46.54 billion). Moreover, the majority of costs were reported from invaders from terrestrial habitats ($643.51 billion, 53%) and agriculture was the most impacted sector ($509.55 billion). From a taxonomic perspective, mammals ($234.71 billion) and insects ($126.42 billion) were the taxonomic groups responsible for the greatest costs. Considering the apparent rising costs of invasions, coupled with increasing numbers of invasive species and the current lack of cost information for most known invaders, our findings provide critical information for policymakers and managers.

category: ecology


title: Systems Biology Analysis of Human Genomes Points to Key Pathways Conferring Spina Bifida Risk

abstract: Spina bifida (SB) is a debilitating birth defect caused by multiple gene and environment interactions. Though SB shows non-Mendelian inheritance, genetic factors contribute to an estimated 70% of cases. Nevertheless, identifying human mutations conferring SB risk is challenging due to its relative rarity, genetic heterogeneity, incomplete penetrance and environmental influences that hamper GWAS approaches to untargeted discovery. Thus, SB genetic studies may suffer from population substructure and/or selection bias introduced by typical candidate gene searches. We report a population based, ancestry-matched whole-genome sequence analysis of SB genetic predisposition using a systems biology strategy to interrogate 298 case-control subject genomes (149 pairs). Genes that were enriched in likely gene disrupting (LGD), rare protein-coding variants were subjected to machine learning analysis to identify genes in which LGD variants occur with a different frequency in cases vs. controls and so discriminate between these groups. Those genes with high discriminatory potential for SB significantly enriched pathways pertaining to carbon metabolism, inflammation, innate immunity, cytoskeletal regulation and essential transcriptional regulation, indicating their impact on the pathogenesis of human SB. Additionally, interrogation of conserved non-coding sequences identified robust variant enrichment in regulatory regions of several transcription factors critical to embryonic development. This genome-wide perspective offers an effective approach to interrogation of coding and non-coding sequence variant contributions to rare complex genetic disorders.

category: genomics


title: A genome-wide association study of serum proteins reveals shared loci with common diseases

abstract: With the growing number of genetic association studies, the genotype-phenotype atlas has become increasingly more complex, yet the functional consequences of most disease associated alleles is not understood. The measurement of protein level variation in solid tissues and biofluids integrated with genetic variants offers a path to deeper functional insights. Here we present a large-scale proteogenomic study in 5,368 individuals, revealing 4,113 independent associations between genetic variants and 2,099 serum proteins, of which 37% are previously unreported. The majority of both cis- and trans-acting genetic signals are unique for a single protein, although our results also highlight numerous highly pleiotropic genetic effects on protein levels and demonstrate that a proteins genetic association profile reflects certain characteristics of the protein, including its location in protein networks, tissue specificity and intolerance to loss of function mutations. Integrating protein measurements with deep phenotyping of the cohort, we observe substantial enrichment of phenotype associations for serum proteins regulated by established GWAS loci, and offer new insights into the interplay between genetics, serum protein levels and complex disease.


title: Implicitly Learned Higher Order Associations Differentiates Recent and Remote Retrieval of Temporal Order Memory

abstract: Memory of an ordered sequence of distinct events requires encoding the temporal order as well as the intervals that separates these events. In this study, using order place association task where the animal learns to associate the location of the food pellet to the order of entry into the event arena, we probe the nature of temporal order memory in mice. In our task, individual trials, become distinct events, as the animal is trained to form unique association between entry order and a correct location. The inter-trial intervals (> 30 mins) are chosen deliberately to minimise the working memory contributions. We develop this paradigm initially using 4 order place associates and later extend it to 5 paired associates. Our results show that animals not only acquire these explicit (entry order to place) associations but also higher order associations that can only be inferred implicitly from the temporal order of these events. As an indicator of such higher order learning during the probe trail the mice exhibit predominantly prospective errors that declines proportionally with temporal distance. On the other hand, prior to acquiring the sequence the retrospective errors are dominant. Additionally, we also tested the nature of such acquisitions when temporal order CS is presented along with flavour as a compound stimulus comprising of order and flavour both simultaneously being paired with location. Results from these experiments indicate that the animal learns both order-place and flavour-place associations. Comparing with pure order place training, we find that the additional flavour in compound training did not interfere with the ability of the animals to acquire the order place associations. When tested remotely, pure order place associations could be retrieved only after a reminder training. Further higher order associations representing the temporal relationship between the events is markedly absent in the remote time.

category: animal behavior and cognition


title: A Novel Art of Electrocardiogram Assessment in Zebrafish for Cardiovascular Disease Studies and Drug Screening

abstract: The zebrafish (Dario rerio) has proven to be an excellent animal model for biological research owing to its small size, low cost for maintenance, short generation time, amenable genetics, and optical transparency. Zebrafish have been extensively used in cardiovascular studies in which mutant lines with cardiovascular defects were introduced and analyzed. Despite the small size, technological advances have paved the way to effectively assess cardiac functions of zebrafish. Here, we present a novel art for long-term simultaneous monitoring and analysis of electrocardiogram (ECG) in multiple zebrafish with controlled environment. The system helps minimize the effect of anesthetic drug and temperature to cardiac rhythm side effects as well as save time and efforts by 40-50 fold compared with the conventional approach. We further employed the system to study the Na+ sensitivity in the development of sinus arrest in Tg(SCN5A-D1275N) fish, a study model of the sick sinus syndrome, as well as the relationship between this variant and drug administration. The novel ECG system developed in this study holds promise to greatly accelerate other cardiovascular studies and drug screening using zebrafish.

category: bioengineering


title: Real-time monitoring of drug pharmacokinetics within tumor tissue in live animals

abstract: The efficacy and safety of a chemotherapy regimen fundamentally depends on its pharmacokinetics. This is currently measured based on blood samples, but the abnormal vasculature and physiological heterogeneity of the tumor microenvironment can produce radically different drug pharmacokinetics relative to the systemic circulation. We have developed an implantable microelectrode array sensor that can collect such tissue-based pharmacokinetic data by simultaneously measuring intratumoral pharmacokinetics from multiple sites. We employ gold nanoporous microelectrodes that maintain robust sensor performance even after repeated tissue implantation and extended exposure to the tumor microenvironment. We demonstrate continuous in vivo monitoring of concentrations of the chemotherapy drug doxorubicin at multiple tumor sites in a rodent model, and demonstrate clear differences in pharmacokinetics relative to the circulation that could meaningfully affect drug efficacy and safety. This platform could prove valuable for preclinical in vivo characterization of cancer therapeutics, and may offer a foundation for future clinical applications.


title: A scalable, multi-wavelength, broad bandwidth frequency-domain near-infrared spectroscopy platform for real-time quantitative tissue optical imaging

abstract: Frequency-domain near-infrared spectroscopy (FD-NIRS) provides quantitative noninvasive measurements of tissue optical absorption and scattering, and provides a safe and accurate method for characterizing tissue composition and metabolism. However, the poor scalability and high complexity of most FD-NIRS systems assembled to date have contributed to its limited clinical impact. To address these shortcomings, we present a scalable, digital-based FD-NIRS platform capable of measuring optical properties and tissue chromophore concentrations in real-time. The system provides single-channel FD-NIRS amplitude/phase, optical property, and chromophore data at a maximum display rate of 36.6 kHz, 17.9 kHz, and 10.2 kHz, respectively, and can be scaled to multiple channels as well as integrated into a handheld format. The entire system is enabled by several innovations including an ultra-high-speed k-nearest neighbor lookup table method (maximum of 250,000 inversions/s for large 2500x700 table of absorption and reduced scattering coefficients), embedded FPGA and CPU high-speed co-processing, and high-speed data transfer (due to on-board processing). We show that our 6-wavelength, broad modulation bandwidth (1-400 MHz) system can be used to perform 2D high-density spatial mapping of optical properties.


