bluuebunny/crossref_metadata_2025 huggingface dataset:
CD34+ Stromal Cell/Telocytes Demonstrate a Dynamic Pattern of Distribution During Healing of Post-Infarcted Myocardium in Middle-Aged Sprague-Dawley Rats
Authors: Schneider Daniel T. , Dedkov Eduard I.
Published: September 2024

Introduction

Myocardial CD34+ stromal cells/telocytes (SC/TCs) have been recently recognized as a novel resident cell which may play an important role in the repair process following acute myocardial infarction (MI). This study aims to determine the spatiotemporal dynamics of CD34+ SC/TCs within the left ventricular (LV) wall during the late inflammatory and proliferative phases of post-MI scar formation.

Methods

A large transmural MI was induced in middle-aged, Sprague-Dawley rats by permanent ligation of the left anterior descending coronary artery. To recognize proliferating cells, rats were infused with 5-bromo-2’-deoxyuridine (BrdU) in a dose of 12.5 mg/kg/day for 72 hours via intraperitoneal osmotic minipumps on day 0, 4, or 11 after surgery. The rats were euthanized on day 3, 7 and 14 after MI, and their hearts were processed for histology and immunostaining.

Results

Three days after MI, CD34+ SC/TCs were absent within the necrotic myocardial tissue but were visible around the surviving cardiac myocytes (CMs) bordering the infarcted region, including those remaining in subepicardial and subendocardial regions, and in the adventitia of residual coronary vessels. Seven days after MI, many of the CD34+ SC/TCs located at the periphery of the developing scar appeared enlarged and contained the BrdU labeling, indicating the cell proliferation. At the same time, elongated CD34+ SC/TCs, which lacked BrdU labeling, were noticed closer to the necrotic zone residing in the interstitial areas between the intact basement membranes left from resorbed CMs, suggesting their migratory activity. Fourteen days after MI, CD34+ SC/TCs were distributed throughout the entire post-infarcted region except for the areas occupied by necrotic tissue, myofibroblast-rich granulation tissue, and the fibroelastic thickenings of the endocardium affected by an MI. Furthermore, accumulated clusters of flattened CD34+ SC/TCs cells were apparent in the areas where the edges of surviving CMs extend into the fibrotic portion of the scar.

Conclusion

These findings, for the first time, demonstrate that a population of myocardial CD34+ SC/TCs follow a dynamic pattern of spatiotemporal distribution within the healing myocardium suggesting their direct involvement in post-MI repair process and scar formation.
Somatic Transthyretin-Related Proteins in C. elegans Govern Reproductive Longevity by Sustaining Sperm Integrity and Timely Ovulation
Authors: Wu Tingshan , Lyu Haochen , Wang Zhao , Jiang Zhaoyang , Qi Yingchuan B.
Published: September 2024

The decline in reproductive capability during adult life is critical for health, but its mechanism is elusive. We systematically analyzed the developmental role of an expanded TTR family of proteins, structurally analogous to mammalian thyroid hormone-transporting Transthyretin, and identified three paralogous proteins, TTR-15, TTR-16, and TTR-17, differentially expressed in somatic cells of the gonads and secreted around gametes inC. elegans. Simultaneous inactivation of TTR-15, TTR-16, and TTR-17 leads to a rapid reduction in reproductive capacity in middle age. While oocyte and sperm production remain unaffected in the triple mutants, late-onset infertility results from stalled ovulation. Mechanistically, the absence of TTR-15, TTR-16, and TTR-17 causes sperm to prematurely deplete the cytoplasmic pool of major sperm protein (MSP), released via non-conventional vesicle budding as a signal for ovulation. We propose that the somatic gonads play a central role in maintaining sperm integrity post-production and determining the duration of the reproductive age.

Highlights

Systematic analysis of TTR family proteins reveals diverse expression and critical functions.

TTR-15, TTR-16, and TTR-17 are secreted around gametes inC. elegans.

TTR-15/16/17 triple KO exhibits middle-age onset infertility due to stalled ovulation.

MSP, a signal for ovulation, is prematurely depleted from sperm in the absence of TTR-15/16/17.
Translation profiling of stress-induced small proteins reveals a novel link among signaling systems
Authors: Vellappan Sangeevan , Sun Junhong , Favate John , Jagadeesan Pranavi , Cerda Debbie , Shah Premal , Yadavalli Srujana S.
Published: September 2024

Signaling networks allow adaptation to stressful environments by activating genes that counteract stressors. Small proteins (≤ 50 amino acids long) are a rising class of stress response regulators.Escherichia coliencodes over 150 small proteins, most of which lack phenotypes and their biological roles remain elusive. Using magnesium limitation as a stressor, we identify stress-induced small proteins using ribosome profiling, RNA sequencing, and transcriptional reporter assays. We uncover 17 small proteins with increased translation initiation, several of them transcriptionally upregulated by the PhoQ-PhoP two-component signaling system, crucial for magnesium homeostasis. Next, we describe small protein-specific deletion and overexpression phenotypes, underscoring their physiological significance in low magnesium stress. Most remarkably, we elucidate an unusual connection via a small membrane protein YoaI, between major signaling networks – PhoR-PhoB and EnvZ-OmpR inE. coli, advancing our understanding of small protein regulators in cellular signaling.

