title: An integrative transcriptional logic model of hepatic insulin resistance

abstract:
Abnormalities of lipid/lipoprotein and glucose metabolism are hallmarks of hepatic insulin resistance in type 2 diabetes. The former antedate the latter, but the latter become progressively refractory to treatment and contribute to therapeutic failures. Its unclear whether the two processes share a common pathogenesis and what underlies their progressive nature. In this study, we investigated the hypothesis that genes in the lipid/lipoprotein pathway and those in the glucose metabolic pathway are governed by different transcriptional logics that affect their response to physiologic (fasting/refeeding) as well as pathophysiologic cues (insulin resistance and hyperglycemia). To this end, we obtained genomic and transcriptomic maps of the key insulin-regulated transcription factor, FoxO1, and integrated them with those of CREB, PPAR, and glucocorticoid receptor. We found an enrichment of glucose metabolic genes among those regulated by intergenic and promoter enhancers in a fasting-dependent manner, while lipid genes were enriched among fasting-dependent intron enhancers and fasting-independent enhancer-less introns. Glucose genes also showed a remarkable transcriptional resiliency, i.e., an enrichment of active marks at shared PPAR/FoxO1 regulatory elements when FoxO1 was inactivated. Surprisingly, the main features associated with insulin resistance and hyperglycemia were a "spreading" of FoxO1 binding to enhancers, and the emergence of target sites unique to this condition. We surmise that this unusual pattern correlates with the progressively intractable nature of hepatic insulin resistance. This transcriptional logic provides an integrated model to interpret the combined lipid and glucose abnormalities of type 2 diabetes.

Significance StatementThe liver is a source of excess lipid, atherogenic lipoproteins, and glucose in patients with type 2 diabetes. These factors predispose to micro- and macrovascular complications. The underlying pathophysiology is not well understood, and mechanistic insight into it may provide better tools to prevent, treat, and reverse the disease. Here we propose an alternative explanation for this pathophysiologic conundrum by illustrating a transcriptional "logic" underlying the regulation of different classes of genes. These findings can be interpreted to provide an integrated stepwise model for the coexistence of lipid and glucose abnormalities in hepatic insulin resistance.

HighlightsO_LIFoxo1 regulates liver metabolism through active enhancers, and hepatocyte maintenance through core promoters
C_LIO_LIFoxo1 regulates glucose genes through fasting-dependent intergenic enhancers
C_LIO_LIBipartite intron regulation of lipid genes is partly fasting-independent
C_LIO_LIPpar contributes to the transcriptional resiliency of Foxo1 metabolic targets
C_LIO_LIInsulin resistance causes de novo recruitment of Foxo1 to active enhancers
C_LIO_LIA stepwise model of insulin resistance
C_LI


title: A gut-restricted lithocholic acid analog as an inhibitor of gut bacterial bile salt hydrolases

abstract: Bile acids play crucial roles in host physiology by acting as both detergents that aid in digestion and as signaling molecules that bind to host receptors. Gut bacterial bile salt hydrolase (BSH) enzymes perform the gateway reaction leading to the conversion of host-produced primary bile acids into bacterially modified secondary bile acids. Small molecule probes that target BSHs will help elucidate the causal roles of these metabolites in host physiology. We previously reported the development of a covalent BSH inhibitor with low gut permeability. Here, we build on our previous findings and describe the development of a second-generation gut-restricted BSH inhibitor with enhanced potency, reduced off-target effects, and durable in vivo efficacy. SAR studies focused on the bile acid core identified a compound, AAA-10, containing a C3-sulfonated lithocholic acid scaffold and an alpha-fluoromethyl ketone warhead as a potent pan-BSH inhibitor. This compound inhibits BSH activity in conventional mouse fecal slurries, bacterial cultures, and purified BSH proteins and displays reduced toxicity against mammalian cells compared to first generation compounds. Oral administration of AAA-10 to wild-type mice for 5 days resulted in a decrease in the abundance of the secondary bile acids deoxycholic acid (DCA) and lithocholic acid (LCA) in the mouse GI tract with low systemic exposure of AAA-10, demonstrating that AAA-10 is an effective tool for inhibiting BSH activity and modulating bile acid pool composition in vivo.

category: biochemistry


title: Predicting Cellular Drug Sensitivity using Conditional Modulation of Gene Expression

abstract: Selecting drugs most effective against a tumors specific transcriptional signature is an important challenge in precision medicine. To assess oncogenic therapy options, cancer cell lines are dosed with drugs that can differentially impact cellular viability. Here we show that basal gene expression patterns can be conditioned by learned small molecule structure to better predict cellular drug sensitivity, achieving an R2 of 0.7190{+/-}0.0098 (a 5.61% gain). We find that 1) transforming gene expression values by learned small molecule representations outperforms raw feature concatenation, 2) small molecule structural features meaningfully contribute to learned representations, and 3) an affine transformation best integrates these representations. We analyze conditioning parameters to determine how small molecule representations modulate gene expression embeddings. This ongoing work formalizes in silico cellular screening as a conditional task in precision oncology applications that can improve drug selection for cancer treatment.

category: bioinformatics


title: Codependency and mutual exclusivity for gene community detection from sparse single-cell transcriptome data

abstract: Single-cell RNA-seq (scRNA-seq) can be used to characterize cellular heterogeneity in thousands of cells. The reconstruction of a gene network based on coexpression patterns is a fundamental task in scRNA-seq analyses, and the mutual exclusivity of gene expression can be critical for understanding such heterogeneity. Here, we propose an approach for detecting communities from a genetic network constructed on the basis of coexpression properties. The community-based comparison of multiple coexpression networks enables the identification of functionally related gene clusters that cannot be fully captured through differential gene expression-based analysis. We also developed a novel metric referred to as the exclusively expressed index (EEI) that identifies mutually exclusive gene pairs from sparse scRNA-seq data. EEI quantifies and ranks the exclusive expression levels of all gene pairs from binary expression patterns while maintaining robustness against a low sequencing depth. We applied our methods to glioblastoma scRNA-seq data and found that gene communities were partially conserved after serum stimulation despite a considerable number of differentially expressed genes. We also demonstrate that the identification of mutually exclusive gene sets with EEI can improve the sensitivity of capturing cellular heterogeneity. Our methods complement existing approaches and provide new biological insights, even for a large, sparse dataset, in the single-cell analysis field.


title: The Most Parsimonious Reconciliation Problem in the Presence of Incomplete Lineage Sorting and Hybridization is NP-Hard

abstract: The maximum parsimony phylogenetic reconciliation problem seeks to explain incongruity between a gene phylogeny and a species phylogeny with respect to a set of evolutionary events. While the reconciliation problem is well-studied for species and gene trees subject to events such as duplication, transfer, loss, and deep coalescence, recent work has examined species phylogenies that incorporate hybridization and are thus represented by networks rather than trees. In this paper, we show that the problem of computing a maximum parsimony reconciliation for a gene tree and species network is NP-hard even when only considering deep coalescence. This result suggests that future work on maximum parsimony reconciliation for species networks should explore approximation algorithms and heuristics.

category: evolutionary biology


title: Age-related neurodegeneration and cognitive impairments of NRMT1 knockout mice are preceded by misregulation of RB and expansion of the neural stem cell population

abstract: N-terminal methylation is an important post-translational modification that regulates protein/DNA interactions and plays a role in many cellular processes, including DNA damage repair, mitosis, and transcriptional regulation. Our generation of a constitutive knockout mouse for the N-terminal methyltransferase NRMT1, demonstrated its loss results in severe developmental abnormalities and premature aging. As premature aging is often accompanied by neurodegeneration, we more specifically examined how NRMT1 loss affects neural pathology and cognitive behaviors. Here we find that Nrmt1-/- mice exhibit postnatal enlargement of the lateral ventricles, age-dependent striatal and hippocampal neurodegeneration, memory impairments, and hyperactivity. These morphological and behavior abnormalities are preceded by alterations in neural stem cell (NSC) development. Depletion of quiescent NSC pools in Nrmt1-/- mice is concurrent with expansion of intermediate progenitor and neuroblast pools. These phenotypes are similar to those seen with loss of the NRMT1 target retinoblastoma protein (RB), and we see that NRMT1 loss leads to derepression of RB target genes and abnormal RB phosphorylation and degradation. As also seen with RB loss, neurons in Nrmt1-/- mice fail to exit cell cycle and ultimately undergo NOXA-mediated apoptosis, indicating that early misregulation of RB in Nrmt1-/- mice promotes premature NSC proliferation and contributes to subsequent neurodegenerative phenotypes.

category: neuroscience


title: Complementary resource preferences spontaneously emerge in diauxic microbial communities

abstract: Many microbes grow diauxically, utilizing the available resources one at a time rather than simultaneously. The properties of communities of microbes growing diauxically remain poorly understood, largely due to a lack of theory and models of such communities. Here, we develop and study a minimal model of diauxic microbial communities assembling in a serially diluted culture. We find that unlike co-utilizing communities, diauxic community assembly repeatably and spontaneously leads to communities with complementary resource preferences, i.e., communities where species prefer different resources as their top choice. Simulations and theory explain that the emergence of complementarity is driven by the disproportionate contribution of the top choice resource to the growth of a diauxic species. Additionally, we develop a geometric approach for analyzing serially diluted communities, with or without diauxie, which intuitively explains several additional emergent community properties, such as the apparent lack of species which grow fastest on a resource other than their most preferred resource. Overall, our work provides testable predictions for the assembly of natural as well as synthetic communities of diauxically shifting microbes.

