title: DeLUCS: Deep Learning for Unsupervised Classification of DNA Sequences

abstract: We present a novel Deep Learning method for the Unsupervised Clustering of DNA Sequences (DeLUCS) that does not require sequence alignment, sequence homology, or (taxonomic) identifiers. DeLUCS uses Frequency Chaos Game Representations (FCGR) of primary DNA sequences, and generates "mimic" sequence FCGRs to self-learn data patterns (genomic signatures) through the optimization of multiple neural networks. A majority voting scheme is then used to determine the final cluster assignment for each sequence. The clusters learned by DeLUCS match true taxonomic groups for large and diverse datasets, with accuracies ranging from 77% to 100%: 2,500 complete vertebrate mitochondrial genomes, at taxonomic levels from sub-phylum to genera; 3,200 randomly selected 400 kbp-long bacterial genome segments, into clusters corresponding to bacterial families; three viral genome and gene datasets, averaging 1,300 sequences each, into clusters corresponding to virus subtypes. DeLUCS significantly outperforms two classic clustering methods (K-means++ and Gaussian Mixture Models) for unlabelled data, by as much as 47%. DeLUCS is highly effective, it is able to cluster datasets of unlabelled primary DNA sequences totalling over 1 billion bp of data, and it bypasses common limitations to classification resulting from the lack of sequence homology, variation in sequence length, and the absence or instability of sequence annotations and taxonomic identifiers. Thus, DeLUCS offers fast and accurate DNA sequence clustering for previously intractable datasets.


title: DeLUCS: Deep Learning for Unsupervised Clustering of DNA Sequences

category: bioinformatics


title: DeLUCS: Deep Learning for (Unsupervised) Clustering of DNA Sequences


title: SCRaPL: hierarchical Bayesian modelling of associations in single cell multi-omics data

abstract: Single-cell multi-omics assays offer unprecedented opportunities to explore gene regulation at cellular level. However, high levels of technical noise and data sparsity frequently lead to a lack of statistical power in correlative analyses, identifying very few, if any, significant associations between different molecular layers. Here we propose SCRaPL, a novel computational tool that increases power by carefully modelling noise in the experimental systems. We show on real and simulated multi-omics single-cell data sets that SCRaPL achieves higher sensitivity and better robustness in identifying correlations, while maintaining a similar level of false positives as standard analyses based on Pearson correlation.


title: Mechanistic model: Analysis of diffusion dynamics of Lugol's chromoendoscopy in Basal layer-type squamous cell carcinoma in situ via Euler's method and Law of mass action

abstract: Basal layer-type squamous cell carcinoma in situ(BLSCC) is an aggressive malignancy tumor. In the past, it usually went ignored because its aggressive biological behavior is different from typical esophageal squamous cancer(SCC). For our mechanistic model, we analyzed diffusion dynamics of iodine stain in BLSCC with the help of Eulers method. We used the law of mass action description of the forming process of the iodine-glycogen Complex. Based on the above analysis, our mechanistic model reveals that the efficacy of Lugols chromoendoscopy is determined by the thickness of the squamous epithelial cell layer, which contains glycogen granules, and the convection of the interpupillary capillary loop(IPCL). A further inference can be made: the unique histological structure of BLSCC suggests Lugols chromoendoscopy does not detect some components of it because these components neither break enough squamous epithelial cells which contain glycogen granules nor contain enough number of IPCL in a specific time frame. Besides, if our mechanistic model starting point is BLSCC and typical SCC share the same evolution path, we found both their cytoplasm tends to solid phase from the iodine diffusion dynamics analysis in "pink color sign."

category: cancer biology


title: Automated, high-accuracy, remote measurement of heart rate

abstract: Arrhythmia is a marked symptom of many cardiovascular diseases (CVDs). The accurate and timely detection of heart rate can greatly reduce the harm of arrhythmia to people. However, it is still a challenge to robustly and remotely measure heart rate in daily life due to the changing environmental conditions during measurement, such as the varying light intensity, the movement of people, and the uncertain distance between the sensor to people. In this study, we propose a method to accurately measure human heart rate within a distance of 4.5 meters under different light intensities by simply using a surveillance camera. After a 20-second color video of a persons hand is captured by the camera, a method based on the Fast Fourier Transform (FFT) algorithm is designed to extract the blood volume pulse wave to calculate the heart rate. According to the comparison between the real heart rate and results measured by electrocardiography (ECG), the proposed method achieves an accuracy of 95.8% when the measurement is performed within a distance of 4.5 meters and 90% when within 5.0 meters. Our experiments show that when the illuminance varies between 100-1000 lux (lighting level indoor), we still get the correct results. Our experiments also demonstrate that the proposed method accurately obtain heart rate even when the light intensity is below 32 lux (300-500 lux in a workplace environment). The methods strong adaptability to changing environmental conditions makes it applicable to many scenarios, such as homes of the elderly, classrooms, and other public spaces.

category: physiology


title: Robust and Remote Measurement of Heart Rate Based on A Surveillance Camera


title: Predicting individual shelter dog behaviour after adoption using longitudinal behavioural assessment: a hierarchical Bayesian approach

abstract: Predicting the behaviour of shelter dogs after adoption is an important, but difficult, endeavour. Differences between shelter and post-adoption environments, between- and within-individual heterogeneity in behaviour, uncertainty in behavioural predictions and measurement error all hinder the accurate assessment of future behaviour. This study integrates 1) a longitudinal behavioural assessment with 2) a novel joint hierarchical Bayesian mixture model that accounts for individual variation, missing data and measurement error to predict behaviour post-adoption. We analysed shelter observations (> 28,000 records) and post-adoption reports (from telephone surveys) on the behaviour of 241 dogs across eight contexts. Dog behaviour at the shelter correlated positively with behaviour post-adoption within contexts (r = 0.38; 95% highest density interval: [0.20, 0.55]), and behavioural repeatability was approximately 20% higher post-adoption than at the shelter for behaviour within contexts. Although measurement error was higher post-adoption than at the shelter, we found few differences in individual-level, latent probabilities of different behaviours post-adoption versus at the shelter. This good predictive ability was aided by accurate representation of uncertainty in individual-level predictions. We conclude that longitudinal assessment paired with a sufficient inferential framework to model latent behavioural profiles with uncertainty enables reasonably accurate estimation of post-adoption behaviour.

category: animal behavior and cognition


title: Syntrophy between fermentative and purple phototrophic bacteria for carbohydrate-based wastewater treatment

abstract:
Fermentative chemoorganoheterotrophic bacteria (FCB) and purple photoorganoheterotrophic bacteria (PPB) are two interesting microbial guilds to process carbohydrate-rich wastewaters. Their interaction has been studied in axenic pure cultures or co-cultures. Little is known about their metabolic interactions in open cultures. We aimed to harness the competitive and syntrophic interactions between PPB and FCB in mixed cultures. We studied the effect of reactor regimes (batch or continuous, CSTR) and illumination modes (continuous irradiation with infrared light, dark, or light/dark diel cycles) on glucose conversions and the ecology of the process. In batch, FCB outcompeted (>80%) PPB, under both dark and infrared light conditions. In CSTR, three FCB populations of Enterobacteriaceae, Lachnospiraceae and Clostridiaceae were enriched (>70%), while Rhodobacteraceae relatives of PPB made 30% of the community. Fermentation products generated from glucose were linked to the dominant FCB. Continuous culturing at a dilution rate of 0.04 h-1 helped maintain FCB and PPB in syntrophy: FCB first fermented glucose into volatile fatty acids and alcohols, and PPB grew on fermentation products. Direct supply of carboxylates like acetate under infrared light enriched for PPB (60%) independent of reactor regimes. Ecological engineering of FCB- and PPB-based biorefineries can help treat and valorize carbohydrate-based waste feedstocks.

GRAPHICAL ABSTRACT

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category: bioengineering


title: Understanding Microbeads Stacking in Deformable Nano-Sieve for Efficient Plasma Separation and Blood Cell Retrieval

abstract: Efficient separation of blood cells and plasma is key for numerous molecular diagnosis and therapeutics applications. Despite various microfluidics-based separation strategies have been developed, a simple, reliable, and multiplexing separation device that can process a large volume of blood is still missing. Here we show a microbead packed deformable microfluidic system that can efficiently separate highly purified plasma from whole blood as well as retrieve blocked blood cells from the device. Combining microscope imaging, optical tomography scanning, and computational fluidic modeling, a highly accurate model is constructed to understand the link between the mechanical properties of the microfluidics, flow rate, and microbeads packing/leaking, which supports and rationalizes the experimental observations. This deformable nano-sieve device establishes a key technology for centrifuge-free diagnosis and treatment of bloodborne diseases and may be important for the design of next-generation deformable microfluidics for separation applications.


title: Discovery of potential drug-like compounds against Viral protein (VP40) of Marburg Virus using pharmacophoric based virtual screening from ZINC database.

abstract: Marburg virus (MARV) has been confirmed to cause extreme hemorrhagic fever (HFM) in human and animals. The effective and suitable vaccine to treat the MARV virus is not commercialized in public and demands rigorously tested on several scales. This research used a CADD (Computer-Aided Drug Design) computational based technology to find novel drug-like compounds that could inhibit the replicating of the VP40. The pharmacophoric features bases screening was done using an online computational based software, "ZINC Pharmer". We retrieved about 32456 compounds mainly focused on the properties of pharmacophores from the ZINC database. Lipinskis rule was also used to predict these drug-like compounds. as well as molecular coupling-dependent screening and selection of VP40 screening ligand complexes based on S-rank (lower than reference) and value of root, mean square (RMSD) (bottom) to examine for reference) using the Molecular Working Environment (MOE) machine. As a result, 100 compounds were found to have a close interaction with MARV VP40, followed by the Binding energy (BE) analysis of these 100 compounds. Only 50 were the strongest binding energy than favipiravir [reference inhibitor] after using the MOE-LigX algorithm to compare their binding energy. After that, ADMET analysis predicted only five compounds (ZINC95457352, ZINC38752258, ZINC38752253, ZINC39272175, and ZINC38752377) passed the ADMET parameters and have the strongest inhibitory effect against the MARVs VP40. It has been suggested that these "drug-like" candidates have an increased ability to inhibit MARV replication, leading to treatment of MARVD.