Synopsis

Ribo-RET identifies 17 small proteins induced under low magnesium (Mg2+) stress inE. coli

Many of these proteins are transcriptionally activated by PhoQP signaling system

Half of the stress-induced small proteins localize to the membrane

Deletion or overexpression of specific small proteins affects growth under stress

Small protein YoaI connects PhoR-PhoB and EnvZ-OmpR signaling networks
Soil redox drives virus-host community dynamics and plant biomass degradation in tropical rainforest soils
Authors: Trubl Gareth , Leleiwi Ikaia , Campbell Ashley , Kimbrel Jeffrey A. , Bhattacharyya Amrita , Riley Robert , Malmstrom Rex R. , Blazewicz Steven J. , Pett-Ridge Jennifer
Published: September 2024

Background

Wet tropical forest soils store a vast amount of organic carbon and cycle over a third of terrestrial net primary production. The microbiomes of these soils have a global impact on greenhouse gases and tolerate a remarkably dynamic redox environment—driven by high availability of reductant, high soil moisture, and fine-textured soils that limit oxygen diffusion. Yet tropical soil microbiomes, particularly virus-host interactions, remain poorly characterized, and we have little understanding of how they will shape future soil carbon cycling as high-intensity drought and precipitation events make soil redox conditions less predictable.

Results

To investigate the effects of shifting soil redox conditions on active viral communities and virus-microbe interactions, we conducted a 44-day redox manipulation experiment using soils from the Luquillo Experimental Forest, Puerto Rico, amended with13C-enriched plant biomass. We sequenced 10 bulk metagenomes and 85 stable isotope probing targeted metagenomes generated by extracting whole community DNA, performing density fractionation, and conducting shotgun sequencing. Viral and microbial genomes were assembled resulting in 5,420 viral populations (vOTUs) and 927 medium-to-high-quality metagenome-assembled genomes across 25 bacterial phyla. Notably, over half (54%) of the vOTUs were13C-enriched, highlighting their active role in microbial degradation of plant litter. These active vOTUs primarily infected bacterial phylaPseudomonadota,Acidobacteriota, andActinomycetota, and 57% were unique to a particular redox treatment. The anoxic samples exhibited the most distinct viral communities, with an increased potential for modulating host metabolism by carrying redox-specific glycoside hydrolases. However, over a third of the vOTUs were present in all redox conditions, suggesting selection for cosmopolitan viruses occurs in these soils that naturally experience dynamic redox conditions.

Conclusions

Our study demonstrates how redox conditions shape viral communities and virus-host interactions in soils. By applying different DNA assembly methods on stable isotope probing targeted metagenomes and incubating soils under various redox regimes, we identified distinct viral populations and observed significant variations in viral community composition and function. These findings highlight the specialized roles of viruses in microbial carbon degradation under diverse environmental conditions, providing important insights into their contributions to carbon cycling and the broader implications for climate change.
Reconstruction of functional olfactory sensory tissue from embryonic nasal stem cells
Authors: Suzuki Kazuya , Wagai Fumi , Eiraku Mototsugu
Published: September 2024

During the development of the olfactory epithelium (OE), olfactory sensory neurons (OSNs) express only one member of the odorant receptor (OR) gene family, and OSNs expressing the same OR converge their axons to the same set of glomeruli on the olfactory bulb (OB). The resulting odor maps allow mice to discriminate more than 100,000 different odorants using about 1,000 ORs. It remains elusive how odor maps are formed. Here, we show a means of forming OE organoids with pseudostratified structure from mouse embryonic OE stem cells. Single-cell RNA sequencing revealed that the OE organoids give rise to all the OE cellular lineages and undergo active neurogenesis. We also found that most OSNs in OE organoids exclusively express only one type of ORs and exhibit a unique molecular code of axon guidance-related genes that can discriminate between OR classes. Thus, OE organoids could be a useful model for studying olfactory nervous system development.
Creation of MLPA: A Multi-level Digital Twin Framework for Personalized Cancer Simulation and Treatment Optimization
Authors: Gu James , Chen Jake Y
Published: September 2024

This research proposes a new personalized cancer modeling and treatment strategy: the Multi-level Parameterized Automata (MLPA), an innovative digital twin framework. The MLPA framework fully integrates macroscopic electronic health records (EHR) and microscopic genomic data for the first time, employing stochastic cellular automata to model tumor progression and treatment efficacy dynamically.

The multi-scale strategy effectively enables MLPA to simulate complex cancer behaviors, including metastasis and pharmacological responses, with remarkable precision. The validation using bioluminescent imaging from mice demonstrates MLPA’s exceptional predictive power, achieving a state-of-the-art R² value of 0.93, improvement over previously reported conventional models, and fitting within 95% confidence intervals.

The proposed MLPA framework accurately captures tumors’ characteristic S-shaped growth curve and shows high fidelity in simulating various scenarios, from natural progression to aggressive growth and drug treatment responses. MLPA’s ability to simulate drug effects through gene pathway perturbation, with predicted tumor cell counts being within a 2.5% equivalence margin interval, underscores its potential as a powerful method for precision oncology.

