title: Profile of the in silico secretome of the palm dieback pathogen, a fungus that puts natural oases at risk

abstract: Understanding biotic changes that occur alongside climate change constitute a research priority of global significance. Here, we address a plant pathogen that poses a serious threat to life on natural oases, where climate change is already taking a toll and severely impacting human subsistence. Fusarium oxysporum f. sp. albedinis is a pathogen that causes dieback disease on date palms, a tree that provides several critical ecosystem services in natural oases; and consequently, of major importance in this vulnerable habitat. Here, we assess the current state of global pathogen spread, we annotate the genome of a sequenced pathogen strain isolated from the native range and we analyse its in silico secretome. The palm dieback pathogen secretes a large arsenal of effector candidates including a variety of toxins, a distinguished profile of secreted in xylem proteins (SIX) as well as an expanded protein family with an N-terminal conserved motif [SG]PC[KR]P that could be involved in interactions with host membranes. Using agrobiodiversity as a strategy to decrease pathogen infectivity, while providing short term resilient solutions, seems to be widely overcome by the pathogen. Hence, the urgent need for future mechanistic research on the palm dieback disease and a better understanding of pathogen genetic diversity.


title: A method to quantitate maternal transcripts localized in sea urchin egg cortex by RT-qPCR with accurate normalization

abstract: The sea urchin egg cortex is a peripheral region of eggs consisting of cell membrane and adjacent cytoplasm, which contains actin and tubulin cytoskeleton, cortical granules and some proteins required for early development. Method for isolation of cortices from sea urchin eggs and early embryos has been developed in 70s of 20th Century. Since that time this method has been reliable tool to study protein localization and cytoskeletal organization in cortex of unfertilized eggs and embryos during first cleavages. This study is an estimation of reliability of RT-qPCR to analyze levels of maternal transcripts that are localized in egg cortex. Firstly, we selected seven potential reference genes, 28S, Cycb, Ebr1, GAPDH, Hmg1, Smtnl1 and Ubb, which transcripts are maternally deposited in sea urchin eggs. The candidate reference genes were ranked by five different algorithms (BestKeeper, CV, {Delta}Ct, geNorm and NormFinder) upon calculated level stability in both eggs and isolated cortices. Our results show that gene ranking differs in total RNA and mRNA samples, though Ubb is most suitable reference gene in both cases. To validate feasibility of comparative analysis of eggs and isolated egg cortices by RT-qPCR, we selected Daglb-2 as a gene of interest, which transcripts potentially localized in cortex, and found increased level of Daglb-2 in egg cortices. This suggests that proposed RNA isolation method with subsequent quantitative RT-qPCR analysis can be used to approve cortical association of transcripts in sea urchin eggs.

category: developmental biology


title: The critical role of the ventral temporal lobe in word retrieval

abstract: Deficits in word retrieval are a hallmark of a variety of neurological illnesses spanning from dementia to traumatic injuries. The role of the dominant temporal lobe in fluent naming has been characterized by lesional analyses, functional imaging, and intracranial recordings, but limitations of each of these measures preclude a clear assessment of which specific constituent of the temporal lobe is critical for naming. We studied a large cohort of patients undergoing surgical resections or laser ablations of the dominant temporal lobe for medically intractable epilepsy (n=95). These techniques are exceedingly effective for seizure control but often result in language declines, particularly in confrontation naming, which can be socio-economically disabling. We used a multivariate voxel-based lesion symptom mapping analysis to localize brain regions significantly associated with visual object naming deficits. We observed that posterior inferior temporal regions, centered around the middle fusiform gyrus, were significantly associated with a decline in confrontation naming. Furthermore, we found that the posterior margin of anterior temporal lobectomies was linearly correlated to a decline in visual naming with a clinically significant decline occurring once the resection extended 6 cm from the anterior tip of the temporal lobe. We integrated these findings with electrocorticography during naming in a subset of this population and found that the majority of cortical regions whose resection was associated with a significant decline overlapped with regions that were functionally most active prior to articulation. Importantly, these loci coincide with the sites of susceptibility artifacts during echo-planar imaging, which explains why this region has not previously been implicated. Taken together, these data highlight the crucial contribution of the posterior ventral temporal cortex in lexical access and its important role in the pathophysiology of anomia following temporal lobe resections. Surgical strategies, including the use of laser ablation to target the medial temporal lobe as well as microsurgical approaches, should attempt to preserve this region to mitigate postoperative language deficits.

category: neuroscience


title: Identification, analysis, and confirmation of seed storability-related loci in Dongxiang wild rice (Oryza rufipogon Griff.)

abstract: Dongxiang wild rice (Oryza rufipogon Griff.) (DXWR) has strong seed storability and identifying its elite gene resources may facilitate genetic improvements in rice seed storability. In this study, we developed two backcross inbred lines (BILs) populations, with DXWR as a common donor parent and two rice varieties (F6 and R974) as recipient parents. Bulked segregant analysis via whole genome sequencing (BSA-seq) was used to identify seed storability-related loci in the DXWR and F6 population. Two main genomic regions containing 18,550,000-20,870,000 bp on chromosome 4 and 7,860,000-9,780,000 bp on chromosome 9 were identified as candidate loci of DXWR seed storability; these overlapped partially with seed storability-related quantitative trait loci (QTLs) discovered in previous studies, suggesting that these loci may provide important regions for isolating the responsible genes. In total, 448 annotated genes were predicted within the identified regions, of which 274 and 82 had nonsynonymous and frameshift mutations, respectively. We detected extensive metabolic activities and cellular processes during seed storability and confirmed the effects of the seed storability-related candidate loci using four BILs from DXWR and R974. These results may facilitate the cloning of DXWR seed storability-related genes, thereby elucidating rice seed storability and its improvement potential.

category: genomics


title: Lateral Line Ablation by Toxins Results in Distinct Rheotaxis Profiles in Fish

abstract: Zebrafish lateral line is an established model for hair cell organ damage, yet few studies link mechanistic disruptions to changes in biologically relevant behavior. We used larval zebrafish to determine how damage via ototoxic chemicals impact rheotaxis. Larvae were treated with CuSO4 or neomycin to disrupt lateral line function then exposed to water flow stimuli. Their swimming behavior was recorded, and DeepLabCut and SimBA software were used to track movements and classify rheotaxis behavior. Lateral line-disrupted fish performed rheotaxis, but they swam greater distances, for shorter durations, and with greater angular variance than controls. Further, spectral decomposition analyses demonstrated that lesioned fish exhibited toxin-specific behavioral profiles with distinct fluctuations in the magnitude, timing, and cross-correlation between changes in linear and angular movements. Our observations support that lateral-line input is needed for fish to perform rheotaxis efficiently in flow and reveals commonly used lesion methods have unique effects on behavior.

category: animal behavior and cognition


title: Biogenic action of Lactobacillus plantarum SBT2227 promotes sleep in Drosophila melanogaster

abstract: Lactic acid bacteria (LAB) influence multiple aspects of host brain function via the production of active metabolites in the gut, which is known as the pre/pro-biotic action. However, little is known about the biogenic effects of LAB on host brain function. Here, we reported that the Lactobacillus plantarum SBT2227 promoted sleep in Drosophila melanogaster. Administration of SBT2227 primarily increased the amount of sleep and decreased sleep latency at the beginning of night-time. The sleep-promoting effects of SBT2227 were independent of the existing gut flora. Furthermore, heat treatment or mechanical crushing of SBT2227 did not suppress the sleep-promoting effects, indicative of biogenic action. Transcriptome analysis, and RNAi mini-screening for gut-derived peptide hormones revealed the requirement of neuropeptide F, a homologue of the mammalian neuropeptide Y, for the action of SBT2227. These biogenic effects of SBT2227 on the host sleep provide new insights into the interaction between the brain and gut bacteria.


title: Transcription Factor Gene Pea3 Regulates Erectile Function in Mice

abstract:
BackgroundMale mice with homozygous loss of function mutations of the ETS transcription factor gene Pea3 (Pea3 null) are infertile due to their inability to deposit semen plugs, however the specific deficits in male sexual behaviors that drive this phenotype are unknown.

AimTo investigate the regulatory role of the Pea3 gene in organizing gross sexual behaviors and erectile functioning during active copulation.

MethodsThe copulatory behavior of male mice (Pea3 null and control) with hormonally primed ovariectomized females was monitored via high-speed and high-resolution digital videography to assess for differences in female-directed social behaviors, gross sexual behaviors (mounting, thrusting), and erectile and ejaculatory function.

OutcomesPea3 null male mice have dramatically reduced erectile function during sexual intercourse, however other aspects of male sexual behaviors are largely intact.

ResultsPea3 null male mice exhibit greatly reduced erectile function, with 44% of males displaying no visible erections during mounting behaviors, and none achieving sustained erections. As such, Pea3 null males are incapable of intromission, and semen plug deposition, despite displaying largely normal female-directed social behaviors, mounting behaviors, and ejaculatory grasping behavior. Additionally, the coordination of the timing of thrusting trains is impaired in Pea3 null males.

Clinical ImplicationsThe identification of the transcription factor Pea3 in regulating erectile function in mice may provide a useful target for understanding the genetics of male sexual dysfunction in human patients.

Strengths and LimitationsHigh-speed and high-resolution videography allows for a detailed analysis of male sexual behaviors and erectile functioning in Pea3 null and control mice. How disruption of the Pea3 gene translates to erectile dysfunction is still unknown.