title: Localization and RNAi-driven inhibition of a Brugia malayi encoded Interleukin-5 Receptor Binding protein

abstract: A molecule termed BmIL5Rbp (aka Bm8757) was identified from Brugia malayi filarial worms and found to competitively inhibit human IL-5 binding to its human receptor. After the expression and purification of a recombinant BmIL5Rbp and generation of BmIL5Rbp-specific rabbit antibody, we localized the molecule on B. malayi worms through immunohistochemistry and immunoelectron microscopy. RNA interference was used to inhibit BmIL5Rbp mRNA and protein production. BmIL5Rbp was shown to localize to the cuticle of Brugia malayi and to be released in their excretory/secretory products. RNAi inhibited BmIL5Rbp mRNA production by 33% and reduced the surface protein expression by [~]50% and suppressed the release of BmIL5Rbp in the excretory/secretory products. RNAi has been used successfully to knock down the mRNA and protein expression of BmIL5Rbp in the early larval stages of B. malayi and provided a proof-of-principle for the local inhibition of the human IL5 receptor. These findings provide evidence that a parasite encoded IL5R antagonist could be utilized therapeutically.

category: pathology


category: molecular biology


title: Identification of mundulone and mundulone acetate as natural products with tocolytic efficacy in mono- and combination-therapy with current tocolytics

abstract:
Currently, there are a lack of FDA-approved tocolytics for the management of preterm labor. We previously observed that the isoflavones mundulone and mundulone acetate (MA) inhibit intracellular Ca2+-regulated myometrial contractility. Here, we further probed the potential of these natural products to be small molecule leads for discovery of novel tocolytics by: (1) examining uterine-selectivity by comparing concentration-response between human primary myometrial cells and a major off-target site, aortic vascular smooth muscle cells (VSMCs), (2) identifying synergistic combinations with current clinical tocolytics to increase efficacy or and reduce off-target side effects, (3) determining cytotoxic effects and (4) investigating the efficacy, potency and tissue-selectivity between myometrial contractility and constriction of fetal ductus arteriosus (DA), a major off-target of current tocolytics. Mundulone displayed significantly greater efficacy (Emax = 80.5% vs. 44.5%, p=0.0005) and potency (IC50 = 27 M and 14 M, p=0.007) compared to MA in the inhibition of intracellular-Ca2+ from myometrial cells. MA showed greater uterine-selectivity, compared to mundulone, based on greater differences in the IC50 (4.3 vs. 2.3 fold) and Emax (70% vs. 0%) between myometrial cells compared to aorta VSMCs. Moreover, MA demonstrated a favorable in vitro therapeutic index of 8.8, compared to TI = 0.8 of mundulone, due to its significantly (p<0.0005) smaller effect on the viability of myometrial (hTERT-HM), liver (HepG2) and kidney (RPTEC) cells. However, mundulone exhibited synergism with two current tocolytics (atosiban and nifedipine), while MA only displayed synergistic efficacy with only nifedipine. Of these synergistic combinations, only mundulone + atosiban demonstrated a favorable TI = 10 compared to TI=0.8 for mundulone alone. While only mundulone showed concentration-dependent inhibition of ex vivo mouse myometrial contractions, neither mundulone or MA affected mouse fetal DA vasoreactivity. The combination of mundulone and atosiban yielded greater tocolytic efficacy and potency on term pregnant mouse and human myometrial tissue compared to single-drugs. Collectively, these data highlight the difference in uterine-selectivity of Ca2+-mobilization, effects on cell viability and tocolytic efficacy between mundulone and MA. These natural products could benefit from medicinal chemistry efforts to study the structural activity relationship for further development into a promising single- and/or combination-tocolytic therapy for management of preterm labor.

Chemical compounds studied in this articleatosiban (Pubchem CID: 5311010); indomethacin (Pubchem CID: 3715); mundulone (Pubchem CID: 4587968); mundulone acetate (Pubchem CID: 6857790); nifedipine (Pubchem CID: 4485); oxytocin acetate (Pubchem CID: 5771); U46619 (Pubchem CID: 5311493)

category: pharmacology and toxicology


title: Light at the end of the tunnel: FRAP assay reveals that plant vacuoles start as a tubular network

abstract:
Plant vacuoles play key roles in cellular homeostasis performing catabolic and storage functions, regulating pH and ion balance. The essential role of vacuoles for plant cell viability makes them a notoriously difficult subject to study impeding reaching the consensus on the mechanism of vacuolar establishment and the source of membrane material for it. Our previous suggestion of endoplasmic reticulum being the main membrane contributor for the tubular network of young vacuoles was recently challenged in a study proposing that young plant vacuoles comprise a set of individual vesicles that are formed de novo via homotypic fusion of multivesicular bodies (MVBs).

To resolve these seemingly contradictory observations we have carefully revaluated both hypotheses. Here we provide a systematic overview of successive vacuolar biogenesis stages in Arabidopsis root, starting from the youngest cells proximate to the quiescent center. We validate our previous conclusions by demonstrating that the vacuolar dye BCECF is fully suitable for studying the organelles morphology and provide 3D models of vacuoles at all developmental stages. Furthermore, we established a customized FRAP assay and proved that even at the earliest stages of biogenesis, vacuoles comprise a connected network. Finally, we summarized the new and pre-existing evidence substantiating that vacuolar structures cannot originate solely from MVBs.

category: plant biology


title: Early induction of hepatic deiodinase type 1 inhibits hepatosteatosis during NAFLD progression

abstract:
ObjectiveNon-alcoholic fatty liver disease (NAFLD) comprises a spectrum ranging from hepatosteatosis to progressive non-alcoholic steatohepatitis that can lead to cirrhosis. Humans with low levels of the prohormone thyroxine (T4) have a higher incidence of NAFLD and thyroid hormone treatment is very promising in all patients with NAFLD. Deiodinase 1 (Dio1) is a hepatic enzyme that converts T4 to the bioactive T3, and therefore regulates intracellular thyroid hormone availability in the liver. The role of this intracellular regulation was investigated during the progression of NAFLD.

MethodsWe investigated intracellular thyroid hormone metabolism in two NAFLD models: wildtype mice fed Western diet with fructose and Leprdp mice fed a methionine- and choline-deficient diet. AAV8-mediated liver-specific Dio1 knockdown was employed to investigate the role of Dio1 during the progression of NAFLD. Intrahepatic thyroid hormone levels, deiodinase activity and metabolic parameters were measured.

ResultsDio1 expression and activity were increased in the early stages of NAFLD and were associated with an increased T3/T4 ratio. Prevention of this increase by AAV8-mediated liverspecific Dio1 knockdown increased hepatic triglycerides and cholesterol as well as decreased pACC/ACC ratio and acylcarnitine levels suggesting there was lower {beta}-oxidation. Dio1 siRNA KD in hepatic cells treated with fatty acids showed increased lipid accumulation and decreased oxidative phosphorylation.

ConclusionHepatic Dio1 gene expression was modulated by dietary conditions, increased during hepatosteatosis and early NASH, and regulated hepatic triglyceride content. These early adaptations likely represent compensatory mechanisms to reduce hepatosteatosis and prevent NASH progression.


title: Competition for fluctuating resources reproduces statistics of species abundance over time across wide-ranging microbiotas

abstract: Across diverse microbiotas, species abundances vary in time with distinctive statistical behaviors that appear to generalize across hosts, but the origins and implications of these patterns remain unclear. Here, we show that many of these patterns can be quantitatively recapitulated by a simple class of resource-competition models, in which the metabolic capabilities of different species are randomly drawn from a common statistical ensemble. Our coarse-grained model parametrizes the intrinsic consumer-resource properties of a community using a small number of macroscopic parameters, including the total number of resources, typical resource fluctuations over time, and the average overlap in resource-consumption profiles across species. We elucidate how variation in these parameters affects various time series statistics, enabling macroscopic parameter estimation and comparison across wide-ranging microbiotas, including the human gut, saliva, and vagina, as well as mouse gut and rice. The successful recapitulation of time series statistics across microbiotas suggests that resource competition generally acts as a dominant driver of community dynamics. Our work unifies numerous time series patterns under one model, clarifies their origins, and provides a framework to infer macroscopic parameters of resource competition from longitudinal studies of microbial communities.

category: ecology


title: Increasing temperature weakens the positive effect of genetic diversity on population growth

abstract: Genetic diversity and temperature increases associated with global climate change, are known to independently influence population growth and extinction risk. Whether increasing temperature may influence the effect of genetic diversity on population growth, however, is not known. We address this issue in the model protist system Tetrahymena thermophila. We test the hypothesis that at temperatures closer to the species thermal optimum (i.e., the temperature at which population growth is maximal), genetic diversity should have a weaker effect on population growth compared to temperatures away from the thermal optimum. To do so, we grew populations of T. thermophila with varying levels of genetic diversity at increasingly warmer temperatures and quantified their intrinsic population growth rate, r. We found that genetic diversity increases population growth at cooler temperatures, but that as temperature increases, this effect almost completely disappears. We also show that a combination of changes in the amount of expressed genetic diversity (G), plastic changes in population growth across temperatures (E), and strong GxE interactions, underlie this temperature effect. Our results uncover important but largely overlooked temperature effects that have implications for the management of small populations with depauperate genetic stocks in an increasingly warming world.


title: RNA-seq and differential expression analysis of the duck transcriptome: The effect of short-term cage-rearing

abstract: Ducks are an important source of meat and egg products for human beings. In China, duck breeding has gradually changed from the traditional floor-water combination system to multilayer cage breeding. Therefore, the present study collected the hypothalamus and pituitary of 113-day-old ducks after being caged for 3 days, in order to investigate the effect of cage-rearing on the birds. In addition, the same tissues (hypothalamus and pituitary) were collected from ducks raised in the floor-water combination system, for comparison. Thereafter, the transcriptomes were sequenced and the expression level of genes were compared. The results of sequencing analysis showed that a total of 506 and 342 genes were differentially expressed in the hypothalamus and pituitary, respectively. Additionally, the differentially expressed genes were mainly enriched in signaling pathways involved in processing environmental information, including ECM-receptor interaction, neuroactive ligand-receptor interaction and focal adhesion. The findings also showed that there was a change in the alternative splicing of genes when ducks were transferred into the cage rearing system. However, there was no difference in the expression of some genes although there was a change in the expression of the isoforms of these genes. The findings herein can therefore help in understanding the mechanisms underlying the effect of caging on waterfowl. The results also highlight the gene regulatory networks involved in animal responses to acute stress.

