title: To rarefy or not to rarefy: Enhancing diversity analysis of microbial communities through next-generation sequencing and rarefying repeatedly

abstract: Amplicon sequencing has revolutionized our ability to study DNA collected from environmental samples by providing a rapid and sensitive technique for microbial community analysis that eliminates the challenges associated with lab cultivation and taxonomic identification through microscopy. In water resources management, it can be especially useful to evaluate ecosystem shifts in response to natural and anthropogenic landscape disturbances to signal potential water quality concerns, such as the detection of toxic cyanobacteria or pathogenic bacteria. Amplicon sequencing data consist of discrete counts of sequence reads, the sum of which is the library size. Groups of samples typically have different library sizes that are not representative of biological variation; library size normalization is required to meaningfully compare diversity between them. Rarefaction is a widely used normalization technique that involves the random subsampling of sequences from the initial sample library to a selected normalized library size. Rarefying is often dismissed as statistically invalid because subsampling effectively discards a portion of the observed sequences. Nonetheless, it remains prevalent in practice. Notably, the superiority of rarefying relative to many other normalization approaches has been argued in diversity analysis. Here, repeated rarefying is proposed as a tool for diversity analyses to normalize library sizes. This enables (i) proportionate representation of all observed sequences and (ii) characterization of the random variation introduced to diversity analyses by rarefying to a smaller library size shared by all samples. While many deterministic data transformations are not tailored to produce equal library sizes, repeatedly rarefying reflects the probabilistic process by which amplicon sequencing data are obtained as a representation of the source microbial community. Specifically, it evaluates which data might have been obtained if a particular samples library size had been smaller and allows graphical representation of the effects of this library size normalization process upon diversity analysis results.


title: Novel regulatory and transcriptional networks associated with resistance to platinum-based chemotherapy in ovarian cancer

abstract:
BackgroundHigh-grade serous ovarian cancer (HGSOC) is a highly lethal gynecologic cancer, in part due to resistance to platinum-based chemotherapy reported among 20% of patients. This study aims to elucidate the biological mechanisms underlying chemotherapy resistance, which remain poorly understood.

MethodsSequencing data (mRNA and microRNA) from HGSOC patients were analyzed to identify differentially expressed genes and co-expressed transcript networks associated with chemotherapy response. Initial analyses used datasets from The Cancer Genome Atlas and then replicated in two independent cancer cohorts. Moreover, transcript expression datasets and genomics data (i.e. single nucleotide polymorphisms) were integrated to determine potential regulation of the associated mRNA networks by microRNAs and expression quantitative trait loci (eQTLs).

ResultsIn total, 196 differentially expressed mRNAs were enriched for adaptive immunity and translation, and 21 differentially expressed microRNAs were associated with angiogenesis. Moreover, co-expression network analysis identified two mRNA networks associated with chemotherapy response, which were enriched for ubiquitination and lipid metabolism, as well as three associated microRNA networks enriched for lipoprotein transport and oncogenic pathways. In addition, integrative analyses revealed potential regulation of the mRNA networks by the associated microRNAs and eQTLs.

ConclusionWe report novel transcriptional networks and pathways associated with resistance to platinum-based chemotherapy among HGSOC patients. These results aid our understanding of the effector networks and regulators of chemotherapy response, which will improve drug efficacy and identify novel therapeutic targets for ovarian cancer.

category: cancer biology


title: FMRP sustains presynaptic function via control of activity-dependent bulk endocytosis

abstract:
Synaptic vesicle (SV) recycling defects are linked to neurodevelopmental disorders, including fragile X syndrome (FXS), which results from loss of fragile X mental retardation protein (FMRP) encoded by the FMR1 gene. Hyperexcitability of neuronal circuits is a key feature of FXS, therefore we investigated whether SV recycling was affected by the absence of FMRP during increased neuronal activity. We revealed that primary neuronal cultures from a Fmr1 knockout rat model display a specific defect in activity-dependent bulk endocytosis (ADBE). This defect resulted in an inability of Fmr1 knockout neurons to sustain SV recycling during high frequency stimulation. Using a molecular replacement strategy, we also revealed that a human FMRP mutant that cannot bind BK channels failed to correct ADBE dysfunction in knockout neurons, however this dysfunction was corrected by BK channel agonists. Therefore, FMRP performs a key role in sustaining neurotransmitter release via selective control of ADBE, suggesting intervention via this endocytosis mode may correct hyperexcitabiltiy observed in FXS.

SUMMARYFragile X syndrome (FXS) is caused by loss of fragile X mental retardation protein (FMRP). Bonnycastle et al show that FMRP is specifically required for activity-dependent bulk endocytosis (ADBE), revealing 1) FMRP sustains neurotransmitter release and 2) intervention via ADBE may correct circuit hyperexcitabilty in FXS.

category: neuroscience


title: In situ photopatterning of cell laden biomaterials for spatially organized 3D cell cultures in a microfluidic chip

abstract: Micropatterning techniques for 3D cell cultures enable the recreation of tissue-level structures, but their combination with well-defined, microscale fluidic systems for perfusion remains challenging. To address this technological gap, we developed a user-friendly in-situ micropatterning protocol that integrates photolithography of crosslinkable, cell-laden hydrogels with a simple microfluidic housing, and tested the impact of crosslinking chemistry on stability and spatial resolution. Working with gelatin functionalized with photo-crosslinkable moieties, we found that inclusion of cells at high densities ([≥] 107/mL) during crosslinking did not impede thiol-norbornene gelation, but decreased the storage moduli of methacryloyl hydrogels. Hydrogel composition and light dose were selected to match the storage moduli of soft tissues. The cell-laden precursor solution was flowed into a microfluidic chamber and exposed to 405 nm light through a photomask to generate the desired pattern. The on-chip 3D cultures were self-standing, and the designs were interchangeable by simply swapping out the photomask. Thiol-ene hydrogels yielded highly accurate feature sizes from 100 - 900 m in diameter, whereas methacryloyl hydrogels yielded slightly enlarged features. Furthermore, only thiol-ene hydrogels were mechanically stable under perfusion overnight. Repeated patterning readily generated multi-region cultures, either separately or adjacent, including non-linear boundaries that are challenging to obtain on-chip. As a proof-of-principle, primary human T cells, were patterned on-chip with high regional specificity. Viability remained high (> 85%) after overnight culture with constant perfusion. We envision that this technology will enable researchers to pattern 3D cultures under fluidic control in biomimetic geometries that were previously difficult to obtain.

category: bioengineering


title: Generation of nonlinear and spatially-organized 3D cultures on a microfluidic chip using photoreactive thiol-ene and methacryloyl hydrogels


title: LIQA: Long-read Isoform Quantification and Analysis

abstract: Long-read RNA sequencing (RNA-seq) technologies have made it possible to sequence full-length transcripts, facilitating the exploration of isoform-specific gene expression (isoform relative abundance and isoform-level TPM) over conventional short-read RNA-seq. However, long-read RNA-seq suffers from high per-base error rate, presence of chimeric reads or alternative alignments, and other biases, which require different analysis methods than short-read RNA-seq. Here we present LIQA (Long-read Isoform Quantification and Analysis), an Expectation-Maximization based statistical method to quantify isoform expression and detect differential alternative splicing (DAS) events using long-read RNA-seq data. Rather than summarizing isoform-specific read counts directly as done in short-read methods, LIQA incorporates base-pair quality score and isoform-specific read length information to assign different weights across reads, which reflects alignment confidence. Moreover, LIQA can detect DAS events between conditions using isoform usage estimates. We evaluated LIQAs performance on simulated data and demonstrated that it outperforms other approaches in characterizing isoforms with low read coverage and in detecting DAS events between two groups. We also generated one direct mRNA sequencing dataset and one cDNA sequencing dataset using the Oxford Nanopore long-read platform, both with paired short-read RNA-seq data and qPCR data on selected genes, and we demonstrated that LIQA performs well in isoform discovery and quantification. Finally, we evaluated LIQA on a PacBio dataset on esophageal squamous epithelial cells, and demonstrated that LIQA recovered DAS events that failed to be detected in short-read data. In summary, LIQA leverages the power of long-read RNA-seq and achieves higher accuracy in estimating isoform abundance than existing approaches, especially for isoforms with low coverage and biased read distribution. LIQA is freely available at https://github.com/WGLab/LIQA.

category: bioinformatics


title: OPTOGENETIC STIMULATION OF LATERAL HYPOTHALAMIC OREXIN/DYNORPHIN INPUTS IN THE VENTRAL TEGMENTAL AREA POTENTIATES MESOLIMBIC DOPAMINE NEUROTRANSMISSION AND PROMOTES REWARD-SEEKING BEHAVIOURS

abstract: Reward and reinforcement processes are critical for survival and propagation of genes. While numerous brain systems underlie these processes, a cardinal role is ascribed to mesolimbic dopamine. However, ventral tegmental area (VTA) dopamine neurons receive complex innervation and various neuromodulatory factors, including input from lateral hypothalamic (LH) orexin/hypocretin neurons which also express and co-release the neuropeptide, dynorphin. Dynorphin in the VTA induces aversive conditioning through the Kappa opioid receptor (KOR) and decreases dopamine when administered intra-VTA. Exogenous application of orexin or orexin 1 receptor (oxR1) antagonists in the VTA bidirectionally modulates dopamine-driven motivation and reward-seeking behaviours, including the attribution of motivational value to primary rewards and associated conditioned stimuli. However, the effect of endogenous stimulation of LH orexin/dynorphin-containing projections to the VTA and the potential contribution of co-released dynorphin on mesolimbic dopamine and reward related processes remains uncharacterised. We combined optogenetic, electrochemical, and behavioural approaches to examine this. We found that optical stimulation of LH orexin/dynorphin inputs in the VTA potentiates mesolimbic dopamine neurotransmission in the nucleus accumbens (NAc) core, produces real time and conditioned place preference, and increases the food cue-directed orientation in a Pavlovian conditioning procedure. LH orexin/dynorphin potentiation of NAc dopamine release and real time place preference was blocked by an oxR1, but not KOR antagonist. Thus, rewarding effects associated with optical stimulation of LH orexin/dynorphin inputs in the VTA are predominantly driven by orexin rather than dynorphin.


title: Optogenetic stimulation of lateral hypothalamic orexin/dynorphin inputs in the ventral tegmental area potentiates mesolimbic dopamine neurotransmission and promotes reward-seeking behaviours.


title: Gene exchange networks define species-like units in marine prokaryotes

abstract:
Post-submission note. Since the original submission of this manuscript to bioRxiv, we discovered that some of our results may be impacted by the limitations of some of the comparative genomics tools used in this study. We are working on a revised version of the manuscript.

