bluuebunny/crossref_metadata_2025 huggingface dataset:
Making the case for an International Decade of Radiocarbon
Authors: Eglinton Timothy I. , Graven Heather D. , Raymond Peter A. , Trumbore Susan E. , Aluwihare Lihini , Bard Edouard , Basu Sourish , Friedlingstein Pierre , Hammer Samuel , Lester Joanna , Sanderman Jonathan , Schuur Edward A. G. , Sierra Carlos A. , Synal Hans-Arno , Turnbull Jocelyn C. , Wacker Lukas
Published: October 2023

Radiocarbon (
14
C) is a critical tool for understanding the global carbon cycle. During the Anthropocene, two new processes influenced
14
C in atmospheric, land and ocean carbon reservoirs. First,
14
C-free carbon derived from fossil fuel burning has diluted
14
C, at rates that have accelerated with time. Second, ‘bomb’
14
C produced by atmospheric nuclear weapon tests in the mid-twentieth century provided a global isotope tracer that is used to constrain rates of air–sea gas exchange, carbon turnover, large-scale atmospheric and ocean transport, and other key C cycle processes. As we write, the
14
C/
12
C ratio of atmospheric CO
2
is dropping below pre-industrial levels, and the rate of decline in the future will depend on global fossil fuel use and net exchange of bomb
14
C between the atmosphere, ocean and land. This milestone coincides with a rapid increase in
14
C measurement capacity worldwide. Leveraging future
14
C measurements to understand processes and test models requires coordinated international effort—a ‘decade of radiocarbon’ with multiple goals: (i) filling observational gaps using archives, (ii) building and sustaining observation networks to increase measurement density across carbon reservoirs, (iii) developing databases, synthesis and modelling tools and (iv) establishing metrics for identifying and verifying changes in carbon sources and sinks.

This article is part of the Theo Murphy meeting issue 'Radiocarbon in the Anthropocene'.
Ontogeny drives shifts in skin bacterial communities in facultatively paedomorphic salamanders
Authors: Hartmann Arik M. , McGrath-Blaser Sarah E. , Colón-Piñeiro Zuania , Longo Ana V.
Published: October 2023

Microbiomes are major determinants of host growth, development and survival. In amphibians, host-associated bacteria in the skin can inhibit pathogen infection, but many processes can influence the structure and composition of the community. Here we quantified the shifts in skin-associated bacteria across developmental stages in the striped newt (Notophthalmus perstriatus), a threatened salamander species with a complex life history and vulnerable to infection by the amphibian chytrid fungus Batrachochytrium dendrobatidis and ranavirus. Our analyses show that pre-metamorphic larval and paedomorphic stages share similar bacterial compositions, and that the changes in the microbiome coincided with physiological restructuring during metamorphosis. Newts undergoing metamorphosis exhibited microbiome compositions that were intermediate between paedomorphic and post-metamorphic stages, further supporting the idea that metamorphosis is a major driver of host-associated microbes in amphibians. We did not find support for infection-related disruption of the microbiome, though infection replicates were small for each respective life stage.
Warming and altered precipitation independently and interactively suppress alpine soil microbial growth in a decadal-long experiment
Authors: Ruan Yang , Ling Ning , Jiang Shengjing , Jing Xin , He Jin-Sheng , Shen Qirong , Nan Zhibiao
Published: October 2023

Warming and precipitation anomalies affect terrestrial carbon balance partly through altering microbial eco-physiological processes (e.g., growth and death) in soil. However, little is known about how such processes responds to simultaneous regime shifts in temperature and precipitation. We used the18O-water quantitative stable isotope probing approach to estimate bacterial growth in alpine meadow soils of the Tibetan Plateau after a decade of warming and altered precipitation manipulation. Our results showed that the growth of major taxa was suppressed by the single and combined effects of temperature and precipitation, eliciting 40-90% of growth reduction of whole community. The antagonistic interactions of warming and altered precipitation on population growth were common (~70% taxa), represented by the weak antagonistic interactions of warming and drought, and the neutralizing effects of warming and wet. The members inSolirubrobacterandPseudonocardiagenera had high growth rates under changed climate regimes. These results are important to understand and predict the soil microbial dynamics in alpine meadow ecosystems suffering from multiple climate change factors.
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

The 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

The 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

Cancer 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

Despite 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

The 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.