The proposed MLPA framework not only offers a more reliable platform for exploring personalized treatment strategies, but also potentially transforms patient outcomes by optimizing therapy based on individual human biological profiles. As clinically adopted technology progresses towards precision medicine, MLPA stands at the forefront, offering new possibilities in cancer simulation and treatment optimization. The code and imaging dataset used is available athttps://github.com/alphamind-club/MLPA.
Normal feeding movements expressed by dimensionality reduction of whole-body joint motions using principal component analysis
Authors: Nakatake Jun , Miyazaki Shigeaki , Arakawa Hideki , Chosa Etsuo
Published: September 2024

Background. Understanding elementary feeding movements and postures is essential for improving assessment and intervention strategies in occupational therapy, particularly for individuals with eating difficulties, and for educating caregivers and students. However, the current assessment tools lack precision in evaluating complex feeding movements and often rely on subjective judgments rather than objective measures. We aimed to determine elementary movements and postures corresponding to different feeding phases using principal component analysis (PCA). Methods. This cross sectional-observational study was conducted at a Local National University Hospital and included 45 healthy, right-handed adult volunteers (23 men and 22 women) aged 20-39 years (mean age, 27.3 years), with no neurological or musculoskeletal impairments. Movements during yogurt feeding using a spoon were captured with a three-dimensional inertial sensor motion capture system. Principal components (PCs) and their scores were derived from PCA of whole-body joint motion data across four feeding phases. PC scores were compared between phases using Friedman and post hoc tests. Results. The primary PC, representing whole body movement, accounted for 50.0% of the variance; the second PC, associated with hand direction changes, accounted for 13.7%. The cumulative variance of the first six PCs was 87.4%, including individual body part movements and fixations or combinations of these. Significant differences existed between feeding phases, particularly in the reaching and transport phases, which showed greater whole-body movement than that during the spooning and mouth phases. Hand direction changes were more prominent during the spooning phase than during the mouth phase. Conclusions. PCA helped determine key elementary movements and their corresponding feeding phases, which can be used to assess patients with feeding difficulties and guide occupational therapy interventions.
Effects ofNf1on sleep behavior are mediated through starvation caused by deficits in SARM1 dependent NAD+ metabolism
Authors: Sofela Folasade A. , Lopez Valencia Mariela , Jongens Thomas A. , Sehgal Amita
Published: September 2024

Neurofibromatosis 1 (NF1) is a relatively common autosomal dominant disease which predisposes to the formation of tumors, and is also associated with behavioral phenotypes, including sleep disturbances. As loss of the NF1 protein has been recently associated with metabolic dysfunction, we explored the relationship between metabolic and behavioral phenotypes through metabolomic analysis ofDrosophila Nf1-null mutants.Nf1-null mutants exhibit a metabolic signature indicative of starvation, with diminished metabolites related to glucose, glycogen, and fatty acid processing and increased mRNA ofAkh, a hormone that promotes foraging during starvation. Reduced sleep inNf1-null mutants was rescued by genetic manipulation of the AKH pathway and by a high-sucrose diet, which also partially corrected hypolipidemia, suggesting that sleep loss is due to starvation-induced foraging. Interestingly, behavioral phenotypes can be recapitulated by loss of NF1 only in the periphery and trace to mitochondrial defects that include elevated levels of the NADase SARM1. Indeed, inhibition of SARM1 activity rescues sleep behavior inNf1-null flies. These findings suggest a novel connection between loss of NF1 and mitochondrial dysfunction caused by SARM1 hyperactivation, setting the scene for new pharmacological and dietary approaches that could provide relief to NF1 patients.
Neurovascular Impulse Response Function (IRF) during spontaneous activity differentially reflects intrinsic neuromodulation across cortical regions
Authors: Rauscher Bradley C. , Fomin-Thunemann Natalie , Kura Sreekanth , Doran Patrick R. , Perez Pablo D. , Kılıç Kıvılcım , Martin Emily A. , Balog Dora , Chai Nathan X. , Froio Francesca A. , Bloniasz Patrick F. , Herrema Kate E. , Tang Rockwell , Knudstrup Scott G. , Garcia Andrew , Jiang John X. , Gavornik Jeffrey P. , Kleinfeld David , Hasselmo Michael E. , Lewis Laura D. , Sakadzic Sava , Tian Lei , Mishne Gal , Stephen Emily P. , Thunemann Martin , Boas David A. , Devor Anna
Published: September 2024