Although horizontal gene transfer is recognized as a major evolutionary process in Bacteria and Archaea, its general patterns remain elusive, due to difficulties tracking genes at relevant resolution and scale within complex microbiomes. To circumvent these challenges, we analyzed a randomized sample of >12,000 genomes of individual cells of Bacteria and Archaea in the tropical and subtropical ocean - a well-mixed, global environment. We found that marine microorganisms form gene exchange networks (GENs) within which transfers of both flexible and core genes are frequent, including the rRNA operon that is commonly used as a conservative taxonomic marker. The data revealed efficient gene exchange among genomes with <28% nucleotide difference, indicating that GENs are much broader lineages than the nominal microbial species, which are currently delineated at 4-6% nucleotide difference. The 42 largest GENs accounted for 90% of cells in the tropical ocean microbiome. Frequent gene exchange within GENs helps explain how marine microorganisms maintain millions of rare genes and adapt to a dynamic environment despite extreme genome streamlining of their individual cells. Our study suggests that sharing of pangenomes through horizontal gene transfer is a defining feature of fundamental evolutionary units in marine planktonic microorganisms and, potentially, other microbiomes.

category: microbiology


title: Spatial analysis of ligand-receptor interaction in skin cancer at genome-wide and single-cell resolution

abstract: The ability to study cancer-immune cell communication across the whole tumor section without tissue dissociation is needed for cancer immunotherapies, to understand molecular mechanisms and to discover potential druggable targets. In this work, we developed a powerful experimental and analytical toolbox to enable genome-wide scale discovery and targeted validation of cellular communication. We assessed the utilities of five sequencing and imaging technologies to study cancer tissue, including single-cell RNA sequencing and Spatial Transcriptomic (measuring over >20,000 genes), RNA In Situ Hybridization (multiplex 4-12 genes), digital droplet PCR, and Opal multiplex protein staining (4-9 proteins). To spatially integrate multimodal data, we developed a computational method called STRISH that can automatically scan across the whole tissue section for local expression of gene and/or protein markers to recapitulate an interaction landscape across the whole tissue. We evaluated the unique ability of this toolbox to discover and validate cell-cell interaction in situ through in-depth analysis of two types of cancer, basal cell carcinoma and squamous cell carcinoma, which account for over 70% of cancer cases. We expect that the approach described here will be widely applied to discover and validate ligand receptor interaction in different types of solid cancer tumors.


title: Inflammatory response in hematopoietic stem and progenitor cells triggered by activating SHP2 mutations potentiates leukemogenesis

abstract: Gain-of-function mutations in the protein-tyrosine phosphatase SHP2 are the most frequently occurring mutations in sporadic juvenile myelomonocytic leukemia (JMML) and JMML-like myeloproliferative neoplasm (MPN) associated with Noonan syndrome (NS). Hematopoietic stem and progenitor cells (HSPCs) are the disease propagating cells of JMML. Here, we explored transcriptomes of HSPCs with Shp2 mutations derived from JMML patients and a novel NS zebrafish model. In addition to major NS traits, CRISPR/Cas9 knock-in Shp2D61G mutant zebrafish recapitulated a JMML-like MPN phenotype, including myeloid lineage hyperproliferation, ex vivo growth of myeloid colonies and in vivo transplantability of HSPCs. Single cell mRNA sequencing of HSPCs from Shp2D61G zebrafish embryos and bulk sequencing of HSPCs from JMML patients revealed an overlapping inflammatory gene expression pattern. Strikingly, an anti-inflammatory agent rescued JMML-like MPN in Shp2D61G zebrafish embryos. Our results indicate that a common inflammatory response was triggered in the HSPCs from sporadic JMML patients and syndromic NS zebrafish, which potentiated MPN and may represent a future target for JMML therapies.

category: developmental biology


title: Inflammatory response in hematopoietic stem and progenitor cells triggered by activating SHP2 mutations evokes blood defects


title: Ribosome stalling caused by the Argonaute-microRNA-SGS3 complex regulates the production of secondary siRNAs in plants

abstract: The path of ribosomes on mRNAs can be impeded by various obstacles. One such example is halting of ribosome movement by microRNAs, though the exact mechanism and physiological role remain unclear. Here, we find that ribosome stalling caused by the Argonaute-microRNA-SGS3 complex regulates the production of secondary small interfering RNAs (siRNAs) in plants. We show that the double-stranded RNA-binding protein SGS3 directly interacts with the 3' end of the microRNA in an Argonaute protein, resulting in ribosome stalling. Importantly, microRNA-mediated ribosome stalling positively correlates with efficient production of secondary siRNAs from target mRNAs. Our results illustrate a role for paused ribosomes in regulation of small RNA function that may have broad biological implications across the plant kingdom.

category: molecular biology


title: DyNeuMo Mk-1: Design and Pilot Validation of an Investigational Motion-Adaptive Neurostimulator with Integrated Chronotherapy

abstract: There is growing interest in using adaptive neuro-modulation to provide a more personalized therapy experience that might improve patient outcomes. Current implant technology, however, can be limited in its adaptive algorithm capability. To enable exploration of adaptive algorithms with chronic implants, we designed and validated the  Picostim DyNeuMo Mk-1 (DyNeuMo Mk-1 for short), a fully-implantable, adaptive research stimulator that titrates stimulation based on circadian rhythms (e.g. sleep, wake) and the patients movement state (e.g. posture, activity, shock, free-fall). The design leverages off-the-shelf consumer technology that provides inertial sensing with low-power, high reliability, and relatively modest cost. The DyNeuMo Mk-1 system was designed, manufactured and verified using ISO 13485 design controls, including ISO 14971 risk management techniques to ensure patient safety, while enabling novel algorithms. The system was validated for an intended use case in movement disorders under an emergency-device authorization from the Medicines and Healthcare Products Regulatory Agency (MHRA). The algorithm configurability and expanded stimulation parameter space allows for a number of applications to be explored in both central and peripheral applications. Intended applications include adaptive stimulation for movement disorders, synchronizing stimulation with circadian patterns, and reacting to transient inertial events such as posture changes, general activity, and walking. With appropriate design controls in place, first-in-human research trials are now being prepared to explore the utility of automated motion-adaptive algorithms.


title: Quantification and demonstration of the collective constriction-by-ratchet mechanism in the dynamin molecular motor

abstract: Dynamin oligomerizes into helical filaments on tubular membrane templates and, through constriction, cleaves them in a GTPase-driven way. Structural observations of GTP-dependent cross-bridges between neighboring filament turns have led to the suggestion that dynamin operates as a molecular ratchet motor. However, the proof of such mechanism remains absent. Particularly, it is not known whether a powerful enough stroke is produced and how the motor modules would cooperate in the constriction process. Here, we characterized the dynamin motor modules by single molecule (sm) FRET and found strong nucleotide-dependent conformational changes. Integrating smFRET with molecular dynamics simulations allowed us to determine the forces generated in a power stroke. Subsequently, the quantitative force data and the measured kinetics of the GT-Pase cycle were incorporated into a model including both a dynamin filament, with explicit motor cross-bridges, and a realistic deformable membrane template. In our simulations, collective constriction of the membrane by dynamin motor modules, based on the ratchet mechanism, is directly reproduced and analyzed. Functional parallels between the dynamin system and actomyosin in the muscle are seen. Through concerted action of the motors, tight membrane constriction to the hemifission radius can be reached. Our experimental and computational study provides an example of how collective motor action in megadalton molecular assemblies can be approached and explicitly resolved.

category: biophysics


title: Stability by gating plasticity in recurrent neural networks

abstract:
With Hebbian learning  who fires together wires together, well-known problems arise. Hebbian plasticity can cause unstable network dynamics and overwrite stored memories. Unstable dynamics can partly be addressed with homeostatic plasticity mechanisms. Unfortunately, the time constants of homeostatic mechanisms required in network models are much shorter than those measured experimentally.

We propose that homeostatic time constants can be slow if plasticity is gated. We investigate how gating plasticity influences network stability and memories in plastic balanced spiking networks of neurons with dendrites. We compare how different factors such as excitability, learning rate, and inhibition lift the requirements for homeostatic time constants. We investigate how dendritic versus perisomatic gating allows for different amounts of weight changes in stable networks. We suggest that the compartmentalisation of pyramidal cells enables dendritic synaptic changes while maintaining stability. We show that spatially restricted plasticity improves stability. Finally, we compare how different gates protect memories.