Teaser

Zaxinone 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

Here, 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

The 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.
Sliding windows analysis can undo the effects of preprocessing when applied to fMRI data
Authors: Lindquist Martin A
Published: October 2023

Resting-state fMRI (rs-fMRI) data is used to study the intrinsic functional connectivity (FC) in the human brain. In the past decade, interest has focused on studying the temporal dynamics of FC on short timescales, ranging from seconds to minutes. These studies of time-varying FC (TVFC) have enabled the classification of whole-brain dynamic FC profiles into distinct "brain states", defined as recurring whole-brain connectivity profiles reliably observed across subjects and sessions. The analysis of rs-fMRI data is complicated by the fact that the measured BOLD signal consists of changes induced by neuronal activation, as well as non-neuronal nuisance fluctuations that should be removed prior to further analysis. Thus, the data undergoes significant preprocesing prior to analysis. In previous work, we illustrated the potential pitfalls involved with using modular preprocessing pipelines, showing how later preprocessing steps can reintroduce correlation with signal previously removed from the data. Here we show that the problem runs deeper, and that certain statistical analysis techniques can potentially interact with preprocessing and reintroduce correlations with previously removed signal. One such technique is the popular sliding window analysis, used to compute TVFC. In this paper, we discuss the problem both theoretically and empirically in application to test-retest rs-fMRI data. Importantly, we show that we are able to obtain essentially the same brain states and state transitions when analyzing motion induced signal as we do when analyzing the preprocessed but windowed data. Our results cast doubt on whether the estimated brain states obtained using sliding window analysis are neuronal in nature, or simply reflect non-neuronal nuisance signal variation (e.g., motion).
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

Genetic 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

The 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

Social 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

The 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

Background

Mortality 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.

Methods

We 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.

Results

Overall, 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).

Conclusions

Whole 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

T 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.
A translation proofreader of archaeal origin imparts multialdehyde stress tolerance to land plants
Authors: Kumar Pradeep , Roy Ankit , Mukul Shivapura Jagadeesha , Singh Avinash Kumar , Singh Dipesh Kumar , Nalli Aswan , Banerjee Pujaita , Babu Kandhalu Sagadevan Dinesh , Raman Bakthisaran , Kruparani Shobha P. , Siddiqi Imran , Sankaranarayanan Rajan
Published: October 2023

Aldehydes, being an integral part of carbon metabolism, energy generation and signalling pathways, are ingrained in plant physiology. Land plants have developed intricate metabolic pathways which involve production of reactive aldehydes and its detoxification to survive harsh terrestrial environments. Here, we show that physiologically produced aldehydes i.e., formaldehyde and methylglyoxal in addition to acetaldehyde, generate adducts with aminoacyl-tRNAs, a substrate for protein synthesis. Plants are unique in possessing two distinct chiral proofreading systems, D-aminoacyl-tRNA deacylase1 (DTD1) and DTD2, of bacterial and archaeal origins, respectively. Extensive biochemical analysis revealed that only archaeal DTD2 can remove the stable D-aminoacyl adducts on tRNA thereby shielding archaea and plants from these system-generated aldehydes. Using Arabidopsis as a model system, we have shown that the loss of DTD2 gene renders plants susceptible to these toxic aldehydes as they generate stable alkyl modification on D-aminoacyl-tRNAs, which are recycled only by DTD2. Bioinformatic analysis identifies the expansion of aldehyde metabolising repertoire in land plant ancestors which strongly correlates with the recruitment of archaeal DTD2. Finally, we demonstrate that the overexpression of DTD2 offers better protection against aldehydes than in wild-type Arabidopsis highlighting its role as a multi-aldehyde detoxifier that can be explored as a transgenic crop development strategy.
Depletion of SMN Protein in Mesenchymal Progenitors Impairs the Development of Bone and Neuromuscular Junction in Spinal Muscular Atrophy
Authors: Hann Sang-Hyeon , Kim Seon-Yong , Kim Ye Lynne , Jo Young-Woo , Kang Jong-Seol , Park Hyerim , Choi Se-Young , Kong Young-Yun
Published: October 2023

