bluuebunny/crossref_metadata_2025_split huggingface dataset:
MPK4 mediated phosphorylation of PIF4 controls thermosensing by regulation of H2A.Z deposition in Arabidopsis
Authors: Verma Neetu , Singh Dhanraj , Mittal Lavanya , Banerjee Gopal , Noryang Stanzin , Sinha Alok Krishna 
Published: July 2023

AbstractPlants have the ability to perceive a slight upsurge in ambient temperature and respond by undergoing morphological changes, such as elongated hypocotyls and early flowering. The dynamic functioning of PHYTOCHROME INTERACTING FACTOR4 (PIF4) in thermomorphogenesis has been well established, although the regulatory pathway involved in thermosensing is not deciphered completely. In our study, we demonstrate that an increase in temperature from 22℃ to 28℃ induces the phosphorylation of PIF4 by MITOGEN-ACTIVATED PROTEIN KINASE 4 (MPK4) which shows high expression and activation at 28℃. Apparently, phosphorylated PIF4 represses the expression ofACTIN-RELATED PROTEIN 6(ARP6) that is required for mediating histone variant H2A.Z deposition at its target gene loci. We demonstrate that variation ofARP6expression in PIF4 phosphor -null and phosphor-mimetic seedlings affects hypocotyl growth and flowering at 22℃ and 28℃. Further, we show that change inARP6expression affects H2A.Z deposition at the loci of genes involved in hypocotyl elongation using PIF4 phosphor -null and phosphor-mimetic seedlings. Interestingly, the expression ofMPK4is also controlled by H2A.Z deposition in temperature dependent manner. Taken together, our findings highlight the cumulative molecular interplay between MPK4, PIF4, and chromatin modification by ARP6-mediated H2A.Z deposition as a regulatory mechanism of thermosensing.
Vascularized Brain Assembloids with Enhanced Cellular Complexity Provide Insights into The Cellular Deficits of Tauopathy
Authors: Kofman Simeon , Sun Xiaohuan , Ogbolu Victor C. , Ibric Larisa , Qiang Liang 
Published: July 2023

AbstractAdvanced technologies have enabled the engineering of self-organized 3-dimensional (3D) cellular structures from human induced pluripotent stem cells (hiPSCs), namely organoids, which recapitulate some key features of tissue development and functions of the human central nervous system (CNS). While hiPSC-derived 3D CNS organoids hold promise in providing a human-specific platform for studying CNS development and diseases, most of them do not incorporate the full range of implicated cell types, including vascular cell components and microglia, limiting their ability to accurately recreate the CNS environment and their utility in the study of certain aspects of the disease. Here we’ve developed a novel approach, called vascularized brain assembloids, for constructing hiPSC-derived 3D CNS structures with a higher level of cellular complexity. This is achieved by integrating forebrain organoids with common myeloid progenitors and phenotypically stabilized human umbilical vein endothelial cells (VeraVecs™), which can be cultured and expanded in serum-free conditions. Compared with organoids, these assembloids exhibited enhanced neuroepithelial proliferation, advanced astrocytic maturation, and increased synapse numbers. Strikingly, the assembloids derived from hiPSCs harboring the tauP301Smutation exhibited increased levels of total tau and phosphorylated tau, along with a higher proportion of rod-like microglia-like cells and enhanced astrocytic activation, when compared to the assembloids derived from isogenic hiPSCs. Additionally, they showed an altered profile of neuroinflammatory cytokines. This innovative assembloid technology serves as a compelling proof-of-concept model, opening new avenues for unraveling the intricate complexities of the human brain and accelerating progress in the development of effective treatments for neurological disorders.Significance StatementModeling neurodegeneration in humanin vitrosystems has proved challenging and requires innovative tissue engineering techniques to create systems that can accurately capture the physiological features of the CNS to enable the study of disease processes. The authors develop a novel assembloid model which integrates neuroectodermal cells with endothelial cells and microglia, two critical cell types that are commonly missing from traditional organoid models. They then apply this model to investigate early manifestations of pathology in the context of tauopathy and uncover early astrocyte and microglia reactivity as a result of the tauP301Smutation.
PAK3 downregulation induces cognitive impairment following cranial irradiation
Authors: Lee Haksoo , Kang Hyunkoo , Moon Changjong , Youn BuHyun 
Published: July 2023

