bluuebunny/crossref_metadata_2025_split huggingface dataset:
TMEM65 regulates NCLX-dependent mitochondrial calcium efflux
Authors: Garbincius Joanne F. , Salik Oniel , Cohen Henry M. , Choya-Foces Carmen , Mangold Adam S. , Makhoul Angelina D. , Schmidt Anna E. , Khalil Dima Y. , Doolittle Joshua J. , Wilkinson Anya S. , Murray Emma K. , Lazaropoulos Michael P. , Hildebrand Alycia N. , Tomar Dhanendra , Elrod John W. 
Published: October 2023

AbstractThe balance between mitochondrial calcium (mCa2+) uptake and efflux regulates ATP production, but if perturbed causes energy starvation ormCa2+overload and cell death. The mitochondrial sodium-calcium exchanger, NCLX, is a critical route ofmCa2+efflux in excitable tissues, such as the heart and brain, and animal models support NCLX as a promising therapeutic target to limit pathogenicmCa2+overload. However, the mechanisms that regulate NCLX activity remain largely unknown. We used proximity biotinylation proteomic screening to identify the NCLX interactome and define novel regulators of NCLX function. Here, we discover the mitochondrial inner membrane protein, TMEM65, as an NCLX-proximal protein that potently enhances sodium (Na+)-dependentmCa2+efflux. Mechanistically, acute pharmacologic NCLX inhibition or genetic deletion of NCLX ablates the TMEM65-dependent increase inmCa2+efflux. Further, loss-of-function studies show that TMEM65 is required for Na+-dependentmCa2+efflux. Co-fractionation andin silicostructural modeling of TMEM65 and NCLX suggest these two proteins exist in a common macromolecular complex in which TMEM65 directly stimulates NCLX function. In line with these findings, knockdown ofTmem65in mice promotesmCa2+overload in the heart and skeletal muscle and impairs both cardiac and neuromuscular function. We further demonstrate thatTMEM65deletion causes excessive mitochondrial permeability transition, whereas TMEM65 overexpression protects against necrotic cell death during cellular Ca2+stress. Collectively, our results show that loss of TMEM65 function in excitable tissue disrupts NCLX-dependentmCa2+efflux, causing pathogenicmCa2+overload, cell death and organ-level dysfunction, and that gain of TMEM65 function mitigates these effects. These findings demonstrate the essential role of TMEM65 in regulating NCLX-dependentmCa2+efflux and suggest modulation of TMEM65 as a novel strategy for the therapeutic control ofmCa2+homeostasis.
Multifunction Fluorescence Open-SourceIn Vivo/In VitroImaging System (openIVIS)
Authors: Branning John M. , Faughnan Kealy A. , Tomson Austin A. , Bell Grant J. , Isbell Sydney M. , DeGroot Allen , Jameson Lydia , Kilroy Kramer , Smith Michael , Smith Robert , Mottel Landon , Branning Elizabeth G. , Worrall Zoe , Anderson Frances , Panditaradyula Ashrit , Yang William , Abdelmalek Joseph , Brake Joshua , Cash Kevin J. 
Published: October 2023

AbstractThe widespread availability and diversity of open-source microcontrollers paired with off-the-shelf electronics and 3D printed technology has led to the creation of a wide range of low-cost scientific instruments, including microscopes, spectrometers, sensors, data loggers, and other tools that can be used for research, education, and experimentation. These devices can be used to explore a wide range of scientific topics, from biology and chemistry to physics and engineering. In this study we designed and built a multifunction fluorescent open-source in-vivo/in-vitro imaging system (openIVIS) fluorescent imaging system that integrates a Raspberry Pi with commercial cameras and LEDs with 3D printed structures combined with an acrylic housing. Our openIVIS provides three excitation wavelengths of 460 nm, 520 nm, and 630 nm integrated with Python control software to enable fluorescent measurements across the full visible light spectrum. To demonstrate the various potential applications of our system, we tested its performance against a diverse set of experiments including laboratory type assays (measuring fluorescent dyes, using optical nanosensors, and DNA gel electrophoresis) to potentially fieldable applications (plant and mineral imaging). We also tested the potential use for a high school biology environment by imaging small animals and tracking their development over the course of a couple of weeks. Our system demonstrated its ability to measure a wide dynamic range fluorescent response from millimolar to picomolar concentrations in the same sample while measuring responses across visible wavelengths. These results demonstrate the power and flexibility of open-source hardware and software and how it can be integrated with customizable manufacturing to create low-cost scientific instruments with a wide range of applications. Our study provides a promising model for the development of low-cost instruments that can be used in both research and education.
G6PD Maintains Redox Homeostasis and Biosynthesis in LKB1-Deficient KRAS-Driven Lung Cancer
Authors: Lan Taijin , Arastu Sara , Wang Samuel , Lam Jarrick , Wang Wenping , Bhatt Vrushank , Lopes Eduardo Cararo , Hu Zhixian , Sun Michael , Luo Xuefei , Ghergurovich Jonathan M. , Li Changlong , Su Xiaoyang , Rabinowitz Joshua D. , White Eileen , Guo Jessie Yanxiang 
Published: October 2023