Ascending neuromodulatory projections from deep brain nuclei generate internal brain states that differentially engage specific neuronal cell types. Because neurovascular coupling is cell-type specific and neuromodulatory transmitters have vasoactive properties, we hypothesized that the impulse response function (IRF) linking spontaneous neuronal activity with hemodynamics would depend on neuromodulation. To test this hypothesis, we used optical imaging to measure (1) release of neuromodulatory transmitters norepinephrine (NE) or acetylcholine (ACh), (2) Ca2+activity of local cortical neurons, and (3) changes in hemoglobin concentration and oxygenation across the dorsal surface of cerebral cortex during spontaneous neuronal activity in awake mice. A canonical convolution model with a stationary IRF (e.g., the convolution kernel) describing evolution of total hemoglobin (HbT, reflective of dilation dynamics) with respect to Ca2+, resulted in a poor fit to the data. However, the HbT time-course was well predicted, pixel-by-pixel, by a weighted sum of Ca2+and NE time-courses. The weighting coefficients, calculated using linear regression, varied smoothly across the cortical space. Consistent with this result, modeling HbT as a weighted sum of stationary Ca2+- and NE-specific IRFs convolved with the respective time-courses dramatically improved the fit compared to the invariant IRF. In both the linear regression and the Double-IRF convolution models, Ca2+and NE weighting was positive and negative, respectively. In contrast to NE, ACh was largely redundant with Ca2+and therefore did not improve HbT estimation. Because NE covaried with arousal, we observed instances of the diminished hemodynamic coherence between cortical regions during high arousal despite coherent behavior of the underlying neuronal Ca2+activity. We conclude that while neurovascular coupling with respect to neuronal Ca2+is a dynamic and seemingly complex phenomenon, hemodynamic fluctuations can be captured by a simple linear model with stationary IRFs with respect to the underlying dilatory and constrictive forces. In the current study, these forces were captured by the positive Ca2+(dilation) and negative NE (constriction) coefficients. Without accounting for NE neuromodulation and the associated vasoconstriction, diminished hemodynamic coherence, commonly referred to as ″functional (dys)connectivity″ in BOLD fMRI studies, can be falsely interpreted as neuronal desynchronizations.
Immune-like glycan-sensing and horizontally-acquired glycan-processing orchestrate host control in a microbial endosymbiosis
Authors: Jenkins Benjamin H. , Kilias Estelle S. , Savory Fiona R. , Sørensen Megan E. S. , Poirier Camille , Attah Victoria , Drew Georgia C. , Galindo Luis J. , Leonard Guy , Cameron Duncan D. , Brockhurst Michael A. , Milner David S. , Richards Thomas A.
Published: September 2024

Endosymbiosis was a key factor in the evolution of eukaryotic cellular complexity. Yet the mechanisms that allow host regulation of intracellular symbionts, a pre-requisite for stable endosymbiosis and subsequent organelle evolution, are largely unknown. Here, we describe an immune-like glycan-sensing/processing network, partly assembled through horizontal gene-transfers (HGTs), that enablesParamecium bursariato control its algal endosymbionts. Using phylogenetics, RNA-interference (RNAi), and metabolite exposure experiments, we show thatP. bursariaregulates endosymbiont destruction using glycan-sensing/processing – a system that includes a eukaryotic-wide chitin-binding chitinase-like protein (CLP) localized to the host phago-lysosome. RNAi ofCLPalters expression of eight glycan-processing genes, including two prokaryote-derived HGTs, during endosymbiont destruction. Furthermore, glycan-sensing/processing dynamically regulates endosymbiont number inP. bursaria, plasticity crucial to maximize host fitness across ecological conditions.CLPis homologous to a human phagocyte-associated innate immune factor, revealing how immune functions can be alternatively adapted and expanded, partly through HGT, enabling endosymbiotic control.

Graphical Abstract
Neural dynamics of reversal learning in the prefrontal cortex and recurrent neural networks
Authors: Kim Christopher M. , Chow Carson C. , Averbeck Bruno B.
Published: September 2024

In probabilistic reversal learning, the choice option yielding reward at higher probability switches at a random trial. To perform optimally in this task, one has to accumulate evidence across trials to infer the probability that a reversal has occurred. In this study, we investigated how this reversal probability is represented in cortical neurons by analyzing the neural activity in prefrontal cortex of monkeys and recurrent neural networks trained on the task. We found that neural trajectories encoding reversal probability had substantial dynamics associated with intervening behaviors necessary to perform the task. Furthermore, the neural trajectories were translated systematically in response to whether outcomes were rewarded, and their position in the neural subspace captured information about reward outcomes. These findings suggested that separable dynamic trajectories, instead of fixed points on a line attractor, provided a better description of neural representation of reversal probability. Near the behavioral reversal, in particular, the trajectories shifted monotonically across trials with stable ordering, representing varying estimates of reversal probability around the reversal point. Perturbing the neural trajectory of trained networks biased when the reversal trial occurred, showing the role of reversal probability activity in decision-making. In sum, our study shows that cortical neurons encode reversal probability in a family of dynamic neural trajectories that accommodate flexible behavior while maintaining separability to represent distinct probabilistic values.
Spike Count Analysis for MultiPlexing Inference (SCAMPI)
Authors: Chen Yunran , Groh Jennifer M , Tokdar Surya T
Published: September 2024

Understanding how neurons encode multiple simultaneous stimuli is a fundamental question in neuroscience. We have previously introduced a novel theory of stochastic encoding patterns wherein a neuron’s spiking activity dynamically switches among its constituent single-stimulus activity patterns when presented with multiple stimuli (Groh et al., 2024). Here, we present an enhanced, comprehensive statistical testing framework for such “multiplexing” or “code juggling”. Our new approach evaluates whether dual-stimulus responses can be accounted for as mixtures of Poissons either anchored to or bounded by single-stimulus benchmarks.