ConclusionThe transcription factor gene Pea3 regulates the ability to achieve and maintain erections in male mice.


title: Localized delivery of β-NGF via injectable microrods accelerates endochondral fracture repair

abstract: Currently, there are no biological approaches to accelerate bone fracture repair. Osteobiologics that promote endochondral ossification are an exciting alternative to surgically implanted bone grafts, however, the translation of osteobiologics remains elusive because of the need for localized and sustained delivery that is both safe and effective. In this regard, an injectable system composed of hydrogel-based microparticles designed to release osteobiologics in a controlled and localized manner is ideal in the context of bone fracture repair. Here, we describe poly (ethylene glycol) dimethacrylate (PEGDMA)-based microparticles, in the form of microrods, engineered to be loaded with beta nerve growth factor ({beta}-NGF) for use in a murine tibial fracture model. In-vitro studies demonstrated that protein-loading efficiency is readily altered by varying PEGDMA macromer concentration and that {beta}-NGF loaded onto PEGDMA microrods exhibited sustained release over a period of 7 days. In-vitro bioactivity of {beta}-NGF was confirmed using a tyrosine receptor kinase A (Trk-A) expressing cell line, TF-1. Moreover, TF-1 cell proliferation significantly increased when incubated with {beta}-NGF loaded PEGDMA microrods versus {beta}-NGF in media. In-vivo studies show that PEGDMA microrods injected into the fracture calluses of mice remained in the callus for over 7 days. Importantly, a single injection of {beta}-NGF-loaded PEGDMA microrods resulted in significantly improved fracture healing as indicated by significant increases in bone volume, trabecular connective density, and bone mineral density and a significant decrease in cartilage despite a remarkably lower dose ([~]111 fold) than the {beta}-NGF in media. In conclusion, we demonstrate a novel and translational method of delivering {beta}-NGF via injectable PEGDMA microrods to improve bone fracture repair.

category: bioengineering


title: Quantifying the Morphology and Mechanisms of Cancer Progression in 3D in-vitro environments: Integrating Experiments, Multiscale Models, and Spatial Validation

abstract: Mathematical models of cancer growth have become increasingly more accurate both in the space and time domains. However, the limited amount of data typically available has resulted in a larger number of qualitative rather than quantitative studies. In the present study, we provide an integrated experimental-computational framework for the quantification of the morphological characteristics and the mechanistic modelling of cancer progression in 3D environments. The proposed framework allows for the calibration of multiscale, spatiotemporal models of cancer growth using state-of-the-art 3D cell culture data, and their validation based on the resulting experimental morphological patterns. Its implementation enabled us to pursue two goals; first, the quantitative description of the morphology of cancer progression in 3D cultures, and second, the relation of tumour morphology with underlying biophysical mechanisms that govern cancer growth and migration. We applied this framework to the study of the spatiotemporal progression of Triple Negative Breast Cancer cells cultured in Matrigel scaffolds, and validated the hypothesis of chemotactic migration using a multiscale Keller-Segel model. The results revealed transient, non-random spatial distributions of cancer cells that consist of clustered, and dispersion patterns. The proposed model was able to describe the general characteristics of the experimental observations and suggests that cancer cells exhibited chemotactic migration and accumulation, as well as random motion during the examined time period of development. To our knowledge, this is the first time that a multiscale model is used to quantify the relationship between the spatial patterns and the underlying mechanisms of cancer growth in 3D environments.


title: Quantifying the Morphology and Mechanisms of Cancer Progression in 3D in-vitro environments: Integrating Experiments and Multiscale Models


category: systems biology


title: NAD precursors cycle between host tissues and the gut microbiome

abstract: Nicotinamide adenine dinucleotide (NAD) is an essential redox cofactor in both mammals and microbes. Here we use isotope tracing to investigate the precursors supporting NAD synthesis in the gut microbiome. We find that preferred dietary NAD precursors are absorbed in the proximal part of the gastrointestinal tract and not available to microbes in the distal gut. Instead, circulating host nicotinamide enters the gut lumen and supports gut microbiome NAD synthesis. In addition, the microbiome converts nicotinamide, originating from the host circulation, into nicotinic acid. Host tissues uptake and utilize this microbiome-derived nicotinic acid for NAD synthesis, maintaining circulating nicotinic acid levels even in the absence of dietary consumption. Moreover, the main route from oral nicotinamide riboside, a widely used nutraceutical, to host NAD is via conversion into nicotinic acid by the gut microbiome. Thus, NAD precursors cycle between the host and gut microbiome to maintain NAD homeostasis.

category: physiology


title: Dual roles of mTORC1-dependent activation of the ubiquitin-proteasome system in muscle proteostasis

abstract: Muscle size is controlled by the PI3K-PKB/Akt-mTORC1-FoxO pathway, which integrates signals from growth factors, energy and amino acids to activate protein synthesis and inhibit protein breakdown. While mTORC1 activity is necessary for PKB/Akt-induced muscle hypertrophy, its constant activation alone induces muscle atrophy. Here we show that this paradox is based on mTORC1 activity promoting protein breakdown through the ubiquitin-proteasome system (UPS) by simultaneously inducing ubiquitin E3 ligase expression via feedback inhibition of PKB/Akt and proteasome biogenesis via Nuclear Factor Erythroid 2-Like 1 (Nrf1). Muscle growth was restored by reactivation of PKB/Akt, but not by Nrf1 knockdown, implicating ubiquitination as the limiting step. However, both PKB/Akt activation and proteasome depletion by Nrf1 knockdown led to an immediate disruption of proteome integrity with rapid accumulation of damaged material. These data highlight the physiological importance of mTORC1-mediated PKB/Akt inhibition and point to juxtaposed roles of the UPS in atrophy and proteome integrity.


title: Intrinsic bursts facilitate learning of Levy flight movements in recurrent neural network models

abstract: Isolated spikes and bursts of spikes are thought to provide the two major modes of information coding by neurons. Bursts are known to be crucial for fundamental processes between neuron pairs, such as neuronal communications and synaptic plasticity. Deficits in neuronal bursting can also impair higher cognitive functions and cause mental disorders. Despite these findings on the roles of bursts, whether and how bursts have an advantage over isolated spikes in the network-level computation remains elusive. Here, we demonstrate in a computational model that not isolated spikes but intrinsic bursts can greatly facilitate learning of Levy flight random walk trajectories by synchronizing burst onsets across neural population. Levy flight is a hallmark of optimal search strategies and appears in cognitive behaviors such as saccadic eye movements and memory retrieval. Our results suggest that bursting is a crucial component of sequence learning by recurrent neural networks in the brain.


title: Genetic polymorphisms in COMT and BDNF influence synchronization dynamics of human neuronal oscillations

abstract: Neuronal oscillations, their inter-areal synchronization, and scale-free dynamics constitute fundamental mechanisms for cognition by regulating communication in neuronal networks. These oscillatory dynamics have large inter-individual variability that is partly heritable. However, the genetic underpinnings of oscillatory dynamics have remained poorly understood. We recorded resting-state magnetoencephalography (MEG) from 82 healthy participants and investigated whether oscillation dynamics were influenced by genetic polymorphisms in Catechol-O-methyltransferase (COMT) Val158Met and brain-derived neurotrophic factor (BDNF) Val66Met. Both COMT and BDNF polymorphisms influenced local oscillation amplitudes and their long-range temporal correlations (LRTCs), while only BDNF polymorphism affected the strength of large-scale synchronization. Our findings demonstrate that COMT and BDNF genetic polymorphisms contribute to inter-individual variability in local and large-scale synchronization dynamics of neuronal oscillations. Comparison of these results to computational modelling of near-critical synchronization dynamics further suggested that COMT and BDNF polymorphisms influenced local oscillations by modulating the excitation-inhibition balance according to the brain criticality framework.


title: Reversible inactivation of ferret auditory cortex impairs spatial and non-spatial hearing

abstract: A key question in auditory neuroscience is how far brain regions are functionally specialized for processing specific sound features such as sound location and identity. In auditory cortex, correlations between neural activity and sounds support both the specialization of distinct cortical subfields, and encoding of multiple sound features within individual cortical areas. However, few studies have tested the causal contribution of auditory cortex to hearing in multiple contexts. Here we tested the role of auditory cortex in both spatial and non-spatial hearing. We reversibly inactivated the border between middle and posterior ectosylvian gyrus using cooling (n=2) or optogenetics (n=1) as ferrets discriminated vowel sounds in discriminated vowel sounds in noise. Animals with cooling loops were also presented with vowels in clean conditions, and then retrained to localize noise-bursts from multiple locations and tested with cooling. Cortical inactivation impaired sound localization and vowel discrimination in noise, but not discrimination in clean conditions. We also tested the effects of cooling on vowel discrimination in noise when vowel and noise were colocated or spatially separated. Here, cooling impaired discriminating vowels with colocalized but not spatially separated noise, such that we could observe spatial release from masking during cortical inactivation. Together our results show that auditory cortex contributes to both spatial and non-spatial hearing, consistent with single unit recordings in the same brain region. The deficits we observed did not reflect general impairments in hearing, but rather are consistent with a role for auditory cortex in auditory scene analysis.


title: The landscape of metabolic brain alterations in Alzheimer's disease

abstract: We present a comprehensive reference map of metabolic brain changes in Alzheimers disease (AD). In a multi-center study within the Accelerating Medicines Partnership in AD, we metabolically profiled 500 samples from the dorsolateral prefrontal cortex (DLPFC) and 83 samples from the temporal cortex (TCX). In the DLPFC, 298 metabolites were correlated with AD-related traits, including late-life cognitive performance and neuropathological {beta}-amyloid and tau tangle burden. Out of these 298 metabolites, 35 replicated in TCX and a previous study. A conditional analysis suggests that metabolic associations with tangle burden were largely independent of {beta}-amyloid load in the brain. Our results provide evidence of brain alterations in bioenergetic pathways, cholesterol metabolism, neuroinflammation, osmoregulation, and other pathways. In a detailed investigation of the glutamate/GABA neurotransmitter pathway, we demonstrate how integration of complementary omics data can provide a comprehensive view of dysregulated biochemical processes. All associations are available as an interactive network at https://omicscience.org/apps/brainmwas/.