AbstractCancer cells depend on nicotinamide adenine dinucleotide phosphate (NADPH) to combat oxidative stress and support reductive biosynthesis. One major NAPDH production route is the oxidative pentose phosphate pathway (committed step: glucose-6-phosphate dehydrogenase, G6PD). Alternatives exist and can compensate in some tumors. Here, using genetically-engineered lung cancer model, we show that ablation of G6PD significantly suppressesKrasG12D/+;Lkb1-/-(KL) but notKrasG12D/+;p53-/-(KP) lung tumorigenesis.In vivoisotope tracing and metabolomics revealed that G6PD ablation significantly impaired NADPH generation, redox balance andde novolipogenesis in KL but not KP lung tumors. Mechanistically, in KL tumors, G6PD ablation caused p53 activation that suppressed tumor growth. As tumor progressed, G6PD-deficient KL tumors increased an alternative NADPH source, serine-driven one carbon metabolism, rendering associated tumor-derived cell lines sensitive to serine/glycine depletion. Thus, oncogenic driver mutations determine lung cancer dependence on G6PD, whose targeting is a potential therapeutic strategy for tumors harboring KRAS and LKB1 co-mutations.
Nitric Oxide controls shoot meristem activity via regulation of DNA methylation
Authors: Zeng Jian , Zhao Xin’Ai , Liang Zhe , Hidalgo Inés , Gebert Michael , Fan Pengfei , Wenzl Christian , Gornik Sebastian G. , Lohmann Jan U. 
Published: October 2023

AbstractDespite the importance of Nitric Oxide (NO) as signaling molecule in both plant and animal development1–7, the regulatory mechanisms downstream of NO remain largely unclear. Here, we show that NO is involved inArabidopsisshoot stem cell control via modifying expression and activity ofARGONAUTE 4(AGO4), a core component of the RNA directed DNA Methylation (RdDM) pathway. Mutations in components of the RdDM pathway cause meristematic defects, and reduce responses of the stem cell system to NO signaling. Importantly, we found that the stem cell inducing WUSCHEL transcription factor directly interacts with AGO4 in an NO dependent manner, explaining how these two signaling systems may converge to modify DNA methylation patterns. Taken together, our results reveal that NO signaling plays an important role in controlling plant stem cell homeostasis via the regulation ofde novoDNA methylation.
Zaxinone Synthaseoverexpression modulates rice physiology and metabolism, improving growth and productivity under normal and low phosphate supply
Authors: Ablazov Abdugaffor , Jamil Muhammad , Haider Imran , Wang Jian You , Melino Vanessa , Maghrebi Moez , Vigani Gianpiero , Liew Kit Xi , Lin Pei-Yu , Chen Guan-Ting , Kuijer Hendrik NJ , Berqdar Lamis , Mazzarella Teresa , Fiorilli Valentina , Lanfranco Luisa , Zheng Xiongjie , Dai Nai-Chiang , Lai Ming-Hsin , Hsing Yue-Ie Caroline , Tester Mark , Blilou Ikram , Al-Babili Salim 
Published: October 2023