AbstractCranial irradiation is used for prophylactic brain radiotherapy as well as treatment of primary brain tumors. Despite its high efficiency, it often induces unexpected side effects, including cognitive dysfunction. Herein, we observed that mice exposed to cranial irradiation exhibited cognitive dysfunction, including altered spontaneous behavior, decreased spatial memory, and reduced novel object recognition. Analysis of actin cytoskeleton revealed that ionizing radiation (IR) disrupted the filamentous/globular actin (F/G-actin) ratio and downregulated the actin turnover signaling pathway p21-activated kinase 3 (PAK3)-LIM kinase 1 (LIMK1)-cofilin. Furthermore, we found that IR could upregulate microRNA-206-3p (miR-206-3p) targeting PAK3. As the inhibition of miR-206-3p through antagonist (antagomiR), IR-induced disruption of PAK3 signaling is restored. In addition, intranasal administration of antagomiR-206-3p recovered IR-induced cognitive impairment in mice. Our results suggest that cranial irradiation-induced cognitive impairment could be ameliorated by regulating PAK3 through antagomiR-206-3p, thereby affording a promising strategy for protecting cognitive function during cranial irradiation, and promoting quality of life in patients with radiation therapy.
From the shallows to the depths: A new probe set to target ultraconserved elements for Malacostraca
Authors: Geburzi Jonas C. , Rodríguez-Flores Paula C. , Derkarabetian Shahan , Giribet Gonzalo 
Published: July 2023

AbstractSince its introduction about a decade ago, target enrichment sequencing of ultraconserved elements (UCEs) has proven to be an invaluable tool for studies across evolutionary scales, and thus employed from population genetics, to historical biogeography and deep phylogenetics. UCE probe sets are available for an increasing range of major taxonomic groups, including cnidarians, vertebrates, terrestrial arthropods, and mollusks. Here, we present the first probe set targeting UCEs in crustaceans, specifically designed for decapods and other malacostracan lineages. Probes were designed using published genomes of nine decapod and one peracarid species, as well as raw Nanopore long reads of one additional brachyuran species. The final probe set consists of about 20,000 probes, targeting 1,348 unique UCE loci. Preliminary analyses of UCE data obtained from an intertidal mangrove crab, and from deep-sea squat lobsters indicate high UCE recovery rates (about 1,000 loci per sample) in evolutionarily shallow datasets. To test the probe set at deeper phylogenetic levels, we compiled a dataset across Malacostraca (including representatives of Decapoda, Peracarida, Euphausiacea, Stomatopoda, and Phyllocarida), and were able to recover hundreds of UCEs for the non-decapod species, expanding the targeted use of this UCE probeset to all Malacostraca. Additionally, we recovered similar numbers of UCEs from historical museum specimens up to > 150 years old, that were included in all datasets, confirming that UCEs are a fruitful technique for leveraging museum specimens for genomic studies. Overall, our results highlight the versatility of this UCE probe set and its high potential for crustacean evolutionary studies.
Predictors of mortality among low birth weight neonates after hospital discharge in a low-resource setting: A case study in Uganda
Authors: Nsubuga Ronald , Rujumba Joseph , Nyende Saleh , Kisaka Stevens , Idro Richard , Nankunda Jolly 
Published: July 2023

