bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogenetic distribution and experimental characterization of corrinoid production and dependence in soil bacterial isolates
Authors: Alvarez-Aponte Zoila I. , Govindaraju Alekhya M. , Hallberg Zachary F. , Nicolas Alexa M. , Green Myka A. , Mok Kenny C. , Fonseca-Garcia Citlali , Coleman-Derr Devin , Brodie Eoin L. , Carlson Hans K. , Taga Michiko E. 
Published: December 2023

ABSTRACTSoil microbial communities impact carbon sequestration and release, biogeochemical cycling, and agricultural yields. These global effects rely on metabolic interactions that modulate community composition and function. However, the physicochemical and taxonomic complexity of soil and the scarcity of available isolates for phenotypic testing are significant barriers to studying soil microbial interactions. Corrinoids—the vitamin B12family of cofactors—are critical for microbial metabolism, yet they are synthesized by only a subset of microbiome members. Here, we evaluated corrinoid production and dependence in soil bacteria as a model to investigate the ecological roles of microbes involved in metabolic interactions. We isolated and characterized a taxonomically diverse collection of 161 soil bacteria from a single study site. Most corrinoid-dependent bacteria in the collection prefer B12over other corrinoids, while all tested producers synthesize B12, indicating metabolic compatibility between producers and dependents in the collection. Furthermore, a subset of producers release B12at levels sufficient to support dependent isolates in laboratory culture at estimated ratios of up to 1,000 dependents per producer. Within our isolate collection, we did not find strong phylogenetic patterns in corrinoid production or dependence. Upon investigating trends in the phylogenetic dispersion of corrinoid metabolism categories across sequenced bacteria from various environments, we found that these traits are conserved in 47 out of 85 genera. Together, these phenotypic and genomic results provide evidence for corrinoid-based metabolic interactions among bacteria and provide a framework for the study of nutrient-sharing ecological interactions in microbial communities.
Leveraging machine learning and citizen science data to describe flowering phenology across South Africa
Authors: Stewart R. D. , Bard N. , van der Bank M. , Davies T. J. 
Published: December 2023

SummaryPhenology — the timing of recurring life history events—is strongly linked to climate. Shifts in phenology have important implications for trophic interactions, ecosystem functioning and community ecology. However, data on plant phenology can be time consuming to collect and current records are biased across space and taxonomy.Here, we explore the performance of Convolutional Neural Networks (CNN) for classifying flowering phenology on a very large and taxonomically diverse dataset of citizen science images. We analyse >1.8 million iNaturalist records for plants listed in the National Botanical Gardens within South Africa, a country famed for its floristic diversity (∼21,000 species) but poorly represented in phenological databases.We were able to correctly classify images with >90% accuracy. Using metadata associated with each image, we then reconstructed the timing of peak flower production and length of the flowering season for the 6,986 species with >5 iNaturalist records.Our analysis illustrates how machine learning tools can leverage the vast wealth of citizen science biodiversity data to describe large-scale phenological dynamics. We suggest such approaches may be particularly valuable where data on plant phenology is currently lacking.
Lumen pressure modulation in chicken embryos
Authors: McLaren Susannah B.P. , Xiong Fengzhu 
Published: December 2023

AbstractPressure exerted by fluid contained within a lumen plays a crucial role in the growth, morphogenesis and patterning of epithelial organs. Accurate modulation of lumen pressure in the developing embryo requires sensitive and robust methods that can detect and vary pressure in the range of tens to hundreds of Pascals (Pa). Here we describe a simple, cost- effective method for setting up a pressure modulation apparatus combining a high-sensitivity pressure sensor and a water column whose height can be finely tuned. We demonstrate lumen pressure control using the developing brain of early chicken embryos.
Task-Switch Related Reductions in Neural Distinctiveness in Children and Adults: Commonalities and Differences
Authors: Schwarze Sina A. , Bonati Sara , Cichy Radoslaw M. , Lindenberger Ulman , Bunge Silvia A. , Fandakova Yana 
Published: December 2023