category: ecology


title: Powering electronic implants by high frequency volume conduction: in human validation

abstract: Wireless power transfer (WPT) is frequently used as an alternative to batteries to accomplish miniaturization in electronic medical implants (eMIs). However, established WPT methods require bulky parts within the implant or cumbersome external systems, hindering minimally invasive deployments and the development of networks of eMIs. As an alternative, we propose a WPT approach based on volume conduction of high frequency (HF) current bursts. These currents are applied through external textile electrodes and are collected by the eMIs through two electrodes at their opposite ends. This approach avoids bulky components to obtain power, making it possible to develop implants with a flexible threadlike conformation. In here we study in humans if HF (6.78 MHz) current bursts complying with safety standards and applied through two textile electrodes strapped around a limb can provide substantial powers from pairs of implanted electrodes. Time averaged electric powers obtained from needle electrodes (diameter = 0.4 mm, length = 3 mm, separation = 30 mm) inserted into arms and lower legs of five healthy participants were 5.9 {+/-} 0.7 mW and 2.4 {+/-} 0.3 mW respectively. We also report a procedure to characterize the coupling between the external system and the implants using two-port impedance models generated from medical images. The results demonstrate for the first time in humans that innocuous and imperceptible HF current bursts that flow through the tissues by volume conduction can be used to wirelessly power threadlike eMIs, overcoming the limitations of existing WPT methods in terms of minimal invasiveness and usability.

category: bioengineering


title: Circular RNA Vaccines against SARS-CoV-2 and Emerging Variants

abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its emerging variants of concern (VOC), such as Delta (B.1.617.2) and Omicron (B.1.1.529), has continued to drive the worldwide pandemic. Therefore, there is a high demand for vaccines with enhanced efficacy, high thermostability, superior design flexibility, and fast manufacturing speed. Here, we report a circular RNA (circRNA) vaccine that encodes the trimeric RBD of SARS-CoV-2 Spike protein. Without the need of nucleotide modification, 5-capping or 3-polyadenylation, circRNA could be rapidly produced via in vitro transcription and is highly thermostable whether stored in naked or lipid-nanoparticle (LNP)-encapsulated format. LNP-encapsulated circRNARBD elicited potent neutralizing antibodies and T cell responses, providing robust protection against Beta (B.1.351) and native viruses in mice and rhesus macaques, respectively. Notably, circRNA vaccine enabled higher and more durable antigen production than 1m{Psi}-modified mRNA vaccine, eliciting a higher proportion of neutralizing antibodies and stronger Th1-biased immune responses. Importantly, we found that circRNARBD-Omicron vaccine induced effective neutralizing antibodies against only Omicron but not Delta variant. By contrast, circRNARBD-Delta could elicit high level of neutralizing antibodies against both Delta and Omicron. Following two doses of either native- or Delta-specific vaccination, circRNARBD-Delta, but not Omicron or Beta vaccines, could effectively boost the neutralizing antibodies against both Delta and Omicron variants. These results suggest that circRNARBD-Delta is a favorable choice for vaccination to provide a broad-spectrum protection against the current variants of concern of SARS-CoV-2.

category: immunology


title: Programming Cell-Free Biosensors with DNA Strand Displacement Circuits

abstract: Cell-free biosensors are emerging as powerful platforms for monitoring human and environmental health. Here, we expand the capabilities of biosensors by interfacing their outputs with toehold-mediated strand displacement circuits, a dynamic DNA nanotechnology that enables molecular computation through programmable interactions between nucleic acid strands. We develop design rules for interfacing biosensors with strand displacement circuits, show that these circuits allow fine-tuning of reaction kinetics and faster response times, and demonstrate a circuit that acts like an analog-to-digital converter to create a series of binary outputs that encode the concentration range of the target molecule being detected. We believe this work establishes a pathway to create "smart" diagnostics that use molecular computations to enhance the speed, robustness and utility of biosensors.

category: synthetic biology


title: Climate Change Controls Phosphorus Transport from the Watershed into Lake Kinneret (Israel)

abstract: Part of the Kinneret watershed, the Hula Valley, was modified from wetlands - shallow lake for agricultural cultivation. Enhancement of nutrient fluxes into Lake Kinneret was predicted. Therefore, a reclamation project was implemented and eco-tourism partly replaced agriculture. Since the mid-1980s, regional climate change has been documented. Statistical evaluation of long-term records of TP (Total Phosphorus) concentrations in headwaters and potential resources in the Hula Valley was carried out to identify efficient management design targets. Significant correlation between major headwater river discharge and TP concentration was indicated, whilst the impact of external fertilizer loads and 50,000 winter migratory cranes was probably negligible. Nevertheless, confirmed severe bdamage to agricultural crops carried out by cranes led to their maximal deportation and optimization of their feeding policy. Consequently, the continuation of the present management is recommended.


title: Targeting Glioblastoma Signaling and Metabolism with A Re-Purposed Brain-Penetrant Drug

abstract: The highly lethal brain cancer glioblastoma (GBM) poses a daunting challenge because the blood-brain barrier renders potentially druggable amplified or mutated oncoproteins relatively inaccessible. Here, we identify SMPD1, an enzyme that regulates the conversion of sphingomyelin to ceramide and a critical regulator of plasma membrane structure and organization, as an actionable drug target in glioblastoma. We show that the safe and highly brain-penetrant antidepressant fluoxetine, potently inhibits SMPD1 activity, killing GBMs, in vitro and in patient-derived xenografts, through inhibition of EGFR signaling and via activation of lysosomal stress. Combining fluoxetine with the chemotherapeutic agent temozolomide, a standard of care for GBM patients, causes massive increases in GBM cell death, and complete and long-lived tumor regression in mice. Incorporation of real-world evidence from electronic medical records from insurance databases, reveals significantly increased survival in glioblastoma patients treated with fluoxetine, which was not seen in patients treated with other SSRI anti-depressants. These results nominate the repurposing of fluoxetine as a potentially safe and promising therapy for GBM patients and suggest prospective randomized clinical trials.

category: cancer biology


title: Diverse mobile genetic elements support the persistence of listeria monocytogenes on dairy farms

abstract:
Listeria monocytogenes is a food-borne pathogen and a resilient environmental saprophyte. Dairy farms are a reservoir of L. monocytogenes and strains can persist on farms for years. Here, we sequenced the genomes of 250 L. monocytogenes isolates to investigate the persistence and mobile genetic elements of Listeria inhabiting dairy farms. We performed a SNP-based phylogenomic analysis to identify 14 monophyletic clades of L. monocytogenes that persistent on the farms for [≥] 6 months. We found that prophages and other mobile genetic elements were on average more numerous among isolates in persistent than nonpersistent clades, and demonstrated that resistance genes against bacitracin, arsenic and cadmium were significantly more prevalent among isolates in persistent than nonpersistent clades. We identified a diversity of mobile elements among the 250 farm isolates, including three novel plasmids, three novel transposons and a novel prophage harbouring cadmium resistance genes. Several of the mobile elements we identified in Listeria were identical to the mobile elements of Enterococci, indicative of recent transfer between these genera. Finally, we demonstrated that the CRISPR-cas IIa system and a type II restriction-modification system were negatively associated with persistence on farms. Our findings suggest that mobile elements support the persistence of L. monocytogenes on dairy farms and that L. monocytogenes inhabiting the agroecosystem is a potential reservoir of mobile elements that may spread to the food industry.

ImportanceAnimal derived raw materials are an important source of L. monocytogenes for the food industry. Knowledge of the factors contributing to the pathogens transmission and persistence on farms are essential for designing effective strategies against the spread of the pathogen from farm to fork. An increasing body of evidence suggests that mobile genetic elements support the adaptation and persistence of L. monocytogenes in the food industry, as these elements contribute to the dissemination of genes encoding favourable phenotypes, such as resilience against biocides and thermal stress. Understanding the role of farms as a potential reservoir of these elements is needed for managing the transmission of mobile elements across the food chain. Because L. monocytogenes coinhabits the farm ecosystem with a diversity of other bacterial species, it is important to assess the degree to which genetic elements are exchanged between Listeria and other species, as such exchanges may contribute to rise the novel resistance phenotypes.

category: microbiology


title: Mobile elements harbouring heavy metal and bacitracin resistance cassettes are common among Listeria monocytogenes persisting on dairy farms


title: Moving outside the lab: markerless motion capture accurately quantifies sagittal plane kinematics during the vertical jump

abstract: Markerless motion capture using deep learning approaches have potential to revolutionize the field of biomechanics by allowing researchers to collect data outside of the laboratory environment, yet there remain questions regarding the accuracy and ease of use of these approaches. The purpose of this study was to apply a markerless motion capture approach to extract lower limb angles in the sagittal plane during the vertical jump and to evaluate agreement between the custom trained model and gold stand motion capture. We performed this study using a large open source data set (N=84) that included synchronized commercial video and gold standard motion capture. We split these data into a training set for model development (n=69) and test set to evaluate capture performance relative to gold standard motion capture using coefficient of multiple correlations (CMC) (n=15). We found very strong agreement between the custom trained markerless approach and marker-based motion capture within the test set across the entire movement (CMC>0.991, RMSE<3.22{degrees}), with at least strong CMC values across all trials for the hip (0.853 {+/-} 0.23), knee (0.963 {+/-} 0.471), and ankle (0.970 {+/-} 0.055). The strong agreement between markerless and marker-based motion capture provides evidence that markerless motion capture is a viable tool to extend data collection to outside of the laboratory. As biomechanical research struggles with representative sampling practices, markerless motion capture has potential to transform biomechanical research away from traditional laboratory settings into venues convenient to populations that are under sampled without sacrificing measurement fidelity.


title: Buffering Updates Enables Efficient Dynamic de Bruijn Graphs

abstract:
MotivationThe de Bruijn graph has become a ubiquitous graph model for biological data ever since its initial introduction in the late 1990s. It has been used for a variety of purposes including genome assembly (Zerbino and Birney, 2008; Bankevich et al., 2012; Peng et al., 2012), variant detection (Alipanahi et al., 2020b; Iqbal et al., 2012), and storage of assembled genomes (Chikhi et al., 2016). For this reason, there have been over a dozen methods for building and representing the de Bruijn graph and its variants in a space and time efficient manner.

ResultsWith the exception of a few data structures (Muggli et al., 2019; Holley and Melsted, 2020; Crawford et al., 2018), compressed and compact de Bruijn graphs do not allow for the graph to be efficiently updated, meaning that data can be be added or deleted. The most recent compressed dynamic de Bruijn graph (Alipanahi et al., 2020a), relies on dynamic bit vectors which are slow in theory and practice. To address this shortcoming, we present a compressed dynamic de Bruijn graph that removes the necessity of dynamic bit vectors by buffering data that should be added or removed from the graph. We implement our method, which we refer to as BufBOSS, and compare its performance to Bifrost, DynamicBOSS, and FDBG. Our experiments demonstrate that BufBOSS achieves attractive trade-offs compared to other tools in terms of time, memory and disk, and has the best deletion performance by an order of magnitude.