AbstractBackgroundMost neonatal deaths occur among low birth weight infants. However, in resource-limited settings, these infants are commonly discharged early which further exposes them to mortality. Previous studies on morbidity and mortality among low birth weight infants after early discharge mainly focused on very low birth weight infants, and none described post-discharge neonatal mortality. This study aimed to determine the proportion and predictors of mortality among low birth weight neonates discharged from the Special Care Baby Unit at Mulago National Referral Hospital in Uganda.MethodsThis was a prospective cohort study of 220 low birth weight neonates discharged from the Special Care Baby Unit at Mulago National Referral Hospital. These were followed up to 28 completed days of life, or death, whichever occurred first. Proportions were used to express mortality. To determine the predictors of mortality, Cox hazards regression was performed.ResultsOf the 220 enrolled participants, 216 (98.1%) completed the follow-up. The mean gestational age of study participants was 34 ±3 weeks. The median weight at discharge was 1,650g (IQR: 1,315g -1,922g) and 46.1% were small for gestational age. During follow-up, 14/216 (6.5%) of neonates died. Mortality was highest (7/34, 20.6%) among neonates with discharge weights less than 1,200g. The causes of death included presumed neonatal sepsis (10/14, 71.4%), suspected aspiration pneumonia (2/14, 14.3%), and suspected cot death (2/14, 14.3%). The median time to death after discharge was 11 days (range 3-16 days). The predictors of mortality were a discharge weight of less than 1,200g (adj HR: 23.47,p<0.001), a 5-minute Apgar score of less than 7 (adj HR: 4.25,p= 0.016), and a diagnosis of neonatal sepsis during admission (adj HR: 7.93,p =0.009).ConclusionPost-discharge mortality among low birth weight neonates at Mulago National Referral Hospital is high. A discharge weight of less than 1,200g may be considered unsafe among neonates. Caregiver education about neonatal danger signs, and measures to prevent sepsis, aspiration, and cot death should be emphasized before discharge and during follow-up visits.
Small extracellular vesicles promote stiffness-mediated metastasis
Authors: Sneider Alexandra , Liu Ying , Starich Bartholomew , Du Wenxuan , Marar Carolyn , Faqih Najwa , Ciotti Gabrielle E. , Kim Joo Ho , Krishnan Sejal , Ibrahim Salma , Igboko Muna , Locke Alexus , Lewis Daniel M. , Hong Hanna , Karl Michelle , Vij Raghav , Russo Gabriella C. , Nair Praful , Gómez-de-Mariscal Estibaliz , Habibi Mehran , Muñoz-Barrutia Arrate , Gu Luo , Eisinger-Mathason T.S. Karin , Wirtz Denis 
Published: July 2023

SummaryTissue stiffness is a critical prognostic factor in breast cancer and is associated with metastatic progression. Here we show an alternative and complementary hypothesis of tumor progression whereby physiological matrix stiffness affects the quantity and protein cargo of small EVs produced by cancer cells, which in turn drive their metastasis. Primary patient breast tissue produces significantly more EVs from stiff tumor tissue than soft tumor adjacent tissue. EVs released by cancer cells on matrices that model human breast tumors (25 kPa; stiff EVs) feature increased adhesion molecule presentation (ITGα2β1, ITGα6β4, ITGα6β1, CD44) compared to EVs from softer normal tissue (0.5 kPa; soft EVs), which facilitates their binding to extracellular matrix (ECM) protein collagen IV, and a 3-fold increase in homing ability to distant organs in mice. In a zebrafish xenograft model, stiff EVs aid cancer cell dissemination through enhanced chemotaxis. Moreover, normal, resident lung fibroblasts treated with stiff and soft EVs change their gene expression profiles to adopt a cancer associated fibroblast (CAF) phenotype. These findings show that EV quantity, cargo, and function depend heavily on the mechanical properties of the extracellular microenvironment.Graphical Abstract
Configurational entropy is an intrinsic driver of tissue structural heterogeneity
Authors: Srivastava Vasudha , Hu Jennifer L. , Garbe James C. , Veytsman Boris , Shalabi Sundus F. , Yllanes David , Thomson Matt , LaBarge Mark A. , Huber Greg , Gartner Zev J. 
Published: July 2023

SUMMARYTissues comprise ordered arrangements of cells that can be surprisingly disordered in their details. How the properties of single cells and their microenvironment contribute to the balance between order and disorder at the tissue-scale remains poorly understood. Here, we address this question using the self-organization of human mammary organoids as a model. We find that organoids behave like a dynamic structural ensemble at the steady state. We apply a maximum entropy formalism to derive the ensemble distribution from three measurable parameters – the degeneracy of structural states, interfacial energy, and tissue activity (the energy associated with positional fluctuations). We link these parameters with the molecular and microenvironmental factors that control them to precisely engineer the ensemble across multiple conditions. Our analysis reveals that the entropy associated with structural degeneracy sets a theoretical limit to tissue order and provides new insight for tissue engineering, development, and our understanding of disease progression.
Optimal Transport Method-Based Gene Filter (GF) Denoising Algorithm for Enhancing Spatially Resolved Transcriptomics Data
Authors: Du Lin , Kang Jingmin , Sun Haixi , Zhang Bohan 
Published: July 2023

