bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA supercoiling-induced shapes alter minicircle hydrodynamic properties
Authors: Waszkiewicz Radost , Ranasinghe Maduni , Fogg Jonathan M. , Catanese Daniel J. , Ekiel-Jeżewska Maria L. , Lisicki Maciej , Demeler Borries , Zechiedrich Lynn , Szymczak Piotr 
Published: January 2023

ABSTRACTDNA in cells is organized in negatively supercoiled loops. The resulting torsional and bending strain allows DNA to adopt a surprisingly wide variety of 3-D shapes. This interplay between negative supercoiling, looping, and shape influences how DNA is stored, replicated, transcribed, repaired, and likely every other aspect of DNA activity. To understand the consequences of negative supercoiling and curvature on the hydrodynamic properties of DNA, we submitted 336 bp and 672 bp DNA minicircles to analytical ultracentrifugation (AUC). We found that the diffusion coefficient, sedimentation coefficient, and the DNA hydrodynamic radius strongly depended on circularity, loop length, and degree of negative supercoiling. Because AUC cannot ascertain shape beyond degree of non-globularity, we applied linear elasticity theory to predict DNA shapes, and combined these with hydrodynamic calculations to interpret the AUC data, with reasonable agreement between theory and experiment. These complementary approaches, together with earlier electron cryotomography data, provide a framework for understanding and predicting the effects of supercoiling on the shape and hydrodynamic properties of DNA.
Comment on “Connexins evolved after early chordates lost innexin diversity”
Authors: Kelmanson Ilya V. , Bakin Evgeny A. , Karbat Izhar , Slivko-Koltchik Georgy A. , Reuveny Eitan , Panchin Yuri V. 
Published: January 2023

AbstractGap junctional (GJ) intercellular channels are an important way of intercellular communication. Currently, two unrelated families of GJ proteins, innexins/pannexins, and connexins, are known, either or both of which are present in most multicellular animals. A striking exception is the echinoderms which have functional GJs but until recently were believed to be lacking both innexins and connexins, which suggests the presence of the third, yet the unknown family of GJ proteins. In the recent work Welzel and Schuster (Welzel and Schuster, 2022) have reported several putative innexins and one connexin from echinoderms, therefore undermining such a hypothesis. Here we provide evidence showing that all reported connexin and innexin sequences from echinoderms are cross-species contaminations, indicating that a search for a third GJ protein family is still a subject of immediate scientific research interest.
Segmenting functional tissue units across human organs using community-driven development of generalizable machine learning algorithms
Authors: Jain Yashvardhan , Godwin Leah L. , Joshi Sripad , Mandarapu Shriya , Le Trang , Lindskog Cecilia , Lundberg Emma , Börner Katy 
Published: January 2023

AbstractThe development of a reference atlas of the healthy human body requires automated image segmentation of major anatomical structures across multiple organs based on spatial bioimages generated from various sources with differences in sample preparation. We present the setup and results of the “Hacking the Human Body” machine learning algorithm development competition hosted by the Human Biomolecular Atlas (HuBMAP) and the Human Protein Atlas (HPA) teams on the Kaggle platform. We showcase how 1,175 teams from 78 countries engaged in community- driven, open-science code development that resulted in machine learning models which successfully segment anatomical structures across five organs using histology images from two consortia and that will be productized in the HuBMAP data portal to process large datasets at scale in support of Human Reference Atlas construction. We discuss the benchmark data created for the competition, major challenges faced by the participants, and the winning models and strategies.
The “replacing surgery” of cpDNA:de novochemical synthesis andin vivofunctional testing ofChlamydomonaschloroplast genome
Authors: Guo Chunli , Zhang Guiying , Wang Hui , Mei Rui , Li Xinyi , Li Hui , Jia Bin , Wang Chaogang , Hu Zhangli 
Published: January 2023

