bluuebunny/crossref_metadata_2025_split huggingface dataset:
The cytochrome P450 enzyme WsCYP71B35 fromWithania somniferahas a role in withanolides biosynthesis and defense against bacteria
Authors: Shilpashree H.B. , Narayanan Ananth Krishna , Kumar Sarma Rajeev , Barvkar Vitthal , Nagegowda Dinesh A. 
Published: October 2023

AbstractThe medicinal properties of Ashwagandha (Withania somniferaL. Dunal) are attributed to withanolides, which belong to the triterpenoid steroidal lactones class of compounds. Though it is proposed that intermediates of the universal phytosterol pathway are utilized by cytochrome P450 (CYP450) enzymes to form withanolides, studies on functional characterization of these enzymes has been sparse. This study reports the functional characterization of a CYP450 candidate fromW. somnifera(WsCYP71B35) that exhibited induced expression in response to methyl jasmonate treatment and showed higher expression in tissues that accumulate withanolides. Biochemical assay with yeast microsomal fraction expressing recombinant WsCYP71B35 indicated no activity when phytosterols and their intermediate 24-methylene cholesterol were used as substrates. However, WsCYP71B35 catalyzed product formation with withaferin A, withanolide A, withanolide B, and withanoside IV among the tested substrates. Moreover, virus-induced gene silencing (VIGS) and transient overexpression ofWsCYP71B35inW. somniferaleaves modulated the levels of withaferin A, withanolide A, and withanolide B, indicating the role ofWsCYP71B35in withanolides pathway. Furthermore, VIGS ofWsCYP71B35inW. somniferareduced its tolerance toPseudomonas syringae(DC3000) infection, whereas overexpression enhanced the tolerance to the bacterium inW. somniferaand transgenic tobacco. Overall, these results provide insights into the role ofW. somniferaWsCYP71B35 in withanolides biosynthesis and bacterial defense.
Biosensor capability of the endometrium is mediated in part, by altered miRNA cargo from conceptus-derived extracellular vesicles
Authors: De Bem Tiago H. C. , Bridi Alessandra , Tinning Haidee , Sampaio Rafael Vilar , Malo-Estepa Irene , Wang Dapeng , Vasconcelos Elton J. R. , Nociti Ricardo Perecin , de Ávila Ana C. F. C. M. , Sangalli Juliano Rodrigues , Motta Igor Garcia , Ataíde Gilmar Arantes , da Silva Júlio C. B. , Watanabe Yeda Fumie , Gonella-Diaza Angela , da Silveira Juliano C. , Pugliesi Guilherme , Meirelles Flávio Vieira , Forde Niamh 
Published: October 2023