title: RNA modification mapping with JACUSA2

abstract: A whole series of high-throughput antibody-free methods for RNA modification detection from sequencing data emerged lately. We present JACUSA2 as a versatile software solution and comprehensive analysis framework for RNA modification detection assays that are based on either the Illumina or Nanopore platform. Importantly, JACUSA2 can integrate information from multiple experiments (e.g. replicates and different conditions) and different library types (e.g. first- or secondstrand libraries). We demonstrate its utility by example, showing three analysis workflows for m6A detection on published data sets: 1) MazF m6a-sensitive RNA digestion (FTO+ vs FTO-), 2) DART-seq (YTHwt vs YTHmut) and 3) Nanopore profiling (METTL3 +/+ vs -/-). All assays have been conducted in HEK293 cells and complement one another.


title: Combining Attention-based Multiple Instance Learning and Gaussian Processes for CT Hemorrhage Detection

abstract: Intracranial hemorrhage (ICH) is a life-threatening emergency with high rates of mortality and morbidity. Rapid and accurate detection of ICH is crucial for patients to get a timely treatment. In order to achieve the automatic diagnosis of ICH, most deep learning models rely on huge amounts of slice labels for training. Unfortunately, the manual annotation of CT slices by radiologists is time-consuming and costly. To diagnose ICH, in this work, we propose to use an attention-based multiple instance learning (Att-MIL) approach implemented through the combination of an attention-based convolutional neural network (Att-CNN) and a variational Gaussian process for multiple instance learning (VGP-MIL). Only labels at scan-level are necessary for training. Our method trains the model using scan labels and assigns each slice with an attention weight, which can be used to provide slice-level predictions, and uses the VGPMIL model based on low-dimensional features extracted by the Att-CNN to obtain improved predictions both at slice and scan levels. To analyze the performance of the proposed approach, our model has been trained on 1150 scans from an RSNA dataset and evaluated on 490 scans from an external CQ500 dataset. Our method outperforms other methods using the same scan-level training and is able to achieve comparable or even better results than other methods relying on slicelevel annotations.


title: Single cell tools for WormBase

abstract: We present two web apps for interactively performing common tasks with single cell RNA sequencing data: scdefg for interactive differential expression and wormcells-viz for visualization of gene expression. We made these tools available with public C. elegans datasets curated by WormBase at single-cell.wormbase.org. They can also be readily deployed for use with any other datasets using the source code available at github.com/WormBase/scdefg and at github.com/WormBase/wormcells-viz.


title: Using Progressive Context Encoders for Anomaly Detection in Digital Pathology Images

abstract: Whole slide imaging (WSI) is transforming the practice of pathology, converting a qualitative discipline into a quantitative one. However, one must exercise caution in interpreting algorithm assertions, particularly in pathology where an incorrect classification could have profound impacts on a patient, and rare classes exist that may not have been seen by the algorithm during training. A more robust approach would be to identify areas of an image for which the pathologist should concentrate their effort to make a final diagnosis. This anomaly detection strategy would be ideal for WSI, but given the extremely high resolution and large file sizes, such an approach is difficult. Here, we combine progressive generative adversarial networks with a flexible adversarial autoencoder architecture capable of learning the "normal distribution" of WSIs of normal skin tissue at extremely high resolution and demonstrate its anomaly detection performance. Our approach yielded pixel-level accuracy of 89% for identifying melanoma, suggesting that our label-free anomaly detection pipeline is a viable strategy for generating high quality annotations - without tedious manual segmentation by pathologists. The code is publicly available at https://github.com/Steven-N-Hart/P-CEAD.

category: pathology


title: An executive center for the intake of liquids

abstract: It has long been known that orofacial movements for feeding can be triggered, coordinated, and often rhythmically organized at the level of the brainstem, without input from higher centers. We uncover two nuclei that can organize the movements for ingesting fluids in mammals. These neuronal groups, defined by unique transcriptional codes and developmental origins, IRtPhox2b and Peri5Atoh1, are located, respectively, in the intermediate reticular formation of the medulla and around the motor nucleus of the trigeminal nerve. They are premotor to all jaw-opening and tongue muscles. Stimulation of either, in awake animals, opens the jaw, while IRtPhox2b alone also protracts the tongue. Moreover, stationary stimulation of IRtPhox2b entrains a rhythmic alternation of tongue protraction and retraction, synchronized with jaw opening and closing, that mimics lapping. Finally, fiber photometric recordings show that IRtPhox2b is active during volitional lapping. Our study identifies one of the long hypothesized subcortical nuclei underpinning a stereotyped feeding behavior.


title: Historical climate change and megafaunal extinctions linked to genetic diversity declines in shorebirds

abstract: The impact of accelerated climate change on extinction risk is not well-characterised despite its increasing relevance. Comparative genomics of extinct versus extant species might be useful in elucidating broad trends in faunal endangerment. We investigated fluctuations in genetic diversity and extinction timing in our genomic dataset of nine species of particularly vulnerable migratory shorebirds (Numenius), including two species widely thought to be extinct. Most species faced generally sharp declines in effective population sizes, a proxy for genetic diversity, soon after the Last Glacial Maximum. During this time, a warming climate supported forest expansions at the expense of open habitats, exacerbated by human-induced mass extinctions of megafauna only a few thousand years prior, resulting in unprecedented reductions in shorebird breeding habitat. Species breeding in temperate regions, where they widely overlap with human populations, have been most strongly affected. Late Quaternary events can exert long-lasting effects on some species' susceptibility to extinction. Genomic inquiry is crucial in informing conservation actions in the fight against ongoing biodiversity loss.

category: evolutionary biology


title: 3D printed lung on a chip device with a stretchable nanofibrous membrane for modeling ventilator induced lung injury

abstract: Mechanical ventilation is often required in patients with pulmonary disease to maintain adequate gas exchange. Despite improved knowledge regarding the risks of over ventilating the lung, ventilator induced lung injury (VILI) remains a major clinical problem due to inhomogeneities within the diseased lung itself as well as the need to increase pressure or volume of oxygen to the lung as a life-saving measure. VILI is characterized by increased physical forces exerted within the lung, which results in cell death, inflammation and long-term fibrotic remodeling. Animal models can be used to study VILI, but it is challenging to distinguish the contributions of individual cell types in such a setup. In vitro models, which allow for controlled stretching of specific lung cell types have emerged as a potential option, but these models and the membranes used in them are unable to recapitulate some key features of the lung such as the 3D nanofibrous structure of the alveolar basement membrane while also allowing for cells to be cultured at an air liquid interface (ALI) and undergo increased mechanical stretch that mimics VILI. Here we develop a lung on a chip device with a nanofibrous synthetic membrane to provide ALI conditions and controllable stretching, including injurious stretching mimicking VILI. The lung on a chip device consists of a thin (i.e. [~]20 {micro}m) stretchable poly(caprolactone) (PCL) nanofibrous membrane placed between two channels fabricated in polydimethylsiloxane (PDMS) using 3D printed molds. We demonstrate that this lung on a chip device can be used to induce mechanotrauma in lung epithelial cells due to cyclic pathophysiologic stretch ([~]25%) that mimics clinical VILI. Pathophysiologic stretch induces cell injury and subsequently cell death, which results in loss of the epithelial monolayer, a feature mimicking the early stages of VILI. We also validate the potential of our lung on a chip device to be used to explore cellular pathways known to be altered with mechanical stretch and show that pathophysiologic stretch of lung epithelial cells causes nuclear translocation of the mechanotransducers YAP/TAZ. In conclusion, we show that a breathable lung on a chip device with a nanofibrous membrane can be easily fabricated using 3D printing of the lung on a chip molds and that this model can be used to explore pathomechanisms in mechanically induced lung injury.