Our enhanced framework improves upon previous methods in two key ways. First, it introduces a stronger set of foils for multiplexing, including an “overreaching” category that captures overdispersed activity patterns unrelated to the single-stimulus benchmarks, reducing false detection of multiplexing/code-juggling. Second, it detects faster fluctuations - i.e. at sub-trial timescales - that would have been overlooked before. We utilize a Bayesian inference framework, considering the hypothesis with the highest posterior probability as the winner, and employ predictive recursion marginal likelihood method for the involving nonparametric density estimation.

Reanalysis of previous findings confirms the general observation of “code juggling” and indicates that such juggling may well occur on faster timescales than previously suggested. We further confirm that juggling is more prevalent in (a) the inferotemporal face patch system for combinations of face stimuli than for faces and non-face objects; and (b) the primary visual cortex for distinct vs fused objects.
Two new species ofGraphium(Microascales, Ascomycota) associated with pine-infesting bark beetles in China
Authors: Li Jie , Gao Xiang , Liu Kun , Chen Minjie , Ran Yutong , Liu Congwang , Lin Tong , Yin Mingliang
Published: September 2024

Graphiumis a genus of fungi that falls under the order Microascales of Ascomycota. Some species in this genus can establish a unique symbiotic relationship with the pine-infesting bark beetles, while others are typically found in wood or soil habitats. To comprehensively investigate the diversity of species of these fungi, recent field trips were conducted in seven provinces (Fujian, Guangdong, Guizhou, Guangxi, Liaoning, Shaanxi, and Shandong) in China. 96 pure isolates ofGraphiumwere obtained by sequences from 361 samples. Nineteen representative strains were carefully selected to generate sequencing data from four gene regions (ITS, LSU, EF1A and TUBB), then used to construct phylogenetic trees for the genus. The results revealed the discovery of two new species, namelyG. armandiisp. nov. andG. massonianasp. nov., andG. pseudoumiticumwas the most common species in various pine hosts.
Spinal and cortical premotor control of primate dexterous hand movements
Authors: Takei Tomohiko , Oya Tomomichi , Seki Kazuhiko
Published: September 2024

Skilled hand movements are an evolutionary advance in primates. Phylogenetically distinct corticospinal pathways are involved in hand control: “newer” direct corticomotoneuronal (CM) pathways and “older” indirect corticospinal pathways mediated by spinal premotor interneurons (PreM-INs). However, the functional differences of these pathways remain unclear. Here we show that CM cells and PreM-INs have distinct physiological properties for the activation of hand muscles and provide different types of movement control signals while monkeys perform a precision grip task. Spike-triggered averaging of electromyographic activity indicated that PreM-INs coactivate a larger number of muscles, whereas CM cells more selectively control fewer muscles. The firing activity of PreM-INs was tightly correlated with their target muscle activity and had a greater contribution to generating hand muscle activity. In contrast, CM cell activity diverged temporally from the target muscle activity and had a smaller contribution to its generation. On the basis of these results, we hypothesize that PreM-INs produce gross muscle activity by activating synergistic muscles, whereas CM cells fine-tune target muscle activity. This idea was supported by dimensional reduction analyses of hand muscle activity, as PreM-IN activity was specifically correlated with lower dimensional control of muscle activity, and CM cell activity was correlated with higher dimensional control. These results indicate that the two pathways have distinct functions, synergistic control and fine tuning of hand muscle activity, both of which are essential for the development of dexterous hand movement in primates.
Co-transcriptional RNA processing boosts zygotic gene activation
Authors: Xu Jingzhao , Li XiaoJing , Hao Xiaowen , Hu Xinyun , Ma Shaoqian , Hong Yantao , Zhang Jing , Yan Dingfei , Deng Haiteng , Na Jie , Ji Xiong , Chang Zai , Shen Xiaohua
Published: September 2024

Transcription decodes protein-coding genes and interprets regulatory information embedded in the genome by generating RNA. In eukaryotes, gene transcription is coupled with RNA processing via the carboxyl terminal domain (CTD) of RNA polymerase (Pol) II, which enhances messenger RNA (mRNA) production. We propose that co-transcriptional RNA processing is essential for zygotic gene activation (ZGA), transitioning the transcription program from noncoding to protein-coding after fertilization. Truncating the CTD in mouse cells disrupts this coupling, halting global mRNA synthesis and increasing noncoding RNA (ncRNA) levels through enhanced intergenic transcription and RNA stabilization. CTD truncation also triggers epigenetic reprogramming and nuclear reorganization towards totipotency, resembling early cleavage embryos. Mechanistically, the CTD restrains nonproductive polymerase activity in noncoding sequences, while at protein-coding genes requiring RNA processing, it promotes elongation by facilitating polymerase promoter-proximal pausing, transcription directionality, and velocity. Longer CTD lengths enhance gene activity, likely evolving to accommodate the increasing noncoding sequences in mammalian genomes.
Environmental surveillance of soil-transmitted helminths and other enteric pathogens in settings without networked wastewater infrastructure
Authors: Siko Joël Edoux Eric , Dahmer Kendra Joy , Manoharan Zayina Zondervenni , Muthukumar Ajithkumar , Amato Heather K. , LeBoa Christopher , Harris Michael , Janagaraj Venkateshprabhu , Manuel Malathi , Varghese Tintu , Houngbegnon Parfait , Pilotte Nils , Bouko Bernadin , Saïdou Souad , Luty Adrian J. F. , Ramesh Rohan Michael , Ibikounlé Moudachirou , Ajjampur Sitara S.R. , Pickering Amy J.
Published: September 2024