Significance statementHow does the brain maintain stable neural activity in the presence of synaptic changes? This question has been studied extensively in the past, but we argue that one crucial aspect is missing in previous studies. While all theoretical work has assumed plasticity to be on all the time, plasticity is in fact heavily gated. In this light, we must reconsider the theories on stability and homeostasis of neural activity. In particular, theoretical studies show that neural networks undergoing plasticity require fast compensatory homeostatic mechanisms to be stable. However, experimentally measured homeostatic processes operate on much slower time scales. We studied how the gating of plasticity can improve network stability and thereby reduce the discrepancy in the homeostatic time constant between models and experiments.


title: A simple permutation-based test of intermodal correspondence

abstract: Many key findings in neuroimaging studies involve similarities between brain maps, but statistical methods used to measure these findings have varied. Current state-of-the-art methods involve comparing observed group-level brain maps (after averaging intensities at each image location across multiple subjects) against spatial null models of these group-level maps. However, these methods typically make strong and potentially unrealistic statistical assumptions, such as covariance stationarity. To address these issues, in this paper we propose using subject-level data and a classical permutation testing framework to test and assess similarities between brain maps. Our method is comparable to traditional permutation tests in that it involves randomly permuting subjects to generate a null distribution of intermodal correspondence statistics, which we compare to an observed statistic to estimate a p-value. We apply and compare our method in simulated and real neuroimaging data from the Philadelphia Neurodevelopmental Cohort. We show that our method performs well for detecting relationships between modalities known to be strongly related (cortical thickness and sulcal depth), and it is conservative when an association would not be expected (cortical thickness and activation on the n-back working memory task). Notably, our method is the most flexible and reliable for localizing intermodal relationships within subregions of the brain and allows for generalizable statistical inference.


title: Two Are Better Than One: Solving the Problem of Vertical Sound Source Localization via Binaural Integration of HRTFs

abstract: Early studies have shown that the localization of a sound source in the vertical plane can be accomplished with only a single ear, thus assumed the localization mechanism to be based on monaural cues. Such cues are induced by the pinna and consist of notches and peaks in the perceived spectrum which vary systematically with the elevation of sound sources. These processes pose several problems to the auditory system like identifying and extracting spectral cues on a neural level, as well as, distinguishing pinna induced peaks and notches from features already present in the source spectrum. Interestingly, at the stage of elevation estimate binaural information from both ears is already available and it seems plausible that the auditory system takes advantage of this information. Especially, since such a binaural integration can improve the localization performance dramatically as we demonstrate in the current study. For that, we first introduce a computational model architecture that takes advantage of binaural signal integration to localize sound sources in the median plane. Model performance is tested under different conditions which reveal that localization of monaural, as well as binaural inputs is best when the model is trained with binaural inputs. Furthermore, modeling results lead to the hypothesis that sound type specific prior information is taken into account to further improve localization quality. This deduced hypothesis about vertical sound source localization is confirmed in a behavioral experiment. Based on these results, we propose that elevation estimation of sound sources is facilitated by an early binaural signal integration and can incorporate sound type specific prior information for higher accuracy.


title: Microbial colonization induces histone acetylation critical for inherited gut-germline-neural signaling

abstract: The gut-neural axis plays a critical role in the control of several physiological processes, including the communication of signals from the microbiome to the nervous system, which affects learning, memory, and behavior. However, the pathways involved in gut-neural signaling of gut-governed behaviors remain unclear. We found that the intestinal distension caused by the bacterium Pseudomonas aeruginosa induces histone H4 Lys8 acetylation (H4K8ac) in the germline of Caenorhabditis elegans, which is required for both a bacterial aversion behavior and its transmission to the next generation. We show that induction of H4K8ac in the germline is essential for bacterial aversion and that a 14-3-3 chaperone protein family member, PAR-5, is required for H4K8ac. Our findings highlight a role for H4K8ac in the germline not only in the intergenerational transmission of pathogen avoidance but also in the transmission of pathogenic cues that travel through the gut-neural axis to control the aversive behavior.

category: immunology


title: Nuclear total RNA sequencing reveals primary sequence context of recursive splicing in long genes

abstract: Recursive splicing (RS) is a splicing mechanism to remove long introns from messenger RNA precursors of long genes. Compared to the hundreds of RS events identified in humans and drosophila, only ten RS events have been reported in mice. To further investigate RS in mice, we analyzed RS in the mouse brain, a tissue that is enriched in the expression of long genes. We found that nuclear total RNA sequencing is an efficient approach to investigate RS events. We analyzed 1.15 billion uniquely mapped reads from the nuclear total RNA sequencing data in the mouse cerebral cortex. Unexpectedly, we only identified 20 RS sites, suggesting that RS is a rare event in the mouse brain. We also identified that RS is constitutive between excitatory and inhibitory neurons and between sexes in the mouse cerebral cortex. In addition, we found that the primary sequence context is associated with RS splicing intermediates and distinguishes RS AGGT site from non-RS AGGT sites, indicating the importance of the primary sequence context in RS sites. Moreover, we discovered that cryptic exons may use an RS-like mechanism for splicing. Overall, our findings provide novel insights into RS in long genes.

category: genomics


title: Recursive splicing is a rare event in the mouse brain


title: Deletion of Stim1 in hypothalamic arcuate nucleus Kiss1 neurons potentiates synchronous GCaMP activity and protects against diet-induced obesity

abstract:
Kisspeptin (Kiss1) neurons are essential for reproduction, but their role in the control of energy balance and other homeostatic functions remains unclear. High frequency firing of hypothalamic arcuate Kiss1 (Kiss1ARH) neurons releases kisspeptin into the median eminence, and neurokinin B (NKB) and dynorphin onto neighboring Kiss1ARH neurons to generate a slow excitatory postsynaptic potential (EPSP) mediated by TRPC5 channels that entrains intermittent, synchronous firing of Kiss1ARH neurons. High frequency optogenetic stimulation of Kiss1ARH neurons releases glutamate to excite the anorexigenic proopiomelanocortin (POMC) neurons and inhibit the orexigenic neuropeptide Y/agouti-related peptide (AgRP) neurons via metabotropic glutamate receptors. At the molecular level, the endoplasmic reticulum calcium-sensing protein stromal interaction molecule 1 (STIM1) is critically involved in the regulation of neuronal Ca2+ signaling and neuronal excitability through its interaction with plasma membrane calcium (e.g., TRPC) channels. 17{beta}-estradiol (E2) downregulates Stim1 mRNA expression in female arcuate neurons. Therefore, we hypothesized that deletion of Stim1 in Kiss1ARH neurons would increase neuronal excitability and their synchronous firing, which ultimately would affect energy homeostasis. Using optogenetics in combination with whole-cell recording and GCaMP6 imaging in slices, we discovered that the deletion of Stim1 in Kiss1 neurons significantly increased the amplitude of the slow EPSP and augmented synchronous [Ca2+]i oscillations in Kiss1ARH neurons. Deletion of Stim1 in Kiss1ARH neurons amplified the actions of NKB and protected ovariectomized female mice from developing obesity and glucose intolerance with high-fat dieting. Therefore, STIM1 appears to play a critical role in regulating synchronous firing of Kiss1ARH neurons, which ultimately affects energy homeostasis.

Significance StatementHypothalamic arcuate kisspeptin (Kiss1ARH) neurons are essential for stimulating the pulsatile release of gonadotropin releasing hormone (GnRH) and maintaining fertility. However, Kiss1ARH neurons appear to be a key player in coordinating energy balance with reproduction. The regulation of calcium channels and hence calcium signaling is critically dependent on the endoplasmic reticulum calcium-sensing protein stromal interaction molecule 1 (STIM1), which interacts with the plasma membrane calcium channels. We have conditionally deleted Stim1 in Kiss1ARH neurons and found that it significantly increased the excitability of Kiss1ARH neurons and protected ovariectomized female mice from developing obesity and glucose intolerance with high-fat dieting.


title: Modulating the activities of chloroplasts and mitochondria promotes ATP production and plant growth

abstract: Efficient photosynthesis requires a balance of ATP and NADPH production/consumption in chloroplasts and the exportation of reducing equivalents from chloroplasts is important for balancing stromal ATP/NADPH ratio. Here we showed that the overexpression of purple acid phosphatase 2 on the outer membranes of chloroplasts and mitochondria can streamline the production and consumption of reducing equivalents in these two organelles, respectively. A higher capacity of consumption of reducing equivalents in mitochondria can indirectly help chloroplasts to balance the ATP/NADPH ratio in stroma and recycle NADP+, the electron acceptors of the linear electron flow. A higher rate of ATP and NADPH production from the linear electron flow, a higher capacity of carbon fixation by the Calvin-Benson-Bassham cycle and a greater consumption of NADH in mitochondria, enhance photosynthesis in the chloroplasts, ATP production in the mitochondria, sucrose synthesis in the cytosol, and eventually boosting plant growth and seed yields in the overexpression lines.

category: plant biology


title: Distinct place cell dynamics in CA1 and CA3 encode experience in new contexts

abstract: When exploring new environments animals form spatial memories that are updated with experience and retrieved upon re-exposure to the same environment. The hippocampus is thought to support these memory processes, but how this is achieved by different subnetworks such as CA1 and CA3 remains unclear. To understand how hippocampal spatial representations emerge and evolve during familiarization, we performed 2-photon calcium imaging in mice running in new virtual environments and compared the trial-to-trial dynamics of place cells in CA1 and CA3 over days. We find that place fields in CA1 emerge rapidly but tend to shift backwards from trial-to-trial and remap upon re-exposure to the environment a day later. In contrast, place fields in CA3 emerge gradually but show more stable trial-to-trial and day-to-day dynamics. These results reflect different roles in CA1 and CA3 in spatial memory processing during familiarization to new environments and constrain the potential mechanisms that support them.


title: Effects of order on memory of event times

abstract: Memorizing time of an event may employ two processes (i) encoding of the absolute time of events within an episode, (ii) encoding of its relative order. Here we study interaction between these two processes. We performed experiments in which one or several items were presented, after which participants were asked to report the time of occurrence of items. When a single item was presented, the distribution of reported times was quite wide. When two or three items were presented, the relative order among them strongly affected the reported time of each of them. Bayesian theory that takes into account the memory for the events order is compatible with the experimental data, in particular in terms of the effect of order on absolute time reports. Our results suggest that people do not deduce order from memorized time, instead peoples memory for absolute time of events relies critically on memorized order of the events.