AbstractGoal-directed behavior requires the ability to flexibly switch between task sets with changing environmental demands. Switching between tasks generally comes at the cost of slower and less accurate responses. Compared to adults, children show greater switch costs, presumably reflecting the protracted development of the ability to flexibly update task-set representations. To examine whether the distinctiveness of neural task-set representations is more strongly affected by a task switch in children compared to adults, we examined multi-voxel patterns of fMRI activation in 88 children (8–11 years, 49 girls) and 53 adults (20–30 years, 28 women) during a task-switching paradigm. Using multivariate pattern analysis (MVPA), we investigated whether task-set representations were less distinct on switch than on repeat trials across frontoparietal, cingulo-opercular, and temporo-occipital regions. Children and adults showed lower accuracy and longer response times on switch than on repeat trials, with higher accuracy costs in children. Decoding accuracy across regions was lower on switch than repeat trials, consistent with the notion that switching reduces the distinctiveness of task-set representations. Reliable age differences in switch-related representational distinctiveness reductions were absent, pointing to a remarkable degree of maturity of neural representations of task-relevant information in late childhood. However, we also observed that switch-related reductions in distinctiveness were more highly correlated across frontoparietal and cingulo-opercular regions in children than in adults, potentially reflecting the ongoing specialization of different control networks with respect to the representation of task features.Significance statementThe ability to flexibly switch between tasks enables goal-directed behavior, but is particularly challenging for children, potentially due to protracted development in the ability to represent multiple and overlapping task rules that link stimuli to appropriate responses. We tested this hypothesis by using neuroimaging to measure brain activity during task switching in 8–11-year-olds and adults. Activation patterns in frontal, parietal, and temporal regions could tell us with above-chance accuracy which task a person was performing when the task remained the same, but not when it had switched. Adults showed greater differentiation across regions in terms of switch-related reductions in distinctiveness than children, suggesting that the relevant functional circuity is present but has not yet fully matured by late childhood.
A novelKCNJ16kidney organoid model recapitulates the disease phenotype and shows restoration of lipid accumulation upon treatment with statins
Authors: Sendino Garví E. , van Slobbe G. , Zaal E.A. , de Baaij J. H. F. , Hoenderop J.G. , Masereeuw R. , Janssen M. J. , van Genderen A. M. 
Published: December 2023

AbstractBackgroundtheKCNJ16gene has been associated with a novel kidney tubulopathy phenotype,viz.disturbed acid-base homeostasis, hypokalemia and altered renal salt transport.KCNJ16encodes for Kir5.1, which together with Kir4.1 constitutes a potassium channel located at kidney tubular cell basolateral membranes. Preclinical studies provided mechanistical links between Kir5.1 and a disease phenotype, however, the disease pathology remains poorly understood. Here, we aimed at generating and characterizing a novel advancedin vitrohuman kidney model that recapitulates the disease phenotype to investigate further the pathophysiological mechanisms underlying the disease and potential therapeutic interventions.Methodswe used CRISPR/Cas9 to generateKCNJ16mutant (KCNJ16+/-andKCNJ16-/-) cell lines from healthy human induced pluripotent stem cells (iPSC)KCNJ16control (KCNJ16WT). The iPSCs were differentiated following an optimized protocol into kidney organoids in an air-liquid interface.ResultsKCNJ16-depleted kidney organoids showed transcriptomic and potential functional impairment of key voltage-dependent electrolyte and water-balance transporters. We observed cysts formation, lipid droplet accumulation and fibrosis upon Kir5.1 function loss. Furthermore, a large scale, glutamine tracer flux metabolomics analysis demonstrated thatKCNJ16-/-organoids display TCA cycle and lipid metabolism impairments. Drug screening revealed that treatment with statins, particularly the combination of simvastatin and C75, prevented lipid droplet accumulation and collagen-I deposition inKCNJ16-/-kidney organoids.Conclusionsmature kidney organoids represent a relevantin vitromodel for investigating the function of Kir5.1. We discovered novel molecular targets for this genetic tubulopathy and identified statins as a potential therapeutic strategy forKCNJ16defects in the kidney.Significance StatementIn this study, the use of CRISPR/Cas9 technology resulted in the establishment of aKCNJ16-depleted kidney organoid model, instrumental in elucidating the pathophysiology of the recently reportedKCNJ16-associated kidney tubulopathy. Our study substantiates the role of Kir5.1 (KCNJ16) in kidney disease, confirming already described phenotypes, as well as aiding to gain insight in the causal role of Kir5.1 loss in the disease phenotype. Our approach increases the knowledge onKCNJ16-related kidney phenotype, and it states the importance of combining CRISPR/Cas9 technology and advancedin vitromodels for complex disease modeling and therapy testing. Furthermore, we encourage the application of our approach to thein vitromodeling of rare and/or underrepresented genetic kidney diseases, for which the availability of patient material is limited.
Bi-allelic variants inWDR47lead to neuronal loss causing a rare neurodevelopmental syndrome with corpus callosum dysgenesis in humans
Authors: Bayam Efil , Tilly Peggy , Collins Stephan C. , Alvarez José Rivera , Kannan Meghna , Tonneau Lucile , Rinaldi Bruno , Lecat Romain , Schwaller Noémie , Maddirevula Sateesh , Monteiro Fabiola , Kitajima João Paulo , Kok Fernando , Kato Mitsuhiro , Hamed Ahlam A. A. , Salih Mustafa A. , Tala Saeed Al , Hashem Mais , Tada Hiroko , Saitsu Hirotomo , Friant Sylvie , Yüksel Zafer , Nakashima Mitsuko , Alkuraya Fowzan S. , Yalcin Binnaz , Godin Juliette D. 
Published: December 2023