AbstractThe riceZaxinone Synthase (ZAS)gene encodes a carotenoid cleavage dioxygenase (CCD) that forms the apocarotenoid growth regulator zaxinone. Here, we generated and characterized constitutiveZAS-overexpressing rice lines, to better understandZASrole in determining zaxinone content and regulating growth and architecture.ZASoverexpression enhanced endogenous zaxinone level, promoted root growth and meristem size, and increased the number of productive tillers, leading to an up to 30% higher grain yield per plant. Hormone analysis revealed a decrease in strigolactone (SL) content, which we confirmed by rescuing the high-tillering phenotype through application of a SL analog. Metabolomics analysis revealed thatZASoverexpressing plants accumulate higher amounts of monosaccharide sugars, in line with transcriptome analysis. Moreover, transgenic plants showed higher carbon (C) assimilation rate and elevated root phosphate, nitrate and sulfate level, enhancing the tolerance towards low phosphate (Pi) and indicating a generally better nutrient uptake. Our study shows thatZASregulates hormone homeostasis and a combination of physiological processes to promote growth and grain yield, which makes this gene an excellent candidate for sustainable crop improvement.TeaserZaxinone Synthaseoverexpression modulates rice metabolism and physiology and improves growth and phosphate uptake.
REM-like Oscillatory Theta Activity Predicts a Reduction in the Recuperative Value of Natural Human Sleep
Authors: Vattikuti Shashaank , Doty Tracy J , Riedy Samantha , Braun Allen , Balkin Thomas J , Hughes John D 
Published: October 2023

AbstractHere, using data from two independent studies, we examine whether all of sleep is restorative or paradoxically whether some sleep processes incur a sleep debt that impacts next-day wakefulness. Specifically, we examine whether rapid eye movement (REM) sleep is such a process due to its similarity to wake activity, which is causal for sleep debt. To investigate this, we first develop a novel measure of REM neural activity (REM-like oscillatory theta activity (OTA)), overcoming limitations of current sleep scoring. We find that naturally occurring average REM-like OTA across individuals: 1) is associated with increased neurobehavioral sleep debt; 2) explains 25-38% (p ≤ 0.001) of sleep debt differences across individuals the following day; 3) occurs throughout sleep to various degrees, contrary to current sleep scoring; and 4) can be measured automatically, without cumbersome manual scoring.
Dopamine lesions alter the striatal encoding of single-limb gait
Authors: Yang Long , Singla Deepak , Wu Alexander K. , Cross Katy A. , Masmanidis Sotiris C. 
Published: October 2023

ABSTRACTThe striatum an important role in motor control, and neurons in this area encode the body’s initiation, cessation, and speed of locomotion. However, it remains unclear whether the same neurons also encode the step-by-step rhythmic motor patterns of individual limbs that characterize gait. By combining high-speed video tracking, electrophysiology, and optogenetic tagging, we found that a sizable population of both D1 and D2 receptor expressing medium spiny projection neurons (MSNs) were phase-locked to the gait cycle of individual limbs in mice. Healthy animals showed balanced limb phase-locking between D1 and D2 MSNs, while dopamine depletion led to stronger phase-locking in D2 MSNs. These findings indicate that striatal neurons represent gait on a single-limb and step basis, and suggest that elevated limb phase-locking of D2 MSNs may underlie some of the gait impairments associated with dopamine loss.
The response of Dual-leucine zipper kinase (DLK) to nocodazole: evidence for a homeostatic cytoskeletal repair mechanism
Authors: DeVault Laura , Mateusiak Chase , Palucki John , Brent Michael , Milbrandt Jeffrey , DiAntonio Aaron 
Published: October 2023

AbstractGenetic and pharmacological perturbation of the cytoskeleton enhances the regenerative potential of neurons. This response requires Dual-leucine Zipper Kinase (DLK), a neuronal stress sensor that is a central regulator of axon regeneration and degeneration. The damage and repair aspects of this response are reminiscent of other cellular homeostatic systems, suggesting that a cytoskeletal homeostatic response exists. In this study, we propose a framework for understanding DLK mediated neuronal cytoskeletal homeostasis. We demonstrate that a) low dose nocodazole treatment activates DLK signaling and b) DLK signaling mitigates the microtubule damage caused by the cytoskeletal perturbation. We also perform RNA-seq to discover a DLK-dependent transcriptional signature. This signature includes genes likely to attenuate DLK signaling while simultaneously inducing actin regulating genes and promoting actin-based morphological changes to the axon. These results are consistent with the model that cytoskeletal disruption in the neuron induces a DLK-dependent homeostatic mechanism, which we term the Cytoskeletal Stress Response (CSR) pathway.
Joint sequence & chromatin neural networks characterize the differential abilities of Forkhead transcription factors to engage inaccessible chromatin
Authors: Arora Sonny , Yang Jianyu , Akiyama Tomohiko , James Daniela Q. , Morrissey Alexis , Blanda Thomas R. , Badjatia Nitika , Lai William K.M. , Ko Minoru S.H. , Pugh B. Franklin , Mahony Shaun 
Published: October 2023