SUMMARYWe have successfully designed and synthesized the 221,372-bp cpDNA SynCpV1.0 with the native cpDNA ofChlamydomonas reinhardtiias the template. Homoplasmic SynCpv1.0-harboring algal strains were obtained by biolistic transformation and selected with an ascending gradient of antibiotic pressure. Meanwhile, we were pleasantly surprised to find that SynCpV1.0 was able to re-introduce and replicate normally after the total DNA of transplastomic algal strains were transformed toEscherichia coli, it indicated that SynCpV1.0 was able to shuttle betweenC. reinhardtiiandE. coli. Finally, we analyzed the photosynthetic properties of SynCpV1.0-harboring transplastomic strains, the results showed that they exhibited the same photosynthetic efficiency as the wild strain ofC. reinhardtiiCC125, and could rescue the photosynthetic defect in mutant strain ofC. reinhardtiiCC5168. Herein, we have performed the “replacing surgery” of cpDNA and established an ideal platform to complete multiple cycles of “Design-Build-Test” for optimizing the cpDNA of photosynthetic organisms.HighlightAn artificial cpDNA SynCpV1.0 is constructed byde novochemical synthesis.The “replacing surgery” of cpDNA was performed in the chloroplast ofC. reinhardtiiIt is found that artificial cpDNA was able to shuttle betweenChlamydomonaschloroplast andE. coli.Establish an ideal platform to complete multiple cycles of “Design-Build-Test” for optimizing the cpDNA.One-Sentence SummaryThe chloroplast genome can be replaced by a complete synthesized genome and performs the designed biological function inC. reinhardtii.
Decapping factor Dcp2 controls mRNA abundance and translation to adjust metabolism and filamentation to nutrient availability
Authors: Vijjamarri Anil Kumar , Niu Xiao , Vandermeulen Matthew D. , Onu Chisom , Zhang Fan , Qiu Hongfang , Gupta Neha , Gaikwad Swati , Greenberg Miriam L. , Cullen Paul J. , Lin Zhenguo , Hinnebusch Alan G. 
Published: January 2023

ABSTRACTDegradation of most yeast mRNAs involves decapping by Dcp1/Dcp2. DEAD-box protein Dhh1 has been implicated as an activator of decapping, in coupling codon non-optimality to enhanced degradation, and as a translational repressor, but its functions in cells are incompletely understood. RNA-Seq analyses coupled with CAGE sequencing of all capped mRNAs revealed increased abundance of hundreds of mRNAs indcp2Δ cells that appears to result directly from impaired decapping rather than elevated transcription, which was confirmed by ChIP-Seq analysis of RNA Polymerase II occupancies genome-wide. Interestingly, only a subset of mRNAs requires Dhh1 for targeting by Dcp2, and also generally requires the other decapping activators Pat1, Lsm2, Edc3 or Scd6; whereas most of the remaining transcripts utilize NMD factors for Dcp2-mediated turnover. Neither inefficient translation initiation nor stalled elongation appears to be a major driver of Dhh1-enhanced mRNA degradation. Surprisingly, ribosome profiling revealed thatdcp2Δ confers widespread changes in relative TEs that generally favor well-translated mRNAs. Because ribosome biogenesis is reduced while capped mRNA abundance is increased bydcp2Δ, we propose that an increased ratio of mRNA to ribosomes increases competition among mRNAs for limiting ribosomes to favor efficiently translated mRNAs indcp2Δ cells. Interestingly, genes involved in respiration or utilization of alternative carbon or nitrogen sources are derepressed, and both mitochondrial function and cell filamentation (a strategy for nutrient foraging) are elevated bydcp2Δ, suggesting that mRNA decapping sculpts gene expression post-transcriptionally to fine-tune metabolic pathways and morphological transitions according to nutrient availability.
Highly multiplexed ddPCR-amplicon sequencing reveals strongPlasmodium falciparumpopulation structure and isolated populations amenable to local elimination efforts in Zanzibar
Authors: Holzschuh Aurel , Lerch Anita , Gerlovina Inna , Fakih Bakar S. , Al-mafazy Abdul-wahid H. , Reaves Erik J. , Ali Abdullah , Abbas Faiza , Ali Mohamed Haji , Ali Mohamed Ali , Hetzel Manuel W. , Yukich Joshua , Koepfli Cristian 
Published: January 2023