category: genetics


title: Beyond resting state neuronal avalanches in the somatosensory barrel cortex

abstract: Since its first experimental signatures, the so called  critical brain hypothesis has been extensively studied. Yet, its actual foundations remain elusive. According to a widely accepted teleological reasoning, the brain would be poised to a critical state to optimize the mapping of the noisy and ever changing real-world inputs, thus suggesting that primary sensory cortical areas should be critical. We investigated whether a single barrel column of the somatosensory cortex of the anesthetized rat displays a critical behavior. Neuronal avalanches were recorded across all cortical layers in terms of both spikes and population local field potentials, and their behavior during spontaneous activity compared to the one evoked by a controlled single whisker deflection. By applying a maximum likelihood statistical method based on timeseries undersampling to fit the avalanches distributions, we show that neuronal avalanches are power law distributed for both spikes and local field potentials during spontaneous activity, with exponents that are spread along a scaling line. Instead, after the tactile stimulus, activity switches to an across-layers synchronization mode that appears to dominate during cortical representation of the single sensory input.

category: neuroscience


title: Chromosome length and gene density contribute to micronuclear membrane stability

abstract: Micronuclei are derived from missegregated chromosomes and frequently lose membrane integrity, leading to DNA damage, innate immune activation, and metastatic signaling. Here we demonstrate that two characteristics of the trapped chromosome, length and gene density, are key contributors to micronuclei membrane stability in human cells. Chromosome length is proportional to micronuclei size, and gene density has an additive effect with micronucleus size on membrane stability. We demonstrate that these results are not due to chromosome-specific differences in spindle position or initial nuclear pore complex recruitment during post-mitotic nuclear envelope assembly. We find that chromosome length and micronuclei size strongly correlate with lamin B1 and nuclear pore density in intact micronuclei. Unexpectedly, lamin B1 levels do not predict nuclear lamina organization and membrane stability. Instead, small gene-dense micronuclei have decreased nuclear lamina gaps compared to large micronuclei, despite very low levels of lamin B1. Our data strongly suggest that nuclear envelope composition defects previously correlated with membrane rupture only partly explain membrane stability in micronuclei. We propose that an unknown factor linked to gene density has a separate function that inhibits the appearance of nuclear lamina gaps and delays membrane rupture until late in the cell cycle.

category: cell biology


title: Piezo1 activation using Yoda1 inhibits macropinocytosis and proliferation of cancer cells

abstract: Macropinocytosis is a type of endocytosis accompanied by actin rearrangement-driven membrane deformation, such as lamellipodia formation and membrane ruffling, followed by macropinosome formation. A certain number of mammalian mechanosensors are sensitive to membrane deformation and tension. However, it remains unclear whether macropinocytosis is regulated by mechanosensors. Focusing on the mechanosensitive ion channel Piezo1, we found that Yoda1, a Piezo1 agonist, potently inhibits macropinocytosis induced by epidermal growth factor (EGF). Although studies with Piezo1 knockout cells suggest that Piezo1 itself is not physiologically indispensable for macropinocytosis regulation, Yoda1 inhibited ruffle formation depending on the extracellular Ca2+ influx through Piezo1 and on the activation of the calcium-activated potassium channel KCa3.1. This suggests that Ca2+ ions can regulate EGF-stimulated macropinocytosis. Moreover, Yoda1 impaired cancer cell proliferation, suggesting the impact of macropinocytosis inhibition. We propose the potential for cancer therapy by macropinocytosis inhibition through the regulation of a mechanosensitive channel activity.


title: Potent macrocycle inhibitors of the human SAGA deubiquitinating module

abstract: The SAGA transcriptional coactivator contains a four-protein subcomplex called the DUB module that removes ubiquitin from histone H2B-K120. The human DUB module contains the catalytic subunit, USP22, which is overexpressed in a number of cancers that are resistant to available therapies. We screened a massive combinatorial library of cyclic peptides and identified potent inhibitors of USP22. The top hit was highly specific for USP22 as compared to a panel of 44 other human DUBs. Cells treated with peptide had increased levels of H2B monoubiquitination, demonstrating the ability of the cyclic peptides to enter human cells and inhibit H2B deubiquitination. These macrocycle inhibitors are, to our knowledge, the first reported inhibitors of USP22/SAGA DUB module and show promise for development.

category: biochemistry


title: Nitric oxide synthase neurons in the preoptic hypothalamus are sleep-active and contribute to regulating NREM and REM sleep and lowering body temperature.

abstract: When mice are exposed to external warmth, nitric oxide synthase (NOS1) neurons in the median and medial preoptic (MnPO/MPO) hypothalamus induce sleep and concomitant body cooling. However, how these neurons regulate baseline sleep and body temperature is unknown. Using calcium photometry, we show that NOS1 neurons in MnPO/MPO are predominantly NREM active. This is the first instance of a predominantly NREM-active population in the PO area, or to our knowledge, elsewhere in the brain. In addition to releasing nitric oxide, NOS1 neurons in MnPO/MPO can release GABA, glutamate and peptides. We expressed tetanus-toxin light-chain in MnPO/MPO NOS1 cells to reduce vesicular release of transmitters. This induced changes in sleep structure: over 24 hours, mice had less NREM sleep in their dark (active) phase, and more NREM sleep in their light (sleep) phase. REM sleep episodes in the dark phase were longer, and there were fewer REM transitions between other vigilance states. REM sleep had less theta power. Mice with synaptically blocked MnPO/MPO NOS1 neurons were also warmer. In particular, mice were warmer than control mice at the dark-light transition (ZT0), as well as during the dark phase siesta (ZT16-20), where there is usually a body temperature dip. Also, at this siesta point of cooled body temperature, mice usually have more NREM, but mice with synaptically blocked MnPO/MPO NOS1 cells showed reduced NREM sleep at this time. Overall, MnPO/MPO NOS1 neurons promote both NREM and REM sleep and contribute to chronically lowering body temperature, particularly at transitions where the mice normally enter NREM sleep.


title: Using ephaptic coupling to estimate the synaptic cleft resistivity of the calyx of Held synapse.

abstract:
At synapses, the pre- and postsynaptic cell get so close that currents entering the cleft do not flow exclusively along its conductance, gcl. A prominent example is found in the calyx of Held synapse in the medial nucleus of the trapezoid body (MNTB), where the presynaptic action potential can be recorded in the postsynaptic cell in the form of a prespike. Here, we developed a theoretical framework for ephaptic coupling via the synaptic cleft, and we tested its predictions using the MNTB prespike recorded in voltage-clamp. The shape of the prespike is predicted to resemble either the first or the second derivative of the inverted, presynaptic action potential if cleft currents dissipate either mostly capacitively or resistively, respectively. We found that the resistive dissipation scenario provided a better description of the prespike shape. Its size is predicted to scale with the fourth power of the radius of the synapse, explaining why intracellularly recorded prespikes are uncommon in the central nervous system. We show that presynaptic calcium currents also contribute to the prespike shape. This calcium prespike resembled the first derivative of the inverted calcium current, again as predicted by the resistive dissipation scenario. Using this calcium prespike, we obtained an estimate for gcl of ~1 S. We demonstrate that, for a circular synapse geometry, such as in conventional boutons or the immature calyx of Held, gcl is scale-invariant and only defined by extracellular resistivity, which was ~75 {Omega}cm, and by cleft height. During development the calyx of Held develops fenestrations. We show that these fenestrations effectively minimize the cleft potentials generated by the adult action potential, which might otherwise interfere with calcium channel opening. We thus provide a quantitative account of the dissipation of currents by the synaptic cleft, which can be readily extrapolated to conventional, bouton-like synapses.

Author SummaryAt chemical synapses two neurons are separated by a cleft, which is very narrow. As a result, the concentration of released neurotransmitter can rapidly peak, which is essential for fast synaptic transmission. At the same time, the currents that flow across the membranes that face the synaptic cleft are also substantial, and a fraction of these currents will enter the other cell. We made an electronic model of the synaptic cleft, which indicated that if the shape and fraction of these currents are known, the electrical resistance of the synaptic cleft can be inferred. We tested several of the predictions of our model by comparing the membrane currents during a presynaptic action potential in a giant terminal, the calyx of Held, with the much smaller prespike evoked by these currents in the postsynaptic cell. We estimate the cleft resistance to be about 1 M{Omega}, which means that the changes in the cleft potential due to the membrane currents can become large enough to have an impact on voltage-dependent calcium channels controlling neurotransmitter release.


title: WASP integrates substrate topology and cell polarity to guide neutrophil migration

abstract: To control their shape and movement, cells leverage nucleation promoting factors (NPFs) to regulate when and where they polymerize actin. Here we investigate the role of the immune-specific NPF WASP during neutrophil migration. Endogenously-tagged WASP localizes to substrate-induced plasma membrane deformations. Super-resolution imaging of live cells reveals that WASP preferentially enriches to the necks of these substrate-induced membrane invaginations, a distribution that could support substrate pinching. Unlike other curvature-sensitive proteins, WASP only enriches to membrane deformations at the cell front, where it controls Arp2/3 complex recruitment and actin polymerization. Despite relatively normal migration on flat substrates, WASP depletion causes defects in topology sensing and directed migration on textured substrates. WASP therefore both responds to and reinforces cell polarity during migration. Surprisingly, front-biased WASP puncta continue to form in the absence of Cdc42. We propose that WASP integrates substrate topology with cell polarity for 3D guidance by selectively polymerizing actin around substrate-induced membrane deformations at the leading edge. A misregulation of WASP-mediated contact guidance could provide insight into the immune disorder Wiskott-Aldrich syndrome.


title: Quantitative proteomics identifies the universally conserved ATPase Ola1p as a positive regulator of heat shock response in Saccharomyces cerevisiae

abstract: The universally conserved P-loop ATPase Ola1 is implicated in various cellular stress response pathways, as well as in cancer and tumor progression. However, Ola1p functions are divergent between species and the involved mechanisms are only poorly understood. Here, we studied the role of Ola1p in the heat shock response of the yeast Saccharomyces cerevisiae using a combination of quantitative and pulse labeling-based proteomics approaches, in vitro studies and cell-based assays. Our data show that when heat stress is applied to cells lacking Ola1p, the expression of stress-protective proteins is enhanced. During heat stress Ola1p associates with detergent-resistant protein aggregates and rapidly forms assemblies that localize to stress granules. The assembly of Ola1p was also observed in vitro using purified protein and conditions, which resembled those in living cells. We show that loss of Ola1p results in increased protein ubiquitination of detergent-insoluble aggregates recovered from heat-shocked cells. When subsequently cells lacking Ola1p were relieved from heat stress, reinitiation of translation was delayed, whereas, at the same time, de novo synthesis of central factors required for protein refolding and the clearance of aggregates was enhanced when compared to wildtype cells. The combined data suggest that upon acute heat stress, Ola1p is involved in the stabilization of misfolded proteins, which become sequestered in cytoplasmic stress granules. This function of Ola1p enables cells to resume translation in a timely manner as soon as heat stress is relieved.