title: Estimating the time since admixture from phased and unphased molecular data

abstract: After admixture, recombination breaks down genomic blocks of contiguous ancestry. The breakdown of these blocks forms a new  molecular clock, that ticks at a much faster rate than the mutation clock, enabling accurate dating of admixture events in the recent past. However, existing theory on the break down of these blocks, or the accumulation of delineations between blocks, so called  junctions, has mostly been limited to using regularly spaced markers on phased data. Here, we present an extension to the theory of junctions using the Ancestral Recombination Graph that describes the expected number of junctions for any distribution of markers along the genome. Furthermore, we provide a new framework to infer the time since admixture using unphased data. We demonstrate both the phased and unphased methods on simulated data and show that our new extensions performs better than previous methods, especially for smaller population sizes and for more ancient admixture times. Lastly, we demonstrate the applicability of our method on an empirical dataset of labcrosses of yeast (Saccharomyces cerevisae) and on two case studies of hybridization in swordtail fish and Populus trees.

category: evolutionary biology


title: Striatal BOLD and midfrontal theta power express motivation for action

abstract: Action selection is biased by the valence of anticipated outcomes. To assess mechanisms by which these motivational biases are expressed and controlled, we measured simultaneous EEG-fMRI during a motivational Go/NoGo learning task (N=36), leveraging the temporal resolution of EEG and subcortical access of fMRI. VmPFC BOLD encoded cue valence, importantly predicting trial-by-trial valence-driven response speed differences and EEG theta power around cue onset. In contrast, striatal BOLD encoded selection of active Go responses and correlated with theta power around response time. Within trials, theta power ramped in the fashion of an evidence accumulation signal for the value of making a  Go response, capturing the faster responding to reward cues. Our findings reveal a dual nature of midfrontal theta power, with early components reflecting the vmPFC contribution to motivational biases, and late components reflecting their striatal translation into behavior, in line with influential recent "value of work" theories of striatal processing.


title: Cell population migration cycle and response to environmental pH in Bacillus subtilis

abstract: Microbial populations are ubiquitous and some form a robust, multicellular structure called biofilm that protects the cells from environmental damage. The dispersion cycle is critical for controlling the population of important target microbes (both pathogenic and beneficial). Here, we show that the hysteresis of Bacillus subtilis cell-type regulation with respect to auto-inducing signal strength triggers the migration cycle of the cell population. We investigate migration cycle and its dependence on environmental conditions by quantitative analysis of cyclically expanding, concentric circular colonies. Next, we construct an input/output model that controls cell types in response to environmental conditions and signal density. On the basis of this model, we propose a migration cycle model for cell populations. The proposed model will widely predict biofilm-related phenomena and provide the basis for the description of highly self-regulating multicellular systems.


title: Gut microbiota survey at species- and strain-level using long-amplicon sequencing, and its application to trace species engraftment

abstract:
The precise identification of bacterial species inhabiting the human gut is essential to define the role of certain gut microbiota in human health and disease unambiguously. At this regard, the sequencing of bacterial rrn regions (16S-ITS-23S) has provided reliable identification of microbiota at the species level previously. On the other hand, fecal microbiota transplantation (FMT) is a clinical approach with recognized performance for treating infection, immune and metabolic disease. However, the demonstration of its underlying species engraftment is challenging because there are no cost-effective strategies for accurately identification and tracing the transfer of donor microbiota to recipients. We used Nanopore-based device to sequence long amplicons from bacterial rrn operons to reveal strain-level variation in predominant members of the human gut microbiota. By assessing the donor and recipient microbiota before and after FMT, we evaluated whether this molecular approach helps to reveal strain-level genetic variation and demonstrate microbe engraftment. We reconstructed several rrn regions derived from predominant gut microbiota, revealing novel genetic variation. Strict control over sequencing data quality and major microbiota covariates was critical for accurately estimating the changes in gut microbial species abundance in the recipients after FMT. Despite the modest per-base accuracy of Nanopore data, we could detect strain-level variation by predicting single-nucleotide variants (SNVs) at rrn regions in a species-specific manner. We showed that the FMT trial explored successfully induced donor-strain (e.g., Parabacteroides merdae) engraftment in recipients according to the mapping and assessment of nucleotide frequencies at selected SNVs. Despite the modest per-base accuracy of Nanopore reads, the data showed sufficient quality to allow the accurate estimation of SNVs and the tracing of microbe engraftment. This methodology and data analysis represent a cost-effective approach for tracing genetic variability, which is necessary to better understand the health effects of the human microbiome under the application of microbiota replacement strategies.

Trial registrationThe study was prospectively registered at the Dutch Trial registry - NTR4488 (https://www.trialregister.nl/trial/4488).


title: A comparative survey of Betacoronavirus binding dynamics relevant to the functional evolution of the highly transmissible SARS-CoV-2 variant N501Y

abstract: Comparative functional analysis of the dynamic interactions between various Betacoronavirus mutant strains and broadly utilized target proteins such as ACE2 and CD26, is crucial for a more complete understanding of zoonotic spillovers of viruses that cause diseases such as COVID-19. Here, we employ machine learning to replicated sets of nanosecond scale GPU accelerated molecular dynamics simulations to statistically compare and classify atom motions of these target proteins in both the presence and absence of different endemic and emergent strains of the viral receptor binding domain (RBD) of the S spike glycoprotein. Machine learning was used to identify functional binding dynamics that are evolutionarily conserved from bat CoV-HKU4 to human endemic/emergent strains. Conserved dynamics regions of ACE2 involve both the N-terminal helices, as well as a region of more transient dynamics encompassing K353, Q325 and a novel motif AAQPFLL 386-92 that appears to coordinate their dynamic interactions with the viral RBD at N501. We also demonstrate that the functional evolution of Betacoronavirus zoonotic spillovers involving ACE2 interaction dynamics are likely pre-adapted from two precise and stable binding sites involving the viral bat progenitor strains interaction with CD26 at SAMLI 291-5 and SS 333-334. Our analyses further indicate that the human endemic strains hCoV-HKU1 and hCoV-OC43 have evolved more stable N-terminal helix interactions through enhancement of an interfacing loop region on the viral RBD, whereas the highly transmissible SARS-CoV-2 variants (B.1.1.7, B.1.351 and P.1) have evolved more stable viral binding via more focused interactions between the viral N501 and ACE2 K353 alone.


title: Betacoronavirus binding dynamics relevant to the functional evolution of the highly transmissible SARS-CoV-2 variant N501Y


title: Functional binding dynamics relevant to the evolution of zoonotic spillovers in endemic and emergent Betacoronavirus strains


title: Treatment of the X chromosome in mapping multiple quantitative trait loci

abstract: Statistical methods to map quantitative trait loci (QTL) often neglect the X chromosome and may focus exclusively on autosomal loci. But the X chromosome often requires special treatment: sex and cross-direction covariates may need to be included to avoid spurious evidence of linkage, and the X chromosome may require a separate significance threshold. In multiple-QTL analyses, including the consideration of epistatic interactions, the X chromosome also requires special care and consideration. We extend a penalized likelihood method for multiple-QTL model selection, to appropriately handle the X chromosome. We examine its performance in simulation and by application to a large eQTL data set. The method has been implemented in the package R/qtl.

category: genetics


title: Co-targeting myelin inhibitors and CSPGs markedly enhances regeneration of GDNF-stimulated, but not conditioning-lesioned, sensory axons into the spinal cord

abstract: A major barrier to intraspinal regeneration after dorsal root (DR) injury is the DR entry zone (DREZ), the CNS/PNS interface. DR axons stop regenerating at the DREZ, even if regenerative capacity is increased by a nerve conditioning lesion. This potent blockade has long been attributed to myelin-associated inhibitors and CSPGs, but incomplete lesions and conflicting reports have prevented conclusive agreement. Here we evaluated DR regeneration in mice, using novel strategies to facilitate complete lesions and analyses, selective tracing of proprioceptive and mechanoreceptive axons, and the first simultaneous targeting of Nogo/Reticulon-4, MAG, OMgp, CSPGs and GDNF. Co-eliminating myelin inhibitors and CSPGs elicited regeneration of only a few conditioning-lesioned DR axons across the DREZ. Their absence, however, markedly and synergistically enhanced regeneration of GDNF-stimulated axons, highlighting the importance of sufficiently elevating intrinsic growth capacity. We also conclude that myelin inhibitors and CSPGs are not the primary mechanism stopping axons at the DREZ.


title: Cevipabulin-tubulin complex reveals a novel agent binding site on α-tubulin with tubulin degradation effect

abstract: Microtubule, composed of {beta}-tubulin heterodimers, remains as one of the most popular anticancer targets for decades. To date, anti-microtubule drugs are mainly functionally divided into microtubule-destabilizing and microtubule-stabilizing agents while microtubule- or tubulin-degradation agents are rarely reported. Six known binding sites on tubulin dimer are identified with five sites on {beta}-tubulin and only one site on -tubulin (pironetin site), hinting compounds binding to -tubulin are less well characterized. Cevipabulin, a microtubule-active antitumor clinical candidate, is widely accepted as a microtubule-stabilizing agent by binding to the vinblastine site. Our X-ray crystallography study reveals that, in addition binding to the vinblastine site, cevipabulin also binds to a novel site on -tubulin (named the seventh site) which located near the nonexchangeable GTP. Interestingly, we find the binding of cevipabulin to the seventh site induces tubulin degradation. As the non-exchangeable GTP has structural role and is important for the stability of tubulin dimers, we propose and confirm the tubulin degradation mechanism as: Cevipabulin at the seventh site puts the T5 loop outward to make the non-exchangeable GTP exchangeable, which reduces the stability of tubulin and results in its destabilization and degradation. Our results confirm a novel agent binding site on -tubulin and shed light on the development of tubulin degraders as a new generation of anti-microtubule drugs targeting this novel site.

category: cell biology


title: SOX9 acts as a dynamic pioneer factor inducing stable changes in the chromatin landscape to reprogram endothelial cells.

abstract:
The transcription factor SOX9 is expressed in multiple tissues during embryogenesis and directs developmental processes. SOX9 is activated upon endothelial-to-mesenchymal transition (EndMT) in the developing heart, but its role in regulating this process is less clear. Using human umbilical vein endothelial cells as an EndMT model, we show that SOX9 expression alone is sufficient to activate mesenchymal enhancers and steer endothelial cells towards a mesenchymal fate. By genome-wide mapping of the chromatin landscape, we show that SOX9 acts as a pioneer transcription factor, having the ability to open chromatin and lead to deposition of active histone marks at a specific subset of previously silent enhancers, guided by SOX motifs and H2A.Z enrichment. This leads to a switch in enhancer activity states resulting in activation of mesenchymal genes and concurrent suppression of endothelial genes to drive EndMT. Moreover, we show that SOX9 chromatin binding is dynamic, but induces stable changes in the chromatin landscape. Our data also show widespread SOX9 chromatin scanning in silent chromatin that is not associated with SOX motifs or H2A.Z enrichment. Our study highlights the crucial developmental role of SOX9 and provides new insight into key molecular functions of SOX9 in the chromatin landscape and mechanisms of EndMT.