Soil-transmitted helminths (STH) are one of the most prevalent enteric infections world-wide. To control STH-related morbidity, the World Health Organization recommends targeted deworming and improvements in water, sanitation and hygiene. Current surveillance strategies for STH focus on identifying and quantifying eggs in stool samples via microscopy, which exhibits poor specificity and sensitivity, especially in settings with low-intensity infections. Wastewater-based epidemiology is a surveillance tool used to monitor pathogen circulation and could replace stool- based approaches for STH detection. However, sampling strategies for settings lacking networked sanitation outside large urban settlements are not well developed. Here, we report evaluation of sampling strategies for soil and wastewater STH surveillance in rural and peri-urban settings without networked sanitation. We used multi-parallel qPCR assays to detect STH DNA in soil collected from high foot-traffic locations and three types of wastewater samples (passive Moore swabs, grab samples, and sediment from drainage ditches) in Comé, Benin and Timiri and Jawadhu Hills in Tamil Nadu, India. We detected STH in soil (India = 32/95, Benin = 39/121) and wastewater (India = 24/60, Benin = 8/64) with a detection frequency across all sample types of 36% in India and 25% in Benin. We evaluated which sample locations and types allowed for more sensitive detection of STH DNA and determined that STH prevalence varied by sample site but did not vary significantly within a given sample site location (e.g., samples collected from multiple locations within one market). Further, we determined that wastewater sediment samples outperformed grab and Moore swab sample types for STH detection. Finally, we expanded our methods to include detection of other enteric pathogens using multiplexed qPCR for wastewater samples. Our results establish sampling strategies for environmental and wastewater surveillance of a wide range of enteric pathogens in settings without networked sanitation.
Sleep-wake states are encoded across emotion-regulation regions of the mouse brain
Authors: Walder-Christensen Kathryn K. , Goffinet Jack , Bey Alexandra L. , Syed Reah , Benton Jacob , Mague Stephen D. , Adamson Elise , Vera Sophia , Soliman Hannah , Kansagra Sujay , Carlson David , Dzirasa Kafui
Published: September 2024

Emotional dysregulation is highly comorbid with sleep disturbances. Sleep is comprised of unique physiological states that are reflected by conserved brain oscillations. Though the role of these state-dependent oscillations in cognitive function has been well established, less is known regarding the nature of state-dependent oscillations across brain regions that strongly contribute to emotional function. To characterize these dynamics, we recorded local field potentials simultaneously from multiple cortical and subcortical regions implicated in sleep and emotion-regulation and characterize widespread patterns of spectral power and synchrony between brain regions during sleep/wake states. First, we showed that these brain regions encode sleep state, albeit to various degrees of accuracy. We then identified network-based classifiers of sleep based on the combination of features from all recorded brain regions. Spectral power and synchrony from brain networks allowed for automatic, accurate and rapid discrimination of wake, non-REM sleep (NREM) and rapid eye movement (REM) sleep. When we examined the impact of commonly prescribed sleep promoting medications on neural dynamics across these regions, we found disparate alterations to both cortical and subcortical activity across all three states. Finally, a we found that a stress manipulation that disrupts circadian rhythm produced increased sleep fragmentation without altering the underlying average brain dynamics across sleep-wake states. Thus, we characterized state dependent brain dynamics across regions canonically associated with emotions.

Significance Statement

Sleep and emotion regulation are known to be intertwined at the level of behavior and in neuropsychiatric illnesses. Here, we examined how brain regions involved in emotion regulation encode wake and sleep states by performing multi-site electrophysiological recordings in mice. We developed sleep-wake state classifiers that rapidly labeled sleep-wake states from brain activity alone. We then identified how commonly prescribed sleep-inducing medications have unique impacts on brain activity throughout these emotion-regulation regions. Finally, we explored the impact of circadian rhythm disruption on sleep architecture and brain activity. Together, these data shed light on how brain regions which regulate emotion behave during sleep so that one day, treatments to improve both sleep and emotional well-being may be developed.
YAP/TAZ signaling in allantois-derived cells is required for placental vascularization
Authors: Gao Siqi , Thillaikumaran Triloshan , Dominguez Martin H. , Giang William , Hayes Kevin , Chen Xiaowen , Pace Jesse , Bockman Jenna , Jathan Danielle , Sung Derek , Narayan Sweta , Frankfurter Maxwell , Mericko-Ishizuka Patricia , Yang Jisheng , Castro Marco , Potente Michael , Kahn Mark L.
Published: September 2024