Contactalanko.jarno@gmail.com


title: Fast holographic scattering compensation for deep tissue biologicalimaging

abstract: Scattering in biological tissues is a major barrier for in vivo optical imaging of all but the most superficial structures. Progress toward overcoming the distortions caused by scattering in turbid media has been made by shaping the excitation wavefront to redirect power into a single point in the imaging plane. However, fast, non-invasive determination of the required wavefront compensation remains challenging. Here, we introduce a quickly converging algorithm for non-invasive scattering compensation, termed DASH, in which holographic phase stepping interferometry enables new phase information to be updated after each measurement. This leads to rapid improvement of the wavefront correction, forming a focus after just one measurement iteration and achieving an order of magnitude higher signal enhancement at this stage than the previous state-of-the-art. Using DASH, we demonstrate two-photon fluorescence imaging of microglia cells in highly turbid mouse hippocampal tissue down to a depth of 530 m.

category: biophysics


title: Structure of SOQ1 lumenal domains identifies potential disulfide exchange for negative regulation of photoprotection, qH

abstract: Non-photochemical quenching (NPQ) plays an important role for phototrophs in decreasing photo-oxidative damage. qH is a sustained component of NPQ and depends on the plastid lipocalin (LCNP). A thylakoid membrane-anchored protein SUPPRESSOR OF QUENCHING1 (SOQ1) prevents qH formation by inhibiting LCNP. SOQ1 suppresses qH with its lumen-located C-terminal Trx-like and NHL domains. Here we report crystal structures and biochemical characterization of SOQ1 lumenal domains. Our results show that the Trx-like and NHL domains are stably associated, with the potential redox-active motif located at their interface. Residue E859 essential for SOQ1 function is pivotal for mediating the inter-domain interaction. Moreover, the C-terminal region of SOQ1 forms an independent {beta}-stranded domain, which possibly interacts with the Trx-like domain through disulfide exchange. Furthermore, SOQ1 is susceptible to cleavage at the loops connecting the neighboring domains both in vitro and in vivo, which could be a regulatory process for its suppression function of qH.

category: plant biology


title: Population differences in the length, early-life dynamics, and heritability of telomeres among European pied flycatchers

abstract: Telomere length and shortening rate are increasingly used as biomarkers for long-term costs in ecological and evolutionary studies because of their relationships with survival and fitness. Both early-life conditions and growth, and later-life stressors can create variation in telomere shortening rate. Studies on between- population telomere length and dynamics are scarce, despite the expectation that populations exposed to varying environmental constraints would present divergent telomere length patterns. The pied flycatcher (Ficedula hypoleuca) is a passerine bird breeding across Eurasia (from Spain to western Siberia) and migrating through the Iberian Peninsula to spend the non-breeding period in sub-Saharan Africa. Thus, different populations show marked differences in migration distance. We studied the large-scale variation of telomere length and early-life dynamics in the pied flycatcher by comparing six European populations across a north- south gradient (Finland, Estonia, England, and Spain) predicting negative effect of migration distance on adult telomere length, and of nestling growth on nestling telomere dynamics. There were clear population differences in telomere length, with English birds from mid-latitudes having the longest telomeres. Telomere length did not thus show consistent latitudinal variation and was not linearly linked to differences in migration distance. Early-life telomere shortening rate tended to vary between populations. Fast growth was associated with shorter telomeres in the early life, but faster nestling growth affected telomeres more negatively in northern than southern populations. While the sources of between-population differences in telomere-related biology remain to be more intensively studied, our study illustrates the need to expand telomere studies at the between-population level.

category: zoology


title: Population differences in the length and early-life dynamics of telomeres among European pied flycatchers


title: Loss of the glial glutamate transporter eaat2a leads to a combined developmental and epileptic encephalopathy in zebrafish

abstract: Astroglial excitatory amino acid transporter 2 (EAAT2, GLT-1, SLC1A2) regulates the duration and extent of neuronal excitation by removing glutamate from the synaptic cleft. Hence, an impairment in EAAT2 function could lead to an imbalanced neural network excitability. Here, we investigated the functional alterations of neuronal and astroglial networks associated with the loss of function in the astroglia predominant eaat2a gene in zebrafish. We observed that eaat2a-/- mutant zebrafish larvae display recurrent spontaneous and light-induced seizures in neurons and astroglia, which coincide with an abrupt increase in extracellular glutamate levels. In stark contrast to this hyperexcitability, basal neuronal and astroglial activity was surprisingly reduced in eaat2a-/- mutant animals, which manifested in decreased overall locomotion. Our results reveal an essential and mechanistic contribution of EAAT2a in balancing brain excitability, and its direct link to epileptic seizures.


title: Loss of glutamate transporter eaat2a leads to aberrant neuronal excitability, recurrent epileptic seizures and hypoactivity


title: Source imaging of high-density visual evoked potentials with multi-scale brain parcellations and connectomes

abstract: We describe the multimodal neuroimaging dataset VEPCON (OpenNeuro Dataset ds003505). It includes raw data and derivatives of high-density EEG, structural MRI, diffusion weighted images (DWI) and single-trial behavior (accuracy, reaction time). Visual evoked potentials (VEPs) were recorded while participants (n=20) discriminated briefly presented faces from scrambled faces, or coherently moving stimuli from incoherent ones. EEG and MRI were recorded separately from the same participants. The dataset contains pre-processed EEG of single trials in each condition, behavioral measures, structural MRIs, individual brain parcellations at 5 spatial resolutions (83 to 1015 regions), and the corresponding structural connectomes computed from fiber count, fiber density, average fractional anisotropy and mean diffusivity maps. For source imaging, VEPCON provides EEG inverse solutions based on individual anatomy, with Python and Matlab scripts to derive activity time-series in each brain region, for each parcellation level. The BIDS-compatible dataset can contribute to multimodal methods development, studying structure-function relations, and to unimodal optimization of source imaging and graph analyses, among many other possibilities.


title: Fitness costs and benefits of gene expression plasticity in rice under drought

abstract: Genome-wide gene expression changes in response to environmental variability have been widely documented, but we lack detailed and comprehensive understanding of the interplay between this form of phenotypic plasticity and natural selection. Selection on expression plasticity may be limited by environment-specific costs, and plasticity may in turn affect selection on baseline expression levels. Here, we address this fundamental issue by measuring selection on drought-induced plasticity of leaf transcripts in field-grown rice populations. Selection disfavored switching off housekeeping genes under drought. This stress-induced dysregulation did not constrain selection on baseline transcript levels, suggesting compensatory evolution may be possible. Selection rarely acted strongly on individual transcripts but worked polygenically on gradual (continuous) plasticity of co-expressed gene modules regulating photosynthesis via known drought-responsive transcription factors. Finally, selection was tied to inefficient gene architectural features and metabolic costs of expression. Our study provides a genome-wide view of costs and benefits of gene expression plasticity.


title: Deconvolution of Expression for Nascent RNA Sequencing Data (DENR) Highlights Pre-RNA Isoform Diversity in Human Cells

abstract: Quantification of mature-RNA isoform abundance from RNA-seq data has been extensively studied, but much less attention has been devoted to quantifying the abundance of distinct precursor RNAs based on nascent RNA sequencing data. Here we address this problem with a new computational method called Deconvolution of Expression for Nascent RNA sequencing data (DENR). DENR models the nascent RNA read counts at each locus as a mixture of user-provided isoforms. The performance of the baseline algorithm is enhanced by the use of machine-learning predictions of transcription start sites (TSSs) and an adjustment for the typical "shape profile" of read counts along a transcription unit. We show using simulated data that DENR clearly outperforms simple read-count-based methods for estimating the abundances of both whole genes and isoforms. By applying DENR to previously published PRO-seq data from K562 and CD4+ T cells, we find that transcription of multiple isoforms per gene is widespread, and the dominant isoform frequently makes use of an internal TSS. We also identify > 200 genes whose dominant isoforms make use of different TSSs in these two cell types. Finally, we apply DENR and StringTie to newly generated PRO-seq and RNA-seq data, respectively, for human CD4+ T cells and CD14+ monocytes, and show that entropy at the pre-RNA level makes a disproportionate contribution to overall isoform diversity, especially across cell types. Altogether, DENR is the first computational tool to enable abundance quantification of pre-RNA isoforms based on nascent RNA sequencing data, and it reveals high levels of pre-RNA isoform diversity in human cells.

category: genomics


title: Integration of plant carbohydrate dynamics by Fourier polynomials

abstract:
Quantification of system dynamics is a central aim of mathematical modelling in biology. Defining experimentally supported functional relationships between molecular entities by mathematical terms enables the application of computational routines to simulate and analyse the underlying molecular system. In many fields of natural sciences and engineering, trigonometric functions are applied to describe oscillatory processes. As biochemical oscillations occur in many aspects of biochemistry and biophysics, Fourier analysis of metabolic functions promises to quantify, describe and analyse metabolism and its reaction towards environmental fluctuations. Here, Fourier polynomials were developed from experimental time-series data and combined with block diagram simulation of plant metabolism to study heat shock response of photosynthetic CO2 assimilation and carbohydrate metabolism. Findings suggest that increased capacities of starch biosynthesis stabilize photosynthetic CO2 assimilation under transient heat exposure. Among soluble sugars, fructose concentrations were observed to fluctuate least under heat exposure which might be the consequence of high respiration rates under elevated temperature. Finally, Col-0 and two mutants of Arabidopsis thaliana with deficiencies in starch and sucrose metabolism were discriminated by fundamental frequencies of Fourier polynomials across different experiments. This suggests balance modelling based on Fourier polynomials as a suitable approach for mathematical analysis of dynamic plant-environment interactions.