ABSTRACTOver the past 15 years, Zanzibar has made great strides towards malaria elimination; yet progress has stalled. Parasite genetic data ofPlasmodium falciparummay inform strategies for malaria elimination by helping to identify contributory factors to parasite persistence. Here we elucidate fine-scale parasite population structure and infer relatedness and connectivity of infections using an identity-by-descent (IBD) approach. We sequenced 518P. falciparumsamples from 5 districts covering both main islands using a novel, highly multiplexed droplet digital PCR (ddPCR)-based amplicon deep sequencing method targeting 35 microhaplotypes and drug-resistance loci. Despite high genetic diversity, we observe strong fine-scale spatial and temporal structure of local parasite populations, including isolated populations on Pemba Island and genetically admixed populations on Unguja Island, providing evidence of ongoing local transmission. We observe a high proportion of highly related parasites in individuals living closer together, including between clinical index cases and the mostly asymptomatic cases surrounding them, consistent with isolation-by-distance. We identify a substantial fraction (2.9%) of related parasite pairs between Zanzibar, and mainland Tanzania and Kenya, consistent with recent importation. We identify haplotypes known to confer resistance to known antimalarials in all districts, including multidrug-resistant parasites, but most parasites remain sensitive to current first-line treatments. Our study provides a high-resolution view of parasite genetic structure across the Zanzibar archipelago and reveals actionable patterns, including isolated parasite populations, which may be prioritized for malaria elimination.
Label-free high-resolution infrared spectroscopy for spatiotemporal analysis of complex living systems
Authors: Gvazava Nika , Konings Sabine , Cepeda-Prado Efrain , Skoryk Valeriia , Umeano Chimezie H. , Dong Jiao , Silva Iran A.N. , Ottosson Daniella Rylander , Leigh Nicholas D. , Wagner Darcy E. , Klementieva Oxana 
Published: January 2023

AbstractLabel-free chemical and structural imaging of complex living tissue and biological systems is the holy grail of biomedical research and clinical diagnostics. The current analysis techniques are time-consuming and/or require extensive sample preparation, often due to the presence of interfering molecules such as water, making them unsuitable for the analysis of such systems. Here, we demonstrate a proof-of-principle study using label-free optical photothermal mid-infrared microspectroscopy (O-PTIR) for fast, direct spatiotemporal chemical analysis of complex living biological systems at submicron resolution. While other analytical methods can provide only static snapshots of molecular structures, our O-PTIR approach enables time-resolved and in situ investigation of chemical and structural changes of diverse biomolecules in their native conditions. This comprises a technological breakthrough in infrared spectroscopy to analyze biomolecules under native conditions over time: in fresh unprocessed biopsies, living brain tissue, and vertebrates without compromising their viability.One-Sentence SummaryProof-of-principle application of non-destructive O-PTIR for high-resolution spatiotemporal chemical and structural analysis of unprocessed biopsies, living brain tissue, and vertebrates.
Realistic simulation of time-course measurements in systems biology
Authors: Egert Janine , Kreutz Clemens 
Published: January 2023

AbstractMotivationIn systems biology, the analysis of complex nonlinear systems faces many methodological challenges. However, the performance evaluation of competing methods is limited by the small amount of publicly available data from biological experiments. Therefore, simulation studies with a realistic representation of the data are a promising alternative and bring the advantage of knowing the ground truth.ResultsWe present an approach for designing a realistic simulation study. Based on 19 published systems biology models with experimental data, we assess typical measurement characteristics such as observables, observation type, measurement error, and observation times. For the latter, we estimate typical time features by fitting a transient response function. We demonstrate the approach on a meal model of the glucose insulin system, a mitogen-activated protein-kinase cascade and a model for the epidermal growth factor signaling. The performance of the realistic design is validated on 9 systems biology models in terms of optimization, integration and identifiability. For any dynamic model downloaded from an online database, our algorithm analyzes the model dynamics and specifies a realistic experimental design. The approach is specifically suited for systematic benchmarking of methods for timecourse data in the context of systems biology. In particular, various application settings such as number of parameters, initial conditions, error model etc. can be tested.AvailabilityThe approach is implemented in the MATLAB-based modelling toolbox Data2Dynamics and available athttps://github.com/Data2Dynamics/d2d.
Ythdf2ablation protects aged retina from RGC dendrite shrinking and visual decline
Authors: Niu Fugui , Long Gaoxin , Zhang Jian , She Yuanchu , Yu Jun , Ji Sheng-Jian 
Published: January 2023