title: Chromatin loading of MCM hexamers is associated with di-/tri-methylation of histone H4K20 toward S phase entry

abstract: DNA replication is a key step in initiating cell proliferation. Loading hexameric complexes of minichromosome maintenance (MCM) helicase onto DNA replication origins during the G1 phase is essential for initiating DNA replication. Here, we examined MCM hexamer states during the cell cycle in human hTERT-RPE1 cells using multicolor immunofluorescence-based, single-cell plot analysis, and biochemical size fractionation. Experiments involving cell-cycle arrest at the G1 phase and release from the arrest revealed that a double MCM hexamer was formed via a single hexamer during G1 progression. A single MCM hexamer was recruited to chromatin in the early G1 phase. Another single hexamer was recruited to form a double hexamer in the late G1 phase. We further examined relationship between the MCM hexamer states and the methylation levels at lysine 20 of histone H4 (H4K20) and found that the double MCM hexamer state was correlated with di/trimethyl-H4K20 (H4K20me2/3). Inhibiting the conversion from monomethyl-H4K20 (H4K20me1) to H4K20me2/3 retained the cells in the single MCM hexamer state. Non-proliferative cells, including confluent cells or Cdk4/6 inhibitor-treated cells, also remained halted in the single MCM hexamer state. We propose that the single MCM hexamer state is a halting step in the determination of cell cycle progression.


title: Selective ablation of Nfix in Macrophages preserves Muscular Dystrophy by inhibiting FAPs-dependent fibrosis

abstract: Muscular dystrophies are genetic diseases characterized by chronic inflammation and fibrosis. Macrophages are immune cells that sustain muscle regeneration upon acute injury but seem deleterious in the context of chronic muscle injury such as muscular dystrophies. Here we observed that the number of macrophages expressing the transcription factor Nfix increases in two distinct murine models of muscular dystrophies. Plus, we showed that the deletion of Nfix in macrophages in dystrophic mice delays fibrosis establishment and muscle wasting until 6 months of life. Indeed, macrophages lacking Nfix express more TNF and less TGF{beta}1 thus promoting apoptosis of fibro-adipogenic progenitors. Moreover, pharmacological treatment of dystrophic mice with ROCK inhibitor accelerates fibrosis through the increase of Nfix expression by macrophages. Thus, we identify Nfix as a macrophage profibrotic actor in muscular dystrophies, whose inhibition could be a therapeutic way to rescue the dystrophic disease.


title: Elevated Neuropeptide Y1 Receptor Signaling Contributes to β-cell Dysfunction and Failure in Type 2 Diabetes

abstract: Loss of functional {beta}-cell mass is a key factor contributing to the poor glycaemic control in type 2 diabetes. However, therapies that directly target these underlying processes remains lacking. Here we demonstrate that gene expression of neuropeptide Y1 receptor and its ligand, neuropeptide Y, was significantly upregulated in human islets from subjects with type 2 diabetes. Importantly, the reduced insulin secretion in type 2 diabetes was associated with increased neuropeptide Y and Y1 receptor expression in human islets. Consistently, pharmacological inhibition of Y1 receptors by BIBO3304 significantly protected {beta}-cells from dysfunction and death under multiple diabetogenic conditions in islets. In a preclinical study, Y1 receptor antagonist BIBO3304 treatment improved {beta}-cell function and preserved functional {beta}-cell mass, thereby resulting in better glycaemic control in both high-fat-diet/multiple low-dose streptozotocin- and db/db type 2 diabetic mice. Collectively, our results uncovered a novel causal link of increased islet NPY-Y1 receptor signaling to {beta}-cell dysfunction and failure in human type 2 diabetes. These results further demonstrate that inhibition of Y1 receptor by BIBO3304 represents a novel and effective {beta}-cell protective therapy for improving functional {beta}-cell mass and glycaemic control in type 2 diabetes.


title: The environmental stress response regulates ribosome content in cell cycle-arrested S. cerevisiae

abstract: Temperature sensitive cell division cycle (cdc-ts) cells are unable to progress through the cell cycle at the restrictive temperature due to mutations in genes essential to cell cycle progress. Cells harboring cdc-ts mutations increase in cell volume upon arrest but eventually stop growing. We found that this attenuation in growth was due to selective downregulation of ribosome concentration. We saw similar ribosome downregulation in cells arrested in the cell cycle through alpha factor addition, rapamycin addition, and entrance into stationary phase. In all cell cycle arrests studied, cells activated the Environmental Stress Response (ESR), a key transcriptional response to many stressors in S. cerevisiae. When we combined cell cycle arrest with hyperactivation of the Ras/PKA pathway, ESR activation was prevented, cells were unable to downregulate their ribosomes, and cell viability was decreased. Our work uncovers a key role for the environmental stress response in coupling cell cycle progression to biomass accumulation.


title: Structural Basis for Membrane Recruitment of ATG16L1 by WIPI2 in Autophagy

abstract: Autophagy is a cellular process that degrades cytoplasmic cargo by engulfing it in a double membrane vesicle, known as the autophagosome, and delivering it to the lysosome. The ATG12-5-16L1 complex is responsible for conjugating members of the ubiquitin-like ATG8 protein family to phosphatidylethanolamine in the growing autophagosomal membrane, known as the phagophore. ATG12-5-16L1 is recruited to the phagophore by a subset of the phosphatidylinositol 3-phosphate-binding seven bladed {beta}-propeller WIPI proteins. We determined the crystal structure of WIPI2d in complex with the WIPI2 interacting region (W2IR) of ATG16L1 comprising residues 207-230 at 1.85 [A] resolution. The structure shows that the ATG16L1 W2IR adopts an alpha helical conformation and binds in an electropositive and hydrophobic groove between WIPI2 {beta}-propeller blades 2 and 3. Mutation of residues at the interface reduces or blocks the recruitment of ATG12-5-16L1 and the conjugation of the ATG8 protein LC3B to synthetic membranes. Interface mutants show a decrease in starvation-induced autophagy. Comparisons across the four human WIPIs suggest that WIPI1 and 2 belong to a W2IR-binding subclass responsible for localizing ATG12-5-16L1 and driving ATG8 lipidation, whilst WIPI3 and 4 belong to a second W34IR-binding subclass responsible for localizing ATG2, and so directing lipid supply to the nascent phagophore. The structure provides a framework for understanding the regulatory node connecting two central events in autophagy initiation, the action of the autophagic PI 3-kinase complex on the one hand, and ATG8 lipidation on the other.


title: Paternal chromosome elimination and X non-disjunction on asymmetric spindles in Sciara male meiosis

abstract: Meiosis in male Sciara is unique with a single centrosome. A monopolar spindle forms in meiosis I, but a bipolar spindle forms in meiosis II. The imprinted paternal chromosomes are eliminated in meiosis I; there is non-disjunction of the X in meiosis II. Despite differences in spindle construction and chromosome behavior, both meiotic divisions are asymmetric, producing a cell and a small bud. Observations of live spermatocytes made with the LC-PolScope, differential interference contrast optics and fluorescence revealed maternal and paternal chromosome sets on the monopolar spindle in meiosis I and formation of an asymmetric monastral bipolar spindle in meiosis II where all chromosomes except the X congress to the metaphase plate. The X remains near the centrosome after meiosis I and stays with it as the spindle forms in meiosis II. Electron microscopy revealed amorphous material between the X and the centrosome. Immunofluorescence with an antibody against the checkpoint protein Mad2 stains the centromeres of the maternal X dyad in late meiosis I and in meiosis II where it fails to congress to the metaphase plate. Mad2 is also present throughout the paternal chromosomes destined for elimination in meiosis I, suggesting a possible role in chromosome imprinting. If Mad2 on the X dyad mediates a spindle checkpoint in meiosis II, it may delay metaphase to facilitate formation of the second half spindle through a non-centrosomal mechanism.


title: Chaperones directly and efficiently disperse stress-triggered biomolecular condensates

abstract: Heat shock triggers formation of intracellular protein aggregates and induction of a molecular disaggregation system. Although this system (Hsp100/Hsp70/Hsp40 in most cellular life) can disperse aggregates of model misfolded proteins, its activity on these model substrates is puzzlingly weak, and its endogenous heat-induced substrates have largely eluded biochemical study. Recent work has revealed that several cases of apparent heat-induced aggregation instead reflect evolved, adaptive biomolecular condensation. In budding yeast Saccharomyces cerevisiae, the resulting condensates depend on molecular chaperones for timely dispersal in vivo, hinting that condensates may be major endogenous substrates of the disaggregation system. Here, we show that the yeast disaggregation system disperses heat-induced biomolecular condensates of poly(A)-binding protein (Pab1) orders of magnitude more rapidly than aggregates of the most commonly used model substrate, firefly luciferase. Pab1 condensate dispersal also differs from aggregate dispersal in its molecular requirements, showing no dependence on small heat-shock proteins and a strict requirement for type II Hsp40. Unlike luciferase, Pab1 is not fully threaded (and thus not fully unfolded) by the disaggregase Hsp104 during dispersal, which we show can contribute to the extreme differences in dispersal efficiency. The Hsp70-related disaggregase Hsp110 shows some Pab1 dispersal activity, a potentially important link to animal systems, which lack cytosolic Hsp104. Finally, we show that the long-observed dependence of the disaggregation system on excess Hsp70 stems from the precise mechanism of the disaggregation system, which depends on the presence of multiple, closely spaced Hsp70s for Hsp104 recruitment and activation. Our results establish heat-induced biomolecular condensates of Pab1 as a direct endogenous substrate of the disaggregation machinery which differs markedly from previously studied foreign substrates, opening a crucial new window into the native mechanistic behavior and biological roles of this ancient system.


title: Efficient and stochastic mouse action switching during probabilistic decision making

abstract:
In probabilistic and nonstationary environments, individuals must use internal and external cues to flexibly make decisions that lead to desirable outcomes. To gain insight into the process by which animals choose between actions, we trained mice in a task with time-varying reward probabilities. In our implementation of such a "two-armed bandit" task, thirsty mice use information about recent action and action-outcome histories to choose between two ports that deliver water probabilistically. Here, we comprehensively modeled choice behavior in this task, including the trial-to-trial changes in port selection - i.e. action switching behavior. We find that mouse behavior is, at times, deterministic and, at others, apparently stochastic. The behavior deviates from that of a theoretically optimal agent performing Bayesian inference in a Hidden Markov Model (HMM). We formulate a set of models based on logistic regression, reinforcement learning, and  sticky Bayesian inference that we demonstrate are mathematically equivalent and that accurately describe mouse behavior. The switching behavior of mice in the task is captured in each model by a stochastic action policy, a history-dependent representation of action value, and a tendency to repeat actions despite incoming evidence. The models parsimoniously capture behavior across different environmental conditionals by varying the  stickiness parameter, and, like the mice, they achieve nearly maximal reward rates. These results indicate that mouse behavior reaches near-maximal performance with reduced action switching and can be described by a set of equivalent models with a small number of relatively fixed parameters.