title: RAFFT: Efficient prediction of RNA folding pathways using the fast Fourier transform

abstract: We propose a novel heuristic to predict RNA secondary structure formation pathways that has two components: (i) a folding algorithm and (ii) a kinetic ansatz. This heuristic is inspired by the kinetic partitioning mechanism, by which molecules follow alternative folding pathways to their native structure, some much faster than others. Similarly, our algorithm RAFFT starts by generating an ensemble of concurrent folding pathways ending in multiple metastable structures, which is in contrast with traditional thermodynamic approaches that find single structures with minimal free energies. When we constrained the algorithm to predict only 50 structures per sequence, nearnative structures were found for RNA molecules of length [≤] 200 nucleotides. Our heuristic has been tested on the coronavirus frameshifting stimulation element (CFSE): an ensemble of 68 distinct structures allowed us to produce complete folding kinetic trajectories, whereas known methods require evaluating millions of sub-optimal structures to achieve this result. Thanks to the fast Fourier transform on which RAFFT is based, these computations are efficient, with complexity [O](L2 log L).


title: HAPPILEE: The Harvard Automated Processing Pipeline In Low Electrode Electroencephalography, a standardized software for low density EEG and ERP data

abstract: Low-density Electroencephalography (EEG) recordings (e.g. fewer than 32 electrodes) are widely-used in research and clinical practice and enable scalable brain function measurement across a variety of settings and populations. Though a number of automated pipelines have recently been proposed to standardize and optimize EEG preprocessing for high-density systems with state-of-the-art methods, few solutions have emerged that are compatible with low-density systems. However, low-density data often include long recording times and/or large sample sizes that would benefit from similar standardization and automation with contemporary methods. To address this need, we propose the HAPPE In Low Electrode Electroencephalography (HAPPILEE) pipeline as a standardized, automated pipeline optimized for EEG recordings with low density channel layouts of any size. HAPPILEE processes task-free (e.g. resting-state) and task-related EEG, and event-related potential (ERP) data, from raw files through a series of processing steps including filtering, line noise reduction, bad channel detection, artifact rejection from continuous data, segmentation, and bad segment rejection that have all been optimized for low density data. HAPPILEE also includes post-processing reports of data and pipeline quality metrics to facilitate the evaluation and reporting of data quality and processing-related changes to the data in a standardized manner. We describe multiple approaches with both recorded and simulated EEG data to optimize and validate pipeline performance. The HAPPILEE pipeline is freely available as part of HAPPE 2.0 software under the terms of the GNU General Public License at: https://github.com/PINE-Lab/HAPPE.


title: Multivalency enhances the specificity of Fc-cytokine fusions

abstract:
The common {gamma}-chain receptor cytokines are promising immune therapies due to their central role in coordinating the proliferation and activity of various immune cell populations. One of these cytokines, interleukin (IL)-2, has potential as a therapy in autoimmunity but is limited in effectiveness by its modest specificity toward regulatory T cells (Tregs). Therapeutic ligands are often made dimeric as antibody Fc fusions to confer desirable pharmacokinetic benefits, with under-explored consequences on signaling. Here, we systematically profiled the signaling responses to a panel of wild type and mutein IL-2 molecules in various Fc fusion configurations. We used a tensor-structured dimensionality reduction scheme to decompose the responses of each cell population to each ligand over a range of time points and cytokine concentrations. We found that dimeric muteins are uniquely specific for Tregs at intermediate ligand concentrations. We then compared signaling response across all treatments to a simple, two-step multivalent binding model. Our model was able to predict cellular responses with high accuracy. Bivalent Fc fusions display enhanced specificity and potency for Tregs through avidity effects toward IL-2R. We then utilize our model to identify the potential benefits conferred by valency engineering as an additional mechanism for cytokines with optimized therapeutic benefits. In total, these findings represent a comprehensive analysis of how ligand properties, and their consequent effects on surface receptor-ligand interactions, translate to selective activation of immune cell populations. It also identifies a new route toward engineering even more selective therapeutic cytokines.

Significance StatementSignaling in off-target immune cells has hindered the effectiveness of IL-2 as an immunotherapeutic. We show that bivalent IL-2 muteins exhibit more regulatory T cell-selective signaling than monovalent forms. This altered selectivity is explained by altered surface receptor-ligand binding kinetics and can be quantitatively predicted using a multivalent binding model. Finally, our model shows that even more selective IL-2 therapies may be developed by designing cytokines in higher valency formats, revealing valency as an unexplored mechanism for engineering specific IL-2 responses.


title: Enzymatic and structural characterization of HAD5, an essential phosphomannomutase of malaria parasites

abstract: The malaria parasite Plasmodium falciparum is responsible for over 200 million infections and 400,000 deaths per year. At multiple stages during its complex life cycle, P. falciparum expresses several essential proteins tethered to its surface by glycosylphosphatidylinositol (GPI) anchors, which are critical for biological processes such as parasite egress and reinvasion of host red blood cells. Targeting this pathway therapeutically has the potential to broadly impact parasite development across several life stages. Here, we characterize an upstream component of GPI anchor biosynthesis, the putative phosphomannomutase (EC 5.4.2.8) of the parasites, HAD5 (PF3D7_1017400). We confirm the phosphomannomutase and phosphoglucomutase activity of purified recombinant HAD5. By regulating expression of HAD5 in transgenic parasites, we demonstrate that HAD5 is required for malaria parasite egress and erythrocyte reinvasion. Finally, we determine the three-dimensional crystal structure of HAD5 and identify a substrate analog that specifically inhibits HAD5, compared to orthologous human phosphomannomutases. These findings demonstrate that the GPI anchor biosynthesis pathway is exceptionally sensitive to inhibition, and that HAD5 has potential as a multi-stage antimalarial target.


title: A multi-gene region targeted capture approach to detect plant DNA in environmental samples: A case study from coastal environments

abstract: Metabarcoding of plant DNA recovered from environmental samples, termed environmental DNA (eDNA), has been used to detect invasive species, track biodiversity changes and reconstruct past ecosystems. The P6 loop of the trnL intron is the most widely utilized gene region for metabarcoding plants due to the short fragment length and subsequent ease of recovery from degraded DNA, which is characteristic of environmental samples. However, the taxonomic resolution for this gene region is limited, often precluding species level identification. Additionally, targeting gene regions using universal primers can bias results as some taxa will amplify more effectively than others. To increase the ability of DNA metabarcoding to better resolve flowering plant species (angiosperms) within environmental samples, and reduce bias in amplification, we developed a multi-gene targeted capture method that simultaneously targets 20 chloroplast gene regions in a single assay across all flowering plant species. Using this approach, we effectively recovered multiple chloroplast gene regions for three species within artificial DNA mixtures down to 0.001 ng/{micro}L of DNA. We tested the detection level of this approach, successfully recovering target genes for 10 flowering plant species. Finally, we applied this approach to sediment samples containing unknown compositions of environmental DNA and confidently detected plant species that were later verified with observation data. Targeting multiple chloroplast gene regions in environmental samples enabled species-level information to be recovered from complex DNA mixtures. Thus, the method developed here, confers an improved level of data on community composition, which can be used to better understand flowering plant assemblages in environmental samples.