title: Successive bleaching events (2019-2020) in Northeast Peninsular Malaysia revealed selective thermal acclimatization and susceptibility of hard corals at biophysical reef scale

abstract: Due to current greenhouse gas emissions, Malaysian coral reefs are predicted to experience severe annual coral bleaching events by 2043, threatening the survival of coral reefs within this century. However, there is no field data on how Malaysian coral reefs respond to successive events of coral bleaching. Despite the notion that many scleractinian taxa exhibit increased thermal tolerance over the last decade, it remains unresolved whether these changes are a result of  weeding out thermally susceptible species and actually ameliorate accelerating warming rates and increasing frequencies of heat disturbances. Moreover, complex interaction of environmental and biological factors that underlie differences in the bleaching response necessitate conducting studies at the within-reef scale (i.e., leeward shallow, windward shallow). Here, we studied two successive thermal stress events starting during the 2019 El Nino Southern Oscillation (ENSO), and determined bleaching trajectories of 29 hard coral taxa across fine spatio-temporal gradients in Northeast Peninsular Malaysia. Analysis of climate trajectories affirms accelerating warming rates (0.17{degrees}C per decade) and higher return-frequency of heat disturbance. Despite high annual maximum temperatures above the putative bleaching threshold (31.07{degrees}C and 31.74{degrees}C, respectively), accumulated thermal stress was low during both bleaching episodes (Degree Heating Weeks of 1.05{degrees}C-weeks and 0.18{degrees}C-weeks, respectively), suggesting widespread thermal sensitivity of hard coral taxa (55.21% and 26.63% bleaching incidence in 2019 and 2020, respectively). However, significant discrepancies between satellite and in-situ temperature data were found (0.63{degrees}C; SD{+/-}0.26). Bleaching severity was highly taxon-specific, varied across and within reef scales due to wind exposure and depth (e.g., less bleaching at shallow windward sites), and partially contrasted historical bleaching observations (e.g., Acropora and Montipora were less susceptible, Cyphastrea, Echinopora, Goniastrea, Heliopora and Porites were highly susceptible). While bleaching severity was higher in 2019, Galaxea and Leptastrea were bleaching more in 2020 despite lower heat stress, suggesting negative legacy effects of the 2019 bleaching event on these taxa. In conclusion, hard corals were subjected to more frequent heat stress during the last decade and remain highly vulnerable to marine heatwaves across all biophysical reef scales. Annual coral bleaching impacted all hard coral taxa and reduced thermal tolerance in at least two taxa.

category: ecology


title: Highly variable response of hard coral taxa to successive coral bleaching events (2019-2020) and rising ocean temperatures in Northeast Peninsular Malaysia.


title: The Prevalence of Litter Foraging Among UK Birds: Lessons Learned From A Citizen Science Project

abstract: 1.Anthropogenic food sources, such as litter, are readily available to birds in urban areas. As an overly anthropogenic diet can have negative health consequences for wildlife, monitoring the frequency of foraging in litter compared to natural food resources can be an important component of wildlife conservation efforts. To understand how common litter foraging is among different bird species, we conducted a citizen science project with volunteers across the UK. Through this project, we also tried to engage people in birdwatching and bird surveys who would not normally participate in these activities. A particular focus was on recruiting respondents from underrepresented groups, and the methodology was designed to accommodate people without any background knowledge of birds. While we did not receive enough observations to draw conclusions about the litter foraging rates of different bird species across the UK, we report the submissions we received, as well as the demographic composition of the volunteer group. We successfully reached volunteers who did not participate in birdwatching or BTO bird surveys before, as well as some young volunteers, but were unsuccessful in reaching respondents from diverse socioeconomic backgrounds. We hope that the successes and failures of our methods reported here can be useful to others designing citizen science studies, so that birdwatching and volunteering for bird surveys will be equally accessible to all in the future.


title: A genome in flux: homoeologous exchanges, subgenome dominance, and gene dosage balance constraints in resynthesized allopolyploid Brassica napus

abstract: Allopolyploidy involves the hybridization of two evolutionary diverged species and the doubling of genomic material. Frequently, allopolyploids exhibit genomic rearrangements that recombine, duplicate, or delete homoeologous regions of the newly formed genome. While decades of investigation have focused on how genome duplication leads to systematic differences in the retention and expression of duplicate genes, the impact of genomic rearrangements on genome evolution has received less attention. We used genomic and transcriptomic data for six independently resynthesized, isogenic Brassica napus lines in the first, fifth, and tenth generation to identify genomic rearrangements and assess their impact on gene expression dynamics related to subgenome dominance and gene dosage constraint. We find that dosage constraints on the gene expression response to polyploidy begin to loosen within the first ten generations of evolution and systematically differ between dominant and non-dominant subgenomes. We also show that genomic rearrangements can bias estimation of homoeolog expression bias, but fail to fully obscure which subgenome is dominantly expressed. Finally, we demonstrate that dosage-sensitive genes exhibit the same kind of coordinated response to homoeologous exchange as they do for genome duplication, suggesting constraint on dosage balance also acts on these changes to gene dosage.

category: evolutionary biology


title: Rapid adaptation often occurs through mutations to the most highly conserved positions of the RNA polymerase core enzyme

abstract: Mutations to the genes encoding the RNA polymerase core enzyme (RNAPC) and additional housekeeping regulatory genes were found to be involved in rapid adaptation, in the context of numerous evolutionary experiments, in which bacteria were exposed to diverse selective pressures. This provides a conundrum, as the housekeeping genes that were so often mutated in response to these diverse selective pressures tend to be among the genes that are most conserved in their sequences across the bacterial phylogeny. In order to further examine this apparent discrepancy, we characterized the precise positions of the RNAPC involved in adaptation to a large variety of selective pressures. We found that different positions of the RNAPC are involved in adaptation to various stresses, with very little overlap found between stresses. We further found that RNAPC positions involved in adaptation tended to be more evolutionary conserved, were more likely to occur within defined protein domains, and tended to be closer to the complexs active site, compared to all other RNAPC positions. Finally, we could show that this observed trend of higher conservation of positions involved in rapid adaptation extends beyond the RNAPC to additional housekeeping genes. Combined, our results demonstrate that the positions that change most readily in response to well defined selective pressures exerted in lab environments are also those that evolve most slowly in nature. This suggests that such adaptations may not readily occur in nature, due to their antagonistically pleiotropic effects, or that if they do occur in nature, they are highly transient.


title: Best BLAST hit alone cannot be used as evidence of fraud

abstract: In a recent study, Blanco-Fernandez, et al. 1 applied molecular tools to authenticate fish products and conclude evidence of "worrying international fraud". They revealed mislabeling in recognizable and unrecognizable fish products labeled as anchovy, hake and tuna commercialized by European companies. Their analyses consisted on extracting DNA from the fish product to be authenticated followed by amplification and sequencing of a suite of DNA markers and on comparing the resulting sequences to the GenBank sequence database using BLAST (Basic Tool Alignment Search Tool) (https://blast.ncbi.nlm.nih.gov/Blast.cgi). By carefully reanalyzing their data, we identify errors in their species identification and conclude that best BLAST hit alone cannot be used as evidence of fraud.

category: genetics


title: cSurvival: a web resource for biomarker interactions in cancer outcomes

abstract:
Survival analysis is a technique to identify prognostic biomarkers and genetic vulnerabilities in cancer studies. Large-scale consortium-based projects have profiled >11,000 adult and >4,000 paediatric tumor cases with clinical outcomes and multi-omics approaches. This provides a resource for investigating molecular-level cancer etiologies using clinical correlations. Although cancers often arise from multiple genetic vulnerabilities and have deregulated gene sets (GSs), existing survival analysis protocols can report only on individual genes. Additionally, there is no systematic method to connect clinical outcomes with experimental (cell line) data. To address these gaps, we developed cSurvival (https://tau.cmmt.ubc.ca/cSurvival). cSurvival provides a user-adjustable analytical pipeline with a curated, integrated database, and offers three main advances: (a) joint analysis with two genomic predictors to identify interacting biomarkers, including new algorithms to identify optimal cutoffs for two continuous predictors; (b) survival analysis not only at the gene, but also the GS level; and (c) integration of clinical and experimental cell line studies to generate synergistic biological insights. To demonstrate these advances, we report three case studies. We confirmed findings of autophagy-dependent survival in colorectal cancers and of synergistic negative effects between high expression of SLC7A11 and SLC2A1 on outcomes in several cancers. We further used cSurvival to identify high expression of the Nrf2-antioxidant response element pathway as a main indicator for lung cancer prognosis and for cellular resistance to oxidative stress-inducing drugs. Together, these analyses demonstrate cSurvivals ability to support biomarker prognosis and interaction analysis via gene- and GS-level approaches and to integrate clinical and experimental biomedical studies.

Key pointsO_LIWe developed cSurvival, an advanced framework using clinical correlations to study biomarker interactions in cancers, with source code and curated datasets freely available for all
C_LIO_LIcSurvival includes new algorithms to identify optimal cutoffs for two continuous predictors to stratify patients into risk groups, enabling for the first time joint analysis with two genomic predictors;
C_LIO_LIcSurvival allows survival analysis at the gene set (GS) level with comprehensive and up-to-date GS libraries
C_LIO_LIThe cSurvival pipeline integrates clinical outcomes and experimental cancer cell line data to generate synergistic biological insights and to mine for appropriate preclinical cell line tools
C_LIO_LIcSurvival is built on a manually curated cancer outcomes database
C_LI


title: Disentangling signatures of selection before and after European colonization in Latin Americans

abstract: Throughout human evolutionary history, large-scale migrations have led to intermixing (i.e., admixture) between previously separated human groups. While classical and recent work have shown that studying admixture can yield novel historical insights, the extent to which this process contributed to adaptation remains underexplored. Here, we introduce a novel statistical model, specific to admixed populations, that identifies loci under selection while determining whether the selection likely occurred post-admixture or prior to admixture in one of the ancestral source populations. Through extensive simulations we show that this method is able to detect selection, even in recently formed admixed populations, and to accurately differentiate between selection occurring in the ancestral or admixed population. We apply this method to genome-wide SNP data of ~4,000 individuals in five admixed Latin American cohorts from Brazil, Chile, Colombia, Mexico and Peru. Our approach replicates previous reports of selection in the HLA region that are consistent with selection post-admixture. We also report novel signals of selection in genomic regions spanning 47 genes, reinforcing many of these signals with an alternative, commonly-used local-ancestry-inference approach. These signals include several genes involved in immunity, which may reflect responses to endemic pathogens of the Americas and to the challenge of infectious disease brought by European contact. In addition, some of the strongest signals inferred to be under selection in the Native American ancestral groups of modern Latin Americans overlap with genes implicated in energy metabolism phenotypes, plausibly reflecting adaptations to novel dietary sources available in the Americas.


title: The haplotype-resolved chromosome pairs and transcriptome of a heterozygous diploid African cassava cultivar

abstract:
BackgroundCassava (Manihot esculenta) is an important clonally propagated food crop in tropical and sub-tropical regions worldwide. Genetic gain by molecular breeding is limited because cassava has a highly heterozygous, repetitive and difficult to assemble genome.