Graphical abstract

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title: Optimizing Mitochondrial Maintenance in Extended Neuronal Projections

abstract:
Neurons rely on localized mitochondria to fulfill spatially heterogeneous metabolic demands. Mitochondrial aging occurs on timescales shorter than the neuronal lifespan, necessitating transport of fresh material from the soma. Maintaining an optimal distribution of healthy mitochondria requires an interplay between a stationary pool localized to sites of high metabolic demand and a motile pool capable of delivering new material. Interchange between these pools can occur via transient fusion / fission events or by halting and restarting entire mitochondria. Our quantitative model of neuronal mitostasis identifies key parameters that govern steady-state mitochondrial health at discrete locations. Very infrequent exchange between stationary and motile pools optimizes this system. Exchange via transient fusion allows for robust maintenance, which can be further improved by selective recycling through mitophagy. These results provide a framework for quantifying how perturbations in organelle transport and interactions affect mitochondrial homeostasis in neurons, a key aspect underlying many neurodegenerative disorders.

Author summaryNeurons contain long projections termed axons and dendrites and a small central body that is responsible for much of cellular biosynthesis. Mitochondria, the energy hubs of a cell, are synthesized in the soma and actively transported to distant sites of high energy demand. Given the extreme distances between these sites and the soma, maintaining distal mitochondrial health poses a substantial challenge. Defects in mitochondrial transport and maintenance are associated with several neurological disorders.

Fortunately, mitochondria stationed at distant sites can be  serviced by passing mitochondria that emerge from the soma and move around the neuron, as well as through low levels of local protein synthesis. We develop mathematical models for two strategies of mitochondrial maintenance: one with direct protein exchange between moving and stationary mitochondria ( Space Station) and the other with moving mitchondria occasionally replacing stationary ones at the demand sites ( Changing of the Guard). We find that only a few servicing events and a small motile pool form optimal conditions for maintaining mitochondrial health. The system can be improved further by selectively removing and recycling some unhealthy mitochondria. Our results are consistent with observations of mitochondrial behavior in neurons and form a basis for future quantitative study of mitochondrial maintenance.


title: Principles of resilient coding for plant ecophysiologists

abstract: Plant ecophysiology is founded on a rich body of physical and chemical theory, but it is challenging to connect theory with data in unambiguous, analytically rigorous, and reproducible ways. Custom scripts written in computer programming languages (coding) enable plant ecophysiologists to model plant processes and fit models to data reproducibly using advanced statistical techniques. Since many ecophysiologists lack formal programming education, we have yet to adopt a unified set of coding principles and standards that could make coding easier to learn, use, and modify. We identify eight principles to help in plant ecophysiologists without much programming experience to write resilient code: 1) standardized nomenclature, 2) consistency in style, 3) increased modularity/extensibility for easier editing and understanding, 4) code scalability for application to large datasets, 5) documented contingencies for code maintenance, 6) documentation to facilitate user understanding; 7) extensive tutorials, and 8) unit testing. We illustrate these principles using a new R package, {photosynthesis}, which provides a set of analytical and simulation tools for plant ecophysiology. Our goal with these principles is to advance scientific discovery in plant ecophysiology by making it easier to use code for simulation and data analysis, reproduce results, and rapidly incorporate new biological understanding and analytical tools.


title: NuMorph: tools for cellular phenotyping in tissue cleared whole brain images

abstract: Tissue clearing methods allow every cell in the mouse brain to be imaged without physical sectioning. However, the computational tools currently available for cell quantification in cleared tissue images have been limited to counting sparse cell populations in stereotypical mice. Here we introduce NuMorph, a group of image analysis tools to quantify all nuclei and nuclear markers within the mouse cortex after tissue clearing and imaging by a conventional light-sheet microscope. We applied NuMorph to investigate two distinct mouse models: a Topoisomerase 1 (Top1) conditional knockout model with severe neurodegenerative deficits and a Neurofibromin 1 (Nf1) conditional knockout model with a more subtle brain overgrowth phenotype. In each case, we identified differential effects of gene deletion on individual cell-type counts and distribution across cortical regions that manifest as alterations of gross brain morphology. These results underline the value of 3D whole brain imaging approaches and the tools are widely applicable for studying 3D structural deficits of the brain at cellular resolution in animal models of neuropsychiatric disorders.


title: The temporal and spectral characteristics of expectations and prediction errors in pain and thermoception

abstract: In the context of a generative model, such as predictive coding, pain and heat perception can be construed as the integration of expectation and input with their difference denoted as a prediction error. In a previous neuroimaging study (Geuter et al., 2017) we observed an important role of the insula in such a model, but could not establish its temporal aspects. Here we employed electroencephalography to investigate neural representations of predictions and prediction errors in heat and pain processing. Our data show that alpha-to-beta activity was associated with stimulus intensity expectation, followed by a negative modulation of gamma band activity by absolute prediction errors. This is in contrast to prediction errors in visual and auditory perception, which are associated with increased gamma band activity, but is in agreement with observations in working memory and word matching, which show gamma band activity for correct, rather than violated predictions.


title: Induction of AmpC-mediated-βlactam resistance requires a single lytic transglycosylase in Agrobacterium tumefaciens

abstract:
The remarkable ability of Agrobacterium tumefaciens to transfer DNA to plant cells has allowed the generation of important transgenic crops. One challenge of A. tumefaciens-mediated transformation is eliminating the bacteria after plant transformation to prevent detrimental effects to plants and the release of engineered bacteria to the environment. Here we use a reverse genetics approach to identify genes involved in ampicillin resistance with the goal of utilizing these antibiotic-sensitive strains for plant transformations. We show that treating A. tumefaciens C58 with ampicillin led to increased {beta}-lactamase production, a response dependent on the broad-spectrum {beta}-lactamase AmpC and its transcription factor AmpR. Loss of the putative ampD orthologue, atu2113, led to constitutive production of AmpC-dependent {beta}-lactamase activity and ampicillin resistance. Finally, one cell wall remodeling enzyme, MltB3, was necessary for the AmpC-dependent {beta}-lactamase activity and its loss elicited ampicillin and carbenicillin sensitivity in the A. tumefaciens C58 and GV3101 strains. Furthermore, GV3101{Delta} mltB3 transforms plants with comparable efficiency to wildtype but can be cleared with sub-lethal concentrations of ampicillin. The functional characterization of the genes involved in the inducible ampicillin resistance pathway of A. tumefaciens constitutes a major step forward in efforts to reduce the intrinsic antibiotic resistance of this bacterium.

IMPORTANCEAgrobacterium tumefaciens, a significant biotechnological tool for production of transgenic plant lines, is highly resistant to a wide variety of antibiotics, posing challenges for various applications. One challenge is the efficient elimination of A. tumefaciens from transformed plant tissue without using levels of antibiotics that are toxic to the plants. Here, we present the functional characterization of genes involved in {beta}-lactam resistance in A. tumefaciens. Knowledge about proteins that promote or inhibit {beta}-lactam resistance will enable the development of strains to improve the efficiency of Agrobacterium-mediated plant genetic transformations. Effective removal of Agrobacterium from transformed plant tissue has the potential to maximize crop yield and food production, improving the outlook for global food security.


title: Bulk segregant analysis reveals environment x genotype interactions determining malaria parasite growth

abstract: What genes determine growth and nutrient utilization in asexual blood-stage malaria parasites? Competition experiments between a lab-adapted African parasite (NF54), and a recently isolated Asian parasite (NHP4026) reveal contrasting outcomes in different media: NF54 outcompetes NHP4026 in media containing human serum, while NHP4026 outcompetes NF54 in media containing AlbuMAX, a lipid-rich bovine serum formulation. We conducted parasite genetic crosses and compared genome-wide allele frequency changes in progeny populations cultured in media containing serum or AlbuMAX: this bulk segregant analysis (BSA) reveals three quantitative trait loci (QTL) underlying differential growth. The strongest QTL (chromosome 13) contains EBA-140: competition experiments between EBA-140-knockout and isogenic wildtype parasites showed fitness reversals in the two media types, validating this locus as the causative gene. These results (i) demonstrate the effectiveness of BSA for dissecting fitness traits in Plasmodium falciparum, and (ii) reveal an intimate link between red blood cell invasion and nutrient composition of growth media.


title: RANKL from Bone Marrow Adipocytes Regulates Osteoclast Formation and Bone Loss in Mice

abstract: Receptor activator of NF-{kappa}B ligand (RANKL) is essential for osteoclast formation and bone remodeling. Nevertheless, the cellular source of RANKL for osteoclastogenesis has not been fully uncovered. Different from peripheral adipose tissue, bone marrow (BM) adipose lineage cells originate from bone marrow mesenchymal stromal cells(BMSCs). Here we demonstrate that adiponectin promoter-driven Cre expression (AdipoqCre) can target bone marrow adipose lineage cells. We cross the AdipoqCre mice with ranklfl/fl mice to conditionally delete RANKL from BM adipose lineage cells. Conditional deletion of RANKL increases cancellous bone mass of long bones in mice by reducing the formation of trabecular osteoclasts and inhibiting bone resorption but does not affect cortical bone thickness or resorption of calcified cartilage. AdipoqCre; ranklfl/fl mice exhibit resistance to estrogen deficiency and rosiglitazone (ROS) induced trabecular bone loss but show bone loss induced by unloading. BM adipose lineage cells therefore represent an essential source of RANKL for the formation of trabecula osteoclasts and resorption of cancellous bone during remodeling under physiological and pathological conditions. Targeting bone marrow adiposity is a promising way of preventing pathological bone loss.