SignificanceTo obtain rewards in changing and uncertain environments, animals must adapt their behavior. We found that mouse choice and trial-to-trial switching behavior in a dynamic and probabilistic two-choice task could be modeled by equivalent theoretical, algorithmic, and descriptive models. These models capture components of evidence accumulation, choice history bias, and stochasticity in mouse behavior. Furthermore, they reveal that mice adapt their behavior in different environmental contexts by modulating their level of  stickiness to their previous choice. Despite deviating from the behavior of a theoretically ideal observer, the empirical models achieve comparable levels of near-maximal reward. These results make predictions to guide interrogation of the neural mechanisms underlying flexible decision-making strategies.


title: Regulatory interplay between RNase III and asRNAs in E. coli; the case of AsflhD and the master regulator of motility, flhDC

abstract:
In order to respond to ever-changing environmental cues, bacteria have evolved resilient regulatory mechanisms controlling gene expression. At the post-transcriptional level, this is achieved by a combination of RNA-binding proteins, such as ribonucleases (RNases) and RNA chaperones, and regulatory RNAs including antisense RNAs (asRNAs). AsRNAs bound to their complementary mRNA are primary targets for the double-strand-specific endoribonuclease, RNase III. By comparing primary and processed transcripts in an rnc strain, mutated for RNase III, and its isogenic wild type strain, we detected several asRNAs. We confirmed the existence of RNase III-sensitive asRNA for crp, ompR, phoP and flhD genes, encoding master regulators of gene expression. AsflhD, the asRNA to the master regulator of motility flhDC, is slightly induced under heat-shock conditions in a sigma24 (RpoE)-dependent manner. We demonstrate that expression of AsflhD asRNA is involved in the transcriptional attenuation of flhD and thus participates in the control of the whole motility cascade. This study demonstrates that AsflhD and RNase III are additional players in the complex regulation ensuring a tight control of flagella synthesis and motility.

ImportanceThe importance of asRNAs in the regulation of gene expression has long been underestimated. Here, we confirm that asRNAs can be part of layered regulatory networks since some are found opposite to genes encoding global regulators. In particular, we show how an antisense RNA (AsflhD) to the gene expressing a transcription factor serving as the primary regulator of bacterial swimming motility (FlhD4C2) is involved in the transcriptional attenuation of flhD, which in turn impacts the expression of other genes of the motility cascade. The role of AsflhD highlights the importance of discrete fine-tuning mechanisms in the control of complex regulatory networks.

category: microbiology


title: Siglec-1 on dendritic cells mediates SARS-CoV-2 trans-infection of target cells while on macrophages triggers proinflammatory responses

abstract: COVID-19 pandemic is not yet under control by vaccination, and effective antivirals are critical for preparedness. Here we report that macrophages and dendritic cells, key antigen presenting myeloid cells (APCs), are largely resistant to SARS-CoV-2 infection. APCs effectively captured viruses within cellular compartments that lead to antigen degradation. Macrophages sense SARS-CoV-2 and released higher levels of cytokines, including those related to cytokine storm in severe COVID-19. The sialic acid-binding Ig-like lectin 1 (Siglec-1/CD169) present on APCs, which interacts with sialylated gangliosides on membranes of retroviruses or filoviruses, also binds SARS-CoV-2 via GM1. Blockage of Siglec-1 receptors by monoclonal antibodies reduces SARS-CoV-2 uptake and transfer to susceptible target cells. APCs expressing Siglec-1 and carrying SARS-CoV-2 are found in pulmonary tissues of non-human primates. Single cell analysis reveals the in vivo induction of cytokines in those macrophages. Targeting Siglec-1 could offer cross-protection against SARS-CoV-2 and other enveloped viruses that exploit APCs for viral dissemination, including those yet to come in future outbreaks.


title: Common Mechanism of SARS-CoV and SARS-CoV-2 Pathogenesis across Species

abstract: Sarbecovirus (CoV) infections, including Severe Acute Respiratory CoV (SARS-CoV) and SARS-CoV-2, are considerable human threats. Human GWAS studies have recently identified loci associated with variation in SARS-CoV-2 susceptibility. However, genetically tractable models that reproduce human CoV disease outcomes are needed to mechanistically evaluate genetic determinants of CoV susceptibility. We used the Collaborative Cross (CC) and human GWAS datasets to elucidate host susceptibility loci that regulate CoV infections and to identify host quantitative trait loci that modulate severe CoV and pan-CoV disease outcomes including a major disease regulating loci including CCR9. CCR9 ablation resulted in enhanced titer, weight loss, respiratory dysfunction, mortality, and inflammation, providing mechanistic support in mitigating protection from severe SARS-CoV-2 pathogenesis across species. This study represents a comprehensive analysis of susceptibility loci for an entire genus of human pathogens conducted, identifies a large collection of susceptibility loci and candidate genes that regulate multiple aspects type-specific and cross-CoV pathogenesis, and also validates the paradigm of using the CC platform to identify common cross-species susceptibility loci and genes for newly emerging and pre-epidemic viruses.


title: Transient ribosome slowdown at the decoding step triggers mRNA degradation independent of Znf598 in zebrafish

abstract: The control of mRNA stability plays a central role in regulating gene expression patterns. Recent studies have revealed that codon composition in the open reading frame (ORF) determines mRNA stability in multiple organisms. Based on genome-wide correlation approaches, this previously unrecognized role of the genetic code is attributable to the kinetics of the codon-decoding process by the ribosome. However, complementary experimental analysis is required to define the codon effects on mRNA stability apart from the related cotranslational mRNA decay pathways such as those triggered by aberrant ribosome stalls. In the current study, we performed a set of reporter-based analyses to define codon-mediated mRNA decay and ribosome stall-dependent mRNA decay in zebrafish embryos. Our analysis showed that the effect of codons on mRNA stability stems from the decoding process, independent of Znf598 and stall-dependent mRNA decay. We propose that codon-mediated mRNA decay is triggered by transiently slowed ribosomes engaging in a productive translation cycle in zebrafish embryos.


title: Do soil features condition seed germination of gypsum plants? An analysis of the effect of different natural soils

abstract:
Gypseous soils are widespread across arid and semiarid environments worldwide. They present remarkable challenges to plants and host a unique flora. We aimed to assess up to what point the specificity and distribution of species on gypsum might be driven by species-specific germination responses to soil gypsum availability. We analyzed the germination of six gypsum specialists and four closely related generalist plant species from the Iberian Peninsula and the Chihuahuan Desert in four different field soils with contrasting concentrations of gypsum, pH and soil texture. Plant restriction to gypsum was unrelated to the germinating ability of seeds on different substrates. Irrespective of their affinity for gypsum, most species germinated better on mixed gypsum-calcareous soil and worse in the acidic soil treatment. Our data suggest soil pH was the main soil feature driving seed germination, while the effect of gypsum content was generally not significant. The main exception was the Iberian gypsum specialist Helianthemum squamatum (L.) Dum. Cours., which showed increased germination on gypseous soils and higher germination in response to increased soil gypsum content. Except for this species, our findings indicate alkaline soils favor the germination of most of the species analyzed, irrespectively of their gypsum content.

HighlightsO_LIGypsum soils are one of the most widespread special substrates of the world
C_LIO_LIWe evaluated the effects of natural soils on the germination of gypsum plants
C_LIO_LISoil pH was the main soil feature driving seed germination
C_LIO_LIThe effect of gypsum content was not significant
C_LIO_LIWe suggest a potential origin of gypsophiles from plants adapted to alkaline soils
C_LI


title: Do host-consumed resources increase endoparasitic but decrease ectoparasitic infections?

abstract: Habitat loss and disease outbreak play a major role in the decline of biodiversity. Habitat degradation is often associated with reduced food resources, which can lead to less investment in host immunity and increased infections. However, pathogens use host resources for replication and pathogen traits, such as infecting hosts internally or short generation times, might allow pathogens to rapidly capitalize on host-consumed nutrients. Thus, it is unclear whether increased food consumption by hosts should reduce or amplify pathogen levels. We conducted experiments on Cuban treefrogs (Osteopilus septentrionalis) to test how food availability affects infection levels of Ranavirus and the fungal pathogen Batrachochytrium dendrobatidis (Bd), which are both associated with mass die-offs of amphibians. Given that Ranavirus is an endoparasite with a much shorter generation time than the ectoparasitic Bd, we postulated that Ranavirus might be able to capitalize on host-consumed resources more quickly than Bd. We hypothesized that increased food availability to hosts might reduce Bd infections more than Ranavirus infections. As predicted, augmenting food access decreased Bd infection intensity, but increased Ranavirus infection intensity. Future work should assess whether pathogen traits, such as generation time and endo- versus ectoparasitism, generally affect whether food resources more positively benefit hosts or pathogens.


title: Selection shapes the landscape of functional variation in wild house mice

abstract:
BackgroundThrough human-aided dispersal, house mice have recently colonized new and diverse habitats across the globe, promoting the emergence of new traits that confer adaptive advantages in distinct environments. Despite their status as the premiere mammalian model system, the impact of this demographic and selective history on the global patterning of disease-relevant trait variation in wild mouse populations is poorly understood.