ABSTRACTWe tested the hypothesis that the biosensor capability of the endometrium is mediated in part, by the effect of different cargo contained in the extracellular vesicles secreted by the conceptus during the peri-implantation period of pregnancy. We transferredBos taurus taurusembryos of different origin:In vivo(high developmental potential (IV)),in vitro(intermediate developmental potential (IVF)), or cloned (low developmental potential (NT)), intoBos taurus indicusrecipients. Extracellular vesicles (EVs) recovered from Day 16 conceptus conditioned medium were characterized and their microRNA (miRNA) cargo sequenced alongside RNA sequencing of their respective endometria. There were substantial differences in the endometrial response toin vivoVsin vitroandin vivoVs cloned conceptuses (1153 and 334DEGs respectively) with limited differences betweenin vitroVs cloned conceptuses (36 DEGs). miRNA cargo was similar between all three groups (426 common cargo) differences betweenin vivoand cloned (8 miRNAs), andin vivoandin vitro(6 miRNAs) observed. Treatment of endometrial epithelial cells with mimic or inhibitors for miR-128 and miR-1298 changes to the proteomic content of target cells (96, and 85 respectively) of which mRNAs are altered in the endometriumin vivo(PLXDC2, COPG1, HSPA12A, MCM5, TBL1XR1, and TTF). In conclusion, we have determined that the biosensor capability of the endometrium is mediated in part, by its response to different EVs miRNA cargo produced by the conceptus during the peri-implantation period of pregnancy.SIGNIFICANCE STATEMENTDuring the peri-implantation period of pregnancy in mammals, the endometrium acts as a biosensor for the developmental competency of the embryo. However, the mechanism by which biosensor capability of the endometrium is established, remains elusive. In this study, we show that embryos of different developmental competencies have distinct microRNA cargo contained in their extracellular vesicles (EVs). Exposure of the endometrium to these conceptuses alters the transcriptional response of the endometrium during the process of pregnancy recognition. This differential response is mediated in part, by the delivery and action of the these differentially abundant microRNAs into EVs. Here we propose differences in EV-mediated miRNA cargo are responsible in part for this biosensor capability of the endometrium.
Transport and inhibition mechanism for VMAT2-mediated synaptic loading of monoamines
Authors: Wang Yuwei , Zhang Pei , Chao Yulin , Zhu Zhini , Yang Chuanhui , Zhou Zixuan , Li Yaohui , Long Yonghui , Liu Yuehua , Li Dianfan , Wang Sheng , Qu Qianhui 
Published: October 2023

AbstractMonoamine neurotransmitters such as serotonin and dopamine are loaded by vesicular monoamine transporter 2 (VMAT2) into synaptic vesicles for storage and subsequent release in neurons. Impaired VMAT2 function underlies various neuropsychiatric diseases. VMAT2 inhibitors reserpine and tetrabenazine are used to treat hypertension, movement disorders associated with Huntington’s Disease and Tardive Dyskinesia. Despite its physiological and pharmacological significance, the structural basis underlying substrate recognition, and inhibition by varying mechanisms remains unknown. Here we present cryo-EM structures of human apo VMAT2 in addition to states bound to serotonin, tetrabenazine, and reserpine. These structures collectively capture three states, namely the lumen-facing, occluded, and cytosol-facing conformations. Notably, tetrabenazine induces a substantial rearrangement of TM2 and TM7, extending beyond the typical rocker-switch movement. These functionally dynamic snapshots, complemented by biochemical analysis, unveil the essential components responsible for ligand recognition, elucidate the proton-driven exchange cycle, and provide a framework to design improved pharmaceutics targeting VMAT2.
Machine learning of three-dimensional protein structures to predict the functional impacts of genome variation
Authors: Shukla Kriti , Idanwekhai Kelvin , Naradikian Martin , Ting Stephanie , Schoenberger Stephen P. , Brunk Elizabeth 
Published: October 2023

AbstractResearch in the human genome sciences generates a substantial amount of genetic data for hundreds of thousands of individuals, which concomitantly increases the number of variants with unknown significance (VUS). Bioinformatic analyses can successfully reveal rare variants and variants with clear associations to disease-related phenotypes. These studies have made a significant impact on how clinical genetic screens are interpreted and how patients are stratified for treatment. There are few, if any, comparable computational methods for variants to biological activity predictions. To address this gap, we developed a machine learning method that uses protein three-dimensional structures from AlphaFold to predict how a variant will influence changes to a gene’s downstream biological pathways. We trained state-of-the-art machine learning classifiers to predict which protein regions will most likely impact transcriptional activities of two proto-oncogenes, nuclear factor erythroid 2 (NFE2)-related factor 2 (Nrf2) and c-MYC. We have identified classifiers that attain accuracies higher than 80%, which have allowed us to identify a set of key protein regions that lead to significant perturbations in c-MYC or Nrf2 transcriptional pathway activities.SignificanceThe vast majority of mutations are either unspecified and/or their downstream biological implications are poorly understood. We have created a method that utilizes protein structure to cluster mutations from population-scale repositories to predict downstream functional impacts. The broader impacts of this approach include advanced filtering of mutations that are likely to impact genome function.
Reconstitution of cytolinker-mediated crosstalk between actin and vimentin
Authors: Petitjean Irene Istúriz , Tran Quang D. , Goutou Angeliki , Kabir Zima , Wiche Gerhard , Leduc Cécile , Koenderink Gijsje H. 
Published: October 2023