HighlightA balance equation model is developed to quantify effects of transient heat exposure on plant carbon assimilation. The model is based on Fourier polynomials for quantitative assessment of system dynamics.


title: Accurate reconstruction of dynamic gene expression and growth rate profiles from noisy measurements

abstract:
Cells face changing environments to which they sense and respond in complex ways, changing their rates of gene expression and growth. Measuring these dynamics is therefore essential to understanding natural and synthetic regulatory networks that give rise to functional phenotypes. However, reconstruction of gene expression and growth rate profiles from typically noisy measurements of cell populations is difficult due to the effects of noise at low cell densities among other factors. We present here a method for estimation of dynamic gene expression rates and biomass growth rates from noisy measurement data, and show that it is several times more accurate than current approaches. We applied our method to multiple promoter-reporter fusion genes. Gene expression rates of such promoter-reporter fusions are typically used as a proxy for transcription rates. However, using our method we show that fusion gene expression rate dynamics are determined at least by the promoter of interest and the downstream reporter.

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category: systems biology


title: P-sort: an open-source software for cerebellar neurophysiology

abstract: Analysis of electrophysiological data from Purkinje cells (P-cells) of the cerebellum presents challenges for spike detection. Complex spikes have waveforms that vary significantly from one event to the next, raising the problem of misidentification. Even when complex spikes are detected correctly, the simple spikes may belong to a different P-cell, raising the danger of misattribution. Here, we analyzed data from over 300 P-cells in marmosets, macaques, and mice, using an open-source, semi-automated software called P-sort that addresses the spike identification and attribution problems. Like other sorting software, P-sort relies on nonlinear dimensionality reduction to cluster spikes. However, it also uses the statistical relationship between simple and complex spikes to merge seemingly disparate clusters, or split a single cluster. In comparison with expert manual curation, occasionally P-sort identified significantly more complex spikes, as well as prevented misattribution of clusters. Three existing automatic sorters performed less well, particularly for identification of complex spikes. To improve development of analysis tools for the cerebellum, we provide labeled data for 313 recording sessions, as well as statistical characteristics of waveforms and firing patterns.


title: Signal complexity indicators of health status in clinical-EEG

abstract: Brain signal variability changes across the lifespan in both health and disease, likely reflecting changes in information processing capacity related to development, aging and neurological disorders. While signal complexity, and multiscale entropy (MSE) in particular, has been proposed as a biomarker for neurological disorders, most observations of altered signal complexity have come from studies comparing patients with few to no comorbidities against healthy controls. In this study, we examined whether MSE of brain signals was distinguishable across individuals in a large and heterogeneous set of clinical-EEG data. Using a multivariate analysis, we found unique timescale-dependent differences in MSE across various neurological disorders. We also found MSE to differentiate individuals with non-brain comorbidities, suggesting that MSE is sensitive to brain signal changes brought about by metabolic and other non-brain disorders. Such changes were not detectable in the spectral power density of brain signals. Our findings suggest that brain signal complexity may offer complementary information to spectral power about an individuals health status and is a promising avenue for clinical biomarker development.


title: MDGAs are fast-diffusing molecules that delay excitatory synapse development by altering neuroligin behavior

abstract: MDGAs are molecules that can bind neuroligins in cis and interfere with trans-synaptic neurexin-neuroligin interactions, thereby impairing synapse development. However, the sub-cellular localization and dynamics of MDGAs, as well as their specific mode of action in neurons are still unclear. Here, using both surface immunostaining of endogenous MDGAs and single molecule tracking of recombinant MDGAs in dissociated hippocampal neurons, we show that MDGA1 and MDGA2 molecules are homogeneously distributed and exhibit fast membrane diffusion, with a small reduction in mobility across neuronal maturation in culture Using shRNAs and CRISPR/Cas9 strategies to knock-down/out MDGA1 or MDGA2, we demonstrate an increase in the density of excitatory synapses accompanied by enhanced membrane immobilization and an increase in the phosphotyrosine level of neuroligins associated with excitatory post-synaptic differentiation. Finally, we show that decreasing MDGA expression level reduces the mobility of AMPA receptors and increases the frequency of AMPA receptor mediated mEPSCs. Overall, our results support a mechanism by which interactions between MDGAs and neuroligin-1 delays the assembly of functional excitatory synapses containing AMPA receptors.


title: Cannabidiol attenuates cognitive deficits and neuroinflammation induced by early alcohol exposure in a mice model.

abstract: Foetal alcohol spectrum disorder (FASD) is the umbrella term used to describe the physical and mental disabilities induced by alcohol exposure during development. Early alcohol exposure induces cognitive impairments resulting from damage to the central nervous system (CNS). The neuroinflammatory response accompanied by neurodegenerative mechanisms contribute to those detrimental alterations. Cannabidiol (CBD) has recently emerged as an anti-inflammatory drug that might be useful to treat several neuropsychiatric disorders. In our study, we assessed the effects of CBD on long-lasting cognitive deficits induced by early alcohol exposure. Furthermore, we analysed long-term pro-inflammatory and apoptotic markers within the prefrontal cortex and hippocampus. To model alcohol binge drinking during gestational and lactation periods, we used pregnant C57BL/6 female mice with time-limited access to 20% v/v alcohol solution. Following the prenatal and lactation alcohol exposure (PLAE), we treated the male and female offspring with CBD from post-natal day (PD) 25 until PD34, and we evaluated their cognitive performance at PD60. Our results showed that CBD treatment during peri-adolescence period ameliorates cognitive deficits observed in our FASD-like mouse model, without sex differences. Moreover, CBD restores the PLAE-induced increased levels of TNF and IL-6 in the hippocampus. Thus, our study provides new insights for CBD as a therapeutic agent to counteract cognitive impairments and neuroinflammation caused by early alcohol exposure.


title: Male rat sexual behavior: insights from inter-copulatory intervals

abstract: The assessment of sexual behavior in male rats with the aim of unraveling underlying neurobiological mechanisms has in the recent decades been reduced to the annotation of mounts, intromissions and ejaculations. To provide a better understanding of the structure and patterns of copulation, it is necessary to extend and tailor the analysis to the natural organization of male rat copulation. This will lead to better formulation of hypotheses about neurobiological underpinnings of behavior. Mounts and intromissions are naturally organized in mount bouts consisting of one or more copulatory behaviors and are interspersed with time outs. We hypothesized that time outs and the post-ejaculatory interval (inter-copulatory intervals) are related and possibly under the control of a common copulatory inhibition mechanism that is the result of penile sensory stimulation. To test this hypothesis, we analyzed sexual behavior in male rats of three different cohorts from three different laboratories. Results showed that the post-ejaculatory interval and mean time out duration are strongly correlated in all cohorts analyzed. In addition, we showed that individual time out duration is at least partially predicted by the sum of sensory stimulation of copulatory components in the preceding mount bout, with more penile stimulation associated with longer time outs. These findings suggest that both time out and post-ejaculatory interval duration may be determined by the magnitude of sensory stimulation, which inhibits copulation. Whether the same neural pathways are involved in the central orchestration of both time outs and the post-ejaculatory interval should be subject to future studies.


title: Cellular pathways during spawning induction in the starlet sea anemone Nematostella vectensis

abstract:
In cnidarians, long-term ecological success relies on sexual reproduction. The sea anemone Nematostella vectensis, which has emerged as an important model organism for developmental studies, can be induced for spawning by temperature elevation and light exposure. To uncover molecular mechanisms and pathways underlying spawning, we characterized the transcriptome of Nematostella females before and during spawning induction. We identified an array of processes involving numerous receptors, circadian clock components, cytoskeleton, and extracellular transcripts that are upregulated upon spawning induction. Concurrently, processes related to the cell cycle, fatty acid metabolism, and other housekeeping functions are downregulated. Real-time qPCR revealed that light exposure has a minor effect on expression levels of most examined transcripts, implying that temperature change is a stronger inducer for spawning in Nematostella. Our findings reveal the mechanisms that may enable the mesenteries to serve as a gonad-like tissue for the developing oocytes and expand our understanding of sexual reproduction in cnidarians.

Summary statementAnalysis of transcriptional changes during spawning induction in Nematostella vectensis, revealed upregulation of processes related to signal perception and cytoskeleton rearrangement and downregulation of fatty acid metabolism and housekeeping processes.


title: Timing of increased temperature sensitivity coincides with nervous system development in winter moth embryos

abstract: Climate change is rapidly altering the environment and many species will need to genetically adapt their seasonal timing to keep up with these changes. Insect development rate is largely influenced by temperature, but we know little about the mechanisms underlying temperature sensitivity of development. Here we investigate seasonal timing of egg hatching in the winter moth, one of the few species which has been found to genetically adapt to climate change, likely through selection on temperature sensitivity of egg development rate. To study when during development winter moth embryos are most sensitive to changes in ambient temperature, we gave eggs an increase or decrease in temperature at different moments during their development. We measured their developmental progression and timing of egg hatching, and used fluorescence microscopy to construct a timeline of embryonic development for the winter moth. We found that egg development rate responded more strongly to temperature once embryos were in the fully extended germband stage. This is the phylotypic stage at which all insect embryos have developed a rudimentary nervous system. Furthermore, at this stage timing of ecdysone signaling determines developmental progression, which could act as an environment dependent gateway. Intriguingly, this may suggest that, from the phylotypic stage onward, insect embryos can start to integrate internal and environmental stimuli to actively regulate important developmental processes. As we found evidence that there is genetic variation for temperature sensitivity of egg development rate in our study population, such regulation could be a target of selection imposed by climate change.


title: Cis-regulatory variants affect gene expression dynamics in yeast

abstract: Evolution of cis-regulatory sequences depends on how they effect gene expression and motivates both the identification and prediction of cis-regulatory variants responsible for expression differences within and between species. While much progress has been made in relating cis-regulatory variants to expression levels, the timing of gene activation and repression may also be important to the evolution of cis-regulatory sequences. We investigated allele-specific expression (ASE) dynamics within and between Saccharomyces species during the diauxic shift and found appreciable cis-acting variation in gene expression dynamics. Within species ASE is associated with intergenic variants, but ASE dynamics are more strongly associated with insertions and deletions than ASE levels. To refine these associations we used a high-throughput reporter assay to test promoter regions and individual variants. Within the subset of regions that recapitulated endogenous expression we identified and characterized cis-regulatory variants that affect expression dynamics. Between species, chimeric promoter regions generate novel patterns and indicate constraints on the evolution of gene expression dynamics. We conclude that changes in cis-regulatory sequences can tune gene expression dynamics and that the interplay between expression dynamics and other aspects expression are relevant to the evolution of cis-regulatory sequences.