ResultsHere, we leveraged 154 whole-genome sequences from diverse wild house mouse populations, subspecies, and species to survey the geographic organization of functional variation and systematically identify signals of positive selection. We show that a significant proportion of wild mouse variation is private to single populations, including numerous predicted functional alleles. In addition, we report strong signals of positive selection at numerous genes associated with both complex and Mendelian diseases in humans. Notably, we detect a significant excess of selection signals at disease-associated genes relative to null expectations, pointing to the important role of adaptation in shaping the landscape of functional variation in wild mouse populations. We also uncover strong signals of selection at multiple genes involved in starch digestion, including Mgam and Amy1. We speculate that the successful emergence of the human-mouse commensalism may have been facilitated, in part, by dietary adaptations at these loci. Finally, our work uncovers multiple cryptic structural variants that manifest as putative signals of positive selection, highlighting an important and under-appreciated source of false-positive signals in genome-wide selection scans.

ConclusionsOverall, our findings underscore the role of adaptation in shaping wild mouse genetic variation at human disease-associated genes. Our work highlights the biomedical relevance of wild mouse genetic diversity and unsdercores the potential for targeted sampling of mice from specific populations as a strategy for developing effective new mouse models of both rare and common human diseases.

category: evolutionary biology


title: Phenotypic distribution and selection response for linear-product gene-environment interaction in quantitative traits

abstract: Gene-environment interaction is often described by linear phenotypic plasticity but has recently also been expressed as function of the product of genotype and environmental variables. While this model can be fitted in a multiple regression scenario, little has been written on the distribution of the product of breeding values and environment, GE, its expected moments, and the theoretical impact on phenotypic selection. Here we will explore these topics introducing the distribution for GE, its mean and variance, and its expected impact of lowering realized heritability due to is increasing the phenotypic variance.


title: Saturation variant interpretation using CRISPR prime editing

abstract: Over the last decade, next generation sequencing has become widely implemented in clinical practice. However, as genetic variants of uncertain significance (VUS) are frequently identified, the need for scaled functional interpretation of such variants has become increasingly apparent. One method to address this is saturation genome editing (SGE), which allows for scaled multiplexed functional assessment of single nucleotide variants. The current applications of SGE, however, rely on homology-directed repair (HDR) to introduce variants of interest, which is limited by low editing efficiencies and low product purity. Here, we have adapted CRISPR prime editing for SGE and demonstrated its utility in understanding the functional significance of variants in the NPC1 gene underlying the lysosomal storage disorder Niemann-Pick disease type C1 (NPC). Additionally, we have designed a genome editing strategy that allows for the haploidization of gene loci, which permits isolated variant interpretation in virtually any cell type. By combining saturation prime editing (SPE) with a clinically relevant assay, we have functionally scored and interpreted 256 variants in NPC1 haploidized HEK293T cells. To further demonstrate the applicability of this strategy, we used SPE and cell model haploidization to functionally score 465 variants in the BRCA2 gene. We anticipate that our work will be translatable to any gene with an appropriate cellular assay, allowing for more rapid and accurate diagnosis and improved genetic counselling and ultimately precise patient care.


title: Residue-specific insights into (2x)72 kDa tryptophan synthase obtained from fast-MAS 1H-detected solid-state NMR

abstract: Solid-state NMR has emerged as a potent technique in structural biology, suitable for the study of fibrillar, micro-crystalline, and membrane proteins. Recent developments in fast-magic-angle-spinning and proton-detected methods have enabled detailed insights into structure and dynamics, but molecular-weight limitations for the asymmetric part of target proteins have remained at ~30-40 kDa. Here we employ solid-state NMR for atom-specific characterization of the 72 kDa (asymmetric unit) microcrystalline protein tryptophan synthase, an important target in pharmacology and biotechnology, chemical-shift assignments of which we obtain via higher-dimensionality, 4D and 5D solid-state NMR experiments. The assignments for the first time provide comprehensive data for assessment of side chain chemical properties involved in the catalytic turnover, and, in conjunction with first-principles calculations, precise determination of thermodynamic and kinetic parameters is demonstrated for the essential acid-base catalytic residue {beta}K87. The insights provided by this study expand by nearly a factor of two the size limitations widely accepted for NMR today, demonstrating the applicability of solid-state NMR to systems that have been thought to be out of reach due to their complexity.


title: SARS-CoV-2 Variant of Concern Substitutions Alter Spike Glycoprotein Receptor Binding Domain Structure and Stability

abstract: The emergence of severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) and the subsequent COVID-19 pandemic has visited a terrible cost on the world in the forms of disease, death, and economic turmoil. The rapid development and deployment of extremely effective vaccines against SARS-CoV-2 have seemingly brought within reach the end of the pandemic. However, the virus has acquired mutations; and emerging variants of concern (VOC) are more infectious and reduce the efficacy of existing vaccines. While promising efforts to combat these variants are underway, the evolutionary pressures leading to these variants are poorly understood. To that end, here we have studied the effects on the structure and function of the SARS-CoV-2 spike glycoprotein receptor-binding domain of three amino-acid substitutions found in several variants of concern, including alpha (B.1.1.7), beta (B.1.351), and gamma (P.1). We found that these substitutions alter the RBD structure, stability, and ability to bind to ACE2, in such a way as to possibly have opposing and compensatory effects. These findings provide new insights into how these VOC may have been selected for infectivity while maintaining the structure and stability of the receptor binding domain.


title: SARS-CoV-2 Beta Variant Substitutions Alter Spike Glycoprotein Receptor Binding Domain Structure and Stability


title: iSubGen: Integrative Subtype Generation by Pairwise Similarity Assessment

abstract: There are myriad types of biomedical data- genetics, transcriptomics, clinical, imaging, wearable devices and many more. When a group of patients with the same underlying disease exhibit similarities across multiple types of data, this is called a subtype. Disease subtypes can reflect etiology and sometimes predict clinical behaviour. Existing subtyping approaches struggle to simultaneously handle multiple diverse data types, particularly when there is missing information, as is common in most real-world clinical datasets. To improve subtype discovery, we exploited changes in the correlation-structure between different data types to create iSubGen, an algorithm for integrative subtype generation. iSubGen can combine arbitrary data types for subtype discovery, such as merging molecular, mutational signature, pathway and micro-environmental data. iSubGen recapitulates known subtypes across multiple diseases, even in the face of substantial missing data. It identifies groups of patients with divergent clinical outcomes, and can combine arbitrary data types for subtype discovery, such as merging molecular, mutational signature, pathway and micro-environmental data. iSubGen can accommodate any feature that can be compared with a similarity-metric, and provides a versatile approach for creating subtypes. It is available at https://CRAN.R-project.org/package=iSubGen.


title: All-atom Simulations Uncover the Molecular Terms of NKCC1 Transport Mechanism

abstract:
The secondary-active Na-K-Cl Cotransporter 1 (NKCC1), member of the Cation Chloride Cotransporters (CCC) family, ensures the electroneutral movement of Cl-, Na+, K+ ions across cellular membranes. NKCC1 regulates Cl- homeostasis and cell volume, handling a pivotal role in transepithelial water transport and neuronal excitability. Aberrant NKCC1 transport is hence implicated in a variety of human diseases (hypertension, renal disorders, neuropathies, cancer). Building on the newly-resolved NKCC1 cryo-EM structure, all-atom enhanced sampling simulations unprecedentedly unlock the mechanism of NKCC1-mediated ions transport, assessing the order and the molecular basis of its interdependent ions translocation. Our outcomes strikingly advance the understanding of the physiological mechanism of CCCs transporters and disclose a key role of CCC-conserved asparagine residues, whose side-chain promiscuity ensures the transport of both negatively and positively charged ions along the same translocation route. This study sets a conceptual basis to devise NKCC-selective inhibitors to treat diseases linked to Cl- dishomeostasis.

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/443869v1_ufig1.gif" ALT="Figure 1">
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category: biophysics


title: Frequency Comb Optoacoustic Tomography

abstract: Optoacoustics (OA) is overwhelmingly implemented in the Time Domain (TD) to achieve a high Signal-to-Noise-Ratio (SNR). Implementations in the Frequency Domain (FD) have been proposed, but have not offered competitive advantages over TD methods to reach high dissemination. It is therefore commonly believed that the TD represents the optimal way of performing optoacoustics. Here, we introduce a novel optoacoustic concept based on frequency comb and theoretically demonstrate its superiority to the TD. Then, using recent advances in laser diode illumination, we launch Frequency Comb Optoacoustic Tomography (FCOT), at multiple wavelengths, and experimentally demonstrate its advantages over TD methods in phantoms and in-vivo. We demonstrate that FCOT optimizes the SNR of spectral measurements over TD methods by benefiting from signal acquisition in the TD and processing in the FD, and that it reaches the fastest multi-spectral operation ever demonstrated in optoacoustics while reducing performance compromises present in TD systems.


title: Evaluation of BOLD effects in the rat cortex

abstract:
PurposeThis study aimed to characterize Blood oxygen level-dependent (BOLD) effects in 1H-MR spectra obtained during optogenetic activation of the rat forelimb cortex for the correction and estimation of accurate metabolite concentration changes.

MethodsT2*-induced effects were characterized by linewidth changes and amplitude changes of water, NAA and tCr spectral peaks during the stimulation paradigm. Spectral linewidth-matching procedures were used to correct for the line-narrowing effect induced by BOLD. For an increased understanding of spectroscopic BOLD effects and the optimized way to correct them, a 1 Hz line-narrowing effect was also simulated on mouseproton MR spectrum

 1H-fMRS data acquired using STEAM acquisitions at 9.4T in rats (n=8) upon optogenetic stimulation of the primary somatosensory cortex were used. Data were analyzed with MATLAB routines and LCModel. Uncorrected and corrected 1H-MR spectra of simulated and in-vivo data were quantified and compared. BOLD-corrected difference spectra were also calculated and analyzed.

ResultsSignificant mean increases in water and NAA peak heights (+ 1.1% and +4.5%, respectively) were found accompanied by decreased linewidths (-0.5 Hz and -2.8%) upon optogenetic stimulation. These estimates were used for further definition of an accurate line-broadening factor (lb). Usage of an erroneous lb introduced false-positive errors in metabolite concentration change estimates thereby altering the specificity of findings. Using different water scalings within LCModel, the water and metabolite BOLD contributions were separated.