FindingsHere we demonstrate that Pacific Biosciences high-fidelity (HiFi) sequencing reads, in combination with the assembler hifiasm, produced genome assemblies at near complete haplotype resolution with higher continuity and accuracy compared to conventional long sequencing reads. We present two chromosome scale haploid genomes phased with Hi-C technology for the diploid African cassava variety TME204. Genome comparisons revealed extensive chromosome re-arrangements and abundant intra-genomic and inter-genomic divergent sequences despite high gene synteny, with most large structural variations being LTR-retrotransposon related. Allele-specific expression analysis of different tissues based on the haplotype-resolved transcriptome identified both stable and inconsistent alleles with imbalanced expression patterns, while most alleles expressed coordinately. Among tissue-specific differentially expressed transcripts, coordinately and biasedly regulated transcripts were functionally enriched for different biological processes. We use the reference-quality assemblies to build a cassava pan-genome and demonstrate its importance in representing the genetic diversity of cassava for downstream reference-guided omics analysis and breeding.

ConclusionsThe haplotype-resolved genome allows the first systematic view of the heterozygous diploid genome organization in cassava. The completely phased and annotated chromosome pairs will be a valuable resource for cassava breeding and research. Our study may also provide insights into developing cost-effective and efficient strategies for resolving complex genomes with high resolution, accuracy and continuity.


title: Trajectory Recording and Analysis System for Cockroach Robot

abstract: In this study, We design a trajectory recording and analysis system to record and analysis the changes in the movement behavior of the cockroach robot after stimulation. The external hardware of this system is an infrared touchpad as the experimental platform for the cockroach robot to crawl freely, and the infrared matrices densely distributed in the X and Y directions of the infrared touchpad are used to detect and locate the position of the cockroach robot. The cockroach robots movement trajectory is displayed visually through the projectors interface projection on the infrared touchpad. The system software consists of three main parts: the electrical signal parameter setting module, the movement trajectory recording module, and the data analysis module. The electrical signal parameter setting module sets the stimulation parameters and configures the corresponding serial port to independently stimulate the left and right antenna and cercus of the cockroach; the trajectory recording module is used to record the trajectory of the cockroach robot through the coordinate positioning method. The data analysis module explores the change of motion behavior of the cockroach robot with time after receiving the stimulus by using the stage analysis method, and explores the change of motion of the cockroach robot with different voltage stimulus by using the module analysis method. The system is tested in experiments and the results demonstrated its applicability to the recording and analysis of the cockroach robots trajectories.


title: Hierarchical organization of rhesus macaque behavior

abstract: Primatologists, psychologists and neuroscientists have long hypothesized that primate behavior is highly structured. However, fully delineating that structure has been impossible due to the difficulties of precision behavioral tracking. Here we analyzed a dataset consisting of continuous measures of the 3D position of fifteen body landmarks from two male rhesus macaques (Macaca mulatta) performing three different tasks in a large unrestrained environment over many hours. Using an unsupervised embedding approach on the tracked joints, we identified commonly repeated pose patterns, which we call postures. We found that macaques behavior is characterized by 49 distinct identifiable postures, lasting an average of 0.6 seconds each. We found evidence that behavior is hierarchically organized, in that transitions between poses tend to occur within larger modules, which correspond to intuitively identifiably actions; these actions are in turn organized hierarchically. Our behavioral decomposition allows us to identify universal (cross-individual and cross-task) and unique (specific to each individual and task) principles of behavior. These results demonstrate the hierarchical nature of primate behavior and provide a method for the automated "ethogramming" of primate behavior.


title: WebSeq: A Genomic Data Analytics Platform for Monogenic Disease Discovery

abstract: Whole exome sequencing (WES) is commonly used to study monogenic diseases. The application of this sequencing technology has gained in popularity amongst clinicians and researchers as WES pricing has declined. The accumulation of WES data creates a need for a robust, flexible, scalable and easy-to-use analytics platform to allow researchers to gain biological insight from this genomic data. We present WebSeq, a self-contained server and web interface to facilitate intuitive analysis of WES data. WebSeq provides access to sophisticated tools and pipelines through a user-friendly and modern web interface. WebSeq has modules that support i) FASTQ to VCF conversion, ii) VCF to ANNOVAR1 CSV conversion, iii) family-based analyses for Mendelian disease gene discovery, iv) cohort-wide gene enrichment analyses, (v) an automated IGV2 browser, and (vi) a  virtual gene panel analysis module. WebSeq Pro, our expanded pipeline, also supports SNP genotype analyses such as ancestry inference and kinship testing. WebSeq Lite, our minimal pipeline, supports family-based analyses, cohort-wide gene enrichment analyses, and a virtual gene panel along with the IGV2 browser module. We anticipate that the rigorous use of our web application will allow researchers to expedite discoveries from human genomic data3. WebSeq Lite, WebSeq, and WebSeq Pro are fully containerized using Docker4, run on all major operating systems, and are freely available for personal, academic, and non-profit use at http://bitly.ws/g6cn

category: bioinformatics


title: SC2MeNetDrug: A computational tool to uncover inter-cell signaling targets and identify relevant drugs based on single cell RNA-seq data

abstract: Single cell RNA sequencing (scRNA-seq) is a powerful technology to investigate the transcriptional programs in stromal, immune and tumor cells or neuron cells within the tumor or Alzheimers Disease (AD) brain microenvironment (ME) or niche. Cell-cell communications within ME play important roles in disease progression and immunotherapy response, and are novel and critical therapeutic targets. Though many tools of scRNA-seq analysis have been developed to investigate the heterogeneity and sub-populations of cells, few were designed for uncovering cell-cell communications of ME and predict the potentially effective drugs to inhibit the communications. Moreover, the data analysis processes of discovering signaling communication networks and effective drugs using scRNA-seq data are complex and involving a set of critical analysis processes and external supportive data resources, which are difficult for researchers who have no strong computational background and training in scRNA-seq data analysis. To address these challenges, in this study, we developed a novel computational tool, SC2MeNetDrug (https://fuhaililab.github.io/sc2MeNetDrug/). It was specifically designed using scRNA-seq data to identify cell types within MEs, uncover the dysfunctional signaling pathways within individual cell types, inter-cell signaling communications, and predict effective drugs that can potentially disrupt cell-cell signaling communications. SC2MeNetDrug provided a user-friendly graphical user interface to encapsulate the data analysis modules, which can facilitate the scRNA-seq data based-discovery of novel inter-cell signaling communications and novel therapeutic regimens.


title: Sensitive identification of known and unknown protease activities by unsupervised linear motif deconvolution

abstract:
The cleavage-site specificities for many proteases are not well-understood, restricting the utility of supervised classification methods. We present an algorithm and web interface to overcome this limitation through the unsupervised detection of overrepresented patterns in protein sequence data, providing insight into the mixture of protease activities contributing to a complex system.

Here, we apply the RObust LInear Motif Deconvolution (RoLiM) algorithm to confidently detect substrate cleavage patterns for SARS-CoV-2 Mpro protease in N terminome data of an infected human cell line. Using mass spectrometry-based peptide data from a case-control comparison of 341 primary urothelial bladder cancer cases and 110 controls, we identified distinct sequence motifs indicative of increased MMP activity in urine from cancer patients. Evaluation of N terminal peptides from patient plasma post-chemotherapy detected novel Granzyme B/Corin activity.

RoLiM will enhance unbiased investigation of peptide sequences to establish the composition of known and uncharacterized protease activities in biological systems.


title: FastQTLmapping: an ultra-fast package for mQTL-like analysis

abstract:
SummaryHere we describe fastQTLmapping, a C++ package that is computationally efficient not only for mQTL-like analysis but as a generic solver also for conducting exhaustive linear regressions involving extraordinarily large numbers of dependent and explanatory variables allowing for covariates. Compared to the state-of-the-art MatrixEQTL, fastQTLmapping was an order of magnitude faster with much lower peak memory usage. In a large dataset consisting of 3,500 individuals, 8 million SNPs, 0.8 million CpGs and 20 covariates, fastQTLmapping completed the mQTL analysis in 7 hours with 230GB peak memory usage.

Availability and ImplementationFastQTLmapping is implemented in C++ and released under a GPL license. FastQTLmapping can be downloaded from https://github.com/TianTTL/xQTLmapping.