Spinal Muscular Atrophy (SMA) is a neuromuscular disorder characterized by the deficiency of the survival motor neuron (SMN) protein, which leads to motor neuron dysfunction and muscle atrophy. In addition to the requirement for SMN in motor neurons, recent studies suggest that SMN deficiency in peripheral tissues plays a key role in the pathogenesis of SMA. Using limb mesenchymal progenitor cells (MPCs)-specific SMN-depleted mouse models, we reveal that SMN reduction in chondrocytes and fibro-adipogenic progenitors (FAPs) derived from limb MPCs causes defects in the development of bone and neuromuscular junction (NMJ), respectively. We showed that impaired growth plate homeostasis, which causes skeletal growth defects in SMA, is due to reduced IGF signaling from chondrocytes rather than the liver. Furthermore, the reduction of SMN in FAPs resulted in abnormal NMJ maturation, altered release of neurotransmitters, and NMJ morphological defects. Transplantation of healthy FAPs rescued the morphological deterioration. Our findings highlight the significance of mesenchymal SMN in neuromusculoskeletal pathogenesis in SMA and provide insights into potential therapeutic strategies targeting mesenchymal cells for the treatment of SMA.
Delivery of A Jagged1-PEG-MAL hydrogel with Pediatric Human Bone Cells Regenerates Critically-Sized Craniofacial Bone Defects
Authors: Kamalakar Archana , Tobin Brendan , Kaimari Sundus , Robinson M. Hope , Toma Afra I. , Cha Timothy , Chihab Samir , Moriarity Irica , Gautam Surabhi , Bhattaram Pallavi , Abramowicz Shelly , Drissi Hicham , García Andrés J. , Wood Levi B. , Goudy Steven L.
Published: October 2023

Treatments for congenital and acquired craniofacial (CF) bone abnormalities are limited and expensive. Current reconstructive methods include surgical correction of injuries, short-term bone stabilization, and long-term use of bone grafting solutions, including implantation of (i) allografts which are prone to implant failure or infection, (ii) autografts which are limited in supply. Current bone regenerative approaches have consistently relied on BMP2 application with or without addition of stem cells. BMP2 treatment can lead to severe bony overgrowth or uncontrolled inflammation, which can accelerate further bone loss. Bone marrow-derived mesenchymal stem cell-based treatments, which do not have the side effects of BMP2, are not currently FDA approved, and are time and resource intensive. There is a critical need for novel bone regenerative therapies to treat CF bone loss that have minimal side effects, are easily available, and are affordable. In this study we investigated novel bone regenerative therapies downstream of JAGGED1 (JAG1).

We previously demonstrated that JAG1 induces murine cranial neural crest (CNC) cells towards osteoblast commitment via a NOTCH non-canonical pathway involving JAK2-STAT5 (1) and that JAG1 delivery with CNC cells elicits bone regeneration in vivo. In this study, we hypothesize that delivery of JAG1 and induction of its downstream NOTCH non-canonical signaling inpediatric human osteoblastsconstitute an effective bone regenerative treatment in an in vivo murine bone loss model of a critically-sized cranial defect. Using this CF defect model in vivo, we delivered JAG1 with pediatric human bone-derived osteoblast-like (HBO) cells to demonstrate the osteo-inductive properties of JAG1 in human cells and in vitro we utilized the HBO cells to identify the downstream non-canonical JAG1 signaling intermediates as effective bone regenerative treatments. In vitro, we identified an important mechanism by which JAG1 induces pediatric osteoblast commitment and bone formation involving the phosphorylation of p70 S6K. This discovery enables potential new treatment avenues involving the delivery of tethered JAG1 and the downstream activators of p70 S6K as powerful bone regenerative therapies in pediatric CF bone loss.
Simulating atmospheric drought: Silica gel packets dehumidify mesocosm microclimates
Authors: Varghese S. , Aguirre B.A. , Isbell F. , Wright A.J.
Published: October 2023

As global temperatures rise, droughts are becoming more frequent and severe. To predict how drought might affect plant communities, ecologists have traditionally designed experiments with controlled watering regimes and rainout shelters. Both treatments have proven effective for simulating soil drought. However, neither are designed to directly modify atmospheric drought.

Here, we detail the efficacy of a silica gel atmospheric drought treatment in outdoor mesocosms with and without a cooccurring soil drought treatment. At California State University, Los Angeles, we monitored relative humidity (RH), temperature, and vapor pressure deficit (VPD) every 10 minutes for five months in a bare-ground experiment featuring mesocosms treated with soil drought (reduced watering) and/or atmospheric drought (silica packets suspended 12 cm above soil).

We found that silica packets dehumidified these microclimates most effectively (-5% RH) when combined with reduced soil water, regardless of the ambient humidity levels of the surrounding air. Further, packets increased microclimate VPD most effectively (+0.4 kPa) when combined with reduced soil water and ambient air temperatures above 20°C. Finally, packets simulated atmospheric drought most consistently when replaced within three days of deployment.