title: FastTomo: A SerialEM Script for Collecting Electron Tomography Data

abstract: FastTomo is a SerialEM script for collecting tilted specimen images in transmission electron microscopes to be further used in tomographic reconstruction. It achieves a speedup over conventional tracking methods by minimizing the usage of off-target tracking shots, and instead applies proportional control to the specimen images. Movement in the Z coordinate is estimated prior to each tilt series in a separate calibration routine. Overall, this method is fast and reliable when the field of view is at least 1 um, and can tolerate minor errors in setting eucentric height. The implemented tilt series schemes include the unidirectional, bidirectional, and dose-symmetric schemes.


title: A novel, open source, low-cost bioreactor for load-controlled cyclic loading of tendon explants

abstract: A major risk factor for tendinopathy is tendon overuse (i.e., fatigue loading). Fatigue loading of tendon damages the extracellular matrix and induces tissue degeneration. However, the specific mechanisms linking tendon fatigue damage with tissue degeneration are unclear. While explant models of tendon fatigue loading have been used to address this knowledge gap, they predominantly employ bioreactors that apply cyclic displacements/strains rather than loads/stresses, which are more physiologically relevant. This is because of the technical complexity and cost of building a load-controlled bioreactor, which requires multiple motors, load cells, and computationally intensive feedback loops. Here, we present a novel, low-cost, load-controlled bioreactor that applies cyclic loading to multiple tendon explants by offloading weights from a single motorized stage. Using an optional load cell, we validated that the bioreactor can effectively provide load-controlled fatigue testing of mouse and rat tendon explants while maintaining tissue viability. Furthermore, all the design files, bill of materials, and operating software are available "open source" (https://github.com/Szczesnytendon/Bioreactor) so that anyone can easily manufacture and use the bioreactor for their own research. Therefore, this novel load-controlled bioreactor will enable researchers to study the mechanisms driving fatigue-induced tendon degeneration in a more physiologically relevant and cost-effective manner.


title: BugSeq 16S: NanoCLUST with Improved Consensus Sequence Classification

abstract: NanoCLUST has enabled species-level taxonomic classification from noisy nanopore 16S sequencing data for BugSeqs users and the broader nanopore sequencing community. We noticed a high misclassification rate of NanoCLUST-derived consensus 16S sequences due to its use of BLAST top hit taxonomy assignment. We replaced the consensus sequence classifier of NanoCLUST with QIIME2s VSEARCH-based classifier to enable greater accuracy. We use mock microbial community and clinical 16S sequencing data to show that this replacement results in significantly improved nanopore 16S accuracy (over 5% recall and 19% precision), and make this new tool (BugSeq 16S) freely available for academic use at BugSeq.com/free.


title: GlucoCEST MRI for the early evaluation response to chemotherapeutic and metabolic treatments in a murine triple negative breast cancer: a comparison with 18F-FDG-PET.

abstract:
PurposeTriple-negative breast cancer (TNBC) patients have usually poor outcome after chemotherapy and early prediction of therapeutic response would be helpful. [18F]F-FDG-PET/CT acquisitions are often carried out to monitor variation in metabolic activity associated to response to the therapy, despite moderate accuracy and radiation exposure limit its application. The glucoCEST technique relies on the use of unlabelled D-glucose to assess glucose uptake with conventional MRI scanners and is currently under active investigations at clinical level. This work aims at validating the potential of MRI-glucoCEST in monitoring early therapeutic responses in a TNBC tumor murine model.

ProceduresBreast tumor (4T1) bearing mice were treated with doxorubicin or dichloroacetate for one week. PET/CT with [18F]F-FDG and MRI-glucoCEST were performed at baseline and after 3 cycles of treatment. Metabolic changes measured with [18F]F-FDG-PET and glucoCEST were compared and evaluated with changes in tumor volumes.

ResultsDoxorubicin treated mice showed a significant decrease in tumor growth when compared to the control group. GlucoCEST imaging provided early metabolic response after three cycles of treatment, conversely, no variations were detect by in [18F]F-FDG uptake. Dichloroacetate treated mice did not show any decrease either in tumor volume or in tumor metabolic activity as assessed by both glucoCEST and [18F]F-FDG-PET.

ConclusionsEarly metabolic changes during doxorubicin treatment can be predicted by glucoCEST imaging that appears more sensitive than [18F]F-FDG-PET in reporting on early therapeutic response. These findings support the view that glucoCEST may be a sensitive technique for monitoring metabolic response, but future studies are needed to explore the accuracy of this approach in other tumor types and treatments.


title: The interplay of chromatin phase separation and lamina interactions in nuclear organisation

abstract:
The genetic material of eukaryotes is segregated into transcriptionally active euchromatin and silent heterochromatin compartments. The spatial arrangement of chromatin compartments evolves over the course of cellular life in a process that remains poorly understood. The latest nuclear imaging experiments reveal a number of dynamical signatures of chromatin which are reminiscent of active multi-phase liquids. This includes the observations of viscoelastic response, coherent motions, Ostwald ripening and coalescence of chromatin compartments. There is also growing evidence that liquid-liquid phase separation of protein and nucleic acid components is the underlying mechanism for the dynamical behavior of chromatin. In order to dissect the organizational and dynamical implications of chromatins liquid behavior, we have devised a phenomenological field-theoretic model of nucleus as a multi-phase condensate of liquid chromatin types. Employing the liquid chromatin model of Drosophila nucleus, we have carried out an extensive set of simulations with an objective to shed light on the dynamics and chromatin patterning observed in the latest nuclear imaging experiments. Our simulations reveal the emergence of experimentally detected mesoscale chromatin channels and spheroidal droplets which arise from the dynamic interplay of chromatin type to type interactions and intermingling of chromosomal territories. We also quantitatively reproduce coherent motions of chromatin domains observed in displacement correlation spectroscopy measurements which are explained within the framework of our model by phase separation of chromatin types operating within constrained intra-chromosomal and inter-chromosomal boundaries. Finally, we illuminate the role of heterochromatin-lamina interactions in the nuclear organization by showing that these interactions enhance the mobility of euchromatin and indirectly introduce correlated motions of heterochromatin droplets.

SIGNIFICANCE STATEMENTThe latest super-resolution imaging experiments have revealed a surprisingly dynamic and stochastic nature of chromatin in eukaryotic nuclei which is reminiscent of multi-phase fluid behavior. As a result, the concepts from the theory of complex fluids such as phase separation, viscoelasticity, and droplet nucleation have found widespread utility in understanding salient features of nuclear organization. In order to understand and disentangle the complex interplay of forces that contribute to the emergent patterns of organization and dynamics, we have devised a phenomenological field-theoretic model of nucleus as a multi-phase condensate of liquid chromatin types. Armed with a mesoscopic model of nuclear chromatin, we have shed light on the distinct dynamical and structural contributions of chromatin type interactions intermingling of chromosomal territories and lamina binding. We also shed light on the dynamical heterogeneity and coherent motions of chromatin domains which are fully captured by an interplay of micro-phase separation of chromatin types and lamina binding.


title: The interplay of chromatin phase separation and lamina interactions in nuclear organization


title: The Arabidopsis ORA59 coordinates jasmonic acid- and ethylene-responsive gene expression to regulate plant immunity

abstract: Jasmonic acid (JA) and ethylene (ET) signaling modulate plant defense against necrotrophic pathogens. These hormone pathways lead to transcriptional reprogramming, which is a major part of plant immunity and requires the roles of transcription factors. ET response factors are responsible for the transcriptional regulation of JA/ET-responsive defense genes, among which ORA59 functions as a key regulator of this process and has been implicated in the JA-ET crosstalk. Here, we identified the ERELEE4 as an ORA59-binding cis-element, in addition to the well-characterized GCC box, demonstrating that ORA59 regulates JA/ET-responsive genes through direct binding to these elements in the gene promoters. Notably, ORA59 exhibited differential preference for the GCC box and ERELEE4, depending on whether ORA59 activation is achieved by JA and ET, respectively. Our results provide insights into how ORA59 can generate specific patterns of gene expression dynamics through JA and ET hormone pathways.


title: DeepCob: Precise and high-throughput analysis of maize cob geometry using deep learning with an application in genebank phenomics

abstract:
BackgroundMaize cobs are an important component of crop yield that exhibit a high diversity in size, shape and color in native landraces and modern varieties. Various phenotyping approaches were developed to measure maize cob parameters in a high throughput fashion. More recently, deep learning methods like convolutional neural networks (CNN) became available and were shown to be highly useful for high-throughput plant phenotyping. We aimed at comparing classical image segmentation with deep learning methods for maize cob image segmentation and phenotyping using a large image dataset of native maize landrace diversity from Peru.

ResultsComparison of three image analysis methods showed that a Mask R-CNN trained on a diverse set of maize cob images was highly superior to classical image analysis using the Felzenszwalb algorithm and a Window-based CNN due to its robustness to image quality and object segmentation accuracy (r = 0.99). We integrated Mask R-CNN into a high-throughput pipeline to segment both maize cobs and rulers in images and perform an automated quantitative analysis of eight phenotypic traits, including diameter, length, ellipticity, asymmetry, aspect ratio and average RGB values for cob color. Statistical analysis identified key training parameters for efficient iterative model updating. We also show that a small number of 10-20 images is sufficient to update the initial Mask R-CNN model to process new types of cob images. To demonstrate an application of the pipeline we analyzed phenotypic variation in 19,867 maize cobs extracted from 3,449 images of 2,484 accessions from the maize genebank of Peru to identify phenotypically homogeneous and heterogeneous genebank accessions using multivariate clustering.