ABSTRACTThe corpus callosum (CC) is the largest interhemispheric connection that is largely formed by the axons of layer 2/3 callosal projection neurons (CPNs) through a series of tightly regulated cellular events, including neuronal specification, migration, axon extension and branching. Defects in any of those steps may prevent the proper development of the corpus callosum resulting in a spectrum of disorders collectively referred to as corpus callosum dysgenesis (CCD). Here, we report four unrelated families carrying bi-allelic variants inWDR47presenting with CCD together with other neuroanatomical phenotypes such as microcephaly, cerebellar abnormalities and hydrocephalus. Using a combination ofin vitroandin vivomouse models and complementation assays, we show that independently from its previously identified functions in neuronal migration and axonal extension, WDR47 is required for survival of callosal neurons by contributing to the maintenance of mitochondrial and microtubule homeostasis. We further provide evidence that severity of the CCD phenotype is determined by the degree of the loss of function caused by the human variants. Taken together, we identifyWDR47as a causative gene of a new neurodevelopmental syndrome characterized by corpus callosum abnormalities and other neuroanatomical malformations.
Phytochrome-dependent responsiveness to root-derived cytokinins enables coordinated elongation responses to combined light and nitrate cues
Authors: Gautrat Pierre , Buti Sara , Romanowski Andrés , Buijs Guido , Pierik Ronald 
Published: December 2023

AbstractPlants growing at high densities can detect competitors through changes in the composition of light reflected by neighbours. In response to this far-red-enriched light, plants elicit adaptive shade avoidance responses for light capture, but these need to be balanced against other input signals, such as nutrient availability. Here, we used a combination of transcriptomics, growth assays and dedicated genetic and pharmacological interventions to demonstrate how Arabidopsis integrates light and nitrate signalling. We unveiled that nitrate modulates shade avoidance via a previously unknown shade response pathway that involves root-derived transZeatin (tZ). Under nitrate-sufficient conditions, tZ promotes hypocotyl elongation specifically in the presence of supplemental far-red light. This occurs via PIF transcription factors-dependent inhibition of type-AARRscytokinin response inhibitors. Our data thus reveal how plants co-regulate responses to shade cues with root-derived information about nutrient availability, and how they restrict responses to this information to specific light conditions in the shoot.
ROS-induced translational regulation—through spatiotemporal differences in codon recognition—is a key driver of brown adipogenesis
Authors: Ip Jun Yu , Wijaya Indrik , Lee Li Ting , Lim Yuhua , Teoh Deryn En-Jie , Chan Cheryl Siew Choo , Cui Liang , Begley Thomas J. , Dedon Peter C. , Guo Huili 
Published: December 2023