ABSTRACTThe DNA-binding activities of transcription factors (TFs) are influenced by both intrinsic sequence preferences and extrinsic interactions with cell-specific chromatin landscapes and other regulatory proteins. Disentangling the roles of these binding determinants remains challenging. For example, the FoxA subfamily of Forkhead domain (Fox) TFs are known pioneer factors that can bind to relatively inaccessible sites during development. Yet FoxA TF binding also varies across cell types, pointing to a combination of intrinsic and extrinsic forces guiding their binding. While other Forkhead domain TFs are often assumed to have pioneering abilities, how sequence and chromatin features influence the binding of related Fox TFs has not been systematically characterized.Here, we present a principled approach to compare the relative contributions of intrinsic DNA sequence preference and cell-specific chromatin environments to a TF’s DNA-binding activities. We apply our approach to investigate how a selection of Fox TFs (FoxA1, FoxC1, FoxG1, FoxL2, and FoxP3) vary in their binding specificity. We over-express the selected Fox TFs in mouse embryonic stem cells, which offer a platform to contrast each TF’s binding activity within the same preexisting chromatin background. By applying a convolutional neural network to interpret the Fox TF binding patterns, we evaluate how sequence and preexisting chromatin features jointly contribute to induced TF binding.We demonstrate that Fox TFs bind different DNA targets, and drive differential gene expression patterns, even when induced in identical chromatin settings. Despite the association between Forkhead domains and pioneering activities, the selected Fox TFs display a wide range of affinities for preexiting chromatin states. Using sequence and chromatin feature attribution techniques to interpret the neural network predictions, we show that differential sequence preferences combined with differential abilities to engage relatively inaccessible chromatin together explain Fox TF binding patterns at individual sites and genome-wide.
FARESHARE: An Open-source Apparatus for Assessing Drinking Microstructure in Socially Housed Rats
Authors: Frie Jude A. , Khokhar Jibran Y. 
Published: October 2023

AbstractSocial factors have been shown to play a significant and lasting role in alcohol consumption. Studying the role of social context on alcohol drinking is important to understand the factors that contribute to initiation or maintenance of casual and problematic alcohol use, as well as those that may be protective. A substantial body of preclinical research has shown that social environment such as housing conditions and social rank plays an important role in alcohol consumption and preference, though the extent of these effects have been obfuscated by methodological differences and technical challenges. Robust individual differences in alcohol intake in socially housed animals are difficult to track when animals share a common fluid source. Commercial solutions are prohibitively expensive and are limited by proprietary software and hardware (including caging systems). Here we describe an affordable, open-source solution for tracking fluid consumption in socially housed rats.
Distinct subpopulations of ventral pallidal cholinergic projection neurons encode valence of olfactory stimuli
Authors: Kim Ronald , Ananth Mala , Desai Niraj S. , Role Lorna W. , Talmage David A. 
Published: October 2023

AbstractThe ventral pallidum (VP) mediates motivated behaviors largely via the action of VP GABA and glutamatergic neurons. In addition to these neuronal subtypes, there is a population of cholinergic projection neurons in the VP, whose functional significance remains unclear. To understand the functional role of VP cholinergic neurons, we first examined behavioral responses to an appetitive (APP) odor that elicited approach, and an aversive (AV) odor that led to avoidance. To examine how VP cholinergic neurons were engaged in APP vs. AV responses, we used an immediate early gene marker and in-vivo fiber photometry, examining the activation profile of VP cholinergic neurons in response to each odor. Exposure to each odor led to an increase in the number of cFos counts and increased calcium signaling of VP cholinergic neurons. Activity and cre-dependent viral vectors were designed to label engaged VP cholinergic neurons in two distinct contexts: (1) exposure to the APP odor, (2) followed by subsequent exposure to the AV odor, and vice versa. These studies revealed two distinct, non-overlapping subpopulations of VP cholinergic neurons: one activated in response to the APP odor, and a second distinct population activated in response to the AV odor. These two subpopulations of VP cholinergic neurons are spatially intermingled within the VP, but show differences in electrophysiological properties, neuronal morphology, and projections to the basolateral amygdala. Although VP cholinergic neurons are engaged in behavioral responses to each odor, VP cholinergic signaling is only required for approach behavior. Indeed, inhibition of VP cholinergic neurons not only blocks approach to the APP odor, but reverses the behavior, leading to active avoidance. Our results highlight the functional heterogeneity of cholinergic projection neurons within the VP. These two subpopulations of VP cholinergic neurons differentially encode valence of olfactory stimuli and play unique roles in approach and avoidance behaviors.
Whole blood transcriptional profiles and the pathogenesis of tuberculous meningitis
Authors: Hai Hoang Thanh , Nhat Le Thanh Hoang , Tram Trinh Thi Bich , Vinh Do Dinh , Nath Artika P , Donovan Joseph , Thu Nguyen Thi Anh , Van Thanh Dang , Bang Nguyen Duc , Ha Dang Thi Minh , Phu Nguyen Hoan , Nghia Ho Dang Trung , Van Le Hong , Inouye Michael , Thwaites Guy E , Thuong Nguyen Thuy Thuong 
Published: October 2023