ConclusionsSingle Mask R-CNN model and associated analysis pipeline are widely applicable tools for maize cob phenotyping in contexts like genebank phenomics or plant breeding.


title: Precise measurements of chromatin diffusion dynamics by modeling using Gaussian processes

abstract: The spatiotemporal organization of chromatin influences many nuclear processes: from chromo-some segregation to transcriptional regulation. To get a deeper understanding of these processes it is essential to go beyond static viewpoints of chromosome structures, and to accurately characterize chromatin mobility and its diffusion properties. Here, we present GP-FBM: a new computational framework based on Gaussian processes and fractional Brownian motion to analyze and extract diffusion properties from stochastic trajectories of labeled chromatin loci. GP-FBM is able to optimally use the higher-order correlations present in the data and therefore outperforms existing methods. Furthermore, GP-FBM is able to extrapolate trajectories from missing data and account for substrate movement automatically. Using our method we show that diffusive chromatin diffusion properties are surprisingly similar in interphase and mitosis in mouse embryonic stem cells. Moreover, we observe surprising heterogeneity in local chromatin dynamics, which correlates with transcriptional activity. We also present GP-Tool, a user-friendly graphical interface to facilitate the use of GP-FBM by the research community for future studies of nuclear dynamics.


title: Binary Interactome Models of Inner- Versus Outer-Complexome Organization

abstract: The interactome is often conceived of primarily as a collection of hundreds of multimeric machines, collectively referred to as the "complexome". However, a large proportion of the interactome exists outside of the complexome, or in the "outer-complexome", and may account for most of the functional plasticity exhibited by cellular systems. To compare features of inner- versus outer-complexome organization, we systematically generated a yeast all-by-all binary interactome map, integrated it with previous binary maps, and compared the resulting interactome "atlas" with systematic co-complex association and functional similarity network datasets. Direct protein-protein interactions in the inner-complexome tend to be readily detected in multiple assays and exhibit high levels of coherence with functional similarity relationships. In contrast, pairs of proteins connected by relatively transient, harder-to-detect binary interactions in the outer-complexome, exhibit higher levels of functional heterogeneity. Thus, a small proportion of the interactome corresponds to a stable, functionally homogeneous, inner-complexome, forming quaternary structure, while a much greater proportion consists of transient interactions between pairs of functionally heterogeneous proteins in the outer-complexome, forming quinary structure.


title: OCRbayes: A Bayesian hierarchical modeling framework for Seahorse extracellular flux oxygen consumption rate data analysis

abstract:
BackgroundMitochondrial dysfunction is involved in many complex diseases. Efficient and accurate evaluation of mitochondrial functionality is crucial for understanding pathology as well as facilitating novel therapeutic developments. As a popular platform, Seahorse extracellular flux (XF) analyzer is widely used for measuring mitochondrial oxygen consumption rate (OCR) in living cells. A hidden feature of Seahorse XF OCR data is that it has a complex data structure, caused by nesting and crossing between measurement cycles, wells and plates. Surprisingly, statistical analysis of Seahorse XF data has not received sufficient attention, and current methods completely ignore the complex data structure, impairing the robustness of statistical inference.

ResultsTo rigorously incorporate the complex structure into data analysis, here we developed a Bayesian hierarchical modeling framework, OCRbayes, and demonstrated its applicability based on analysis of published data sets.

ConclusionsWe showed that OCRbayes can analyze Seahorse XF OCR experimental data derived from either single or multiple plates. Moreover, OCRbayes has potential to be used for diagnosing patients with mitochondrial diseases.


title: Growth-Rate Dependent And Nutrient-Specific Gene Expression Resource Allocation In Fission Yeast

abstract: Cellular resources are limited and their relative allocation to gene expression programmes determines physiological states and global properties such as the growth rate. Quantitative studies using various growth conditions have singled out growth rate as a major physiological variable explaining relative protein abundances. Here, we used the simple eukaryote Schizosaccharomyces pombe to determine the importance of growth rate in explaining relative changes in protein and mRNA levels during growth on a series of non-limiting nitrogen sources. Although half of fission yeast genes were significantly correlated with the growth rate, this came alongside wide-spread nutrient-specific regulation. Proteome and transcriptome often showed coordinated regulation but with notable exceptions, such as metabolic enzymes. Genes positively correlated with growth rate participated in every level of protein production with the notable exception of RNA polymerase II, whereas those negatively correlated mainly belonged to the environmental stress response programme. Critically, metabolic enzymes, which represent [~]55-70% of the proteome by mass, showed mainly condition-specific regulation. Specifically, many enzymes involved in glycolysis and NAD-dependent metabolism as well as the fermentative and respiratory pathways were condition-dependent and not consistently correlated with growth. In summary, we provide a rich account of resource allocation to gene expression in a simple eukaryote, advancing our basic understanding of the interplay between growth-rate dependent and nutrient-specific gene expression.


title: L-Thyroxine improves vestibular compensation in a rat model of acute peripheral vestibulopathy

abstract: Unilateral vestibular lesions induce a vestibular syndrome, which recovers over time due to vestibular compensation. The therapeutic effect of L-Thyroxine (L-T4) on vestibular compensation was investigated by behavioral testing and immunohistochemical analysis in a rat model of unilateral vestibular neurectomy (UVN). We demonstrated that an acute L-T4 treatment reduced the vestibular syndrome and significantly promoted vestibular compensation. Thyroid hormone receptors (TR and TR{beta}) and type II iodothyronine deiodinase (DIO2) were present in the vestibular nuclei (VN), supporting a local action of L-T4. We confirmed the T4-induced metabolic effects by demonstrating an increase in the number of cytochrome oxidase-labelled neurons in the VN three days after the lesion. L-T4 treatment modulated glial reaction by decreasing both microglia and oligodendrocytes in the deafferented VN three days after UVN and increased cell proliferation. The survival of newly generated cells was not affected, but neuronal differentiation was altered by the L-T4 treatment.


title: Sex-specific interactions between procedural and deliberative decision-making systems in a mouse model of Alzheimer's disease

abstract: A central question in aging and Alzheimers disease (AD) is when and how neural substrates underlying decision-making are altered. Here we show that while APP mice, a commonly used mouse model of AD, were able to learn Restaurant Row, a complex neuroeconomic decision-making task, they were significantly impaired in procedural, habit-forming, aspects of cognition and relied heavily on deliberation when making decisions. Surprisingly, these behavioral changes are associated with amyloid-beta (A{beta}) pathology and network remodeling in the striatum, a key brain region involved in procedural cognition. Furthermore, APP mice and control mice relied on distinct sex-specific strategies in this neuroeconomic task. These findings provide foundational pillars to examine how aging and age-related neurodegenerative diseases impact decision-making across sexes. They also highlight the need for complex behavioral tasks that allow for the dissociation of competing neurally-distinct decision-making circuits to get an accurate picture of changes in neurodegenerative models of human disease.


title: Sex-specific, pdfr-1-dependent modulation of pheromone avoidance by food abundance enables flexibility in C. elegans foraging behavior

abstract: To make adaptive feeding and foraging decisions, animals must integrate diverse sensory streams with multiple dimensions of internal state. In C. elegans, foraging and dispersal behaviors are influenced by food abundance, population density, and biological sex, but the neural and genetic mechanisms that integrate these signals are poorly understood. Here, by systematically varying food abundance, we find that chronic avoidance of the population-density pheromone ascr#3 is modulated by food thickness, such that hermaphrodites avoid ascr#3 only when food is scarce. The integration of food and pheromone signals requires the conserved neuropeptide receptor PDFR-1, as pdfr-1 mutant hermaphrodites display strong ascr#3 avoidance even when food is abundant. Conversely, increasing PDFR-1 signaling inhibits ascr#3 aversion when food is sparse, indicating that this signal encodes information about food abundance. In both wild-type and pdfr-1 hermaphrodites, chronic ascr#3 avoidance requires the ASI sensory neurons. In contrast, PDFR-1 acts in interneurons, suggesting that it modulates processing of the ascr#3 signal. Although a sex-shared mechanism mediates ascr#3 avoidance, food thickness modulates this behavior only in hermaphrodites, indicating that PDFR-1 signaling has distinct functions in the two sexes. Supporting the idea that this mechanism modulates foraging behavior, ascr#3 promotes ASI-dependent dispersal of hermaphrodites from food, an effect that is markedly enhanced when food is scarce. Together, these findings identify a neurogenetic mechanism that sex-specifically integrates population and food abundance, two important dimensions of environmental quality, to optimize foraging decisions. Further, they suggest that modulation of attention to sensory signals could be an ancient, conserved function of pdfr-1.


title: Adolescent Stress Confers Resilience to Traumatic Stress Later in Life: Role of the Prefrontal Cortex

abstract: Stress during adolescence is usually associated with psychopathology later in life. However, under certain circumstances, developmental stress can promote an adaptive phenotype, allowing individuals to cope better with adverse situations in adulthood, thereby contributing to resilience. The aim of the study was to understand how adolescent stress alters behavioral and physiological responses to traumatic stress in adulthood. Sprague Dawley rats were subjected to adolescent chronic variable stress (adol CVS) followed by single prolonged stress (SPS) in adulthood. One week after SPS, animals were tested for acquisition, extinction, extinction recall and reinstatement of auditory-cued fear conditioning, with neuronal recruitment during reinstatement assessed by Fos expression. Patch clamp electrophysiology was performed to examine physiological changes associated with resilience. We observed that adol CVS blocked SPS-induced impairment of extinction learning (males) and enhancement fear reinstatement (both sexes). SPS effects were associated with a reduction of infralimbic (IL) cortex neuronal recruitment after reinstatement in males and increased engagement of the central amygdala in females, both of which were also prevented by adol CVS. We explored the mechanism behind reduced IL recruitment in male rats by studying the intrinsic excitability of IL pyramidal neurons. SPS reduced excitability of IL neurons and prior adol CVS prevented this effect, indicating that adolescent stress can impart resilience to the effects of traumatic stress by modification of IL output in males. Overall, our study suggests that prior stress exposure can limit the impact of a subsequent severe stress exposure in adulthood, effects that are mediated by sex-specific modification of infralimbic and amygdala signaling.


title: B cells imprint adoptively transferred CD8+ T cells with enhanced tumor immunity

abstract:
Here we report a novel strategy to reverse the tolerant state of adoptively transferred CD8+ T cells against melanoma through ex vivo expansion with the TLR9 agonist CpG. T cells generated in the presence of CpG display potent anti-tumor efficacy without in vivo co-administration of high dose IL-2 or vaccination, which are classically required for effective treatment of solid tumors using adoptive cell therapies. CD8+ T cells adopt a unique proteomic signature and are characterized by an IL-2RhighICOShighCD39low phenotype after CpG-mediated expansion. Surprisingly, we found that the presence of B cells, in the culture, was essential for imprinting CD8+ T cells with this phenotype and moreover purified B cells were sufficient to mediate the CpG-associated changes in T cells. These findings reveal a vital role for B cells in the generation of effective antitumor CD8+ T cells and have immediate implications for profoundly improving immunotherapy for patients.