Our results demonstrate the use of silica packets as effective dehumidification agents in outdoor drought experiments. We emphasize that incorporating atmospheric drought in existing soil drought experiments can improve our understandings of the ecological impacts of drought.
Diet and chemical defenses of the Sonoran Desert toads
Authors: Luccioni Marina D. , Wyman Jules T. , Espinoza Edgard O. , O’Connell Lauren A.
Published: October 2023

The Sonoran Desert Toad (Incilius alvarius) is the only animal known to secrete the psychedelic compound 5-MeO-DMT as a chemical defense, but the source of 5-MeO-DMT inI. alvariusremains unknown. Some amphibians endogenously produce chemical defenses while others acquire them from specialized diets. In this study we analyzed toxin gland secretions and diet profiles from wildI. alvariusand sympatric anurans from native and urban habitats around Tucson, Arizona to explore possible links between diet and 5-MeO-DMT production. AllI. alvariussecreted high concentrations of 5-MeO-DMT, whereas other sympatric toads did not. The diet ofI. alvariuswas similar to that of sympatric anurans, indicating thatI. alvariusdoes not exhibit relative dietary specialization. Slight dietary differences betweenI. alvariusin native and urbanized habitats were observed. Taken together, these lines of evidence suggest that diet is not directly linked to 5-MeO-DMT production, and support the alternative hypotheses that Sonoran Desert toads synthesize 5-MeO-DMT endogenously or via a microbial symbiont.
Mouse Model of Heart Attack and Stroke Shows Improved Survival with MPO Inhibition
Authors: Shamsuzzaman Sohel , Deaton Rebecca A. , Doviak Heather , Evans Megan A. , Salamon Anita , Karnewar Santosh , Serbulea Vlad , Alencar Gabriel F. , Shankman Laura S. , Walsh Kenneth , Bekiranov Stefan , Kocher Olivier , Krieger Monty , Kull Bengt , Persson Marie , Bergenhem Nils , Heydarkhan-Hagvall Sepideh , Owens Gary K.
Published: October 2023

Thromboembolic events, including myocardial infarction (MI) or stroke, caused by the rupture or erosion of unstable atherosclerotic plaques are the leading cause of death worldwide1. Unfortunately, the lack of a mouse model that develops advanced coronary atherosclerosis and that exhibits a high incidence of spontaneous plaque rupture with MI or stroke has greatly stymied development of more effective therapeutic approaches for reducing these events beyond what has been achieved with aggressive lipid lowering. Herein, we describe a novel mouse model that develops widespread advanced atherosclerosis including in coronary, brachiocephalic, and carotid arteries. These mice show high mortality following Western Diet feeding with clear evidence of plaque rupture, MI, and stroke. To validate the utility of this model, mice were treated with the drug candidate AZM198, which inhibits myeloperoxidase, an enzyme primarily produced by activated neutrophils and predictive of rupture of human atherosclerotic lesions2–7. AZM198 treatment resulted in marked improvements in survival with a greater than 60% decrease in the incidence of plaque rupture, MI, and stroke. In summary, our work describes a novel mouse model that closely replicates late-stage clinical events of advanced human atherosclerotic disease and evidence that this model can be used to identify and test potential new therapeutic agents to prevent major adverse cardiac events.
Unifying microorganisms and macrograzers in rocky shore ecological networks
Authors: Arboleda-Baena Clara , Pareja Claudia Belén , Poblete Javiera , Berlow Eric , Sarmento Hugo , Logares Ramiro , De la Iglesia Rodrigo , Navarrete Sergio A.
Published: October 2023

Over the past decades, our understanding of the vital role microbes play in ecosystem processes has greatly expanded. However, we still have limited knowledge about how microbial communities interact with larger organisms. Many existing representations of microbial interactions are based on co-occurrence patterns, which do not provide clear insights into trophic or non-trophic relationships. In this study, we untangled trophic and non-trophic interactions between macroscopic and microscopic organisms on a marine rocky shore. Five abundant mollusk grazers were selected, and their consumptive (grazing) and non-consumptive (grazer pedal mucus) interactions with bacteria in biofilms were measured using 16S rRNA amplicon sequencing. While no significant effects on a commonly used measure of biofilm grazing (Chlorophyll-a concentration) were observed, detailed image analysis revealed that all grazers had a detrimental impact on biofilm cover. Moreover, different grazers exhibited distinct effects on various bacterial groups. Some groups, such as Rhodobacteraceae, Saprospiraceae, Flavobacteriaceae, and Halieaceae, experienced positive effects from specific grazers, while others, like Rhizobiaceae, Rhodobacteraceae, and Flavobacteriaceae were negatively affected by certain grazers. This study presents the first attempt to construct an interaction network between macroorganisms and bacteria. It demonstrates that the strength of trophic and non-trophic interactions varies significantly depending on the mollusk grazer or bacterial group involved. Notably, certain bacterial groups exhibited a generalized response, while others showed specialized responses to specific macroorganisms in trophic or non-trophic interactions. Overall, this work highlights the potential for integrating microbes into ecological networks, providing valuable insights and methodologies for quantifying interactions across Domains. This research complements the previous ecological network, showing that mollusk grazers interact not only trophically but also non-trophically with epilithic biofilms. It identifies three drivers affecting microbial community assembly, crucial for understanding macro-microorganism dynamics in intertidal systems.
Isolating structured salient variations in single-cell transcriptomic data with StrastiveVI
Authors: Qiu Wei , Weinberger Ethan , Lee Su-In
Published: October 2023