AbstractThe role of translational regulation in brown adipogenesis is relatively unknown. Localized translation of mRNAs encoding mitochondrial components enables swift mitochondrial responses, but whether this occurs during brown adipogenesis, which involves massive mitochondrial biogenesis, has not been explored. Here, we used ribosome profiling and RNA-Seq, coupled with cellular fractionation, to obtain spatiotemporal insights into translational regulation. During brown adipogenesis, a translation bias towards G/C-ending codons is triggered first in the mitochondrial vicinity by reactive oxygen species (ROS), which later spreads to the rest of the cell. This translation bias is induced through ROS modulating the activity of the tRNA modification enzyme, ELP3. Intriguingly, functionally relevant mRNAs, including those encoding ROS scavengers, benefit from this bias; in so doing, ROS-induced translation bias both fuels differentiation and concurrently minimizes oxidative damage. These ROS-induced changes could enable sustained mitochondrial biogenesis during brown adipogenesis, and explain in part, the molecular basis for ROS hormesis.
Genomic analysis ofStaphylococcus aureusisolates from bacteremia reveals genetic features associated with the COVID-19 pandemic
Authors: Sánchez-Osuna Miquel , Pedrosa Marc , Bierge Paula , Gómez-Sánchez Inmaculada , Alguacil-Guillén Marina , Espasa Mateu , Erill Ivan , Gasch Oriol , Pich Oscar Q. 
Published: December 2023

ABSTRACTGenomic analyses of bacterial isolates are necessary to monitor the prevalence of antibiotic resistance genes and virulence determinants. Herein, we provide a comprehensive genomic description of a collection of 339Staphylococcus aureusstrains isolated from patients with bacteremia between 2014 and 2022. Nosocomial acquisition accounted for 56.6% of episodes, with vascular catheters being the predominant source of infection (31.8%). Cases of fatality (27.4%), persistent bacteremia (19.5%) and diagnosis of septic emboli (24.2%) were documented. During the COVID-19 pandemic, we observed a 140% increase of the episodes ofS. aureusbacteremia per year, with a concomitant increase of the cases from nosocomial origin. This prompted us to investigate the existence of genetic features associated withS. aureusisolates from the COVID-19 pandemic. While genes conferring resistance to β-lactams (blaI-blaR-blaZ), macrolides (ermA, ermC, ermT, mphC, msrA) and aminoglycosides (ant(4’)-Ia,ant(9)-Ia,aph(3’)-IIIa,aph(2’’)-Ih) were prevalent in our collection, detection of themsrAandmphCgenes increased significantly in pandemicS. aureusisolates. Similarly, we observed a higher prevalence of isolates carrying the genes encoding the Clumping Factors A and B, involved in fibrinogen binding. Of note, macrolides were extensively used as accessory therapy for COVID-19 and fibrinogen levels were usually elevated upon SARS-CoV-2 infection. Therefore, our results reveal a remarkable adaptation of theS. aureusisolates to the COVID-19 pandemic context and demonstrates the potential of whole-genome sequencing to conduct molecular epidemiology studies.
UVB radiation suppresses Dicer expression through β-catenin
Authors: Aktary Zackie , Petit Valérie , Berlin Irina , Charenchaon Nisamanee , Sage Evelyne , Bertrand Juliette , Larue Lionel 
Published: December 2023

ABSTRACTUltraviolet (UV) rays prompt a natural response in epidermal cells, particularly within melanocytes. The changes in gene expression and related signaling pathways in melanocytes following exposure to UVR are still not entirely understood. Our findings reveal that UVB irradiation suppresses the expression of Dicer. This repression is intricately linked to the activation of the PI3K, RSK, and WNT/β-catenin signaling pathways and is directly associated with transcriptional repression by β-catenin. Notably, we have identified specific binding sites for the LEF/β-catenin complex in the Dicer promoter. Collectively, these results emphasize the significance of the UV-induced pathway involving LEF/β-catenin, which impacts Dicer expression. This pathway holds potential importance in governing melanocyte physiology.
Activity of oleo-gum resins of myrrha on the growth of Candidiasis
Authors: Alabdalall Amira H. 
Published: December 2023