Normal placental development and angiogenesis are crucial for fetal growth and maternal health during pregnancy. However, molecular regulation of placental angiogenesis has been difficult to study due to a lack of specific genetic tools that isolate the placenta from the embryo and yolk sac. To address this gap in knowledge we recently developedHoxa13Cremice in which Cre is expressed in allantois-derived cells, including placental endothelial and stromal cells. Mice lacking the transcriptional regulators Yes-associated protein (YAP) and PDZ-binding motif (TAZ) in allantois-derived cells exhibit embryonic lethality at midgestation with compromised placental vasculature. snRNA-seq analysis revealed transcriptional changes in placental stromal cells and endothelial cells. YAP/TAZ mutants exhibited significantly reduced placental stromal cells prior to the endothelial architectural change, highlighting the role of these cells in placental vascular growth. These results reveal a central role for YAP/TAZ signaling during placental vascular growth and implicateHoxa13-derived placental stromal cells as a critical component of placental vascularization.
Inositol Hexaphosphate (InsP6) Activates the HDAC1/3 Epigenetic Axis to Maintain Intestinal Barrier Function
Authors: Chatterjee Sujan , Preval Loretta Viera , Sin Zachary , Tran Nguyen , Ritter Kevin , Su Xue Bessie , Centlivre Jakob P. , Ragsac Saharat Jolak , Van Richard , Park Seungman , Han Mira , Liu Qian , Hedlund Brian P , Saiardi Adolfo , Jessen Henning , Guha Prasun
Published: September 2024

HDACs (histone deacetylase) play a crucial role in regulating gene expression, and the inhibition of these enzymes is gaining attention as a promising therapeutic approach for cancer treatment. Despite their significant physiological and clinical importance, the mechanisms of HDAC activation remain poorly understood. This study reveals that inositol polyphosphate multikinase (IPMK) is essential for activating HDAC1 and HDAC3 in cell lines and mice. IPMK deletion or inactivation of its kinase activity selectively impairs HDAC1/3's deacetylase activity, significantly influencing gene expression. Disruption of the IPMK-HDAC1/3 epigenetic axis results in transcriptional upregulation of matrix metalloproteinase (MMP) genes, exacerbating cell and intestinal permeability. Remarkably, treatment of IPMK KO cells with cell-permeable inositol hexaphosphate (InsP6) rescues these defects. This study elucidates the role of IPMK's kinase activity in HDAC1/3 activation and its implications for intestinal barrier function.
Long-read RNA sequencing of archival tissues reveals novel genes and transcripts associated with clear cell renal cell carcinoma recurrence and immune evasion
Authors: Lee Joshua , Snell Elizabeth A. , Brown Joanne , Booth Charlotte E. , Banks Rosamonde E. , Turner Daniel J. , Vasudev Naveen S. , Lagos Dimitris
Published: September 2024

The use of long-read direct RNA sequencing (DRS) and PCR cDNA sequencing (PCS) in clinical oncology remains limited, with no direct comparison between the two methods. We used DRS and PCS to study clear cell renal cell carcinoma (ccRCC), focusing on new transcript and gene discovery. Twelve primary ccRCC archival tumors, six from patients who went on to relapse, were analyzed. Results were validated in an independent cohort of 20 patients by qRT-PCR and compared to DRS analysis of RCC4 cells. In archival clinical samples and due to the long-term storage, the average read length was lower (400–500 nt) than that achieved through DRS of RCC4 cells (>1100 nt). Still, deconvolution analysis showed a loss of immune infiltrate in primary tumors of patients who relapse as reported by others. Differentially expressed genes in patients who went on to relapse were determined with good overlap between DRS and PCS, identifyingLINC04216and the T-cell exhaustion markerTOXas novel candidate recurrence-associated genes. Novel transcript analysis revealed over 10,000 candidate novel transcripts detected by both methods and in ccRCC cells in vitro, including a novelCD274(PD-L1) transcript encoding for the soluble version of the protein with a longer 3′ UTR and lower stability than the annotated transcript. Both methods identified 414 novel genes, also detected in RCC4 cells, including a novel noncoding gene overexpressed in patients who relapse. Overall, we showcase the use of PCS and DRS in archival tumor samples to uncover unmapped features of cancer transcriptomes, linked to disease progression and immune evasion.
Comprehensive identification of genomic and environmental determinants of phenotypic plasticity in maize
Authors: Tibbs-Cortes Laura E. , Guo Tingting , Andorf Carson M. , Li Xianran , Yu Jianming
Published: September 2024

Maize phenotypes are plastic, determined by the complex interplay of genetics and environmental variables. Uncovering the genes responsible and understanding how their effects change across a large geographic region are challenging. In this study, we conducted systematic analysis to identify environmental indices that strongly influence 19 traits (including flowering time, plant architecture, and yield component traits) measured in the maize nested association mapping (NAM) population grown in 11 environments. Identified environmental indices based on day length, temperature, moisture, and combinations of these are biologically meaningful. Next, we leveraged a total of more than 20 million SNP and SV markers derived from recent de novo sequencing of the NAM founders for trait prediction and dissection. When combined with identified environmental indices, genomic prediction enables accurate performance predictions. Genome-wide association studies (GWASs) detected genetic loci associated with the plastic response to the identified environmental indices for all examined traits. By systematically uncovering the major environmental and genomic factors underlying phenotypic plasticity in a wide variety of traits and depositing our results as a track on the MaizeGDB genome browser, we provide a community resource as well as a comprehensive analytical framework to facilitate continuing complex trait dissection and prediction in maize and other crops. Our findings also provide a conceptual framework for the genetic architecture of phenotypic plasticity by accommodating two alternative models, regulatory gene model and allelic sensitivity model, as special cases of a continuum.
Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects ofSF3B1mutations
Authors: Pacholewska Alicja , Lienhard Matthias , Brüggemann Mirko , Hänel Heike , Bilalli Lorina , Königs Anja , Heß Felix , Becker Kerstin , Köhrer Karl , Kaiser Jesko , Gohlke Holger , Gattermann Norbert , Hallek Michael , Herling Carmen D. , König Julian , Grimm Christina , Herwig Ralf , Zarnack Kathi , Schweiger Michal R.
Published: September 2024