title: Resource-diversity relationships in bacterial communities reflect the network structure of microbial metabolism

abstract: The relationship between the number of available nutrients and community diversity is a central question for ecological research that remains unanswered. Here, we studied the assembly of hundreds of soil-derived microbial communities on a wide range of well-defined resource environments, from single carbon sources to combinations of up to 16. We found that, while single resources supported multispecies communities varying from 8 to 40 taxa, mean community richness increased only one-by-one with additional resources. Cross-feeding could reconcile these seemingly contrasting observations, with the metabolic network seeded by the supplied resources explaining the changes in richness due to both the identity and the number of resources, as well as the distribution of taxa across different communities. By using a consumer-resource model incorporating the inferred cross-feeding network, we provide further theoretical support to our observations and a framework to link the type and number of environmental resources to microbial community diversity.

category: ecology


title: Integration of Biodynamic Imaging and RNA-seq classifies chemotherapy response in canine diffuse large B-cell lymphoma

abstract: Diffuse large B-cell lymphoma (DLBCL) is a common, aggressive cancer of notorious genotypic and phenotypic heterogeneity. A major challenge is predicting response to drug treatment, which has typically been done using genomic tools alone with little success. A novel method that incorporates phenotypic profiling for predicting the effectiveness of therapy for individual patients is desperately needed. BioDynamic Imaging (BDI) is a technique for measuring time-dependent fluctuations in back-scattered light through living tumor tissues to identify critical changes in intracellular dynamics that are associated with phenotypic response to drugs. In this study, BDI and RNA sequencing (RNA-seq) data were collected on tumor samples from dogs with naturally occurring DLBCL, an animal model of increasingly recognized relevance to the human disease. BDI and RNA-seq data were combined to identify correlations between gene co-expression modules and linear combinations of biomarkers to provide biological mechanistic interpretations of BDI biomarkers. Using regularized multivariate logistic regression, we combined RNA-seq and BDI data to develop a novel model to accurately classify the clinical response of canine DLBCL to combination chemotherapy (i.e. CHOP). Our model incorporates data on the expression of 4 genes and 3 BDI-derived phenotypic biomarkers, capturing changes in transcription, microtubule related processes, and apoptosis. This pilot study suggests that the combination of multi-scale transcriptomic and phenotypic data can identify patients that respond to a given treatment a priori in a disease that has been difficult to treat. Our work provides an important framework for future development of strategies and treatments in precision cancer medicine.


title: Combined protein and transcript single cell RNA sequencing in human peripheral blood mononuclear cells

abstract: Cryopreserved peripheral blood mononuclear cells (PBMCs) are frequently collected and provide disease- and treatment-relevant data in clinical studies. Here, we developed combined protein (40 antibodies) and transcript single cell (sc)RNA sequencing in PBMCs. Among 31 participants in the WIHS Study, we sequenced 41,611 cells. Using Boolean gating followed by Seurat UMAPs and Louvain clustering, we identified 58 subsets among CD4 T, CD8 T, B, NK cells and monocytes. This resolution was superior to flow cytometry, mass cytometry or scRNA-sequencing without antibodies. Since the transcriptome was not needed for cell identification, combined protein and transcript scRNA-Seq allowed for the assessment of disease-related changes in transcriptomes and cell type proportion. As a proof-of-concept, we showed such differences between healthy and matched individuals living with HIV with and without cardiovascular disease. In conclusion, combined protein and transcript scRNA sequencing is a suitable and powerful method for clinical investigations using PBMCs.


title: A Hybrid High-Resolution Anatomical MRI Atlas with Sub-parcellation of Cortical Gyri using Resting fMRI

abstract: We present a new high-quality, single-subject atlas with sub-millimeter voxel resolution, high SNR, and excellent grey-white tissue contrast to resolve fine anatomical details. The atlas is labeled into two parcellation schemes: 1) the anatomical BCI-DNI atlas, which is manually labeled based on known morphological and anatomical features, and 2) the hybrid USCBrain atlas, which incorporates functional information to guide the sub-parcellation of cerebral cortex. In both cases, we provide consistent volumetric and cortical surface-based parcellation and labeling. The intended use of the atlas is as a reference template for structural coregistration and labeling of individual brains. A single-subject T1-weighted image was acquired at a resolution of 0.547mm x 0.547mm x 0.800mm five times and averaged. Images were processed by an expert neuroanatomist using semi-automated methods in BrainSuite to extract the brain, classify tissue-types, and render anatomical surfaces. Sixty-six cortical and 29 noncortical regions were manually labeled to generate the BCI-DNI atlas. The cortical regions were further sub-parcellated into 130 cortical regions based on multi-subject connectivity analysis using resting fMRI (rfMRI) data from the Human Connectome Project (HCP) database to produce the USCBrain atlas. In addition, we provide a delineation between sulcal valleys and gyral crowns, which offer an additional set of 26 sulcal subregions per hemisphere. Lastly, a probabilistic map is provided to give users a quantitative measure of reliability for each gyral subdivision. Utility of the atlas was assessed by computing adjusted Rand indices between individual sub-parcellations obtained through structural-only coregistration to the USCBrain atlas and sub-parcellations obtained directly from each subjects resting fMRI data. Both atlas parcellations can be used with the BrainSuite, FreeSurfer, and FSL software packages.


title: Measuring expression heterogeneity of single-cell cytoskeletal protein complexes

abstract: Multimeric cytoskeletal protein complexes orchestrate normal cellular function. However, protein-complex distributions in stressed, heterogeneous cell populations remain unknown. Cell staining and proximity-based methods have limited selectivity and/or sensitivity for endogenous multimeric protein-complex quantification from single cells. We introduce micro-arrayed, differential detergent fractionation to simultaneously detect protein complexes in 100s of individual cells. Fractionation occurs by 60 s size-exclusion electrophoresis with protein complex-stabilizing buffer that minimizes depolymerization. Co-detection of cytoskeletal protein complexes in U2OS cells treated with filamentous actin (F-actin) destabilizing LatA detects a subpopulation (~11%) exhibiting downregulated F-actin, but upregulated microtubule and intermediate filament protein complexes. Thus, some cells upregulate other cytoskeletal complexes to counteract the stress of LatA treatment. We also sought to understand the effect of non-chemical stress on cellular heterogeneity of F-actin. We find heat shock dysregulates F- and G-actin correlation. The assay overcomes selectivity limitations to biochemically quantify single-cell protein complexes perturbed with diverse stimuli.


title: Discovery of a Novel Inhibitor of Coronavirus 3CL Protease as a Clinical Candidate for the Potential Treatment of COVID-19

abstract: COVID-19 caused by the SARS-CoV-2 virus has become a global pandemic. 3CL protease is a virally encoded protein that is essential across a broad spectrum of coronaviruses with no close human analogs. The designed phosphate prodrug PF-07304814 is metabolized to PF-00835321 which is a potent inhibitor in vitro of the coronavirus family 3CL pro, with selectivity over human host protease targets. Furthermore, PF-00835231 exhibits potent in vitro antiviral activity against SARS-CoV-2 as a single agent and it is additive/synergistic in combination with remdesivir. We present the ADME, safety, in vitro, and in vivo antiviral activity data that supports the clinical evaluation of this compound as a potential COVID-19 treatment.

category: pharmacology and toxicology


title: nanoDoc: RNA modification detection using Nanopore raw reads with Deep One-Class Classification

abstract:
Advances in Nanopore single-molecule direct RNA sequencing (DRS) have presented the possibility of detecting comprehensive post-transcriptional modifications (PTMs) as an alternative to experimental approaches combined with high-throughput sequencing. It has been shown that the DRS method can detect the change in the raw electric current signal of a PTM; however, the accuracy and reliability still require improvement. Here, I present a new software program, named as nanoDoc, for detecting PTMs from DRS data using a deep neural network. Current signal deviations caused by PTMs are analyzed via Deep One-Class Classification with a convolutional neural network. Using a ribosomal RNA dataset, the software archive displayed an area under the curve (AUC) accuracy of 0.96 for detecting 23 different types of modifications in Escherichia coli and Saccharomyces cerevisiae. Furthermore, I demonstrated a tentative classification of PTMs using unsupervised clustering. Finally, I applied this software to severe acute respiratory syndrome coronavirus 2 data and identified commonly modified sites among three groups. nanoDoc is an open source software (GPLv3) available at https://github.com/uedaLabR/nanoDoc

Author SummaryRNA post-transcriptional modifications (PTMs) is regulate multiple aspects of RNA function, including alternative splicing, export, stability, and translation, and the method to identify multiple types of PTMs is required for further advancement of this fields called  epitranscriptomics. Nanopore singlemolecule direct RNA sequencing (DRS) can detect such PTMs, however the accuracy of the method needs to be improved. Detecting PTMs can be solved as a One-Class Classification problem, which is widely used in machine learning fields. Thus, a novel software named  nanoDoc for detecting PTMs was developed. The nanoDoc use convolutional neural network to extract the feature signal from nanopore sequencer and Deep One-Class Classification to detect PTMs as an anomaly. The software archive displayed an area under the curve (AUC) accuracy of 0.96 for detecting 23 different types of modifications in Escherichia coli and Saccharomyces cerevisiae. This software is applicable to different samples, and tested on severe acute respiratory syndrome coronavirus 2, and human transcript data as well.


title: Prolonged low-dose dioxin exposure impairs metabolic adaptability to high-fat diet feeding in female but not male mice

abstract:
ObjectiveHuman studies consistently show an association between exposure to persistent organic pollutants, including 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD, aka "dioxin"), and increased diabetes risk, but rarely consider potential sex differences. We previously showed that a single high-dose TCDD exposure (20 {micro}g/kg) decreased plasma insulin levels in both male and female mice in vivo, but effects on glucose homeostasis were sex-dependent. The purpose of the current study was to determine whether prolonged exposure to a physiologically relevant low-dose of TCDD impacts glucose homeostasis and/or the islet phenotype in a sex-dependent manner in either chow-fed or high fat diet (HFD)-fed mice.