AbstractAimsMedicinal plants have a long and significant history of being used for their healing properties. One famous example is Commiphora, which is mostly found in the southern part of Arabia. The objective of this research was to evaluate the effectiveness of a water-based extract obtained from two different varieties of myrrh in suppressing the proliferation ofCandidaspp. at different concentrations. The objective of this research is to determine the chemical composition ofCommiphoraand its capacity to prevent the development ofCandidaspp.Methodology and ResultsA plant specimen traditionally used in Saudi Arabia for its possible effectiveness againstCandida albicans(ATCC 14053),C. neoformans(ATCC 66031),Candida laurentii(ATCC 18803),Candida guilliermondii(ATCC 6260), andCandida tropicalis(ATCC 66029). The results showed that the aqueous extract of both tested species of Myrrha (Commiphora myrrhaandC. molmol) shown inhibitory effects on all tested isolates. Moreover, it was discovered that the inhibitory impact decreased with increasing concentrations of Myrrha. During the chemical examination of the Myrrha, it was noted that the material included 12 components known for their antimicrobial properties. The components described before are as follows: The specified chemical compounds consist of β-Elemene, β-bisabolene, Dihydro butyl bezodoxepin, Tetradecanol, methyl palmitate, Tribenzo-1,2,3,4,5,6 anthracene, 9-Eicosene, 2-bromo-4-fluoro-N-(thiophen-2-ylmethyl) aniline, Octadecenoic acid methyl ester, dehydroabietic acid, and Docosene.ConclusionThe antimicrobial activity of five yeasts was assessed using the diffusion technique. The essential oil derived from two varieties of myrrha shown the most significant effects onCandida tropicalis(ATCC 66029),Candida guilliermondii(ATCC 6260),Candida laurentii(ATCC 18803),C. neoformans(ATCC 66031), andCandida albicans(ATCC 14053). Upon conducting a chemical examination of the myrrha, it was shown that it consists of 19 known components, of which 12 compounds have been proven by research to suppress the growth of microorganisms. Further research is needed to fully explore the potential of these water extracts as innovative antifungal medicines, including their effectiveness against various strains ofCandidaand the processes by which they work, as well as the primary components responsible for their action.
Unravelling Silicon’s Transcriptomic Armor in Soybean againstMacrophomina phaseolinacausing Charcoal Rot Disease
Authors: Jadhav P. V. , Magar S. G. , Sharma P. K. , Vaidya E. R. , Moharil M. P. , Jaiswal S. , Nichal S. S. , Ghawade R. S. , Iquebal M. S. , Kawar P. G. , Jadhav P. R. , Sakhare S. B. , Ghorade R. B. , Deshmukh R. , Sonah H. , Kumar D. , Kharche V. K. , Torop E. A. , Dani R. G. , Mane S. S. 
Published: December 2023

AbstractTheGlycine maxL. has been affected by more than 100 diseases, includingMacrophomina phaseolinaproducing charcoal rot disease, which reduces production by 70%. In this investigation, RNA-Seq analysis is used for the first time to explore role of silicon in preventing soybean charcoal rot. The study explores the molecular mechanism underlying soybeans’ resilience to charcoal rot when treated with potassium silicon. It was meticulously investigated howMacrophomina phaseolinaentered the roots. The SEM, which showed a strong link between potassium silicate accumulation and disease resistance. Further investigation indicates that a potassium silicate concentration of 1.7mM lowers disease incidence. Using Illumina HiSeq NGS data, we present a transcriptome analysis revealing genes associated with charcoal rot resistance, highlighting 3,106 genes with distinct expression patterns. The strong enrichment of pathways including “Biosynthesis of ansamycins” and “Flavone and flavonol biosynthesis,” which contribute to resistance against charcoal rot, is highlighted by KEGG enrichment analysis. The ERF transcription factor and NB leucine-rich repeats stands out among the differentially expressed genes as being particularly connected to resistance. The crucial functions that many other important transcription factors, including as MYB, NAC, and proteins from the FAR1 family, play in enhancing soybeans’ resistance to charcoal rot are also noted. This newly discovered information could help in developing tactics to strengthen soybean’s resistance toMacrophomina phaseolina.
Lethality of West Nile virus strains in a mouse model
Authors: Siniavin A.E. , Dolzhikova I.V. , Pochtovyi A.A. , Reshetnikov D.A. , Gushchin V.A. 
Published: December 2023

AbstractWest Nile fever (WNF) is a viral infection caused by West Nile virus (WNV), a flavivirus of theFlaviviridaefamily. Virus circulates between mosquitoes and wild birds, but can infect other species, including humans. The first cases of West Nile fever were reported in Africa in the 1930s. Currently, WNV has a wide geographic range, which includes countries in Europe, Asia, Africa, Australia, and North and South America, where it periodically causes WNF outbreaks. The disease in human occurs with the development of fever, and in some cases ending up severe neurological complications. Studies of the virus in animal models demonstrate that virulence varies depending on the host species, the genotype of the virus, and the presence of substitutions in key viral proteins, even within the same genotype. These studies highlight the need for comparative studies of different WNV strains to evaluate the impact of amino acid substitutions on WNV pathogenesis. Analysis of key mutations and substitutions will allow the development of a safe and effective vaccine for the prevention of WNF.