SUMMARY STATEMENTThe TLR9 agonist CpG allows B cells to license adoptively transferred CD8+ T cells with potent tumor immunity. These licensed T cells have a unique proteomic signature, are marked by low CD39 and high ICOS and IL-2R expression, and engraft robustly in vivo.


title: Collagen density defines 3D migration of CTLs and their consequent cytotoxicity against tumor cells

abstract: Solid tumors are often characterized by condensed extracellular matrix (ECM). The impact of dense ECM on cytotoxic T lymphocytes (CTL) function is not fully understood. Here, we report that CTL-mediated cytotoxicity is substantially impaired in dense collagen matrices. Although the intrinsic killing machinery including expression of cytotoxic proteins and degranulation was intact, CTL motility was substantially compromised in dense collagen. We found that for 3D CTL migration, persistence and velocity was regulated by collagen stiffness and the porosity, respectively. Interestingly, 3D CTL velocity is strongly correlated with their nuclear deformability/flexibility during migration, which is regulated by the microtubule network. Moreover, CTL migration was completely abolished by inhibition of actin polymerization and or myosin IIA. Remarkably, disruption of the microtubule-networks significantly improves the impaired migration, search efficiency, and cytotoxicity of CTLs in dense collagen. Our work suggests the microtubule network as a promising target to rescue impaired CTL killing capacity in solid tumor related scenarios.


title: Efficacy of two commercial disinfectants on Paenibacillus larvae spores

abstract:
SHORT SUMMARYPaenibacillus larvae is a spore-forming bacterium causing American foulbrood (AFB) in honey bee larvae. The remains of a diseased larva contains billions of extremely resilient P. larvae spores viable for decades. Burning clinically symptomatic colonies is widely considered the only workable strategy to prevent further spread of the disease, and the management practices used for decontamination requires high concentrations of chemicals or special equipment.

The aim of this study was to test and compare the biocidal effect of two commercially available disinfectants, " Disinfection for beekeeping" and Virkon S on P. larvae. The two products were applied to P. larvae spores in suspension as well as inoculated on two common beehive materials, wood and styrofoam.

" Disinfection for beekeeping" had a 100 % biocidal effect on P. larvae spores in suspension compared to 87.0-88.6 % for Virkon S which, however, had a significantly better effect on P. larvae on styrofoam. The two disinfectants had similar effect on infected wood material.


title: A millennium of increasing ecosystem diversity until the mid-20th century

abstract: Land-use change is widely regarded as a simplifying and homogenising force in nature. In contrast, analysing global land-use reconstructions from the 10th to 20th centuries, we found progressive increases in the number, evenness, and diversity of ecosystems (including human-modified land-use types) across the globe. Ecosystem diversity increased more rapidly after [~]1700CE, then slowed or partially reversed (depending on the metric) following the mid-20th century acceleration of human impacts. Differentiation also generally increased across space, with homogenization only evident in the presence-absence analysis of ecosystem types at the global scale. Our results suggest that human land-use changes have primarily driven increases in ecosystem diversity over the last millennium.


title: Neither wood ash application nor phosphorus-fertilisation mitigated the negative effects of whole-tree harvesting on a temperate oligotrophic forest.

abstract:
Background and AimsConcerns about climate change and carbon economy have prompted the promotion of alternative energy sources, including forest-based bioenergy. An evaluation of the environmental consequences of intensive harvests (stumps and roots, and also branches and foliage) for energy wood supply, and use of wood-ash recycling as a compensatory practice, helps in the evaluation of the use of forest biomass for energy production.

MethodsWe made use of records from a split-plot experimental site crossing four different intensities of biomass harvesting (Stem-Only Harvest [SOH], Aboveground Additional Harvest [AAH], Belowground Additional Harvest [BAH], and Whole-Tree Harvest [WTH]) and three compensation methods (control [C], wood ash application [A] and phosphorus fertilisation [P]) to evaluate, in the 11-years-old stand (maritime pine: Pinus pinaster) that followed the biomass exports of the former stand, their effects on nutrient budgets, tree growth, soil fertility, chemical properties and soil carbon. This site is located in a forest on a poor soil, under a warm temperate climate (SW France).

Key resultsDespite their low additional biomass exports (+10% for AAH to +34% for WTH), the non-conventional harvest practices exported much higher quantities of nutrients than the conventional SOH technique (for example +145% for N and K in WTH). Consequently, these treatments had negative effects on the soil nutritive status. Additional biomass harvests impacted the soil organic matter content, with negative effects on P-organic, soil cation exchange capacity, exchangeable Ca, and most extractible nutrients. However, data suggested that tree growth and foliage nutrient content had not yet been significantly impacted by harvest treatments, whereas tree nutritional status was improved by P-fertiliser or wood ash. As expected, we observed a positive effect of wood ash application on soil pH and nutrient content but, like additional harvests, wood ash application decreased the pool of soil organic carbon (~10% of the initial stock with ~7% of N-total losses).

ConclusionsOverall, this factorial experiment showed that exporting more forest biomass due to the additional harvesting of tree canopies, stumps and roots had negative consequences on the ecosystem biogeochemistry. Additional harvests have aggravated the poverty of the already oligotrophic soil, and decreased the soil organic carbon content. Importantly, applying nutrients as fertiliser or wood ash did not compensate for all the negative impacts of biomass exports and the method of wood ash recycling in forests could even decrease the soil organic carbon.


title: Response of soil and vegetation in a warm-temperate Pine forest to intensive biomass harvests, phosphorus fertilisation, and wood ash application.


title: Genome-wide DNA methylation and transcriptome integration reveal distinct sex differences in skeletal muscle.

abstract:
Nearly all human complex traits and diseases exhibit some degree of sex differences, with epigenetics being one of the main contributing factors. Various tissues display sex differences in DNA methylation, however this has not yet been explored in skeletal muscle, despite skeletal muscle being among the tissues with the most transcriptomic sex differences. For the first time, we investigated the effect of sex on autosomal DNA methylation in human skeletal muscle across three independent cohorts (Gene SMART, FUSION, and GSE38291) using a meta-analysis approach, totalling 369 human muscle samples (222 males, 147 females), and integrated this with known sex-biased transcriptomics. We found 10,240 differentially methylated regions (DMRs) at FDR < 0.005, 94% of which were hypomethylated in males, and gene set enrichment analysis revealed that differentially methylated genes were involved in muscle contraction and substrate metabolism. We then investigated biological factors underlying DNA methylation sex differences and found that circulating hormones were not associated with differential methylation at sex-biased DNA methylation loci, however these sex-specific loci were enriched for binding sites of hormone-related transcription factors (with top TFs including androgen (AR), estrogen (ESR1), and glucocorticoid (NR3C1) receptors). Fibre type proportions were associated with differential methylation across the genome, as well as across 16 % of sex-biased DNA methylation loci (FDR < 0.005). Integration of DNA methylomic results with transcriptomic data from the GTEx database and the FUSION cohort revealed 326 autosomal genes that display sex differences at both the epigenome and transcriptome levels. Importantly, transcriptional sex-biased genes were overrepresented among epigenetic sex-biased genes (p-value = 4.6e-13), suggesting differential DNA methylation and gene expression between male and female muscle are functionally linked. Finally, we validated expression of three genes with large effect sizes (FOXO3A, ALDH1A1, and GGT7) in the Gene SMART cohort with qPCR. GGT7, involved in antioxidant metabolism, displays male-biased expression as well as lower methylation in males across the three cohorts. In conclusion, we uncovered 8,420 genes that exhibit DNA methylation differences between males and females in human skeletal muscle that may modulate mechanisms controlling muscle metabolism and health.

SignificanceThe importance of uncovering biological sex differences and their translation to physiology has become increasingly evident. Using a large-scale meta-analysis of three cohorts, we perform the first comparison of genome-wide skeletal muscle DNA methylation between males and females, and identify thousands of genes that display sex-differential methylation. We then explore intrinsic biological factors that may be underlying the DNA methylation sex differences, such as fibre type proportions and sex hormones. Leveraging the GTEx database, we identify hundreds of genes with both sex-differential expression and DNA methylation in skeletal muscle. We further confirm the sex-biased genes with gene expression data from two cohorts included in the methylation meta-analysis. Our study integrates genomewide sex-biased DNA methylation and expression in skeletal muscle, shedding light on distinct sex differences in skeletal muscle.


title: Skeletal muscle methylome and transcriptome integration reveals profound sex differences related to muscle function and substrate metabolism


title: Topography-dependent gene expression and function of common cell archetypes in large and small porcine airways

abstract: The small airways of humans are affected early in several lung diseases. However, because they are relatively inaccessible, little is known about the epithelial cells that line these airways. We performed a single cell RNA-seq census of small and large airways of wild-type pigs and pigs with disrupted cystic fibrosis transmembrane conductance regulator (CFTR) gene. The sequencing data showed that small airway epithelia had similar major cell types as large airways but no ionocytes; moreover, lack of CFTR expression had minimal effect on the transcriptome. Small airway epithelial cells expressed a different transcriptome than large airway cells. Quantitative immunohistochemistry showed that small airway basal cells participate in epithelial barrier function. Finally, sequencing data and in vitro electrophysiologic studies suggest that small airway epithelia have a water and ion transport advantage. Our data highlight the archetypal nature of basal, secretory, and ciliated airway cells with location-dependent gene expression and function.