Contactliufan@big.ac.cn


title: Marker-free characterization of single live circulating tumor cell full-length transcriptomes

abstract: The identification and characterization of circulating tumor cells (CTCs) are important for gaining insights into the biology of metastatic cancers, monitoring disease progression, and medical management of the disease. The limiting factor that hinders enrichment of purified CTC populations is their sparse availability, heterogeneity, and altered phenotypic traits relative to the tumor of origin. Intensive research both at the technical and molecular fronts led to the development of assays that ease CTC detection and identification from the peripheral blood. Most CTC detection methods use a mix of size selection, immune marker based white blood cells (WBC) depletion, and positive enrichment antibodies targeting tumor-associated antigens. However, the majority of these methods either miss out on atypical CTCs or suffer from WBC contamination. Single-cell RNA sequencing (scRNA-Seq) of CTCs provides a wealth of information about their tumors of origin as well as their fate and is a potent method of enabling unbiased identification of CTCs. We present unCTC, an R package for unbiased identification and characterization of CTCs from single-cell transcriptomic data. unCTC features many standard and novel computational and statistical modules for various analysis tasks. These include a novel method of scRNA-Seq clustering, named Deep Dictionary Learning using K-means clustering cost (DDLK), expression based copy number variation (CNV) inference, and combinatorial, marker-based verification of the malignant phenotypes. DDLK enables robust segregation of CTCs and WBCs in the pathway space, as opposed to the gene expression space. We validated the utility of unCTC on scRNA-Seq profiles of breast CTCs from six patients, captured and profiled using an integrated ClearCell(R) FX and PolarisTM workflow that works by the principles of size-based separation of CTCs and marker based WBC depletion.


title: Extending and using anatomical vocabularies in the Stimulating Peripheral Activity to Relieve Conditions (SPARC) project

abstract: The Stimulating Peripheral Activity to Relieve Conditions (SPARC) program is a US National Institutes of Health-funded effort to improve our understanding of the neural circuitry of the autonomic nervous system in support of bioelectronic medicine. As part of this effort, the SPARC program is generating multi-species, multimodal data, models, simulations, and anatomical maps supported by a comprehensive knowledge base of autonomic circuitry. To facilitate the organization of and integration across multi-faceted SPARC data and models, SPARC is implementing the FAIR data principles to ensure that all SPARC products are findable, accessible, interoperable, and reusable. We are therefore annotating and describing all products with a common FAIR vocabulary. The SPARC Vocabulary is built from a set of community ontologies covering major domains relevant to SPARC, including anatomy, physiology, experimental techniques, and molecules. The SPARC Vocabulary is incorporated into tools researchers use to segment and annotate their data, facilitating the application of these ontologies for annotation of research data. However, since investigators perform deep annotations on experimental data, not all terms and relationships are available in community ontologies. We therefore implemented a term management and vocabulary extension pipeline where SPARC researchers may extend the SPARC Vocabulary using InterLex, an online vocabulary management system. To ensure the quality of contributed terms, we have set up a curated term request and review pipeline specifically for anatomical terms involving expert review. Accepted terms are added to the SPARC Vocabulary and, when appropriate, contributed back to community ontologies to enhance autonomic nervous system coverage. Here, we provide an overview of the SPARC Vocabulary, the infrastructure and process for implementing the term management and review pipeline. In an analysis of > 300 anatomical contributed terms, the majority represented composite terms that necessitated combining terms within and across existing ontologies. Although these terms are not good candidates for community ontologies, they can be linked to structures contained within these ontologies. We conclude that the term request pipeline serves as a useful adjunct to community ontologies for annotating experimental data and increases the FAIRness of SPARC data.


title: Extending and using anatomical vocabularies in the Stimulating Peripheral Activity to Relieve Conditions (SPARC) program


title: Reconstructing mutational lineages in breast cancer by multi-patient-targeted single cell DNA sequencing

abstract: Single cell DNA sequencing (scDNA-seq) methods are powerful tools for profiling mutations in cancer cells, however most genomic regions characterized in single cells are non-informative. To overcome this issue, we developed a Multi-Patient-Targeted (MPT) scDNA-seq sequencing method. MPT involves first performing bulk exome sequencing across a cohort of cancer patients to identify somatic mutations, which are then pooled together to develop a single custom targeted panel for high-throughput scDNA-seq using a microfluidics platform. We applied MPT to profile 330 mutations across 23,500 cells from 5 TNBC patients, which showed that 3 tumors were monoclonal and 2 tumors were polyclonal. From this data, we reconstructed mutational lineages and identified early mutational and copy number events, including early TP53 mutations that occurred in all five patients. Collectively, our data suggests that MPT can overcome technical obstacles for studying tumor evolution using scDNA-seq by profiling information-rich mutation sites.

category: cancer biology


title: Association of EBV (Type 1 and 2) with Histopathological Outcomes in Breast Cancer in Pakistani Women

abstract:
IntroductionBreast cancer is one of the major and frequent tumors in the public health sector globally. The rising global prevalence of breast cancer has aroused attention in a viral etiology. Other than genetic and hormonal roles, viruses like Epstein - Barr virus (EBV) also participate in the development and advancement of breast cancer.

AimThis study was conducted to detect the frequency of EBV genotypes in breast cancer patients and compare it with histopathological breast cancer changes.

MethodsFormalin-fixed paraffin-embedded samples of breast cancer (N=60) ages ranged from 22-70 years were collected. EBV DNA was isolated, amplified, typed through PCR, and correlated with histopathological outcomes of breast cancer using SPSS software version 26.

ResultsOur findings suggest that among breast cancer factors, Invasive ductal carcinoma (IDC) was the most common pathological pattern found among patients (90%), observed statistically significant (p= 0.01275). In regards to clinical staging, 8 (13.3 %) patients diagnosed with stage I, 39 (65 %) with stage II, and 13 (21.6 %) with stage III reported statistically significant association (p=0.0003). EBV DNA was detected in 68.3% (41/60) breast cancer patients, reported a statistically significant difference between the prevalence of EBV in breast cancer patients and normal samples (p = 0.001). Of 41 EBV-positive samples, 40 were EBV-1, while only 1 had EBV-2 infection (p < 0.001). No influence on cancer histology was observed. Regarding the association of breast cancer with EBV, histological type (P =0.209), tumor stage (P = 0.48), tumor grade (0.356), tumor sizes (p= 0.976), age (p= 0.1055), tumor laterality (p= 0.533) and ER/PR status (p=0.773) showed no significant association.

ConclusionEBV-1 is prevalent in breast cancer patients and associated with IDC in the study area. For conclusive evidence, more studies are required based on a large sample size and by using more sensitive techniques.


title: Recapitulation of patient-specific 3D chromatin conformation using machine learning and validation of identified enhancer-gene targets

abstract: Regulatory networks containing enhancer to gene edges define cellular state and their rewiring is a hallmark of cancer. While efforts, such as ENCODE, have revealed these networks for reference tissues and cell-lines by integrating multi-omics data, the same methods cannot be applied for large patient cohorts due to the constraints on generating ChIP-seq and three-dimensional data from limited material in patient biopsies. We trained a supervised machine learning model using genomic 3D signatures of physical enhancer-gene connections that can predict accurate connections using data from ATAC-seq and RNA-seq assays only, which can be easily generated from patient biopsies. Our method overcomes the major limitations of correlation-based approaches that cannot distinguish between distinct target genes of given enhancers in different samples, which is a hallmark of network rewiring in cancer. Our model achieved an AUROC (area under receiver operating characteristic curve) of 0.91 and, importantly, can distinguish between active regulatory elements with connections to target genes and poised elements with no connections to target genes. Our predicted regulatory elements are validated by multi-omics data, including histone modification marks from ENCODE, with an average specificity of 0.92. Application of our model on chromatin accessibility and transcriptomic data from 400 cancer patients across 22 cancer types revealed novel cancer-type and subtype-specific enhancer-gene connections for known cancer genes. In one example, we identified two enhancers that regulate the expression of ESR1 in only ER+ breast cancer (BRCA) samples but not in ER-samples. These enhancers are predicted to contribute to the high expression of ESR1 in 93% of ER+ BRCA samples. Functional validation using CRISPRi confirms that inhibition of these enhancers decreases the expression of ESR1 in ER+ samples.


title: Aerobic glycolysis in cancer cells supplies ATP while preventing excess metabolic thermogenesis

abstract: A general feature of cancer metabolism is ATP regeneration via substrate-level phosphorylation even under normoxic conditions (aerobic glycolysis). However, it is unclear why cancer cells prefer the inefficient aerobic glycolysis over the highly efficient process of oxidative phosphorylation for ATP regeneration. Here, we show that a beneficial aspect of aerobic glycolysis is that it reduces metabolic heat generation during ATP regeneration. 13C-metabolic flux analysis of 12 cultured cancer cell lines and in silico metabolic simulation revealed that metabolic heat production during ATP regeneration via aerobic glycolysis was considerably lesser than that produced via oxidative phosphorylation. The dependency on aerobic glycolysis was partly alleviated upon culturing under low temperatures. In conclusion, thermogenesis is required for maintaining thermal homeostasis and can govern aerobic glycolysis in cancer cells.


title: A Poor Research Landscape Hinders the Progression of Knowledge and Treatment of Reproductive Diseases

abstract: Reproductive diseases have gone under the radar for many years, resulting in insufficient diagnostics and treatments. Infertility rates are rising, preeclampsia claims over 70 000 maternal and 500 000 neonatal lives globally per year, and endometriosis affects 10% of all reproductive-aged women but is often undiagnosed for many years. Changes in policy have been enacted to mitigate the gender inequality in research investigators and subjects of medical research. However, the disparities in reproductive research advancement still exist. Here, we analyzed the reproductive science research landscape in attempt to quantify the gravity of the current situation. We find that non-reproductive organs are annually researched 5-20 times more than reproductive organs leading to an exponentially increasing relative knowledge gap in reproductive sciences. Additionally, reproductive organs (breast and prostate) are mainly researched when there is a disease-focus, leading to a lack of basic understanding of the reproductive organs. This gap in knowledge affects reproductive syndromes, as well as other bodily systems and research areas, such as cancer biology and regenerative medicine. Action must be taken by current researchers, funding organizations, and educators to combat this longstanding disregard of reproductive science.