ConclusionThe linewidth-matching procedure using a precise lb factor remains the most performant approach for the accurate quantification of small ({+/-}0.3 mol/g) metabolic changes in 1H-fMRS studies. A simple and preliminary compartmentation of BOLD effects was proposed, which will require validation.


title: Sortilin exhibits tumor suppressor-like activity by limiting EGFR transducing function

abstract: Lung cancer is the leading cause of cancer deaths worldwide and remains one of the most incurable. Tyrosine kinase receptors, such as the epidermal growth factor receptor (EGFR), are often aberrantly activated and drive tumor growth. Monotherapy with tyrosine kinase inhibitors to deactivate EGFR has shown initial efficacy, but their benefits tend to decline over time. EGFR acts as a transcriptional factor promoting the expression of co-oncogenic drivers, which, in turn, interact with canonical EGFR mutations to induce therapeutic relapse. This study reports that sortilin, a crucial regulator of cytoplasmic EGFR, attenuates its transducing function. Genome-wide chromatin binding revealed that sortilin interacts with gene regulatory elements occupied by EGFR. These results suggest a model, in which sortilin exhibits potential tumor suppressor-like activity by concurrently binding to regulatory elements of cMYC. Sortilin expression in lung adenocarcinoma may be predictive of the efficacy of anti-EGFR strategies.


title: Network pharmacology and chemoproteomics unveil the mechanism of Total Flavonoid Aglycones Extract inhibiting EMT in A549 cell line

abstract: Non-small cell lung cancer (NSCLC) is a worldwide disease with high morbidity and mortality, which is most derived from its metastasis. Some researches show that the epithelial-mesenchymal transition (EMT) process promotes lung cancer cells migration and invasion, leading to NSCLC metastasis. Total Flavonoid Aglycones Extract (TFAE) isolated from Scutellaria baicalensis was reported to inhibit tumor growth and induce apoptosis. In this study, we found that baicalein, wogonin, and oroxylin-A were the active compounds of TFAE. After reconstructing with these three compounds (baicalein (65.8%), wogonin (21.2%), and oroxylin-A (13.0%)), the reconstructed TFAE (reTFAE) present inhibitory effect on the EMT process of A549 cells. Then, bioinformatic technology was employed to elucidate the potential pharmacodynamic mechanism network of reTFAE. We identified the relationship between reTFAE and PI3K/Akt signaling pathways, with TWIST1 as the key protein. LY294002, the inhibitor of PI3K/Akt signaling pathway, and knock-down TWIST1 could significantly enhance the efficacy of reTFAE, with increasing expression of epithelial markers and decreasing expression of mesenchymal markers in A549 cells at the same time. Furthermore, stable isotope dimethyl-labeled proteomics technology was conducted to complement the follow-up mechanism that the EMT-inhibition process may be realized through glycolysis pathway. In conclusion, we claim that TWIST1-targeted flavonoids could provide a new strategy to inhibit EMT progress for the treatment of NSCLC.


title: The compound of baicalein, wogonin, and oroxylin-A inhibiting EMT in A549 cell line via PI3K/AKT-TWIST1-glycolysis pathway


title: The compound of baicalein, wogonin, and oroxylin-A inhibits EMT in A549 cell line via PI3K/AKT-TWIST1-glycolysis pathway


title: Functional expression of opioid receptors and other human GPCRs in yeast engineered to produce human sterols

abstract: The yeast Saccharomyces cerevisiae is a powerful tool for studying G protein-coupled receptors (GPCRs) as they can be functionally coupled to its pheromone response pathway. However, some exogenous GPCRs, including the mu opioid receptor, are non-functional in yeast, which may be due to the presence of the fungal sterol ergosterol instead of the animal sterol cholesterol. We engineered yeast to produce cholesterol and introduced the human mu opioid receptor, creating an opioid biosensor capable of detecting the peptide DAMGO at an EC50 of 62 nM and the opiate morphine at an EC50 of 882 nM. Furthermore, introducing mu, delta, and kappa opioid receptors from diverse vertebrates consistently yielded active opioid biosensors that both recapitulated expected agonist binding profiles with EC50s as low as 2.5 nM and were inhibited by the antagonist naltrexone. Additionally, clinically relevant human mu opioid receptor alleles, or variants with terminal mutations, resulted in biosensors that largely displayed the expected changes in activity. We also tested mu opioid receptor-based biosensors with systematically adjusted biosynthetic intermediates of cholesterol, enabling us to relate sterol profiles with biosensor sensitivity. Finally, cholesterol-producing and sterol intermediate biosensor backgrounds were applied to other human GPCRs, resulting in SSTR5, 5-HTR4, FPR1 and NPY1R signaling with varying degrees of cholesterol dependence. Our sterol-optimized platform will be a valuable tool in generating human GPCR-based biosensors, aiding in ongoing receptor deorphanization efforts, and providing a framework for high-throughput screening of receptors and effectors.

category: synthetic biology


title: Dynamic optimization reveals alveolar epithelial cells as key mediators of host defense in invasive aspergillosis

abstract: Aspergillus fumigatus is an important human fungal pathogen and its conidia are constantly inhaled by humans. In immunocompromised individuals, conidia can grow out as hyphae that damage lung epithelium. The resulting invasive aspergillosis is associated with devastating mortality rates. Since infection is a race between the innate immune system and the outgrowth of A. fumigatus conidia, we use dynamic optimization to obtain insight into the recruitment and depletion of alveolar macrophages and neutrophils. Using this model, we obtain key insights into major determinants of infection outcome on host and pathogen side. On the pathogen side, we predict in silico and confirm in vitro that germination speed is a key virulence trait of fungal pathogens due to the vulnerability of conidia against host defense. On the host side, we find that epithelial cells play a so far underappreciated role in fungal clearance and are potent mediators of cytokine release which we confirm ex vivo. Further, our model affirms the importance of neutrophils in invasive aspergillosis and underlines that the role of macrophages remains elusive. We expect that our model will contribute to improvement of treatment protocols by focusing on the critical components of immune response to fungi but also fungal virulence.

category: systems biology


title: Wiring logic of the early rodent olfactory system revealed by high-throughput sequencing of single neuron projections

abstract: The structure of neuronal connectivity often provides insights into the relevant stimulus features, such as spatial location, orientation, sound frequency, etc1-6. The olfactory system, however, appears to lack structured connectivity as suggested by reports of broad and distributed connections both from the olfactory bulb to the piriform cortex7-22 and within the cortex23-25. These studies have inspired computational models of circuit function that rely on random connectivity26-33. It remains, nonetheless, unclear whether the olfactory connectivity contains spatial structure. Here, we use high throughput anatomical methods (MAPseq and BARseq)34-38 to analyze the projections of 5,309 bulb and 30,433 piriform cortex output neurons in the mouse at single-cell resolution. We identify previously unrecognized spatial organization in connectivity along the anterior-posterior axis (A-P) of the piriform cortex. We find that both the bulb projections to the cortex and the cortical outputs are not random, but rather form gradients along the A-P axis. Strikingly, these gradients are matched: bulb neurons targeting a given location within the piriform cortex co-innervate extra-piriform regions that receive strong inputs from neurons within that piriform locus. We also identify signatures of local connectivity in the piriform cortex. Our findings suggest an organizing principle of matched direct and indirect olfactory pathways that innervate extra-piriform targets in a coordinated manner, thus supporting models of information processing that rely on structured connectivity within the olfactory system.


title: Wnt signaling mediates acquisition of blood-brain barrier properties in naïve endothelium derived from human pluripotent stem cells

abstract: Endothelial cells (ECs) in the central nervous system (CNS) acquire their specialized blood-brain barrier (BBB) properties in response to extrinsic signals, with Wnt/{beta}-catenin signaling coordinating multiple aspects of this process. Our knowledge of CNS EC development has been advanced largely by animal models, and human pluripotent stem cells (hPSCs) offer the opportunity to examine BBB development in an in vitro human system. Here we show that activation of Wnt signaling in hPSC-derived naive endothelial progenitors, but not in matured ECs, leads to robust acquisition of canonical BBB phenotypes including expression of GLUT-1, increased claudin-5, and decreased PLVAP. RNA-seq revealed a transcriptome profile resembling ECs with CNS-like characteristics, including Wnt-upregulated expression of LEF1, APCDD1, and ZIC3. Together, our work defines effects of Wnt activation in naive ECs and establishes an improved hPSC-based model for interrogation of CNS barriergenesis.


title: Role of Nrp1 in controlling cortical interhemispheric circuits

abstract: Callosal projections establish topographically organized maps between cortical areas. Neuropilin-1 (Nrp1) cortical gradient induces an early segregation of developing callosal axons. We investigated later roles of Nrp1 on the development of callosal projections from layer (L) 2/3 of the primary (S1) and secondary (S2) somatosensory (SS) areas, which express higher and lower levels of Nrp1, respectively. We used in utero electroporation to knock down or overexpress Nrp1 combined with retrograde tracers, to map connections at postnatal day 16 and 30. High levels of Nrp1 blocked contralateral S2 innervation while promoted the late postnatal growth of homotopic S1L2/3 and heterotopic S2L2/3 branches into S1. Conversely, knocking down Nrp1 increased the growth of heterotopic S1L2/3 projections into S2, and the overall refinement of S2L2/3 branches, thereby diminishing the number of P30 S2L2/3 callosally projecting neurons. Thus, the Nrp1 gradient determines homotopic SSL2/3 callosal connectivity by regulating late postnatal branching and refinement in a topographic manner.


title: How spatial attention affects the decision process: looking through the lens of Bayesian hierarchical diffusion model & EEG analysis

abstract: Model-based cognitive neuroscience elucidates the cognitive processes and neurophysiological oscillations that lead to behavioral performance in cognitive tasks (e.g., response times and accuracy). In this paper we explore the underlying latent process of spatial prioritization in perceptual decision processes, based on one well-known sequential sampling model (SSM), the drift-diffusion model (DDM), and subsequent nested model comparison. Neural components of spatial attention which contributed to the latent process and behavioral performance in a visual face-car perceptual decision were detected based on both time-frequency decomposition and event-related potential (ERP) analysis. For estimating DDM parameters (i.e. the drift rate, the boundary separation, and the non-decision time), a Bayesian hierarchical approach is considered, which allows inferences to be performed simultaneously on the group and individual level. Our cognitive modeling analysis revealed that spatial attention changed the non-decision time parameter across experimental conditions, such that a model with a changing non-decision time parameter provides a better fit to the data than other model parameters, quantified using the deviance information criterion (DIC) score and R-squared. Using multiple regression analysis on the contralateral minus neutral N2 sub-component (N2nc) at central electrodes, it can be concluded that poststimulus N2nc can predict mean response times (RTs) and non-decision time parameters related to spatial prioritization. However the contralateral minus neutral alpha power (Anc) at parieto-occipital electrodes can only predict the mean RTs and not the non-decision time relating to spatial prioritization. It was also found that the difference of contralateral minus neutral neural oscillations were more reflective of the modulation of the top-down spatial attention in comparison to the difference of ipsilateral minus neutral neural oscillations. These results suggest that individual differences in spatial attention are encoded by contralateral (and not ipsilateral) N2 oscillations and non-decision times. This work highlights how model-based Cognitive Neuroscience can further reveal the role of EEG in spatial attention during perceptual decision making.