AbstractCell shape and motility are determined by the cytoskeleton, an interpenetrating network of actin filaments, microtubules, and intermediate filaments. The biophysical properties of each filament type individually have been studied extensively by cell-free reconstitution. By contrast, the interactions between the three cytoskeletal networks are relatively unexplored. They are coupled via crosslinkers of the plakin family such as plectin. These are challenging proteins for reconstitution because of their giant size and multidomain structure. Here we engineer a recombinant actin-vimentin crosslinker protein called ‘ACTIF’ that provides a minimal model system for plectin, recapitulating its modular design with actin-binding and intermediate filament-binding domains separated by a coiled-coil linker for dimerisation. We show by fluorescence and electron microscopy that ACTIF has a high binding affinity for vimentin and actin and creates mixed actin-vimentin bundles. Rheology measurements show that ACTIF-mediated crosslinking strongly stiffens actin-vimentin composites. Finally, we demonstrate the modularity of this approach by creating an ACTIF variant with the intermediate filament binding domain of Adenomatous Polyposis Coli. Our protein engineering approach provides a new cell-free system for the biophysical characterization of intermediate filament-binding crosslinkers and for understanding the mechanical synergy between actin and vimentin in mesenchymal cells.HIGHLIGHTSEngineering of a recombinant actin-vimentin crosslinker called ACTIF with the plectin intermediate filament binding domain (IFBD), calponin homology domains that mediate actin binding, and a coiled-coil linker.ACTIF crosslinks F-actin and vimentin and mediates their co-localizationin vitro.ACTIF has a binding affinity for vimentin that is about 500 times higher than for F-actin.ACTIF forms composite bundles of F-actin and vimentin filaments.Composite F-actin/vimentin networks stiffen upon crosslinking with ACTIF.The design of actin-vimentin crosslinker is modular, as other IFBDs like APCn2 can also be used.
The core microbiome of cultured Pacific oyster spat develops with age but not mortality
Authors: Cho Anna , Finke Jan F. , Zhong Kevin X. , Chan Amy M. , Saunders Rob , Schulze Angela , Warne Snehal , Miller Kristina M. , Suttle Curtis A. 
Published: October 2023

AbstractThe Pacific oyster (Magallana gigas, also known asCrassostrea gigas) is the most widely cultured shellfish worldwide, but production has been affected by mortality events. This includes mortality events in hatcheries that can threaten the seed supply for growers. There are several pathogens that cause disease in oysters, but in many cases mortality events cannot be attributed to a single agent, and appear to be multifactorial and involve a combination of environmental variables, microbial interactions and disbiosis. In many organisms, a mature microbiome provides resilience against pathogens and environmental stressors. In this study we investigated the microbiomes of cohorts of freshly settled oyster spat, some of which experienced notable mortality. Deep sequencing of 16S rRNA gene fragments did not show a significant difference among the microbiomes of cohorts experiencing different levels of mortality, but revealed a characteristic core microbiome with 74 taxa. Irrespective of mortality, the spat core microbiomes changed significantly in the relative abundance of taxa as the spat aged; yet, remained distinct from the microbial community in the surrounding water. The core microbiome was dominated by bacteria in the familiesRhodobacteraceae,Nitrosomonadaceae,Flavobacteriaceae, PirellulaeceaeandSaprospiraceae. Of these, 14 taxa were indicative for the change in the core microbiome, which we designated as the “Hard-Core Microbiome”. The variability in diversity and richess of members of the core taxa decreased with oyster-spat aging, implying niche occupation. The study further accounts for the exchange of microbes with surrounding water during the core microbiome development. The observed shifts in the core microbiome with ageing oyster spat implies a crucial developmental period for the core microbiome of rearing spat.ImportanceThe Pacific oyster (Magallana gigas, also known asCrassostrea gigas) is the most widely cultivated shellfish and is important to the economy of many coastal communities. However, high mortality of spat during the first few days following metamorphosis can affect the seed supply to oyster growers. Here, we show that the microbiome composition of recently settled oyster spat experiencing low or high mortality were not significantly different. Instead, development of the core microbiome were associated with spat aging and was partially driven by dispersal through the water. These findings imply the importance of early stage rearing conditons for spat microbiome development in aquaculture facilities. Furthermore, shellfish growers could gain information about the developmental state of the oyster spat microbiome by assessing key taxa. Additionally, the study provides a baseline micriobiome for future hypothesis testing on developing spat.
Attention, Musicality, and Familiarity Shape Cortical Speech Tracking at the Musical Cocktail Party
Authors: Brown Jane A. , Bidelman Gavin M. 
Published: October 2023