title: HSP90 function is required for T2R bitter taste receptor nitric oxide production and innate immune responses in human airway epithelial cells and macrophages

abstract: Bitter taste receptors (T2Rs) are G protein-coupled receptors (GPCRs) expressed in various cell types including ciliated airway epithelial cells and macrophages. T2Rs in these two airway innate immune cell types are activated by bitter products, including some secreted by Pseudomonas aeruginosa, leading to Ca2+-dependent activation of endothelial nitric oxide (NO) synthase (eNOS). NO enhances mucociliary clearance and has direct antibacterial effects in ciliated epithelial cells and increases phagocytosis by macrophages. Using biochemistry and live cell imaging, we explored the role of heat shock protein 90 (HSP90) in regulating T2R-dependent NO pathways in primary sinonasal epithelial cells, primary monocyte-derived macrophages, and a human bronchiolar cell line (H441). We used immunofluorescence to show that H441 cells express eNOS and certain T2Rs and that the bitterant denatonium benzoate activates NO production in an HSP90-dependent manner in cells grown either as submerged cultures and at air liquid interface. In primary sinonasal epithelial cells, we determined that HSP-90 inhibition reduces T2R-stimulated NO production and ciliary beating which are crucial for pathogen clearance. In primary monocyte-derived macrophages, we found that HSP-90 is integral to T2R-stimulated NO production and phagocytosis of FITC-labeled Escherichia coli and pHrodo-Staphylococcus aureus. Our study demonstrates that HSP90 serves an innate immune role by regulating NO production downstream of T2R signaling by augmenting eNOS activation without impairing upstream calcium signaling. These findings suggest that HSP90 plays an important role in airway antibacterial innate immunity and may be an important target in airway diseases like chronic rhinosinusitis, asthma, or cystic fibrosis.


title: HSP90 modulates T2R bitter taste receptor nitric oxide production and innate immune responses in human airway epithelial cells and macrophages


title: Tunable Transcription Factor Library for Robust Quantification of Gene Expression Dynamics in E. coli

abstract: Predicting the quantitative regulatory function of a TF based on factors such as binding sequence, binding location and promoter type is not possible. The interconnected nature of gene networks and the difficulty in tuning individual TF concentrations makes the isolated study of TF function challenging. Here we present a library of E. coli strains designed to allow for precise control of the concentration of individual TFs enabling the study of the role of TF concentration on physiology and regulation. We demonstrate the usefulness of this resource by measuring the regulatory function of the zinc responsive TF, ZntR and the paralogous TF pair, GalR/GalS. For ZntR, we find that zinc alters ZntR regulatory function in a way that enables activation of the regulated gene to be robust with respect to ZntR concentration. For GalR and GalS, we are able to demonstrate that these parlogous TFs have fundamentally distinct regulatory roles beyond differences in binding affinity.


title: Malathion-resistant Tribolium castaneum has enhanced response to oxidative stress, immunity, and fitness

abstract:
Many cases of insecticide resistance in insect pests give resulting no-cost strains that retain the resistance genes even in the absence of the toxic stressor. Malathion has been widely used against the red flour beetle, Tribolium castaneum Herbst. in stored products although no longer used. Malathion specific resistance in this pest has provided resistance that is long lasting and widely distributed. To understand this resistance a malathion resistant strain was challenged with a range of stressors including starvation, hyperoxia, malathion and a pathogen and the antioxidant responses and some lifecycle parameters were determined.

Adult life span of malathion-specific resistant strain of T. castaneum was significantly shorter than the susceptible. Starvation and/or high oxygen reduced adult life span of both strains. Starving with and without 100% oxygen gave longer lifespan for the resistant strain, but for oxygen alone there was no difference. Under oxygen the proportional survival of the resistant strain to the adult stage was significantly higher, for both larvae and pupae, than the susceptible. The resistant strain when stressed with malathion and/or oxygen significantly increased catalase activity, but the susceptible did not. The resistant strain stressed with Paranosema whitei infection had significantly higher survival compared to the susceptible, and with almost no mortality.

The malathion resistant strain of T. castaneum showed greater vigour than the susceptible in most oxidative stress situations and especially where stressors were combined. The induction of the antioxidant enzyme catalase could have helped the resistant strain to withstand oxidative stresses, including insecticidal and importantly those from pathogens. These adaptations, in the absence of insecticide, seem to support the increased immunity of host insects to pathogens seen in other insect species, such as mosquitoes. By increasing the responses to a range of stressors the resistant strain could be considered as having enhanced fitness.

category: zoology


title: Transcriptomic and proteomic analysis of marine nematode Litoditis marina acclimated to different salinities

abstract: Salinity is a critical abiotic factor for all living organisms. The ability to adapt to different salinity environments determines an organisms survival and ecological niches. Litoditis marina is a euryhaline marine nematode widely distributed in coastal ecosystems all over the world, although numerous genes involved in its salinity response have been reported, the adaptive mechanisms underlying its euryhalinity remain unexplored. Here, we utilized worms which have been acclimated to either low salinity or high salinity conditions and evaluated their basal gene expression at both transcriptomic and proteomic levels. We found that several conserved regulators, including osmolytes biosynthesis genes, transthyretin-like family genes, V-type H+-transporting ATPase and potassium channel genes, were involved in both short-term salinity stress response and long-term acclimation processes. In addition, we identified genes related to cell volume regulation, such as actin regulatory genes, Rho family small GTPases and diverse ion transporters, might contribute to hyposaline acclimation, while the glycerol biosynthesis genes gpdh-1 and gpdh-2 accompanied hypersaline acclimation in L. marina. Furthermore, gpdh-2 might play an essential role in transgenerational inheritance of osmotic stress protection in L. marina as in its relative nematode Caenorhabditis elegans. Hereby, this study paves the way for further in-depth exploration on adaptive mechanisms underlying euryhalinity, and may also contribute to the studies of healthy ecosystems in the context of global climate change.


title: Modulation of cutaneous responses in the cuneate nucleus of macaques during active movement

abstract: AO_SCPLOWBSTRACTC_SCPLOWTo achieve stable and precise movement execution, the sensorimotor system integrates exafferent sensory signals originating from interactions with the external world and reafferent signals caused by our own movements. This barrage of sensory information is regulated such that behaviorally relevant signals are boosted at the expense of irrelevant ones. For example, sensitivity to touch is reduced during movement - when cutaneous signals caused by skin stretch are expected and uninteresting - a phenomenon reflected in a decreased cutaneous responsiveness in thalamus and cortex. Some evidence suggests that movement gating of touch may originate from the cuneate nucleus (CN), the first recipient of signals from tactile nerve fibers along the dorsal column-medial lemniscus pathway. To test this possibility, we intermittently delivered mechanical pulses to the receptive fields (RFs) of identified cutaneous CN neurons as monkeys performed a reach-to-grasp task. As predicted, we found that the cutaneous responses of individual CN neurons were reduced during movement. In contrast, cutaneous signals from neurons with RFs on the hand were enhanced during reach. We conclude that tactile signals are already modulated in the first processing stage along the somatosensory neuraxis. Furthermore, the sign and magnitude of this modulation depends on the behavioral relevance of the sensory signals.


title: A neural mechanism for detecting object motion during self-motion

abstract: Detecting objects that move in a scene is a fundamental computation performed by the visual system. This computation is greatly complicated by observer motion, which causes most objects to move across the retinal image. How the visual system detects scene-relative object motion during self-motion is poorly understood. Human behavioral studies suggest that the visual system may identify local conflicts between motion parallax and binocular disparity cues to depth, and may use these signals to detect moving objects. We describe a novel mechanism for performing this computation based on neurons in macaque area MT with incongruent depth tuning for binocular disparity and motion parallax cues. Neurons with incongruent tuning respond selectively to scene-relative object motion and their responses are predictive of perceptual decisions when animals are trained to detect a moving object during self-motion. This finding establishes a novel functional role for neurons with incongruent tuning for multiple depth cues.


title: Whole transcriptome-sequencing and network analysis of CD1c+ human dendritic cells identifies cytokine-secreting subsets linked to type I IFN-negative autoimmunity to the eye

abstract:
BackgroundInflammatory subsets of CD1c+ conventional dendritic cells (CD1c+ DCs) are promoted by type I interferons (IFN), but the molecular basis for CD1c+ DCs involvement in conditions not driven by type I IFNs is unknown.

MethodsOur objective was to use RNA-sequencing of blood CD1c+ DCs and high-dimensional flow cytometry of two cohorts of autoimmune uveitis patients and healthy donors to characterize the CD1c+ DCs population of type I IFN-negative autoimmune uveitis.

ResultsWe report that the CD1c+ DCs pool from patients with autoimmune uveitis (n=45) is skewed towards a transcriptional network characterized by surface receptor genes CX3CR1, CCR2, and CD36. We confirmed the association of the transcriptional network with autoimmune uveitis by RNA-sequencing in another case-control cohort (n=35) and demonstrated that this network was governed by NOTCH2-RUNX3 signaling. Unbiased flow cytometry analysis based on the transcriptional network identified blood CD1c+ DC subsets that can be distinguished by CX3CR1 and CD36 surface expression. A CD36+CX3CR1+CD1c+ DC subset within the novel DC3 population was diminished in peripheral blood of patients, while CD1c+ DCs expressing CD36 and CX3CR1 accumulate locally in the inflamed eye. The CD36+CX3CR1+CD1c+ DC subset showed a differential capacity to produce cytokines, including TNF-alpha, IL-6, and VEGF, but not IL-23.

ConclusionThese results show that CD1c+ DC subsets defined on the basis of surface expression of CD36 and CX3CR1 are linked to type I IFN-negative human autoimmune uveitis and show a differential capacity to secrete proinflammatory mediators that drive its pathophysiology.