AbstractThe recent advancements in spatially resolved transcriptomics (SRT) technology have enabled the acquisition of gene expression data at near- or sub-single-cell resolution, along with simultaneous imaging of physical locations. Nevertheless, necessary experimental procedures such as tissue fixation, permeabilization, and tissue removal inevitably induce the diffusion of transcribed molecules. Consequently, this leads to the partial capture of ex-situ transcripts in SRT data, thereby introducing a considerable amount of noise into the dataset. To address this issue, in this study, we focused on evaluating the diffusion pattern of individual genes within tissue regions and quantitatively calculating their signal-to-noise ratio (SNR). Through this analysis, we successfully identified “invalid genes” exhibiting widespread expression across tissue regions. Then by filtering out these genes, we effectively reduced the high noise level present in SRT data. To achieve this, we developed the gene filter denoising (GF) algorithm, which utilizes the optimal transport method to compute the gene diffusion coefficient and generate denoised SRT data. One notable advantage of our GF algorithm is its ability to fully “respect” the raw sequencing data, thereby avoiding the introduction of false positives often associated with traditional interpolation and modification denoising methods. Furthermore, we conducted comprehensive validation of GF, and the GF-denoised SRT data demonstrated substantial improvements in clustering, identification of differentially expressed genes (DEGs), and cell type annotation. Taken together, we believe that the GF denoising technique will serve as an essential and crucial step in exploring SRT data and investigating the underlying biological processes.
A sensor complements the steric gate when DNA polymerase ε discriminates ribonucleotides
Authors: Parkash Vimal , Kulkarni Yashraj , Bylund Göran O. , Osterman Pia , Kamerlin Shina Caroline Lynn , Johansson Erik 
Published: July 2023

ABSTRACTThe cellular imbalance between high concentrations of ribonucleotides (NTPs) and low concentrations of deoxyribonucleotides (dNTPs), is challenging for DNA polymerases when building DNA from dNTPs. It is currently believed that DNA polymerases discriminate against NTPs through a steric gate model involving a clash between a tyrosine and the 2’-hydroxyl of the ribonucleotide in the polymerase active site in B-family DNA polymerases. With the help of crystal structures of a B-family polymerase with a UTP or CTP in the active site, molecular dynamics simulations, biochemical assays and yeast genetics, we have identified a mechanism by which the finger domain of the polymerase sense NTPs in the polymerase active site. In contrast to the previously proposed polar filter, our experiments suggest that the amino acid residue in the finger domain senses ribonucleotides by steric hindrance. Furthermore, our results demonstrate that the steric gate in the palm domain and the sensor in the finger domain are both important when discriminating NTPs. Structural comparisons reveal that the sensor residue is conserved among B-family polymerases and we hypothesize that a sensor in the finger domain should be considered in all types of DNA polymerases.
A bistable inhibitory OptoGPCR for multiplexed optogenetic control of neural circuits
Authors: Wietek Jonas , Nozownik Adrianna , Pulin Mauro , Saraf-Sinik Inbar , Matosevich Noa , Malan Daniela , Brown Bobbie J. , Dine Julien , Levy Rivka , Litvin Anna , Regev Noa , Subramaniam Suraj , Bitton Eyal , Benjamin Asaf , Copits Bryan A. , Sasse Philipp , Rost Benjamin R. , Schmitz Dietmar , Soba Peter , Nir Yuval , Wiegert J. Simon , Yizhar Ofer 
Published: July 2023