AbstractBackgroundMortality and morbidity from tuberculous meningitis (TBM) are frequent and strongly associated with the inflammatory response toMycobacterium tuberculosisinfection. However, the mechanisms driving the associations are uncertain. We sought to identify the gene modules, hubs and pathways associated with the pathogenesis and mortality from TBM, and to identify which best-predicted death.MethodsWe used whole blood RNA sequencing to obtain transcriptional profiles from 281 Vietnamese adults with TBM (207 HIV-negative; 74 HIV-positive), 295 with pulmonary TB (PTB), and 30 healthy controls. The TBM cohort was divided randomly into a discovery cohort (n=142) and a validation cohort (n=139). Weighted gene co-expression network analysis identified clusters of genes (or ‘modules’) and hub genes associated with death or disease severity. An overrepresentation analysis identified pathways associated with TBM mortality, with a consensus analysis identifying consensual patterns between HIV-positive and HIV-negative individuals. A multivariate elastic-net Cox regression model selected the candidate predictors of TBM mortality, then model prediction performance using logistic regression and internal bootstrap validation to choose best predictors.ResultsOverall, TBM mortality was associated with increased neutrophil activation and decreased T and B cell activation pathways. Death from TBM was associated with increased angiogenesis in HIV-positive adults, and with activated TNF signaling and down-regulated extracellular matrix organization in HIV-negative adults. PTB and TBM have similar transcriptional profiles compared to healthy controls, although inflammatory genes were more activated in HIV-positive than HIV-negative TBM. The expression of four hub genes –MCEMP1,NELL2,ZNF354CandCD4– were strongly predictive of death from TBM (AUC 0.80 and 0.86 for HIV-negative and HIV-positive, respectively).ConclusionsWhole blood transcriptional profiling revealed that TBM is associated with a characteristic systemic inflammatory response, similar to that invoked by pulmonary tuberculosis, but with key gene modules, hubs and pathways strongly associated with death. Our analysis suggests a novel 4-gene biomarker for predicting death from TBM, but also opens a new window into TBM pathogenesis that may reveal novel therapeutic targets for this lethal disease.
Time- and lineage-resolved transcriptional profiling uncovers gene expression programs and clonal relationships that underlie human T lineage specification
Authors: Michaels Yale S. , Major Matthew C. , Bonham-Carter Becca , Zhang Jingqi , Heydari Tiam , Edgar John M. , Greenstreet Laura , Vilarrasa-Blasi Roser , Kim Seungjoon , Castle Elizabeth L. , Forrow Aden , Ibanez-Rios M Iliana , Zimmerman Carla , Chung Yvonne , Stach Tara , Werschler Nico , Knapp David JHF , Vento-Tormo Roser , Schiebinger Geoffrey , Zandstra Peter W. 
Published: October 2023

AbstractT cells develop from multi-potent hematopoietic progenitors in the thymus and provide adaptive protection against pathogens and cancer. However, the emergence of human T cell-competent blood progenitors, and their subsequent specification to the T lineage, has been challenging to capture in real time. Here, we leveraged a pluripotent stem cell differentiation system to understand the transcriptional dynamics and cell fate restriction events that underlie this critical developmental process. Time-resolved single cell RNA sequencing revealed that cell-cycle exit, downregulation of the multipotent hematopoietic program, and upregulation of >90 lineage-associated transcription factors all occur within a highly co-ordinated and narrow developmental window. Computational gene-regulatory network inference elucidated the transcriptional logic of T lineage specification, uncovering an important role for YBX1. We mapped the differentiation cell fate hierarchy using transcribed lineage barcoding and mathematical trajectory inference and discovered that mast and myeloid potential bifurcate from each other early in haematopoiesis, upstream of T lineage restriction. Collectively, our analyses provide a quantitative, time-resolved model of human T cell specification with relevance for regenerative medicine and developmental immunology.