Graphical Abstract

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category: immunology


title: The stochastic logistic model with correlated carrying capacities reproduces beta-diversity metrics of microbial

abstract:
The large taxonomic variability of microbial community composition is a consequence of the combination of environmental variability, mediated through ecological interactions, and stochasticity. Most of the analysis aiming to infer the biological factors determining this difference in community structure start by quantifying how much communities are similar in their composition, trough beta-diversity metrics. The central role that these metrics play in microbial ecology does not parallel with a quantitative understanding of their relationships and statistical properties. In particular, we lack a framework that reproduces the empirical statistical properties of beta-diversity metrics. Here we take a macroecological approach and introduce a model to reproduce the statistical properties of community similarity. The model is based on the statistical properties of individual communities and on a single tunable parameter, the correlation of species carrying capacities across communities, which sets the difference of two communities. The model reproduces quantitatively the empirical values of several commonly-used beta-diversity metrics, as well as the relationships between them. In particular, this modeling framework naturally reproduces the negative correlation between overlap and dissimilarity, which has been observed in both empirical and experimental communities and previously related to the existence of universal features of community dynamics. In this framework, such correlation naturally emerges due to the effect of random sampling.

AUTHORS SUMMARYSeveral biological and ecological forces shape the composition of microbial communities. But also contingency and stochasticity play an important role. Comparing communities, identifying which conditions are similar in communities with similar species composition, allows to identify which forces shape their structure. Here we introduce a modeling framework which reproduces the statistical features of community similarity. We identify a single relevant parameter that captures in a single number the multidimensional nature of similarity in community composition. These results set the basis for a quantitative, and predicting, theory of the statistical properties of microbial communities.


title: Spatial scale of transmission explains how acute infections circulate at low prevalence

abstract:
Fundamental questions remain about the regulation of acute pathogens in the absence of acquired immunity. This is especially true for canine rabies, a universally fatal zoonosis. From tracing rabies transmission in a population of 50,000 dogs in Tanzania between 2002-2016 we unravel the processes through which rabies is regulated and persists, fitting individual-based models to spatially-resolved data to investigate the mechanisms modulating transmission and the scale over which they operate. We find that while prevalence never exceeds 0.15%, we detect significant susceptible depletion at local scales commensurate with rabid dog movement, reducing transmission through clustering of rabies deaths and individuals incubating infection. Individual variation in rabid dog behaviour facilitates virus dispersal and co-circulation of lineages, enabling metapopulation persistence. These mechanisms likely operate in many pathogens circulating in spatially structured populations, with important implications for prediction and control, yet are unobservable unless the scale of host interactions is identified.

One-Sentence SummaryIdentifying the spatial scale of contact reveals the mechanisms that limit the size of rabies outbreaks and that are critical for predicting transmission dynamics.


title: Tissue-specific impacts of aging and genetics on gene expression patterns in humans

abstract: Age is the primary risk factor for many common human diseases including heart disease, Alzheimers dementias, cancers, and diabetes. Determining how and why tissues age differently is key to understanding the onset and progression of such pathologies. Here, we set out to quantify the relative contributions of genetics and aging to gene expression patterns from data collected across 27 tissues from 948 humans. We show that gene expression patterns become more erratic with age in several different tissues reducing the predictive power of expression quantitative trait loci. Jointly modelling the contributions of age and genetics to transcript level variation we find that the heritability (h2) of gene expression is largely consistent among tissues. In contrast, the average contribution of aging to gene expression variance varied by more than 20-fold among tissues with [Formula] in 5 tissues. We find that the coordinated decline of mitochondrial and translation factors is a widespread signature of aging across tissues. Finally, we show that while in general the force of purifying selection is stronger on genes expressed early in life compared to late in life as predicted by Medawars hypothesis, a handful of highly proliferative tissues exhibit the opposite pattern. In contrast, gene expression variation that is under genetic control is strongly enriched for genes under relaxed constraint. Together we present a novel framework for predicting gene expression phenotypes from genetics and age and provide insights into the tissue-specific relative contributions of genes and the environment to phenotypes of aging.


title: Repeated translocation of a supergene underlying rapid sex chromosome turnover in Takifugu fish

abstract:
Recent studies have revealed a surprising diversity of sex chromosomes in vertebrates. However, the detailed mechanism of their turnover is still elusive. To understand this process, it is necessary to compare closely related species in terms of sex-determining genes and the chromosomes harboring them. Here, we explored the genus Takifugu, in which one strong candidate sex-determining gene, Amhr2, has been identified. To trace the processes involved in transitions in the sex determination system in this genus, we studied 12 species and found that while the Amhr2 locus likely determines sex in the majority of Takifugu species, three species have acquired sex-determining loci at different chromosomal locations. Nevertheless, the generation of genome assemblies for the three species revealed that they share a portion of the male-specific supergene that contains a candidate sex-determining gene, GsdfY, along with genes that potentially play a role in male fitness. The shared supergene span approximately 100 kb and are flanked by two duplicated regions characterized by CACTA transposable elements. These results suggest that the shared supergene has taken over the role of sex-determining locus from Amhr2 in lineages leading to the three species, and repeated translocations of the supergene underlie the turnover of sex chromosomes in these lineages. These findings highlight the underestimated role of a mobile supergene in the turnover of sex chromosomes in vertebrates.

SignificanceAlthough turnover of sex chromosomes is very common in many vertebrate lineages, the transition process is still elusive. We studied the sex-determining region (SDR) of 12 congeneric fish species. We found that while nine species retained their ancestral SDR, three species had acquired derived SDRs. Although the derived SDRs resided in three different chromosomes, they harbored a shared supergene flanked by two putative transposable elements. The results highlight the underestimated role of a mobile supergene in turnover of sex chromosomes in vertebrates.


title: Whole genome sequencing uncovers the structural and transcriptomic landscape of hexaploid wheat/Am. muticum introgression lines

abstract: Wheat is a globally vital crop, but its limited genetic variation creates a challenge for breeders aiming to maintain or accelerate agricultural improvements over time. Introducing novel genes and alleles from wheats wild relatives into the wheat breeding pool via introgression lines is an important component of overcoming this low variation but is limited by poor genomic resolution and limited understanding of the genomic impact of introgression breeding. By sequencing 17 hexaploid wheat/Ambylopyrum muticum introgression lines and the parent lines, we have precisely pinpointed the borders of introgressed segments. We report a genome assembly and annotation of Am. muticum that has facilitated the identification of Am. muticum resistance genes commonly introgressed in lines resistant to stripe rust. Our analysis has identified an abundance of structural disruption and homoeologous pairing across the introgression lines, likely caused by the suppressed Ph1 locus. mRNAseq analysis of six of these introgression lines revealed that introgressed genes tend to be downregulated, shifting the expression balance of triads towards suppression of the introgressed region, with no discernible compensation in the expression of the homoeologous copies. This analysis explores the genomic impact of introgression breeding and provides an affordable way for breeders to better characterise introgression lines and more effectively deploy wild relative variation.


title: Weighing the DNA content of Adeno-Associated Virus vectors with zeptogram precision using nanomechanical resonators

abstract: Quantifying the composition of viral vectors used in vaccine development and gene therapy is critical for assessing their functionality. Adeno-Associated Virus (AAV) vectors, which are the most widely used viral vectors for in-vivo gene therapy, are typically characterized using PCR, ELISA, and Analytical Ultracentrifugation which require laborious protocols or hours of turnaround time. Emerging methods such as Charge-Detection Mass Spectroscopy, Static Light Scattering, and Mass Photometry offer turnaround times of minutes for measuring AAV mass, but mostly require purified AAV-based reference materials for calibration. Here, we demonstrate a method for using Suspended Nanomechanical Resonators (SNR) to directly measure both AAV mass and aggregation from a few microliters of sample within minutes. We achieve a resolution near 10 zeptograms which corresponds to 1% of the genome holding capacity of the AAV capsid. Our results show the potential of our method for providing real-time quality control of viral vectors during biomanufacturing.


title: Characterizing Protein Conformational Spaces using Dimensionality Reduction and Algebraic Topology

abstract: Datasets representing the conformational landscapes of protein structures are high dimensional and hence present computational challenges. Efficient and effective dimensionality reduction of these datasets is therefore paramount to our ability to analyze the conformational landscapes of proteins and extract important information regarding protein folding, conformational changes and binding. Representing the structures with fewer attributes that capture the most variance of the data, makes for quicker and precise analysis of these structures. In this work we make use of dimensionality reduction methods for reducing the number of instances and for feature reduction. The reduced dataset that is obtained is then subjected to topological and quantitative analysis. In this step we perform hierarchical clustering to obtain different sets of conformation clusters that may correspond to intermediate structures. The structures represented by these conformations are then analyzed by studying their high dimension topological properties to identify truly distinct conformations and holes in the conformational space that may represent high energy barriers. Our results show that the clusters closely follow known experimental results about intermediate structures, as well as binding and folding events.


title: PMD Uncovers Widespread Cell-State Erasure by scRNAseq Batch Correction Methods

abstract: Single cell RNAseq (scRNAseq) batches range from technical replicates to multi-tissue atlases, thus requiring robust batch correction methods that operate effectively across this similarity spectrum. Currently, no metrics allow for full benchmarking across this spectrum, resulting in benchmarks that quantify removal of batch effects without quantifying preservation of real batch differences. Here, we address these gaps with a new statistical metric [Percent Maximum Difference (PMD)] that linearly quantifies batch similarity, and simulations generating cells from mixtures of distinct gene expression programs (cell-lineages/-types/-states). Using 690 real-world and 672 simulated integrations (7.2e6 cells total) we compared 7 batch integration approaches across the spectrum of similarity with batch-confounded gene expression. Count downsampling appeared the most robust, while others left residual batch effects or produced over-merged datasets. We further released open-source PMD and downsampling packages, with the latter capable of downsampling an organism atlas (245,389 cells) in tens of minutes on a standard computer.


title: Validation of cervical lesion proportion measure using a gridded imaging techique to assess cervical pathology in women with genital schistosomiasis

abstract:
Female genital schistosomiasis (FGS) is characterized by a pattern of lesions which manifest at the cervix and the vagina, such as homogeneous and grainy sandy patches, rubbery papules in addition to neovascularization. A tool for quantification of the lesions is needed to improve FGS research and control programs. Hitherto, no tools are available to quantify clinical pathology at the cervix in a standardized and reproducible manner. This study aimed to develop and validate a cervical lesion proportion (CLP) measure for quantification of cervical pathology in FGS. A digital imaging technique was applied in which a grid containing 424 identical squares was positioned on high resolution digital images from the cervix of 70 women with FGS. A CLP was made for each image by counting the total number of squares containing at least one type of pathognomonic lesions. For validation of inter- and intra-observer reliability, three different observers estimated CLP independently. In addition, a rubbery papule count (RPC) was determined in a similar manner. The intraclass correlation coefficient was 0.94 (excellent) for the CLP inter-rater reliability and 0.90 (good) for intra-rater reliability and the coefficients for the RPC were 0.88 and 0.80 (good), respectively. The CLP facilitated a reliable and reproducible quantification of the surface of the cervix affected by FGS pathognomonic lesions. Grading of cervical pathology by CLP can provide insight into the natural course of schistosome egg-induced pathology of the cervix. Moreover, CLP provides a measure for the efficacy of treatment.