AbstractInformation is transmitted between brain regions through the release of neurotransmitters from long-range projecting axons. Understanding how the activity of such long-range connections contributes to behavior requires efficient methods for reversibly manipulating their function. Chemogenetic and optogenetic tools, acting through endogenous G-protein coupled receptor (GPCRs) pathways, can be used to modulate synaptic transmission, but existing tools are limited in sensitivity, spatiotemporal precision, or spectral multiplexing capabilities. Here we systematically evaluated multiple bistable opsins for optogenetic applications and found that thePlatynereis dumeriliiciliary opsin (PdCO) is an efficient, versatile, light-activated bistable GPCR that can suppress synaptic transmission in mammalian neurons with high temporal precisionin-vivo.PdCO has superior biophysical properties that enable spectral multiplexing with other optogenetic actuators and reporters. We demonstrate thatPdCO can be used to conduct reversible loss-of-function experiments in long-range projections of behaving animals, thereby enabling detailed synapse-specific functional circuit mapping.
Single Cell Multi-Omics of an iPSC Model of Human Sinoatrial Node Development Reveals Genetic Determinants of Heart Rate and Arrhythmia Susceptibility
Authors: Engel James L. , Zhang Xianglong , Lu Daniel R. , Vila Olaia F. , Arias Vanessa , Lee Jasper , Hale Christopher , Hsu Yi-Hsiang , Li Chi-Ming , Wu Roland S. , Vedantham Vasanth , Ang Yen-Sin 
Published: July 2023

ABSTRACTCellular heterogeneity within the sinoatrial node (SAN) is functionally important but has been difficult to modelin vitro, presenting a major obstacle to studies of heart rate regulation and arrhythmias. Here we describe a scalable method to derive sinoatrial node pacemaker cardiomyocytes (PCs) from human induced pluripotent stem cells that recapitulates differentiation into distinct PC subtypes, including SAN Head, SAN Tail, transitional zone cells, and sinus venosus myocardium. Single cell (sc) RNA-sequencing, sc-ATAC-sequencing, and trajectory analyses were used to define epigenetic and transcriptomic signatures of each cell type, and to identify novel transcriptional pathways important for PC subtype differentiation. Integration of our multi-omics datasets with genome wide association studies uncovered cell type-specific regulatory elements that associated with heart rate regulation and susceptibility to atrial fibrillation. Taken together, these datasets validate a novel, robust, and realisticin vitroplatform that will enable deeper mechanistic exploration of human cardiac automaticity and arrhythmia.
Sequence-dependent orientational coupling and electrostatic attraction in cation-mediated DNA-DNA interactions
Authors: He Weiwei , Qiu Xiangyun , Kirmizialtin Serdal 
Published: July 2023

AbstractCondensation of DNA is vital for its biological functions and controlled nucleic acid assemblies. However, the mechanisms of DNA condensation are not fully understood due to the inability of experiments to access cation distributions and the complex interplay of energetic and entropic forces during assembly. By constructing free energy surfaces using exhaustive sampling, and detailed analysis of cation distributions, we elucidate the mechanism of DNA condensation in different salt conditions and with different DNA sequences. We found that DNA condensation is facilitated by the correlated dynamics of localized cations at the grooves of DNA helices. These dynamics are strongly dependent on salt conditions and DNA sequences. In the presence of magnesium ions, major groove binding facilitates attraction. In contrast, in the presence of poly-valent cations, minor groove binding serves to create charge patterns leading to condensation. Our findings present a novel advancement to the field and have broad implications for understanding and controlling nucleic acid complexesin vivoandin vitro.
Orchestration of differential mesodermal fate choice from ESCs by Wnt-USP3 link and H2A/H2B contextual deubiquitination
Authors: Haran Varun , Lenka Nibedita 
Published: July 2023

AbstractWnt, an evolutionarily conserved morphogen, is vital for various cell fates specification during early development. However, a concrete mechanistic understanding of the precise and fine-tuned regulation of Wnt underlying these processes is yet to be uncovered. Using the murine embryonic stem cells (ESCs) model, we have identified USP3, a histone deubiquitinase (DUB), displaying bimodal action, serving both as a downstream Wnt target and a regulator of canonical Wnt signalling. Using both loss- and gain-of-function approaches, we could identify USP3 as essential for mesoderm specification, exerting a differential influence during further differentiation. While cardiogenic mesoderm was negatively regulated and so also cardiomyogenesis, USP3 positively regulated hemangioblasts differentiation. Interestingly, however, these induced hemangioblasts promoted the haematopoietic program at the expense of endothelial differentiation. The mechanistic underpinning revealed USP3 localizing to chromatin and differentially modulating these fate choices by precise and contextual deposition of H2AUb/H2BUb in the promoters of mesoderm genes. Collectively our study underscored the Wnt-USP3 link underlying differential mesodermal fate modulation.