MethodsMale and female mice were exposed to 20 ng/kg/d TCDD 2x/week for 12 weeks and simultaneously fed standard chow or a 45% HFD. Glucose homeostasis was assessed by glucose and insulin tolerance tests, and glucose-induced plasma insulin levels were measured in vivo. Histological analysis was performed on pancreas from male and female mice, and islets were isolated from females at 12 weeks for Tempo-Seq(R) analysis.

ResultsLow-dose TCDD exposure did not lead to adverse metabolic consequences in chow-fed male or female mice, or in HFD-fed males. However, TCDD accelerated the onset of HFD-induced hyperglycemia and impaired glucose-induced plasma insulin levels in female mice. TCDD caused a modest increase in islet area in males irrespective of diet, but reduced % beta cell area within islets in females. RNAseq analysis of female islets also revealed abnormal changes to endocrine and metabolic pathways in TCDD-exposed HFD-fed females compared chow-fed females.

ConclusionsOur data suggest that prolonged low-dose TCDD exposure has minimal effects on glucose homeostasis and islet morphology in chow-fed male and female mice, but promotes maladaptive metabolic responses in HFD-fed females.


title: Revealing the relevant spatiotemporal scale underlying whole-brain dynamics

abstract: The brain rapidly processes and adapts to new information by dynamically switching between activity in whole-brain functional networks. In this whole-brain modelling study we investigate the relevance of spatiotemporal scale in whole-brain functional networks. This is achieved through estimating brain parcellations at different spatial scales (100-900 regions) and time series at different temporal scales (from milliseconds to seconds) generated by a whole-brain model fitted to fMRI data. We quantify a fingerprint of healthy dynamics quantifying the richness of the dynamical repertoire at each spatiotemporal scale by computing the entropy of switching activity between whole-brain functional networks. The results show that the optimal relevant spatial scale is around 300 regions and a temporal scale of around 150 milliseconds. Overall, this study provides much needed evidence for the relevant spatiotemporal scales needed to make sense of neuroimaging data.


title: DNA damage activates mTORC1 signaling in podocytes leading to glomerulosclerosis

abstract:
DNA repair is essential for preserving genome integrity and ensures cellular functionality and survival. Podocytes have a very limited regenerative capacity, and their survival is essential to maintain kidney function. While podocyte depletion is a hallmark of glomerular diseases, the mechanisms leading to severe podocyte injury and loss remain largely unclear. We detected perturbations in DNA repair in biopsies from patients with various podocyte-related glomerular diseases and identified single-nucleotide polymorphisms associated with the expression of DNA repair genes in patients suffering from proteinuric kidney disease. Genome maintenance through nucleotide excision repair (NER) proved to be indispensable for podocyte homeostasis. Podocyte-specific knockout of the NER endonuclease co-factor Ercc1 resulted in accumulation of DNA damage, proteinuria, podocyte loss and glomerulosclerosis. The response to this genomic stress was fundamentally different to other cell types, as podocytes activate mTORC1 signaling upon DNA damage in vitro and in vivo.

Visual AbstractSchematic overview of main findings - Accumulation of genomic stress in podocytes occurs through endogenous or exogenous agents as well as genetic factors causing decreased DNA repair gene expression. Excessive DNA damage leads to the activation of mTORC1 triggering podocyte effacement, loss, glomerular scarring and proteinuric kidney disease.

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title: Glutamine deprivation triggers NAGK-dependent hexosamine salvage

abstract: Tumors frequently exhibit aberrant glycosylation, which can impact cancer progression and therapeutic responses. The hexosamine biosynthesis pathway (HBP) produces uridine diphosphate N-acetylglucosamine (UDP-GlcNAc), a major substrate for glycosylation in the cell. Prior studies have identified the HBP as a promising therapeutic target in pancreatic ductal adenocarcinoma (PDA). The HBP requires both glucose and glutamine for its initiation. The PDA tumor microenvironment is nutrient poor, however, prompting us to investigate how nutrient limitation impacts hexosamine synthesis. Here, we identify that glutamine limitation in PDA cells suppresses de novo hexosamine synthesis but results in increased free GlcNAc abundance. GlcNAc salvage via N-acetylglucosamine kinase (NAGK) is engaged to feed UDP-GlcNAc pools. NAGK expression is elevated in human PDA, and NAGK deletion from PDA cells impairs tumor growth in mice. Together, these data identify an important role for NAGK-dependent hexosamine salvage in supporting PDA tumor growth.


title: pDeep3: Towards More Accurate Spectrum Prediction with Fast Few-Shot Learning

abstract: Spectrum prediction using deep learning has attracted a lot of attention in recent years. Although existing deep learning methods have dramatically increased the pre-diction accuracy, there is still considerable space for improvement, which is presently limited by the difference of fragmentation types or instrument settings. In this work, we use the few-shot learning method to fit the data online to make up for the shortcoming. The method is evaluated using ten datasets, where the instruments includes Velos, QE, Lumos, and Sciex, with collision energies being differently set. Experimental results show that few-shot learning can achieve higher prediction accuracy with almost negligible computing resources. For example, on the dataset from a untrained instrument Sciex-6600, within about 10 seconds, the prediction accuracy is increased from 69.7% to 86.4%; on the CID (collision-induced dissociation) dataset, the prediction accuracy of the model trained by HCD (higher energy collision dissociation) spectra is increased from 48.0% to 83.9%. It is also shown that, the method is not critical to data quality and is sufficiently efficient to fill the accuracy gap. The source code of pDeep3 is available at http://pfind.ict.ac.cn/software/pdeep3.


title: Sense of self impacts spatial navigation and hexadirectional coding in human entorhinal cortex

abstract: Grid cells in entorhinal cortex (EC) encode an individuals location in space and rely on environmental cues and self-motion cues derived from the individuals body. Body-derived signals are also primary signals for the sense of self and self-identification with a body. However, it is currently unknown whether self-identification impacts grid cells and spatial navigation. Integrating the online manipulation of bodily signals, to modulate self-identification, into a spatial navigation task and with an fMRI measure to detect grid cell-like representation (GCLR) in humans, we report improved spatial navigation performance and decreased GCLR in EC when participants navigated with enhanced self-identification. These changes were further associated with increased activity in posterior parietal and retrosplenial cortex. Modulating self-identification by controlling online body-derived signals during spatial navigation, these data link the sense of self to spatial navigation and to entorhinal grid cell-like activity within a distributed cortical spatial navigation system.


title: Dissociable influences of reward and punishment on adaptive cognitive control

abstract:
To invest effort into any cognitive task, people must be sufficiently motivated. Whereas prior research has focused primarily on how the cognitive control required to complete these tasks is motivated by the potential rewards for success, it is also known that control investment can be equally motivated by the potential negative consequence for failure. Previous theoretical and experimental work has yet to examine how positive and negative incentives differentially influence the manner and intensity with which people allocate control. Here, we develop and test a normative model of control allocation under conditions of varying positive and negative performance incentives. Our model predicts, and our empirical findings confirm, that rewards for success and punishment for failure should differentially influence adjustments to the evidence accumulation rate versus response threshold, respectively. This dissociation further enabled us to infer how motivated a given person was by the consequences of success versus failure.

Author SummaryFrom the school to the workplace, whether someone achieves their goals is determined largely by the mental effort they invest in their tasks. Recent work has demonstrated both why and how people adjust the amount of effort they invest in response to variability in the rewards expected for achieving that goal. However, in the real world, we are motivated both by the positive outcomes our efforts can achieve (e.g., praise) and the negative outcomes they can avoid (e.g., rejection), and these two types of incentives can motivate adjustments not only in the amount of effort we invest but also the types of effort we invest (e.g., whether to prioritize performing the task efficiently or cautiously). Using a combination of computational modeling and a novel task that measures voluntary effort allocation under varying incentive conditions, we show that people should and do engage dissociable forms of mental effort in response to positive versus negative incentives. With increasing rewards for achieving their goal, they prioritize efficient performance, whereas with increasing penalties for failure they prioritize performing cautious performance. We further show that these dissociable strategies enable us to infer how motivated a given person was based on the positive consequences of success relative to the negative consequences of failure.


title: Application of subject-specific adaptive mechanical loading for bone healing in a mouse tail vertebral defect.

abstract: Methods to repair bone defects arising from trauma, resection, or disease, continue to be sought after. Cyclic mechanical loading is well established to influence bone (re)modelling activity, in which bone formation and resorption are correlated to micro-scale strain. Based on this, the application of mechanical stimulation across a bone defect could improve healing. However, if ignoring the mechanical integrity of defected bone, loading regimes have a high potential to either cause damage or be ineffective. This study explores real-time finite element (rtFE) methods that use three-dimensional structural analyses from micro-computed tomography images to estimate effective peak cyclic loads in a subject-specific and time-dependent manner. It demonstrates the concept in a cyclically loaded mouse caudal vertebral bone defect model. Using rtFE analysis combined with adaptive mechanical loading, mouse bone healing was significantly improved over non-loaded controls, with no incidence of vertebral fractures. Such rtFE-driven adaptive loading regimes demonstrated here could be relevant to clinical bone defect healing scenarios, where mechanical loading can become patient-specific and more efficacious. This is achieved by accounting for initial bone defect conditions and spatio-temporal healing, both being factors that are always unique to the patient.


title: The chaos in calibrating crop models

abstract:
Calibration, the estimation of model parameters based on fitting the model to experimental data, is among the first steps in many applications of system models and has an important impact on simulated values. Here we propose and illustrate a novel method of developing guidelines for calibration of system models. Our example is calibration of the phenology component of crop models. The approach is based on a multi-model study, where all teams are provided with the same data and asked to return simulations for the same conditions. All teams are asked to document in detail their calibration approach, including choices with respect to criteria for best parameters, choice of parameters to estimate and software. Based on an analysis of the advantages and disadvantages of the various choices, we propose calibration recommendations that cover a comprehensive list of decisions and that are based on actual practices.