title: Evidence against altered excitatory/inhibitory balance in the posteromedial cortex of young adult APOE E4 carriers: a resting state 1H-MRS study

abstract:
A strategy to gain insight into early changes that may predispose people to Alzheimers disease is to study the brains of younger cognitively healthy people that are at increased genetic risk of AD. The Apolipoprotein (APOE) E4 allele is the strongest genetic risk factor for AD, and several neuroimaging studies comparing APOE E4 carriers with non-carriers at age ~20-30 have detected hyperactivity (or reduced deactivation) in posteromedial cortex (PMC), a key hub of the default network (DN) which has a high susceptibility to early amyloid deposition in AD. Transgenic mouse models suggest such early network activity alterations may result from altered excitatory/inhibitory (E/I) balance, but this is yet to be examined in humans. Here we test the hypothesis that PMC fMRI hyperactivity could be underpinned by altered levels of excitatory (glutamate) and/or inhibitory (GABA) neurotransmitters in this brain region. Forty-seven participants (20 APOE E4 carriers and 27 non-carriers) aged 18-25 underwent resting-state proton magnetic resonance spectroscopy (1H-MRS), a non-invasive neuroimaging technique to measure glutamate and GABA in vivo. Metabolites were measured in a PMC voxel of interest and in a comparison voxel in the occipital cortex (OCC). There was no difference in either glutamate or GABA between the E4 carriers and non-carriers in either MRS voxel, nor in the ratio of glutamate to GABA, a measure of E/I balance. Default Bayesian t-tests revealed evidence in support of this null finding. Results suggest that PMC hyperactivity in APOE E4 carriers is unlikely to be associated with, or indeed may precede, alterations in local resting-state PMC neurotransmitters, thus informing the spatio-temporal order and the cause/effect dynamic of neuroimaging differences in APOE E4 carriers.

HighlightsO_LIHyperactivity in posteromedial (PM) network in people at AD genetic risk (APOE E4)
C_LIO_LISuch PM network hyperactivity may initiate pathogenic cascade that triggers AD
C_LIO_LIAPOE mouse models suggest hyperactivity driven by excitatory/inhibitory imbalance
C_LIO_LIUsing 1H-MRS at 3T we studied PMC E/I balance in young adult APOE E4 carriers
C_LIO_LIFound evidence against altered E/I balance in young adult APOE E4 carriers
C_LI


title: Face identity selectivity in the deep neural network and human brain

abstract: A central challenge in face perception research is to understand how neurons encode various face identities. However, this challenge has not been met largely due to the lack of simultaneous access to the activity of the entire face processing neural network as well as the lack of a comprehensive multifaceted model that is able to characterize a large number of facial features. In this study, we address this challenge by conducting in silico experiments using a deep neural network (DNN) capable of face recognition with a diverse array of stimuli. We identified a subset of DNN neurons selective to face identities, and these identity-selective neurons demonstrated generalized discriminability to novel faces not involved in the training and in many different styles. Visualization of the network explained the response of the DNN neurons and manipulation of the network confirmed the importance of identity-selective neurons in face recognition. Importantly, using our human single-neuron recordings, we directly compared the response of artificial neurons with 490 real human neurons to the same stimuli and found that artificial neurons did share a similar representation of facial features as human neurons. We also observed a novel region-based feature coding mechanism in DNN neurons as in human neurons, which may explain how the DNN performs face recognition. Together, by directly linking between artificial and human neurons, our results shed light on how human neurons encode face identities.


title: Partial response electromyography as a markerof the individual stopping latency

abstract: Response inhibition is among the core constructs of cognitive control. It is notoriously difficult to quantify from overt behavior, since the outcome of successful inhibition is the lack of a behavioral response. Currently, the most common measure of action stopping, and by proxy response inhibition, is the model-based stop signal reaction time (SSRT) derived from the stop signal task. Recently, partial response electromyography (prEMG) has been introduced as a complementary physiological measure to capture individual stopping latencies. PrEMG refers to muscle activity initiated by the go signal that plummets after the stop signal before its accumulation to a full response. Whereas neither the SSRT nor the prEMG is an unambiguous marker for neural processes underlying response inhibition, our analysis indicates that the prEMG peak latency is better suited to investigate brain mechanisms of action stopping. This study is a methodological resource with a comprehensive overview of the psychometric properties of the prEMG in a stop signal task, and further provides practical tips for data collection and analysis.


title: Partial response electromyography as a marker of action stopping


title: Diurnal variation in neuronal chloride levels and seizure susceptibility, in neocortex, reflecting changes in activity of chloride-cation-cotransporters

abstract: The main inhibitory synaptic currents, gated by gamma-aminobutyric acid (GABA), are mediated by Cl--conducting channels1-3, and are therefore sensitive to changes in the chloride electrochemical gradient. GABAergic activity dictates the neuronal firing range4,5 and timing6-9, which in turn influences the rhythms of the brain, synaptic plasticity, and flow of information in neuronal networks7,10-12. The intracellular chloride concentration [Cl-]i is, therefore, ideally placed to be a regulator of neuronal activity. Chloride levels have been thought to be stable in adult cortical networks, except when associated with pathological activation13-16. Here, we used 2-photon LSSmClopHensor imaging, in anaesthetized young adult mice13, to show that [Cl-] inside pyramidal cells shows a physiological diurnal rhythm, with an approximately 1.8-fold range, equating to an ~15mV positive shift in ECl at times when mice are typically awake (midnight), relative to when they are usually asleep (midday). This change of [Cl-]i alters the stability of cortical networks, as demonstrated by a greater than 3-fold longer latency to seizures induced by 4-aminopyridine at midday, compared to midnight. Importantly, both [Cl-]i and latency to seizure, in night-time experiments, were shifted in line with day-time measures, by inhibition of NKCC1. The redistribution of [Cl-]i reflects diurnal changes in surface expression and phosphorylation states of the cation-chloride-co-transporters, KCC2 and NKCC1, leading to a greatly reduced chloride-extrusion capacity at night (awake period). Our data demonstrate a means by which changes in the biochemical state of neurons are transduced into altered brain states.


title: Circadian rhythm in cortical chloride homeostasis underpins variation in network excitability


title: Mapping Interactome Networks of FOSL1 and FOSL2 in Human Th17 Cells

abstract: Dysregulated function of Th17 cells has implications in immunodeficiencies and autoimmune disorders. Th17 cell-differentiation is orchestrated by a complex network of transcription factors, including several members of the activator protein (AP-1) family. Among these, FOSL1 and FOSL2 influence the effector responses of Th17 cells. However, the molecular mechanisms underlying these functions are unclear, owing to the poorly characterized protein interaction networks of these factors. Here, we establish the first interactomes of FOSL1 and FOSL2 in human Th17 cells, using affinity purification-mass spectrometry analysis. In addition to the known JUN proteins, we identified several novel binding partners of FOSL1 and FOSL2. Gene ontology analysis found a major fraction of these interactors to be associated with RNA binding activity, which suggests new mechanistic links. Intriguingly, 29 proteins were found to share interactions with FOSL1 and FOSL2, and these included key regulators of Th17-fate. We further validated the binding partners identified in this study by using parallel reaction monitoring targeted mass-spectrometry and other methods. Our study provides key insights into the interaction-based signaling mechanisms of FOSL factors that potentially govern Th17 cell-differentiation and associated pathologies.

category: immunology


title: Reprogramming adult tendon healing using regenerative neonatal regulatory T cells

abstract: Tendinopathy is a common clinical problem leading to significant musculoskeletal disability. Using a neonatal mouse model of tendon regeneration compared to adult tendon fibrosis, we identified a unique immune profile in regeneration that is associated with type 2 macrophage polarization and regulatory T cell (Treg) infiltration. Neonatal Treg ablation resulted in a dysregulated immune response leading to failed tenocyte recruitment and loss of functional regeneration. Transcriptional profiling of adult and neonatal tendon Tregs revealed distinct type 1 and type 2 immune signatures that facilitate macrophage polarization following injury. Finally, adoptive transfer of mouse and human neonatal Tregs was sufficient to improve functional regeneration, in contrast to adult Treg transfer. Collectively, these studies uncover a critical role for neonatal Tregs in controlling immune polarization to promote an environment permissive for tendon regeneration. Our findings provide a basis for immune modulating therapies to facilitate regenerative adult tendon healing.


title: Human alveolar lining fluid from the elderly promotes Mycobacterium tuberculosis growth in alveolar epithelial cells and bacterial translocation into the cytosol

abstract: The elderly population is at significant risk of developing respiratory diseases, including tuberculosis (TB) caused by the airborne Mycobacterium tuberculosis (M.tb). Once M.tb reaches the alveolar space, it contacts alveolar lining fluid (ALF) which dictates host cell interactions. We previously determined that age-associated dysfunctionality in human ALF soluble innate components lead to accelerated M.tb growth within human alveolar macrophages. Here we determined the impact of human ALF on M.tb infection of alveolar epithelial cells (ATs), another critical cellular determinant of infection. We observed that E-ALF-exposed M.tb had significantly increased intracellular growth in ATs compared to adult ALF (A-ALF)-exposed bacteria. Despite this, there were no alterations in AT inflammatory mediators or cell activation. However, exposure to E-ALF altered endosomal trafficking of M.tb, driving bacterial translocation to both endosomal and cytosolic compartments in ATs. Our results indicate that exposure of M.tb to E-ALF promotes translocation of bacteria into the AT cytosol as a potential favorable niche for rapid bacterial growth and at the same time dampens ATs immune responses. Thus, our findings highlight the influence of the elderly lung mucosa on M.tb infection of ATs, an unexplored contributing factor to the elderly populations increased susceptibility of developing active TB disease.