category: molecular biology


title: SARS-CoV-2 Nsp14 mediates the effects of viral infection on the host cell transcriptome

abstract: Viral infection involves complex set of events orchestrated by multiple viral proteins. To identify functions of SARS-CoV-2 proteins, we performed transcriptomic analyses of cells expressing individual viral proteins. Expression of Nsp14, a protein involved in viral RNA replication, provoked a dramatic remodeling of the transcriptome that strongly resembled that observed following SARS-CoV-2 infection. Moreover, Nsp14 expression altered the splicing of more than 1,000 genes and resulted in a dramatic increase in the number of circRNAs, which are linked to innate immunity. These effects were independent of the Nsp14 exonuclease activity and required the N7-guanine-methyltransferase domain of the protein. Activation of the NFkB pathway and increased expression of CXCL8 occurred early upon Nsp14 expression. We identified IMPDH2, which catalyzes the rate-limiting step of guanine nucleotides biosynthesis, as a key mediator of these effects. Nsp14 expression caused an increase in GTP cellular levels, and the effect of Nsp14 was strongly decreased in presence of IMPDH2 inhibitors. Together, our data demonstrate an unknown role for Nsp14 with implications for therapy.


title: Three-dimensional drug screen identifies HDAC inhibitors as therapeutic agents in mTORC1-driven lymphangioleiomyomatosis

abstract:
Lymphangioleiomyomatosis (LAM) is a rare disease involving cystic lung destruction by invasive LAM cells. These cells harbor loss-of-function mutations in TSC2, conferring constitutive mTORC1 signaling. Rapamycin is the only clinically approved disease-modifying treatment, but its action is cytostatic and disease progresses upon its withdrawal. There is a critical need to identify novel agents that prevent the invasive phenotype and/or eradicate the neoplastic LAM cells. Here, we employed novel cellular and extracellular models to screen for candidate therapeutics in a physiologically relevant setting. We observed that lung-mimetic hydrogel culture of pluripotent stem cell-derived diseased cells more faithfully recapitulates human LAM biology compared to conventional culture on two-dimensional tissue culture plastic. Leveraging our culture system, we conducted a three-dimensional drug screen using a custom 800-compound library, tracking cytotoxicity and invasion modulation phenotypes at the single cell level. We identified histone deacetylase (HDAC) inhibitors as a group of anti-invasive agents that are also selectively cytotoxic towards TSC2-/- cells. Unexpectedly, we observed that next generation ATP-competitive mTORC1/2 inhibitors potentiate invasion. We determined anti-invasive effects of HDAC inhibitors to be independent of genotype, while selective cell death is mTORC1-dependent and mediated by apoptosis. Drug performance was subsequently evaluated at the single cell level in zebrafish xenografts. We observed consistent therapeutic efficacy in vivo at equivalent concentrations to those used in vitro, substantiating HDAC inhibitors as potential therapeutic candidates for pursuit in patients with LAM.

One Sentence SummaryWe performed a drug screen in 3D and discovered HDAC inhibitors exhibit therapeutic efficacy in models of the lung disease lymphangioleiomyomatosis.

category: cell biology


title: Hot and sour: parasite adaptations to honey bee body temperature and pH

abstract:
Host temperature and gut chemistry can shape resistance to parasite infection. Heat and acidity can limit trypanosomatid infection in warm-blooded hosts, and could shape infection resistance in insects as well. The colony-level endothermy and acidic guts of social bees provide unique opportunities to study how temperature and acidity shape insect-parasite associations. We compared temperature and pH tolerance between three trypanosomatid parasites from social bees and a related trypanosomatid from poikilothermic mosquitoes, which have alkaline guts.

Relative to the mosquito parasites, all three bee parasites had higher heat tolerance that reflected levels of endothermy in hosts. Heat tolerance of the honey bee parasite Crithidia mellificae was exceptional for its genus, implicating honey bee endothermy as a filter of parasite establishment. The lesser heat tolerance of the emerging Lotmaria passim suggests possible spillover from a less endothermic host. Whereas both honey bee parasites tolerated the acidic pHs found in bee intestines, mosquito parasites tolerated the alkaline conditions found in mosquito midguts, suggesting that both gut pH and temperature could structure host-parasite specificity. Elucidating how host temperature and gut pH affect infection--and corresponding parasite adaptations to these factors--could help explain trypanosomatids distribution among insects and invasion of mammals.


title: A New Likelihood-based Test for Natural Selection

abstract: We present a new statistic for testing for neutral evolution from allele frequency data summarised as a site frequency spectrum, which we call the relative likelihood neutrality test or{rho} . Classical methods of testing for natural selection, such as Tajimas D and its relatives, require the null model to have constant population size over time and therefore can confound demographic change with natural selection.{rho} can directly incorporate a null hypothesis reflecting general demographic histories. It has a natural Bayesian interpretation as an approximation to the log-probability of the null model, given the data. We use simulations to show that{rho} has greater power than Tajimas D to detect departure from neutrality for a range of scenarios of positive and negative selection. We also show how{rho} can be adapted to account for sequencing error. Application to the ACKR1 (FYO) gene in humans supported previous studies inferring positive selection in sub-Saharan populations which were based on inter-population comparisons. However, we did not find the signal of selection to be maximal in the region of the FY*O or Duffy-null allele in these populations. We also applied{rho} to investigate in greater detail a region on the 2q11.1 band of the human genome that has previously been identified as showing evidence of selection. This was done for a range of populations: for the European populations we incorporated a demographic history with a bottleneck corresponding to the putative out of Africa event. We were able to localise signals of selection to some specific regions and genes. Overall, we suggest that{rho} will be a useful tool for identifying genomic regions that may be subject to natural selection.

category: genetics


title: Combined tumor and immune signals from genomes or transcriptomes predict outcomes of checkpoint inhibition in melanoma

abstract: Cancer immunotherapy with checkpoint blockade (CPB) leads to improved outcomes in melanoma and other tumor types, but a majority of patients do not respond. High tumor mutation burden (TMB) and high levels of tumor-infiltrating T cells have been associated with response to immunotherapy, but integrative models to predict clinical benefit using DNA or RNA alone have not been comprehensively explored. We sequenced DNA and RNA from melanoma patients receiving CPB, and aggregated previously published data, yielding whole exome sequencing data for 189 patients and bulk RNA sequencing data for 178 patients. Using these datasets, we derived genomic and transcriptomic factors that predict overall survival (OS) and response to immunotherapy. Using whole-exome DNA data alone, we calculated T cell burden (TCB) and B cell burden (BCB) based on rearranged TCR/Ig DNA sequences and found that patients whose melanomas have high TMB together with either high TCB or high BCB survived longer and had higher response rates as compared to patients with either low TMB or TCB/BCB. Next, using bulk RNA-Seq data, differential expression analysis identified 83 genes associated with high or low OS. By combining pairs of immune-expressed genes with tumor-expressed genes, we identified three gene pairs associated with response and survival (Bonferroni P<0.05). All three gene pair models were validated in an independent cohort (n=180) (Bonferroni P<0.05). The best performing gene pair model included the lymphocyte-expressed MAP4K1 (Mitogen- Activated Protein Kinase Kinase Kinase Kinase 1) combined with the transcription factor TBX3 (T-Box Transcription Factor 3) which is overexpressed in poorly differentiated melanomas. We conclude that RNA-based (MAP4K1&TBX3) or DNA-based (TCB&TMB) models combining immune and tumor measures improve predictions of outcome after checkpoint blockade in melanoma.