HighlightsO_LIWe propose a new approach to deriving calibration recommendations for system models
C_LIO_LIApproach is based on analyzing calibration in multi-model simulation exercises
C_LIO_LIResulting recommendations are holistic and anchored in actual practice
C_LIO_LIWe apply the approach to calibration of crop models used to simulate phenology
C_LIO_LIRecommendations concern: objective function, parameters to estimate, software used
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title: Sustained neural activity correlates with rapid perceptual learning of auditory patterns

abstract: Repeating structures forming regular patterns are common in sounds. Learning such patterns may enable accurate perceptual organization. In five experiments, we investigated the behavioral and neural signatures of rapid perceptual learning of regular sound patterns. We show that recurring (compared to novel) patterns are detected more quickly and increase sensitivity to pattern deviations and to the temporal order of pattern onset relative to a visual stimulus. Sustained neural activity reflected perceptual learning in two ways. Firstly, sustained activity increased earlier for recurring than novel patterns when participants attended to sounds, but not when they ignored them; this earlier increase mirrored the rapid perceptual learning we observed behaviorally. Secondly, the magnitude of sustained activity was generally lower for recurring than novel patterns, but only for trials later in the experiment, and independent of whether participants attended to or ignored sounds. The late manifestation of sustained activity reduction suggests that it is not directly related to rapid perceptual learning, but to a mechanism that does not require attention to sound. In sum, we demonstrate that the latency of sustained activity reflects rapid perceptual learning of auditory patterns, while the magnitude may reflect a result of learning, such as better prediction of learned auditory patterns.


title: Human skeletal muscle organoids model fetal myogenesis and sustain uncommitted PAX7 myogenic progenitors

abstract: In vitro culture systems that structurally model human myogenesis and promote PAX7+ myogenic progenitor maturation have not been established. Here we report that human skeletal muscle organoids can be differentiated from induced pluripotent stem cell lines to contain paraxial mesoderm and neuromesodermal progenitors and develop into organized structures reassembling neural plate border and dermomyotome. Culture conditions instigate neural lineage arrest and promote fetal hypaxial myogenesis towards limb axial anatomical identity, with generation of sustainable uncommitted PAX7 myogenic progenitors and fibroadipogenic (PDGFRa+) progenitor populations equivalent to those from the second trimester of human gestation. Single cell comparison to human fetal and adult myogenic progenitors reveals distinct molecular signatures for non-dividing myogenic progenitors in activated (CD44High/CD98+/MYOD1+) and dormant (PAX7High/FBN1High/SPRY1High) states. Our approach, further validated with Duchenne and CRISPR/Cas9 genome-edited Limb-girdle muscular dystrophy (LGMD2A) patient iPSC lines, provides a novel robust 3D in vitro developmental system for investigating muscle tissue morphogenesis and homeostasis.


title: Deep learning classification of temporal data in ecology

abstract: Temporal data is ubiquitous in ecology and ecologists often face the challenge of accurately differentiating these data into predefined classes, such as biological entities or ecological states. The usual approach consists of transforming the time series into user-defined features and then using these features as predictors in conventional statistical or machine learning models. Here we suggest the use of deep learning models as an alternative to this approach. Recent deep learning techniques can perform the classification directly from the time series, eliminating subjective and resource-consuming data transformation steps, and potentially improving classification results. We describe some of the deep learning architectures relevant for time series classification and show how these architectures and their hyper-parameters can be tested and used for the classification problems at hand. We illustrate the approach using three case studies from distinct ecological subdisciplines: i) insect species identification from wingbeat spectrograms; ii) species distribution modelling from climate time series and iii) the classification of phenological phases from continuous meteorological data. The deep learning approach delivered ecologically sensible and accurate classifications demonstrating its potential for wide applicability across subfields of ecology.


title: A Hierarchical 3D-motion Learning Framework for Animal Spontaneous Behavior Mapping

abstract: Animal behavior usually has a hierarchical structure and dynamics. Therefore, to understand how the neural system coordinates with behaviors, neuroscientists need a quantitative description of the hierarchical dynamics of different behaviors. However, the recent end-to-end machine-learning-based methods for behavior analysis mostly focus on recognizing behavioral identities on a static timescale or based on limited observations. These approaches usually lose rich dynamic information on cross-scale behaviors. Inspired by the natural structure of animal behaviors, we addressed this challenge by proposing a novel parallel and multi-layered framework to learn the hierarchical dynamics and generate an objective metric to map the behavior into the feature space. In addition, we characterized the animal 3D kinematics with our low-cost and efficient multi-view 3D animal motion-capture system. Finally, we demonstrated that this framework could monitor spontaneous behavior and automatically identify the behavioral phenotypes of the transgenic animal disease model. The extensive experiment results suggest that our framework has a wide range of applications, including animal disease model phenotyping and the relationships modeling between the neural circuits and behavior.

category: animal behavior and cognition


title: ASXL1 Directs Neutrophilic Differentiation via Modulation of MYC and RNA Polymerase II.

abstract: Mutations in the gene Additional Sex-Combs Like 1 (ASXL1) are recurrent in myeloid malignancies as well as the pre-malignant condition clonal hematopoiesis, where they are universally associated with poor prognosis. An epigenetic regulator, ASXL1 canonically directs the deposition of H3K27me3 via the polycomb repressive complex 2. However, its precise role in myeloid lineage maturation is incompletely described. We utilized single cell RNA sequencing (scRNA-seq) on a murine model of hematopoietic-specific ASXL1 deletion and identified a specific role for ASXL1 in terminal granulocyte maturation. Terminal maturation is accompanied by down regulation of Myc expression and cell cycle exit. ASXL1 deletion leads to hyperactivation of Myc in granulocyte precursors and a quantitative decrease in neutrophil production. This failure of normal developmentallyassociated Myc suppression is not accompanied by significant changes in the landscape of covalent histone modifications including H3K27me3. Examining the genome-wide localization of ASXL1 in myeloid progenitors revealed strong co-localization with RNA Polymerase II (RNAPII) at the promoters and spread across the gene bodies of transcriptionally active genes. ASXL1 deletion results in a decrease in RNAPII promoter-proximal pausing in granulocyte progenitors, indicative of a global increase in productive transcription, consistent with the known role of ASXL1 as a mediator of RNAPII pause release. These results suggest that ASXL1 inhibits productive transcription in granulocyte progenitors, identifying a new role for this epigenetic regulator and highlighting a novel potential oncogenic mechanism for ASXL1 mutations in myeloid malignancies.

category: cancer biology


title: Memory specificity is linked to repetition effects in event-related potentials across the lifespan

abstract: The specificity with which past experiences can be remembered varies across the lifespan, possibly due to differences in how precisely information is encoded. Memory formation can be investigated through repetition effects, the common finding that neural activity is altered when stimuli are repeated. However, whether differences in this indirect measure of memory formation relate to lifespan differences in memory specificity has not yet been established. In the present study, we examined repetition effects in event-related potentials and their relation to recognition. During incidental encoding, children (aged 7-9 years), young adults (18-30 years), and older adults (65-76 years) viewed repeated object images from different categories. During subsequent recognition, we distinguished memory for the specific items versus the general categories. We identified repetition suppression in all age groups, and repetition enhancement for adults. Furthermore, individual item recognition performance comprising lure discrimination was positively associated with the magnitude of the neural repetition effects, which did not differ between groups, indicating common neural mechanisms of memory formation. Our findings demonstrate that neural repetition effects reflect the formation of highly specific memory representations and highlight their significance as a neural indicator of individual differences in episodic memory encoding across the lifespan.

category: neuroscience


title: Interacting effects of frontal lobe neuroanatomy and working memory capacity to older listeners' speech recognition in noise

abstract:
Many older adults are struggling with understanding spoken language, particularly when background noise interferes with comprehension. In the present study, we investigated a potential interaction between two well-known factors associated with greater speech-in-noise (SiN) reception thresholds in older adults, namely a) lower working memory capacity and b) age-related structural decline of frontal lobe regions.

In a sample of older adults (N=25) and younger controls (N=13) with normal pure-tone thresholds, SiN reception thresholds and working memory capacity were assessed. Furthermore, T1-weighted structural MR-images were recorded to analyze neuroanatomical traits (i.e., cortical thickness (CT) and cortical surface area (CSA)) of the cortex.

As expected, the older group showed greater SiN reception thresholds compared to the younger group. We also found consistent age-related atrophy (i.e., lower CT) in brain regions associated with SiN recognition namely the superior temporal lobe bilaterally, the right inferior frontal and precentral gyrus, as well as the left superior frontal gyrus. Those older participants with greater atrophy in these brain regions also showed greater SiN reception thresholds. Interestingly, the association between CT in the left superior frontal gyrus and SiN reception thresholds was moderated by individual working memory capacity. Older adults with greater working memory capacity benefitted more strongly from thicker frontal lobe regions when it comes to improve SiN recognition.

Overall, our results fit well into the literature showing that age-related structural decline in auditory- and cognition-related brain areas is associated with greater SiN reception thresholds in older adults. However, we highlight that this association changes as a function of individual working memory capacity. We therefore believe that future interventions to improve SiN recognition in older adults should take into account the role of the frontal lobe as well as individual working memory capacity.

HighlightsO_LISpeech-in-noise (SiN) reception thresholds are significantly increased with higher age, independently of pure-tone hearing loss
C_LIO_LIGreater SiN reception thresholds are associated with cortical thinning in several auditory-, linguistic-, and cognitive-related brain areas, irrespective of pure-tone hearing loss
C_LIO_LIGreater cortical thinning in the left superior frontal lobe is detrimental for SiN recognition in older, but not younger adults
C_LIO_LIOlder adults with greater working memory capacity benefit more strongly from structural integrity of left superior frontal lobe for SiN recognition
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