AbstractAging-related retinal degeneration and vision loss have been severely affecting the elder worldwide. Previously we showed that the m6A reader YTHDF2 is a negative regulator for dendrite development and maintenance of retinal ganglion cells (RGC) in mice(Niu et al. 2022). Here, we show that conditional ablation ofYthdf2protects retina from RGC dendrite shrinking and vision loss in the aged mice. Further, we identifyHspa12aandIslr2as the YTHDF2 target mRNAs mediating these effects. Together our results indicate that m6A modification regulates retinal degeneration caused by aging, which might provide therapeutical potentials for developing new treatment approaches against aging-related vision loss.
Spatiotemporal distribution of ROS production, delivery and utilization in Arabidopsis root hairs
Authors: Kuběnová Lenka , Haberland Jan , Dvořák Petr , Šamaj Jozef , Ovečka Miroslav 
Published: January 2023

AbstractFluorescent selective probes for reactive oxygen species (ROS) detection in living cells are versatile tools for the documentation of ROS production in plant developmental or stress reactions. We employed high-resolution live-cell imaging and semi-quantitative analysis ofArabidopsis thalianastained with CM-H2DCFDA, CellROXTMDeep Red and AmplexTMRed for functional characterization of spatiotemporal mode of ROS production, delivery and utilization during root hair formation. Cell viability marker fluorescein diacetate served as a positive control for dye-loading and undisturbed tip growth after staining. Colocalization analysis with subcellular molecular markers and utilization of two root hair mutants with similar phenotype of non-elongating root hairs, but with contrast reasons for this impairment, we found that: i) CM-H2DCFDA is a sensitive probe for ROS generation in cytoplasm, ii) CellROXTMDeep Red labels ROS in mitochondria, iii) AmplexTMRed labels apoplastic ROS and mitochondria, and shows high selectivity to root hairs, iv)rhd2-1mutant with nonfunctional AtRBOHC/RHD2 has a low level of CM-H2DCFDA-reactive ROS in cytoplasm and lacks AmplexTMRed-reactive ROS in apoplast, v)ACTIN2-deficientder1-3mutant is not altered in these aspects. The sensitivity of CellROXTMDeep Red was documented by discrimination between larger ROS-containing mitochondria and small, yet ROS-free pre-mature mitochondria in the growing tip of root hairs. We characterized spatial changes in ROS production and compartmentalization induced by external ROS modulators, ethylene precursor 1-aminocyclopropane-1-carboxylic acid and ionophore valinomycin. This dynamic and high-resolution study of ROS production and utilization opens new opportunities for precise speciation of particular ROS involved in the root hair formation.One sentence summary:High-resolution live-cell imaging of ROS production and subcellular localization in bulges and growing root hairs of Arabidopsis using CM-H2DCFDA, CellROXTMDeep Red and AmplexTMRed selective probes.
Generation of eco-friendly channel catfish,Ictalurus punctatus, harboring alligator cathelicidin gene with robust disease resistance by harnessing different CRISPR/Cas9-mediated systems
Authors: Wang Jinhai , Su Baofeng , Xing De , Bruce Timothy J. , Li Shangjia , Bern Logan , Shang Mei , Johnson Andrew , Simora Rhoda Mae C. , Coogan Michael , Hettiarachchi Darshika U. , Wang Wenwen , Hasin Tasnuba , Al-Armanazi Jacob , Lu Cuiyu , Dunham Rex A. 
Published: January 2023

AbstractThe CRISPR/Cas9 platform holds promise for modifying fish traits of interest as a precise and versatile tool for genome manipulation. To reduce introgression of transgene and control reproduction, catfish species have been studied for upscaled disease resistance and intervening of reproduction to lower the potential environmental risks of introgression of escapees’ as transgenic animals. Taking advantage of the CRISPR/Cas9-mediated system, we succeeded in integrating the cathelicidin gene from an alligator (Alligator sinensis;As-Cath) into the target luteinizing hormone (LH) locus of channel catfish (Ictalurus punctatus) using two delivery systems assisted by double-stranded DNA (dsDNA) and single-stranded oligodeoxynucleotides (ssODNs), respectively. In this study, high knock-in (KI) efficiency (22.38%, 64/286) but low on-target was achieved using the ssODN strategy, whereas adopting a dsDNA as the donor template led to an efficient on-target KI (10.80%, 23/213). On-target KI ofAs-Cathwas instrumental in establishing theLHknockout (LH−_As-Cath+) catfish line, which displayed heightened disease resistance and reduced fecundity compared to the wild-type sibling fish. Furthermore, implanting with HCG and LHRHa can restore the fecundity, spawnability and hatchability of the new transgenic fish line. Overall, we replaced theLHgene with an alligator cathelicidin transgene and then administered hormone therapy to gain complete reproductive control of disease-resistant transgenic catfish in an environmentally sound manner. This strategy not only effectively improves the consumer-valued traits, but also guards against genetic contamination. This is a breakthrough in aquaculture genetics to confine fish reproduction and prevent the establishment of transgenic or domestic genotypes in the natural environment.
Cerebrovascular reactivity increases across development in multiple networks as revealed by a breath-holding task: a longitudinal fMRI study
Authors: Chen Donna Y. , Di Xin , Biswal Bharat 
Published: January 2023