title: Alginate-based microparticles coated with HPMCP/AS cellulose-derivatives enable the Ctx(Ile21)-Ha antimicrobial peptide application as a feed additive

abstract: Microencapsulation is a potential biotechnological tool, which can overcome AMPs instabilities and reduce toxic side effects. Thus, this study evaluates the antibacterial activities of the Ctx(Ile21)-Ha antimicrobial peptide against MDR and non-resistant bacteria, develop and characterize peptide-loaded microparticles coated with HPMCAS and HPMCP. Ctx(Ile21)-Ha microencapsulation was performed by ionic gelation with high-efficiency, maintaining the physical-chemical stability. Ctx(Ile21)-Ha coated-microparticles were characterized, and their hemolytic activity assay demonstrated that hemolysis was decreased up to 95% compared to single molecule. In addition, in vitro release control profile simulating different portions of gastrointestinal tract was performed and showed the microcapsules ability to protect the peptide and release it in the intestine, aimed pathogens location, mainly by Salmonella sp. Therefore, use of microencapsulated Ctx(Ile21)-Ha can be allowed as an antimicrobial controller in monogastric animal production, being a valuable option for molecules with low therapeutic indexes or high hemolytic rates.


title: Modelling Human Gait using a Nonlinear Differential Equation

abstract:
We introduce an innovative method for the investigation of human gait, which is based on the visualisation of the vertical component of the movement of the centre of mass during walking or running, in the space of the coordinates position, velocity, and acceleration of the centre of mass. Collected data has been numerically approximated by the best fitting curve for a non-linear model. The resulting equation for the best fitting plane or curve in this space is a differential equation of second order. The model that we suggest is a Duffing equation with coefficients that depend on the height of a walker or runner and on the angular frequency of the oscillation. Statistics about the distribution of the Duffing stiffness depending on the speed is presented.

1 Author SummaryWe study the human gait modelled by the movement of the centre of mass of the test person. This is an example of a biological process which can be considered as a periodical dynamic system. Roughly, this movement behaves in a similar way to a vibrating mass suspended on a spring, but it is more complex. The vertical component of the movement during walking or running can be visualised as an oscillogram: a graph of the position as a function of time. We suggest a visualisation of the data in 3D space, where the coordinates describe position, velocity, and acceleration. Our new visualisation method allows us to model the movement of a persons centre of mass by a nonlinear differential equation. The resulting curve for an ideal spring-mass movement, without viscosity or external force, is an ellipse in the suggested 3D space. The shape of the data curve shows at which position an additional force was applied, or the movement slowed down. Some deviations are common for all test persons and others are different. In the future we plan to investigate the reasons for these deviations, such as different running techniques or the presence of injuries.


title: Enhancing Drug-Drug Interaction Prediction Using Deep Attention Neural Networks

abstract: Drug-drug interactions are one of the main concerns in drug discovery. Accurate prediction of drug-drug interactions plays a key role in increasing the efficiency of drug research and safety when multiple drugs are c o-prescribed. With various data sources that describe the relationships and properties between drugs, the comprehensive approach that integrates multiple data sources would be considerably effective in making high-accuracy prediction. In this paper, we propose a Deep Attention Neural Network based Drug-Drug Interaction prediction framework, abbreviated as DANN-DDI, to predict unobserved drug-drug interactions. First, we construct multiple drug feature networks and learn drug representations from these networks using the graph embedding method; then, we concatenate the learned drug embeddings and design an attention neural network to learn representations of drug-drug pairs; finally, we adopt a deep neural network to accurately predict drug-drug interactions. The experimental results demonstrate that our model DANN-DDI has improved prediction performance compared with state-of-the-art methods. Moreover, the proposed model can predict novel drug-drug interactions and drug-drug interaction-associated events.


title: Computational Evaluation of DNA Metabarcoding for Universal Diagnostics of Invasive Insect Pests

abstract: Appropriate design and selection of PCR primers plays a critical role in determining the sensitivity and specificity of a metabarcoding assay. Despite several studies applying metabarcoding to insect pest surveillance, the diagnostic performance of the short "mini-barcodes" required by high-throughput sequencing platforms has not been established across the broader taxonomic diversity of invasive insects. We address this by computationally evaluating the diagnostic sensitivity and predicted amplification bias for 68 published and novel cytochrome c oxidase subunit 1 (COI) primers on a curated database of 110,676 insect species, including 2,625 registered on global invasive species lists. We find that mini-barcodes between 125-257 bp can provide comparable resolution to the full-length barcode for both invasive insect pests and the broader Insecta, conditional upon the subregion of COI targeted and the genetic similarity threshold used to identify species. Taxa that could not be identified by any barcode lengths were phylogenetically clustered within  problem groups, many arising through taxonomic inconsistencies rather than insufficient diagnostic information within the barcode itself. Substantial variation in predicted PCR bias was seen across published primers, with those including 4-5 degenerate nucleotide bases showing almost no mismatch to major insect orders. While not completely universal, a single COI mini-barcode can successfully differentiate the majority of pest and non-pest insects from their congenerics, even at the small amplicon size imposed by 2 x 150 bp sequencing. We provide a ranked summary of high-performing primers and discuss the bioinformatic steps required to curate reliable reference databases for metabarcoding studies.


title: RCytoGPS: An R Package for Reading and Visualizing Cytogenetics Data

abstract:
SummaryCytogenetics data, or karyotypes, are among the most common clinically used forms of genetic data. Karyotypes are stored as standardized text strings using the International System for Human Cytogenomic Nomenclature (ISCN). Historically, these data have not been used in large-scale computational analyses due to limitations in the ISCN text format and structure. Recently developed computational tools such as CytoGPS have enabled large-scale computational analyses of karyotypes. To further enable such analyses, we have now developed RCytoGPS, an R package that takes JSON files generated from CytoGPS.org and converts them into objects in R. This conversion facilitates the analysis and visualizations of karyotype data. In effect this tool streamlines the process of performing large-scale karyotype analyses, thus advancing the field of computational cytogenetic pathology.

Availability and ImplementationFreely available at https://CRAN.R-project.org/package=RCytoGPS

Supplementary informationSupplementary data are available at Bioinformatics online.


title: Actin filament alignment causes mechanical hysteresis in cross-linked networks

abstract: Cells dynamically control their material properties through remodeling of the actin cytoskeleton, an assembly of cross-linked networks and bundles formed from the biopolymer actin. We recently found that cross-linked networks of actin filaments reconstituted in vitro can exhibit adaptive behavior and thus serve as a model system to understand the underlying mechanisms of mechanical adaptation of the cytoskeleton. In these networks, training, in the form of applied shear stress, can induce asymmetry in the nonlinear elasticity. Here, we explore control over this mechanical hysteresis by tuning the concentration and mechanical properties of cross-linking proteins in both experimental and simulated networks. We find that this effect depends on two conditions: the initial network must exhibit nonlinear strain stiffening, and filaments in the network must be able to reorient during training. Hysteresis depends strongly and non-monotonically on cross-linker concentration, with a peak at moderate concentrations. In contrast, at low concentrations, where the network does not strain stiffen, or at high concentrations, where filaments are less able to rearrange, there is little response to training. Additionally, we investigate the effect of changing cross-linker properties and find that longer or more flexible cross-linkers enhance hysteresis. Remarkably plotting hysteresis against alignment after training yields a single curve regardless of the physical properties or concentration of the cross-linkers.


title: Characterization of an Agarophyton chilense oleoresin containing PPARγ natural ligands with insulin-sensitizing effects in a C57BL/6J mouse model of diet-induced obesity and antioxidant activity in Caenorhabditis elegans.

abstract:
The biomedical potential of the edible red seaweed Agarophyton chilense (former Gracilaria chilensis) has not been explored. Red seaweeds are enriched in polyunsaturated fatty acids and eicosanoids, which are known natural ligands of the PPAR{gamma} nuclear receptor. PPAR{gamma} is the molecular target of thiazolidinediones (TZDs), drugs used as insulin sensitizers to treat type 2 diabetes mellitus. TZDs medical use is limited due to undesired side effects, the fact that it has triggered the search for partial agonists without the TZDs side effects.

We produced A.chilense oleoresin (Gracilex(R)) that induces the activation of PPAR{gamma} without inducing adipocyte differentiation, similar to PPAR{gamma} partial agonists. In a model of high-fat diet-induced obesity in male mice, we showed that treatment with Gracilex(R) improves insulin sensitivity, normalizing altered glucose and insulin parameters. Gracilex(R) was enriched in palmitic acid, arachidonic acid, oleic acid, and lipophilic antioxidants such as {beta}-carotene and tocopherols. Gracilex(R) possesses antioxidant activity in vitro (CUPRAC) and increased the antioxidant capacity in vivo in Caenorhabditis elegans. These findings support the idea that Gracilex(R) is an excellent source of healthy lipids targeting PPAR{gamma} with antioxidant activity and a high nutraceutical value.

category: physiology


title: Manganese toxicity disrupts indole acetic acid homeostasis and suppresses CO2 assimilation reaction in rice plants

abstract:
Despite the essentiality of Mn in terrestrial plants, its excessive accumulation in plant tissues causes growth defects, known as Mn toxicity. Mn toxicity can be divided into apoplastic and symplastic types depending on its onset. For growth defects, symplastic rather than apoplastic Mn toxicity is hypothesised to be more critical. However, details of the relationship between growth defects and symplastic Mn toxicity remains elusive. In this study, we aimed to elucidate the molecular mechanisms of symplastic Mn toxicity in rice plants. We found that under excess Mn conditions, CO2 assimilation was inhibited by stomatal closure, and both carbon anabolic and catabolic activities were decreased. In addition to stomatal dysfunction, stomatal and leaf anatomical development were also altered by excess Mn accumulation. Furthermore, the indole acetic acid (IAA) concentration was decreased, and auxin-responsive gene expression analyses showed IAA-deficient symptoms in leaves due to excess Mn accumulation. These results suggest that excessive Mn accumulation causes IAA deficiency, and low IAA concentrations suppress plant growth by suppressing stomatal opening and leaf anatomical development for efficient CO2 assimilation in leaves.

HIGHLIGHTIncreased Mn concentration lowers auxin concentrations in rice leaves, which suppresses photosynthesis by changing stomatal function and development.