Mutations in splicing factor 3B subunit 1 (SF3B1) frequently occur in patients with chronic lymphocytic leukemia (CLL) and myelodysplastic syndromes (MDSs). These mutations have different effects on the disease prognosis with beneficial effect in MDS and worse prognosis in CLL patients. A full-length transcriptome approach can expand our knowledge onSF3B1mutation effects on RNA splicing and its contribution to patient survival and treatment options. We applied long-read transcriptome sequencing (LRTS) to 44 MDS and CLL patients, as well as two pairs of isogenic cell lines with and withoutSF3B1mutations, and found >60% of novel isoforms. Splicing alterations were largely shared between cancer types and specifically affected the usage of introns and 3′ splice sites. Our data highlighted a constrained window at canonical 3′ splice sites in which dynamic splice-site switches occurred inSF3B1-mutated patients. Using transcriptome-wide RNA-binding maps and molecular dynamics simulations, we showed multimodal SF3B1 binding at 3′ splice sites and predicted reduced RNA binding at the second binding pocket of SF3B1K700E. Our work presents the hitherto most-complete LRTS study of theSF3B1mutation in CLL and MDS and provides a resource to study aberrant splicing in cancer. Moreover, we showed that different disease prognosises result most likely from the different cell types expanded during carcinogenesis rather than different mechanisms of action of the mutated SF3B1. These results have important implications for understanding the role ofSF3B1mutations in hematological malignancies and other related diseases.
Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing
Authors: Gocuk Sena A. , Lancaster James , Su Shian , Jolly Jasleen K. , Edwards Thomas L. , Hickey Doron G. , Ritchie Matthew E. , Blewitt Marnie E. , Ayton Lauren N. , Gouil Quentin
Published: September 2024

X-linked genetic disorders typically affect females less severely than males owing to the presence of a second X Chromosome not carrying the deleterious variant. However, the phenotypic expression in females is highly variable, which may be explained by an allelic skew in X-Chromosome inactivation. Accurate measurement of X inactivation skew is crucial to understand and predict disease phenotype in carrier females, with prediction especially relevant for degenerative conditions. We propose a novel approach using nanopore sequencing to quantify skewed X inactivation accurately. By phasing sequence variants and methylation patterns, this single assay reveals the disease variant, X inactivation skew, and its directionality and is applicable to all patients and X-linked variants. Enrichment of X Chromosome reads through adaptive sampling enhances cost-efficiency. Our study includes a cohort of 16 X-linked variant carrier females affected by two X-linked inherited retinal diseases: choroideremia andRPGR-associated retinitis pigmentosa. As retinal DNA cannot be readily obtained, we instead determine the skew from peripheral samples (blood, saliva, and buccal mucosa) and correlate it to phenotypic outcomes. This reveals a strong correlation between X inactivation skew and disease presentation, confirming the value in performing this assay and its potential as a way to prioritize patients for early intervention, such as gene therapy currently in clinical trials for these conditions. Our method of assessing skewed X inactivation is applicable to all long-read genomic data sets, providing insights into disease risk and severity and aiding in the development of individualized strategies for X-linked variant carrier females.
Imaging Neural Activity in Intact, SemirestrainedDrosophilaLarvae
Authors: Vasudevan Deeptha , Wreden Chris C. , Heckscher Ellie S.
Published: September 2024

TheDrosophilalarval nerve cord, which is the equivalent of the vertebrate spinal cord, houses the circuits required to process somatosensory stimuli (e.g., tactile, temperature, vibration, and self-movement) and generate the patterned muscle contractions underlying movement and behavior. Within this complex structure reside many cell types and cellular processes, making it difficult to experimentally access, when compared to peripheral parts of the nervous system (i.e., primary sensory neuron dendrites, motor neuron axons and synapses, and muscles). Additionally, the neurons in the larval nerve cord have small cell bodies, precluding traditional electrophysiological approaches. As such, the function of neurons in the nerve cord is less well studied than other parts of the nervous system, severely limiting our understanding of how larvae process sensory information and generate movement. Ca2+-sensitive fluorescent proteins enable the study of neuronal activity in live, genetically tractable animals, even those with small neuronal cell bodies. In addition, live imaging of neurons within the nerve cord in whole, intact animals is possible because larvae are translucent, and the use of intact animals allows for the peripheral sensory neuron circuits to remain intact. Ca2+-sensitive fluorescent proteins increase their fluorescence when voltage-gated Ca2+channels are opened in depolarized neurons. Here, we describe an assay where a Ca2+-sensitive fluorescent protein (GCaMP6m) is expressed under the control of a GAL4 driver in a subset of neurons that reside in a circuit for vibration sensation. External vibration (sound) stimulates sensory neurons that activate the cells expressing the Ca2+-sensitive fluorescent protein. Visualization of the calcium-induced fluorescent signal with microscopy allows for quantification of neuronal activity.