AbstractFunctional magnetic resonance imaging (fMRI) has been widely used to understand the neurodevelopmental changes that occur in cognition and behavior across childhood. The blood-oxygen-level-dependent (BOLD) signal obtained from fMRI is understood to be comprised of both neuronal and vascular information. However, it is unclear whether the vascular response is altered across age in studies investigating development in children. Since the breath-hold task is commonly used to understand cerebrovascular reactivity in fMRI studies, it can be used to account for developmental differences in vascular response. This study examines how the cerebrovascular response changes over age in a longitudinal children’s breath-hold dataset from the Nathan Kline Institute (NKI) Rockland Sample (ages 6 to 18 years old at enrollment). A general linear model (GLM) approach was applied to derive cerebrovascular reactivity from breath-hold data. To model both the longitudinal and cross-sectional effects of age on breath-hold response, we used mixed effects modeling with the following terms: linear, quadratic, logarithmic, and quadratic-logarithmic, to find the best-fitting model. We observed increased breath-hold BOLD signal in multiple networks across age, in which linear and logarithmic mixed effects models provided the best fit with the lowest Akaike Information Criterion (AIC) scores. This shows that the cerebrovascular response increases across development in a brain network-specific manner. Therefore, fMRI studies investigating the developmental period should account for cerebrovascular changes which occur with age.
Dispersal overwhelms variation in host quality to shape nectar microbiome assembly
Authors: Francis Jacob S. , Mueller Tobias G. , Vannette Rachel L. 
Published: January 2023

SummaryEpiphytic microbes frequently impact plant phenotype and fitness, but effects depend on microbe community composition. Deterministic filtering by plant traits and dispersal-mediated processes can affect microbiome assembly yet their relative contribution is poorly understood.We tested the impact of host-plant filtering and dispersal limitation on nectar microbiome abundance and composition. We inoculated bacteria and yeast into 30 plants across 4 phenotypically distinct cultivars ofEpilobium canum. We compared the growth of inoculated communities to openly visited flowers from a subset of the same plants.The abundance and composition of microbial communities differed among plant individuals and cultivars in both inoculated and open flowers. However, plants hosting the highest microbial abundance when inoculated did not have the highest abundances when openly visited. Rather microbial density among open flowers was correlated with pollen receipt, a proxy for animal visitation, suggesting a primary role of deterministic dispersal in floral microbiome assembly despite variation in host-quality.While host-quality can affect microbiome assembly, variation in dispersal was more important here. Host quality could drive microbial community assembly in plant tissues where species pools are large and dispersal is consistent, but dispersal may be more important when microbial dispersal is limited, or arrival order is important.
Loss of secondary motor cortex neurons in chronic neuropathic pain
Authors: Das Gupta Amrita , Zheng Hongwei , John Jennifer , Kaushalya Sanjeev , Asan Livia , Beretta Carlo A. , Kuner Rohini , Knabbe Johannes , Kuner Thomas 
Published: January 2023

AbstractChronic neuropathic pain is associated with structural plasticity of the brain on different spatial scales, yet, little is known on the mesoscopic scale of tissue composition. Here, we determined the cellular composition of cortical areas and structural variability of entire neurons during the development of chronic neuropathic pain using longitudinal in vivo two-photon microscopy and behavioral assessment. When monitoring cell type composition in response to spared-nerve injury in 84 cortical volumes containing ∽25000 cells each, we found neuronal loss in the secondary motor cortex region M2 immediately adjacent to the cingulate cortex already one week after surgery. Loss of mostly interneurons was also evident when monitoring individual M2 neurons over time. This neuronal loss was preceded by decreased spine density and loss of distal dendritic branches. In conclusion, our work delineates M2 as a novel site and neuronal loss as a so far underappreciated mechanism underlying chronic neuropathic pain states.