title: Behavioral performance requirements for division of labor influence adaptive brain mosaicism in a socially complex ant

abstract: Brain evolution is hypothesized to be driven by neuroarchitectural requirements for behavioral performance. Assessments of such needs should be informed by the nature of sensory and motor processes underpinning behavior. We developed a novel metric to estimate the relative neuroanatomical investments required to perform tasks varying in sensorimotor and processing demands across polymorphic and polyethic workers of the leafcutter ant Atta cephalotes and quantified brain size and structure to examine their correspondence with our computational approximations. Investment in multi-sensory integration and motor requirements for task performance was estimated to be greatest for media workers whose leaf-harvesting repertoire involves the most diverse and demanding sensory and motor processes, including plant discrimination, leaf cutting, and fragment transportation. Volumetric analysis of confocal brain images revealed that absolute brain size increased with worker size and compartmental scaling allometries among functionally specialized brain compartments differed among polymorphic workers. The mushroom bodies, centers of sensory integration and learning, and the antennal lobes, which process olfactory inputs, were significantly larger in medias than in minim workers (fungal gardeners) and major workers ("soldiers"), which had lower estimated task-related neural demands. Minims had a proportionally larger central complex, perhaps to control navigation in subterranean fungal garden chambers. These results indicate that variation in task performance requirements has selected for adaptive variation in brain size and mosaic scaling.


title: Allotypic variation in antigen processing controls antigenic peptide generation from SARS-CoV-2 S1 Spike Glycoprotein

abstract: Population genetic variability in immune system genes can often underlie variability in immune responses to pathogens. Cytotoxic T-lymphocytes are emerging as critical determinants of both SARS-CoV-2 infection severity and long-term immunity, either after recovery or vaccination. A hallmark of COVID-19 is its highly variable severity and breadth of immune responses between individuals. To address the underlying mechanisms behind this phenomenon we analyzed the proteolytic processing of S1 spike glycoprotein precursor antigenic peptides by 10 common allotypes of ER aminopeptidase 1 (ERAP1), a polymorphic intracellular enzyme that can regulate cytotoxic T-lymphocyte responses by generating or destroying antigenic peptides. We utilized a systematic proteomic approach that allows the concurrent analysis of hundreds of trimming reactions in parallel, thus better emulating antigen processing in the cell. While all ERAP1 allotypes were capable of producing optimal ligands for MHC class I molecules, including known SARS-CoV-2 epitopes, they presented significant differences in peptide sequences produced, suggesting allotype-dependent sequence biases. Allotype 10, previously suggested to be enzymatically deficient, was rather found to be functionally distinct from other allotypes. Our findings suggest that common ERAP1 allotypes can be a major source of heterogeneity in antigen processing and through this mechanism contribute to variable immune responses to COVID-19.

category: biochemistry


title: Accelerating leaf area measurement using a volumetric approach

abstract: Despite the advances in the techniques of indirect estimation of leaf area, the destructive measurement approaches have still remained as the reference and the most accurate methods. However, even utilizing the modern sensors and applications usually requires the laborious and time-consuming practice of unfolding and analyzing the single leaves, separately. In the present study, a volumetric approach was tested to determine the pile leaf area based on the ratio of leaf volume divided by thickness. For this purpose, the suspension technique was used for volumetry, which is based on the simple practice and calculations of the Archimedes principle. The results indicated that the wheat volumetric leaf area (VLA), had an approximately 1:1 correlation with the conventionally measured optical leaf area (OLA). Exclusion of the midrib volume from calculations, did not affect the estimation error (i.e. NRMSE less than 2.61%); however, improved the slope of the linear model by about 6%. The error of sampling for determining the mean leaf thickness of the pile, was also less than 2% throughout the season. Besides, a more practical and facilitated version of the pile volumetry was tested using a Specific Gravity Bench (SGB), which is currently available as a laboratory equipment. As an important observation, which was also expectable according to the 3D shape of the leaf (i.e. expansion in a 2D plane), it was evidenced that the variations in the OLA exactly follows the pattern of the changes in the leaf volume. Accordingly, it was suggested that the relative leaf areas of various experimental treatments may be compared directly based on the volume, and independently of leaf thickness. Furthermore, no considerable difference was observed among the OLAs measured using various image resolutions (NRMSE < 0.212%); which indicates that even the current superfast scanners with low resolutions as 200 dpi may be used for a precision optical measurement of leaf area. It is expected that utilizing the reliable and simple concept of volumetric leaf area, based on which the measurement time may be independent of the sample size, facilitate the laborious practice of leaf area measurement; and consequently, improve the precision of the field experiments.

category: plant biology


title: Amyloid-β and tau pathologies relate to distinctive brain dysconnectomics in preclinical autosomal-dominant Alzheimer's disease

abstract:
The human brain is composed of functional networks that have a modular topology, where brain regions are organized into communities that form internally dense (segregated) and externally sparse (integrated) subnetworks that underlie higher-order cognitive functioning. It is hypothesized that amyloid-{beta} and tau pathology in preclinical Alzheimers disease (AD) spread through functional networks, disrupting neural communication that results in cognitive dysfunction. We used high-resolution (voxel-level) graph-based network analyses to test whether in vivo amyloid-{beta} and tau burden was associated with the segregation and integration of brain functional connections, and episodic memory, in cognitively-unimpaired Presenilin-1 E280A carriers who are expected to develop early-onset AD dementia in approximately 13 years on average. Compared to non-carriers, mutation carriers exhibited less functional segregation and integration in posterior default-mode network (DMN) regions, particularly the precuneus, and in the retrospenial cortex, which has been shown to link medial temporal regions and cortical regions of the DMN. Mutation carriers also showed greater functional segregation and integration in regions connected to the salience network, including the striatum and thalamus. Greater tau burden was associated with lower segregated and integrated functional connectivity of DMN regions, particularly the precuneus and medial prefrontal cortex. In turn, greater tau pathology was related to higher segregated and integrated functional connectivity in the retrospenial cortex, and the anterior cingulate cortex, a hub of the salience network. These findings enlighten our understanding of how AD-related pathology distinctly alters the brains functional architecture in the preclinical stage, possibly contributing to pathology propagation and ultimately resulting in dementia.