Single-cell RNA sequencing (scRNA-seq) has provided deeper insights into biological processes by highlighting differences at the cellular level. Within these single-cell omics measurements, researchers are often interested in identifying variations associated with a specific covariate. For instance, in aging research, it becomes vital to differentiate variations related to aging. To address this, we introduce StrastiveVI (Structured Contrastive Variational Inference;https://github.com/suinleelab/StrastiveVI), which effectively separates the variations of interest from other dominant biological signals in scRNA-seq datasets. When deployed on aging and Alzheimer’s disease (AD) datasets, StrastiveVI efficiently isolates aging and AD-associated patterns, distinguishing them from dominant variations linked to sex, tissue, and cell type that are unrelated to aging or AD. In doing so, it underscores both well-known genes and potential novel genes related to aging or AD.
Modulation of Calcium Signaling and Metabolic Pathways in Endothelial Cells with Magnetic Fields
Authors: Gorobets Oksana , Gorobets Svitlana , Polyakova Tatyana , Zablotskii Vitalii
Published: October 2023

Calcium signaling plays a crucial role in various physiological processes, including muscle contraction, cell division, and neurotransmitter release. Dysregulation of calcium levels and signaling has been linked to a range of pathological conditions such as neurodegenerative disorders, cardiovascular disease, and cancer. Here, we suggest that in the endothelium, calcium ion channel activity and calcium signaling can be modulated by applying either a time-varying or static gradient magnetic field (MF). This modulation is achieved by exerting magnetic forces or torques on either biogenic or non-biogenic magnetic nanoparticles that are bound to endothelial cell membranes. Since calcium signaling in endothelial cells induces neuromodulation and influences blood flow control, treatment with a magnetic field shows promise for regulating neurovascular coupling and treating vascular dysfunctions associated with aging and neurodegenerative disorders. Furthermore, magnetic treatment can enable control over the decoding of Ca signals, ultimately impacting protein synthesis. The ability to modulate calcium wave frequencies using MFsand the MF-controlled decoding of Ca signaling present promising avenues for treating diseases characterized by calcium dysregulation.
Correlative single-molecule and structured illumination microscopy of fast dynamics at the plasma membrane
Authors: Winkelmann Hauke , Richter Christian P. , Eising Jasper , Piehler Jacob , Kurre Rainer
Published: October 2023

Total internal reflection fluorescence (TIRF) microscopy offers powerful means to uncover the functional organization of proteins in the plasma membrane with very high spatial and temporal resolution. Traditional TIRF illumination, however, shows a Gaussian intensity profile, which is typically deteriorated by overlaying interference fringes hampering precise quantification of intensities – an important requisite for quantitative analyses in single-molecule localization microscopy (SMLM). Here, we combined flat-field illumination by using a standard πShaper with multi-angular TIR illumination by incorporating a spatial light modulator compatible with fast super-resolution structured illumination microscopy (SIM). This unique combination enabled quantitative multi-color SMLM with a highly homogenous illumination. By using a dual camera setup with optimized image splitting optics, we achieved versatile combination of SMLM and SIM with up to three channels. We deployed this setup for establishing robust detection of receptor stoichiometries based on single-molecule intensity analysis and single-molecule Förster resonance energy transfer (smFRET). Homogeneous illumination furthermore enabled long-term tracking and localization microscopy (TALM) of cell surface receptors identifying spatial heterogeneity of mobility and accessibility in the plasma membrane. By combination of TALM and SIM, spatially and molecularly heterogenous diffusion properties could be correlated with nanoscale cytoskeletal organization and dynamics.