Author summaryFemale genital schistosomiasis (FGS) is characterized by development of egg-induced chronic inflammatory lesions of the cervix and the vagina. FGS causes various symptoms such vaginal discharge, dyspareunia and post-coital bleeding, and the disease is further associated with reproductive complications such as ectopic pregnancy and infertility. Moreover, FGS is today considered as a major risk factor for transmission of HIV in Sub-Saharan Africa. General prevention directed against Schistosoma infection and use of praziquantel as anthelmintic drug therapy are cornerstones in the FGS control strategy. In that overall context, we have developed an important new digital image tool for quantitative assessment of FGS evoked cervical lesions, which enables evaluation of treatment outcome at individual as well as community level. The tool will also provide new information in understanding the natural history of FGS including development of clinical pathology.

category: pathology


title: Influence network model uncovers new relations between biological processes and mutational signatures

abstract:
There is a growing appreciation that mutagenic processes can be studied through the lenses of mutational signatures: characteristic mutation patterns attributed to individual mutagens. However, the link between mutagens and observed mutation patterns is not always obvious. In addition, mutational processes interact with each other, as well as with other cellular processes, in ways that are not fully understood. To gain insights into these relationships we developed a new approach, GenSigNet, that leverages a sparse partial correlation technique and a novel confounder-free higher moment-based approach for the construction of a directed network containing nodes representing genes and mutational signatures. When applied to cancer data, GenSigNet allowed to uncover important relations between mutational signatures and cellular processes including a relation between APOBEC hypermutation and activation of regulatory T Cells (Tregs), a relation between APOBEC mutations and changes in DNA conformation, and impact of homologous recombination deficiency on a clustered APOBEC mutations in breast cancer. GenSigNet also exposed a relation between the SBS8 signature of unknown aetiology and the nucleotide excision repair pathway.

GO_SCPLOWENEC_SCPLOWSO_SCPLOWIGC_SCPLOWNO_SCPLOWETC_SCPLOW is freely available at https://github.com/ncbi/GeneSigNet.


title: Exploratory methods for high-performance EEG speech decoding

abstract: State-of-the-art technologies in neural speech decoding utilize data collected from microwires or microarrays implanted directly into the cerebral cortex. Yet as a tool accessible only to individuals with implanted electrodes, speech decoding from devices of this nature is severely limited in its implementation, and cannot be considered a viable solution for widespread application. Speech decoding from non-invasive EEG signals can achieve relatively high accuracy (70-80%), but only from very small classification tasks, with more complex tasks typically yielding a limited (20-50%) classification accuracy. We propose a novel combination of technologies in which transcranial magnetic stimulation (TMS) is first applied to augment the neural signals of interest, producing a greater signal-to-noise ratio in the EEG data. Next, delay differential analysis (DDA) - a cutting-edge computational method based on nonlinear dynamics - is implemented to capture the widest range of information available in the neural signal, by incorporating both linear and nonlinear dynamics.


title: Mitochondrial OPA1 deficiency causes reversible defects in adult neurogenesis-associated spatial memory in mice

abstract:
Mitochondria are integrative hubs central to cellular adaptive pathways. Such pathways are critical in highly differentiated post-mitotic neurons, the plasticity of which sustains brain function. Consequently, defects in mitochondrial dynamics and quality control appear instrumental in neurodegenerative diseases and may also participate in cognitive impairments. To directly test this hypothesis, we analyzed cognitive performances in a mouse mitochondria-based disease model, due to haploinsufficiency in the mitochondrial optic-atrophy-type-1 (OPA1) protein. While in Dominant Optic Atrophy (DOA) models, the known main symptoms are late onset visual deficits, we discovered early impairments in hippocampus-dependent spatial memory attributable to defects in adult neurogenesis. Moreover, less connected hippocampal adult-born neurons showed a decrease in mitochondrial content. Remarkably, modulating mitochondrial function through voluntary exercise or pharmacological treatment restored spatial memory.

Altogether, our study identifies a crucial role for OPA1-dependent mitochondrial functions in adult neurogenesis, and thus in hippocampal-dependent cognitive functions. More generally, our findings show that adult neurogenesis is highly sensitive to mild mitochondrial defects, generating impairments in spatial memory that can be detected at an early stage and counterbalanced by physical exercise and pharmacological targeting of mitochondrial dynamics. Thus, early amplification of mitochondrial function appears beneficial for late-onset neurodegenerative diseases.


title: The sleep EEG envelope: a novel, neuronal firing-based human biomarker

abstract: Sleep EEG reflects instantaneous voltage differences relative to a reference, while its spectrum reflects the degree to which it is comprised of oscillations at various frequencies. In contrast, the envelope of the sleep EEG reflects the instantaneous amplitude of oscillations at specific frequencies, and its spectrum reflects the rhythmicity of the occurrence of these oscillations. The ordinary sleep EEG and its spectrum have been extensively studied and its individual stability and relationship to various demographic characteristics, psychological traits and pathologies is well known. In contrast, the envelope spectrum has not been extensively studied before. In two studies, we explored the generating mechanisms and utility of studying the envelope of the sleep EEG. First, we used human invasive data from cortex-penetrating microelectrodes and subdural grids to demonstrate that the sleep EEG envelope spectrum reflects local neuronal firing. Second, we used a large database of healthy volunteers to demonstrate that the scalp EEG envelope spectrum is highly stable within individuals, especially in NREM sleep, and that it is affected by age and sex. Multivariate models based on a learning algorithm could predict both age (r=0.6) and sex (r=0.5) with considerable accuracy from the EEG envelope spectrum. With age, oscillations characteristically shifted from a 4-5 second rhythm to higher rhythms. The envelope spectrum was not associated with general cognitive ability (IQ). Our results demonstrate that the sleep envelope spectrum is a promising, neuronal firing-based biomarker of various demographic and disease-related phenotypes.


title: The Flip-flop neuron - A memory efficient alternative for solving challenging sequence processing and decision making problems

abstract: Sequential decision making tasks that require information integration over extended durations of time are challenging for several reasons including the problem of vanishing gradients, long training times and significant memory requirements. To this end we propose a neuron model fashioned after the JK flip-flops in digital systems. A flip-flop is a sequential device that can store state information of the previous history. We incorporate the JK flip-flop neuron into several deep network architectures and apply the networks to difficult sequence processing problems. The proposed architectures include flip-flop neural networks (FFNNs), bidirectional flip-flop neural networks (BiFFNNs), convolutional flip-flop neural networks (ConvFFNNs), and bidirectional convolutional flip-flop neural networks (BiConvFFNNs). Learning rules of proposed architectures have also been derived. We have considered the most popular benchmark sequential tasks like signal generation, sentiment analysis, handwriting generation, text generation, video frame prediction, lung volume prediction, and action recognition to evaluate the proposed networks. Finally, we compare the results of our networks with the results from analogous networks with Long Short-Term Memory (LSTM) neurons on the same sequential tasks. Our results show that the JK flip-flop networks outperform the LSTM networks significantly or marginally on all the tasks, with only half of the trainable parameters.


title: Comparison of seven modelling algorithms for GABA-edited 1H-MRS

abstract:
Edited MRS sequences are widely used for studying GABA in the human brain. Several algorithms are available for modelling these data, deriving metabolite concentration estimates through peak fitting or a linear combination of basis spectra. The present study compares seven such algorithms, using data obtained in a large multi-site study.

GABA-edited (GABA+, TE = 68 ms MEGA-PRESS) data from 222 subjects at 20 sites were processed via a standardised pipeline, before modelling with FSL-MRS, Gannet, AMARES, QUEST, LCModel, Osprey and Tarquin, using standardised vendor-specific basis sets (for GE, Philips and Siemens) where appropriate.

After referencing metabolite estimates (to water or creatine), systematic differences in scale were observed between datasets acquired on different vendors hardware, presenting across algorithms. Scale differences across algorithms were also observed.

Using the correlation between metabolite estimates and voxel tissue fraction as a benchmark, most algorithms were found to be similarly effective in detecting differences in GABA+. An inter-class correlation across all algorithms showed single-rater consistency for GABA+ estimates of around 0.38, indicating moderate agreement. Upon inclusion of a basis set component explicitly modelling the macromolecule signal underlying the observed 3.0 ppm GABA peaks, single-rater consistency improved to 0.44. Correlation between discrete pairs of algorithms varied, and was concerningly weak in some cases.

Our findings highlight the need for consensus on appropriate modelling parameters across different algorithms, and for detailed reporting of the parameters adopted in individual studies to ensure reproducibility and meaningful comparison of outcomes between different studies.

HighlightsO_LIGABA-edited MRS data from 222 healthy adults across 20 research sites were analyzed
C_LIO_LIData were modelled using seven different algorithms, yielding GABA+ and Glx estimates
C_LIO_LIModerate agreement was seen across all the tested algorithms
C_LIO_LIAdding a component to represent co-edited macromolecule signals improved concordance
C_LIO_LIBaseline modelling emerged as major factor differentiating outcomes
C_LI