SIGNIFICANCE STATEMENTAmyloid-{beta} and tau pathologies in Alzheimers disease (AD) are hypothesized to propagate through functional networks. Research is needed to elucidate how AD-related pathologies alter the brains functional connections years before symptom-onset to help predict pathology accumulation and dementia risk. Using high-resolution (voxel-level) graph-based network analyses and PET imaging, we showed that greater tau burden was associated with largely dysconnectivity of posterior default-mode network brain regions, and increased connectivity of structures associated with the salience network and others that are critical for integrating information across neural systems in cognitively-unimpaired Presenilin-1 E280A carriers. Findings enlighten how amyloid-{beta} and tau relate to distinct patterns of functional connectivity in regions that underlie memory functioning and are critical for information processing, helping predict disease progression.


title: Neuronal activity drives pathway-specific depolarization of astrocyte distal processes

abstract:
Astrocytes are glial cells that interact with neuronal synapses via their distal processes, where they remove glutamate and potassium (K+) from the extracellular space following neuronal activity. Astrocyte clearance of both glutamate and K+ is voltage-dependent, but astrocyte membrane potential (Vm) has been thought to be largely invariant. As a result, these voltage-dependencies have not been considered relevant to astrocyte function. Using genetically encoded voltage indicators enabling the measurement of Vm at distal astrocyte processes (DAPs), we report large, rapid, focal, and pathway-specific depolarizations in DAPs during neuronal activity. These activity-dependent astrocyte depolarizations are driven by action potential-mediated presynaptic K+ efflux and electrogenic glutamate transporters. We find that DAP depolarization inhibits astrocyte glutamate clearance during neuronal activity, enhancing neuronal activation by glutamate. This represents a novel class of sub-cellular astrocyte membrane dynamics and a new form of astrocyte-neuron interaction.

One Sentence SummaryGenetically encoded voltage imaging of astrocytes shows that presynaptic neuronal activity drives focal astrocyte depolarization, contributing to activity-dependent inhibition of glutamate uptake.


title: Single-cell analysis uncovers differential regulation of lung γδ T cell subsets by the co-inhibitory molecules, PD-1 and TIM-3

abstract: IL-17A-producing {gamma}{delta} T cells within the lung consist of both V{gamma}6+ tissue-resident cells and V{gamma}4+ circulating cells that play important roles in homeostasis, inflammation, infection, tumor progression and metastasis. How these {gamma}{delta} T cell subsets are regulated in the lung environment during homeostasis and cancer remains poorly understood. Using single-cell RNA sequencing and flow cytometry, we show that lung V{gamma}6+ cells express a repertoire of cell surface molecules distinctive from V{gamma}4+ cells, including PD-1 and ICOS. We found that PD-1 functions as a co-inhibitory molecule on V{gamma}6+ cells to reduce IL-17A production, whereas manipulation of ICOS signaling fails to affect IL-17A in V{gamma}6+ cells. In a mammary tumor model, ICOS and PD-1 expression on lung V{gamma}6+ cells remained stable. However, V{gamma}6+ and V{gamma}4+ cells within the lung pre-metastatic niche increased expression of IL-17A, IL-17F, amphiregulin (AREG) and TIM-3 in response to tumor-derived IL-1{beta} and IL-23, where the upregulation of TIM-3 was specific to V{gamma}4+ cells. Inhibition of either PD-1 or TIM-3 in mammary tumor-bearing mice further increased IL-17A by V{gamma}6+ and V{gamma}4+ cells, indicating that both PD-1 and TIM-3 function as negative regulators of IL-17A-producing {gamma}{delta} T cell subsets. Together, these data demonstrate how lung {gamma}{delta} T cell subsets are differentially controlled by co-inhibitory molecules in steady-state and cancer.


title: Network-based identification and pharmacological targeting of host cell master regulators induced by SARS-CoV-2 infection

abstract: Precise characterization and targeting of host cell transcriptional machinery hijacked by SARS-CoV-2 remains challenging. To identify therapeutically targetable mechanisms that are critical for SARS-CoV-2 infection, here we elucidated the Master Regulator (MR) proteins representing mechanistic determinants of the gene expression signature induced by SARS-CoV-2. The analysis revealed coordinated inactivation of MR-proteins linked to regulatory programs potentiating efficiency of viral replication (detrimental host MR-signature) and activation of MR-proteins governing innate immune response programs (beneficial MR-signature). To identify MR-inverting compounds capable of rescuing activity of inactivated host MR-proteins, with-out adversely affecting the beneficial MR-signature, we developed the ViroTreat algorithm. Overall, >80% of drugs predicted to be effective by this methodology induced significant reduction of SARS-CoV-2 infection, without affecting cell viability. ViroTreat is fully generalizable and can be extended to identify drugs targeting the host cell-based MR signatures induced by virtually any pathogen.


title: Consistent changes in the intestinal microbiota of Atlantic salmon fed insect meal diets

abstract: Being part of fishs natural diets, insects have become a realistic, sustainable feed ingredient for aquaculture. While nutritional values of insects have been extensively studied in various fish species, their impact on the fish microbiota remains to be fully explored. In an 8-week freshwater feeding trial, Atlantic salmon (Salmo salar) were fed either a commercially relevant reference diet or an insect meal diet wherein black soldier fly (Hermetia illucens) larvae meal comprised 60% of total ingredients. Microbiota of digesta and mucosa origin from the proximal and distal intestine were collected and profiled along with feed and water samples. The insect meal diet markedly modulated the salmon intestinal microbiota. Overall, the microbial diversity was lower in the digesta of salmon fed the insect meal diet but higher in the mucosa. A group of bacterial genera, dominated by members of the Bacillaceae family, was enriched in salmon fed the insect meal diet, which confirms our previous findings in a seawater feeding trial. We also found that microbiota in the intestine closely resembled that of the feeds but was distinct from the water microbiota. Notably, bacterial genera associated with the diet effects were present in the feeds as well. In conclusion, our results show consistent changes in the intestinal microbiota of Atlantic salmon fed diets containing black soldier fly larvae meal.


title: Cystathionine-β-synthase is essential for AKT-induced senescence and suppresses the development of gastric cancers with PI3K/AKT activation

abstract: Hyperactivation of oncogenic pathways downstream of RAS and PI3K/AKT in normal cells induces a senescence-like phenotype that acts as a tumor-suppressive mechanism that must be overcome during transformation. We previously demonstrated that AKT-induced senescence (AIS) is associated with profound transcriptional and metabolic changes. Here, we demonstrate that human fibroblasts undergoing AIS display increased Cystathionine-{beta}-synthase (CBS) expression and consequent activation of the transsulfuration pathway controlling hydrogen sulfide (H2S) and glutathione (GSH) metabolism. Activated transsulfuration pathway during AIS maintenance enhances the antioxidant capacity, protecting senescent cells from ROS-induced cell death via GSH and H2S. Importantly, CBS depletion allows cells that have undergone AIS to escape senescence and re-enter the cell cycle, indicating the importance of CBS activity in maintaining AIS. Mechanistically, we show this restoration of proliferation is mediated through suppressing mitochondrial respiration and reactive oxygen species (ROS) production and increasing GSH metabolism. These findings implicate a potential tumor-suppressive role for CBS in cells with inappropriately activated PI3K/AKT signaling. Consistent with this concept, in human gastric cancer cells with activated PI3K/AKT signaling, we demonstrate that CBS expression is suppressed due to promoter hypermethylation. CBS loss cooperates with activated PI3K/AKT signaling in promoting anchorage-independent growth of gastric epithelial cells, while CBS restoration suppresses the growth of gastric tumors in vivo. Taken together, we find that CBS is a novel regulator of AIS and a potential tumor suppressor in PI3K/AKT-driven gastric cancers, providing a new exploitable metabolic vulnerability in these cancers.


title: Primary cilia drive postnatal tidemark patterning in articular cartilage by coordinating responses to Indian Hedgehog and mechanical load

abstract: Articular cartilage (AC) is essential for body movement, but is highly susceptible to degenerative diseases and has poor self-repair capacity. To improve current subpar regenerative treatment, developmental mechanisms of AC should be clarified and, specifically, how postnatal multi-zone organization is acquired. Primary cilia are cell surface organelles crucial for mammalian tissue morphogenesis and while the importance of chondrocyte primary cilia is well appreciated their specific roles in postnatal AC morphogenesis remain unclear. To explore these mechanisms, we used a murine conditional loss-of-function approach (Ift88-flox) targeting joint-lineage progenitors (Gdf5Cre) and monitored postnatal knee AC development. Joint formation and growth up to juvenile stages were largely unaffected, however mature AC (aged 2 months) exhibited disorganized extracellular matrix, decreased aggrecan and collagen II due to reduced gene expression (not increased catabolism), and marked reduction of AC modulus by 30-50%. In addition, we discovered the surprising findings that tidemark patterning was severely disrupted and accompanied alterations in hedgehog signaling that were also dependent on regional load-bearing functions of AC. Interestingly, Prg4 expression was also increased in those loaded sites. Together, our data provide evidence that primary cilia orchestrate postnatal AC morphogenesis, dictating tidemark topography, zonal matrix composition and mechanical load responses.

category: developmental biology


title: Impact of cilia-related genes on mitochondrial dynamics during Drosophila spermatogenesis

abstract: Spermatogenesis is a dynamic process of cellular differentiation that generates the mature spermatozoa required for reproduction. Errors that arise during this process can lead to sterility due to low sperm counts and malformed or immotile sperm. While is estimated that 1 out of 7 couples encounter infertility, the underlying cause of male infertility can only be identified in 50% of cases. Here, we describe and examine the genetic requirements for missing minor mitochondria (mmm), sterile affecting ciliogenesis (sac), and testes of unusual size (tous), three previously uncharacterized genes that are predicted to be components of the flagellar axoneme. Using Drosophila, we demonstrate that these genes are essential for male fertility and that loss of mmm, sac, or tous results in complete immotility of the sperm flagellum. Cytological examination uncovered additional roles for sac and tous during cytokinesis and transmission electron microscopy of developing spermatids in mmm, sac, and tous mutant animals revealed defects associated with mitochondria and the accessory microtubules required for the proper elongation of the mitochondria and flagella during ciliogenesis. This study highlights the complex interactions of cilia-related proteins within the cell body and advances our understanding of male infertility by uncovering novel mitochondrial defects during spermatogenesis.


title: Invasive grass causes biotic homogenization in wetland birds

abstract: Plant invasions often lead to homogenization of the plant community, but the potential for plant invasions to cause homogenization of other trophic levels is under-studied in many systems. We tested whether the bird community in Phragmites australis-invaded marsh would exhibit spatial and temporal taxonomic homogenization compared to remnant cattail and meadow marsh. We compared the bird community using marsh invaded by P. australis and remnant, uninvaded marsh vegetation in a year with average water depths and a year with above-average water depths in the coastal marshes of a World Biosphere Reserve. Our results demonstrate strong evidence for spatial and temporal homogenization of the wetland bird community following P. australis invasion. The birds present in P. australis-invaded marsh were a nested subset of those present in remnant marsh, and total beta diversity decreased when water depths were above average. In contrast, total beta diversity was high in remnant marsh vegetation and stable between the two years. The distinctively structured vegetation zones in remnant (uninvaded) marsh yields structural complexity and habitat heterogeneity that supports greater taxonomic turnover in the bird community. Our study provides evidence that invasion by a plant has resulted in biological homogenization of the wetland bird community.


title: Bark beetles locate fungal symbionts by detecting volatile fungal metabolites of host tree resin monoterpenes

abstract: Outbreaks of bark beetles have decimated millions of hectares of conifer forest worldwide in recent years. The ability of these tiny 3-6 mm long insects to kill mature trees over a short period has been ascribed to two factors: (1) mass attacks on the host tree to overcome tree defenses and (2) the presence of fungal symbionts that support successful beetle development in the tree. While the role of pheromones in coordinating mass attacks has been well studied, the role of chemical communication in maintaining the fungal symbiosis is poorly understood. We previously demonstrated that Eurasian spruce bark beetles (Ips typographus) can recognize beneficial fungal symbionts of the genera Grosmannia, Endoconidiophora and Ophiostoma by their de novo synthesized volatile compounds. We hypothesized that the fungal symbionts of the bark beetles might metabolize spruce resin monoterpenes of the beetles host tree, Norway spruce (Picea abies), and that the volatile products could be used as cues by beetles for locating breeding sites with beneficial symbionts. Grosmannia penicillata and other fungal symbionts altered the profile of spruce bark volatiles by converting the major monoterpenes to oxygenated derivatives. Bornyl acetate was metabolized to camphor, and - and {beta}-pinene to trans-4-thujanol and other oxygenated products. Extensive electrophysiological measurements showed that bark beetles possess olfactory sensory neurons that are selective for these oxygenated symbiont metabolites. Compounds such as camphor and trans-4-thujanol attracted beetles at specific doses in olfactory experiments and stimulated the response of female beetles to a mixture of pheromones. Finally, the fungal symbiont was found to stimulate bark beetle tunneling on diets. Collectively, our results show that oxygenated metabolites of conifer monoterpenes produced by fungal symbionts are used by bark beetles as cues to find these essential microbial symbionts. The oxygenated metabolites may aid beetles in assessing the presence of the fungus, the defense status of the host tree and the density of conspecifics at potential feeding and breeding sites.


title: Promoter architecture links gene duplication with transcriptional divergence

abstract:
Gene duplication is thought to be a central mechanism in evolution to gain new functions, but gene families vary greatly in their rates of gene duplication and long-term retention. Here, we discover a link between the promoter architecture of vertebrate genes and their rate of duplication: Genes that harbor CpG Islands in their promoters (CGI genes) - nearly 60% of our genes - have rarely duplicated in recent evolutionary times, and most CGI gene duplication events predate the emergence of CGI as a major regulatory element of vertebrate genes. In contrast, CGI-less genes predominate duplications that have occurred since the divergence of vertebrates. Furthermore, CGI-less paralogs are transcriptionally more divergent than CGI paralogs, even when comparing CGI and CGI-less paralogs that have duplicated at similar evolutionary times - suggesting greater capacity of CGI-less promoters to enable divergence in expression. This higher divergence between CGI-less paralogs is also reflected in lower similarity of transcription factors that bind to the promoters of CGI-less paralog pairs in comparison with CGI paralogs. Finally, CGI-less paralogs have a greater tendency to sub- and neo-functionalize, and they transcriptionally diversify faster following duplication. Our results highlight the links between promoter architecture, gene expression plasticity and their impact on gene expansion, and unravel an unappreciated role of CGI elements in shaping genome evolution.

Significance statementGene duplication generates extra gene copies, providing material for evolution of new functions. However, many duplicated genes are eliminated due to functional and regulatory constraints. The evolutionary processes that govern the elimination and persistence of duplicated genes are not well understood. Here, we focus on CpG Islands (CGIs) - important elements that occur in the majority of gene promoters. We show that genes with CGIs in their promoters have duplicated almost exclusively in ancient times, and nearly all recent duplications involve CGI-less genes. Furthermore, duplicated CGI-less genes diverge more in expression and display more distinctive transcription and cis-regulation compared to duplicated CGI-genes. Our results demonstrate how promoter structure influences transcriptional evolvability and, in turn, the retention of new genes.


title: eQTL mapping using allele-specific gene expression

abstract: Using information from allele-specific gene expression (ASE) can sub-stantially improve the power to map gene expression quantitative trait loci (eQTLs). However, such practice has been limited, partly due to high computational cost and the requirement to access raw data that can take a large amount of storage space. To address these computational challenges, we have developed a computational framework that uses a statistical method named TReCASE as its computational engine, and it is computationally feasible for large scale analysis. We applied it to map eQTLs in 28 human tissues using the data from the Genotype-Tissue Expression (GTEx) project. Compared with a popular linear regression method that does not use ASE data, TReCASE can double the number of eGenes (i.e., genes with at least one significant eQTL) when sample size is relatively small, e.g., n = 200. We also demonstrated how to use the ASE data that we have collected to study dynamic eQTLs whose effect sizes vary with respect to another variable, such as age. We find the majority of such dynamic eQTLs are due to some underlying latent factors, such as cell type proportions. We further compare TReCASE versus another method RASQUAL. TReCASE is ten times or more faster than RASQUAL and it provides more robust type I error control.


title: Synchronized swarming: Harmonic convergence and acoustic mating dynamics in the malaria mosquito Anopheles gambiae

abstract: The mosquito Anopheles gambiae is a major African malaria vector, transmitting parasites responsible for significant mortality and disease burden. Malaria declines have stagnated recently due to widespread insecticide resistance among vector populations. Flight acoustics are essential to mosquito mating biology and represent promising alternative targets for mosquito control. However, mosquito swarm acoustics data are limited. Here, for the first time, we present detailed analyses of free-flying male and female An. gambiae flight tones and their harmonization (harmonic convergence) over a complete swarm sequence. Audio analysis of single-sex swarms showed elevated male or female flight tone frequencies and amplitudes during swarming flight with gradual declines to pre-swarm levels over an approximately 35-min period. Analysis of mixed-sex swarms revealed additional increases in flight tone frequencies and amplitudes due to mating activity. Data from mixed-sex swarms suggest harmonic convergence during swarming enhances the efficiency of female detection by synchronizing male and female baseline swarm tones. Further, data from experiments using female swarm tone playbacks to males indicate that harmonic convergence during mating interactions coordinates male scramble competition by acoustically masking mating couple flight tones. These findings advance our knowledge of mosquito swarm acoustics, providing vital information for reproductive control strategies.


title: Quantifying unusual neurological movement phenotypes in collective movement phenotypes

abstract: Building models of anomalous behaviour in animals is important for monitoring animal welfare as well as assessing the efficacy of therapeutic interventions in preclinical trials. In this paper, we describe methods that allow for the automatic discrimination of sheep with a genetic mutation that causes Batten disease from an age-matched control group, using GPS movement traces as input. Batten disease is an autosomal recessive lysosomal storage abnormality with symptoms that are likely to affect the way that those with it move and socialise, including loss of vision and dementia. The sheep in this study displayed a full range of symptoms and during the experiment, the sheep were mixed with a large group of younger animals. We used data obtained from bespoke raw data GPS sensors carried by all animals, with a sampling rate of 1 sample/second and a positional accuracy of around 30cm. The distance covered in each ten minute period and, more specifically, outliers in each period, were used as the basis for estimating the abnormal behaviour. Our results show that, despite the variability in the sample, the bulk of the outliers during the period of observation across six days came from the sheep with Batten disease. Our results point towards the potential of using relatively simple movement metrics in identifying the onset of a phenotype in symptomatically similar conditions.


title: Accurate Automatic Glioma Segmentation in Brain MRI images Based on CapsNet

abstract: Glioma is a highly invasive type of brain tumor with an irregular morphology and blurred infiltrative borders that may affect different parts of the brain. Therefore, it is a challenging task to identify the exact boundaries of the tumor in an MR image. In recent years, deep learning-based Convolutional Neural Networks (CNNs) have gained popularity in the field of image processing and have been utilized for accurate image segmentation in medical applications. However, due to the inherent constraints of CNNs, tens of thousands of images are required for training, and collecting and annotating such a large number of images poses a serious challenge for their practical implementation. Here, for the first time, we have optimized a network based on the capsule neural network called SegCaps, to achieve accurate glioma segmentation on MR images. We have compared our results with a similar experiment conducted using the commonly utilized U-Net. Both experiments were performed on the BraTS2020 challenging dataset. For U-Net, network training was performed on the entire dataset, whereas a subset containing only 20% of the whole dataset was used for the SegCaps. To evaluate the results of our proposed method, the Dice Similarity Coefficient (DSC) was used. SegCaps and U-Net reached DSC of 87.96% and 85.56% on glioma tumor core segmentation, respectively. The SegCaps uses convolutional layers as the basic components and has the intrinsic capability to generalize novel viewpoints. The network learns the spatial relationship between features using dynamic routing of capsules. These capabilities of the capsule neural network have led to a 3% improvement in results of glioma segmentation with fewer data while it contains 95.4% fewer parameters than U-Net.


title: Trycycler: consensus long-read assemblies for bacterial genomes

abstract:
Assembly of bacterial genomes from long-read data (generated by Oxford Nanopore or Pacific Biosciences platforms) can often be complete: a single contig for each chromosome or plasmid in the genome. However, even complete bacterial genome assemblies constructed solely from long reads still contain a variety of errors, and different assemblies of the same genome often contain different errors. Here, we present Trycycler, a tool which produces a consensus assembly from multiple input assemblies of the same genome. Benchmarking using both simulated and real sequencing reads showed that Trycycler consensus assemblies contained fewer errors than any of those constructed with a single long-read assembler. Post-assembly polishing with Medaka and Pilon further reduced errors and yielded the most accurate genome assemblies in our study. As Trycycler can require human judgement and manual intervention, its output is not deterministic, and different users can produce different Trycycler assemblies from the same input data. However, we demonstrated that multiple users with minimal training converge on similar assemblies that are consistently more accurate than those produced by automated assembly tools. We therefore recommend Trycycler+Medaka+Pilon as an ideal approach for generating high-quality bacterial reference genomes.

Data availabilitySupplementary figures, tables and code can be found at: github.com/rrwick/Trycycler-paper

Reads, assemblies and reference sequences can be found at: bridges.monash.edu/articles/dataset/Trycycler_paper_dataset/14890734

category: bioinformatics


title: Effect of artificial light at night on sleep and metabolism in weaver birds

abstract: Artificial light at night is constantly minimizing the span of dark nights from the natural light-dark cycle of earth. Over the past century, the  lightscape of earth has completely changed owing to technological advancements which subsequently changed the lifestyle of human as well as the nearby animal species. This motivated the present study, wherein we investigated the impact of light at night (LAN) on behavior and physiology of a diurnal passerine finch, baya weaver (Ploceus philippinus). A group of bird (N=10) exposed to 12L:12D photoperiod was initially subjected to dark nights (0 lux) for a period of 10 days followed by 5 lux; night light for a span of 4 weeks. First week in LAN served as acute treatment with respect to fourth week (chronic). Acute exposure had more pronounced impact on the behavioral and physiological observations when compared with chronic treatment. The results reveal significant increase in nighttime activity, sleep loss, significant inclusion of drowsiness behavior during the day in response to LAN. Beside these behavioral alterations, changes in physiological parameters such as; reduction in body mass, loss of gradient between pre- and post-prandial blood glucose levels, elevation in plasma corticosterone levels were more prominent during acute exposure of LAN. Plasma metabolites such as triglycerides, total protein, serum glutamic-oxaloacetic transaminase (SGOT) and creatinine concentrations also hiked in response to LAN treatment. Thus, the study broadly enumerates the impact of acute and chronic exposure of LAN on behavior (rest/sleep) and physiology (metabolism) of birds.

category: zoology