AbstractThe “cocktail party problem” challenges our ability to understand speech in noisy environments, which often include background music. Here, we explored the role of background music in speech-in-noise listening. Participants listened to an audiobook in familiar and unfamiliar music while tracking keywords in either speech or song lyrics. We used EEG to measure neural tracking of the audiobook. When speech was masked by music, the modeled peak latency at 50 ms (P1TRF) was prolonged compared to unmasked. Additionally, P1TRFamplitude was larger in unfamiliar background music, suggesting improved speech tracking. We observed prolonged latencies at 100 ms (N1TRF) when speech was not the attended stimulus, though only in less musical listeners. Our results suggest early neural representations of speech are enhanced with both attention and concurrent unfamiliar music, indicating familiar music is more distracting. One’s ability to perceptually filter “musical noise” at the cocktail party depends on objective musical abilities.
Stringent Control Over Cytoplasmic and Membrane Densities Defines Cell Geometry inEscherichia coli
Authors: Chure Griffin , de Silva Roshali T. , Sharma Richa , Lanz Michael C. , Cremer Jonas 
Published: October 2023

AbstractUnderstanding how cells regulate their growth rate, macromolecular composition, and size have been central topics in the study of microbial physiology for the better part of a century. However, we lack a mechanistic understanding of how cells so tightly coordinate biosynthesis and size control across diverse environments. In this work, we present a biophysical model of cell size control that quantitatively predicts how rod-shaped bacterial cells such asE. coliregulate their surface-to-volume ratio as a function of their composition. Central to this theory is a biochemical constraint that the protein density within the cell membranes and the macromolecular density within the cell cytoplasm are strictly controlled and kept at a constant ratiometric value. Through a reanalysis of more than 30 published data sets coupled with our own experiments, we demonstrate that this theory quantitatively predicts how the surface-to-volume ratio scales with the total RNA-to-protein ratio. We further test and confirm this theory by directly adjusting the RNA-to-protein ratio through genetic control of cellular ppGpp concentrations. This work demonstrates that cellular composition, rather than the growth rate, drives the regulation of cell geometry and provides a candidate biophysical mechanism for how cell size homeostasis is manifest.
Natural genetic variation inGLK1-mediated photosynthetic acclimation in response to light
Authors: Muino Jose M , Großmann Christopher , Kleine Tatjana , Kaufmann Kerstin 
Published: October 2023

ABSTRACTGOLDEN-like (GLK) transcription factors are central regulators of chloroplast biogenesis in Arabidopsis and other species. Findings from Arabidopsis show that these factors also contribute to photosynthetic acclimation, e.g. to variation in light intensity, and are controlled by retrograde signals emanating from the chloroplast. However, the natural variation of GLK1-centered gene-regulatory networks is largely unexplored. By evaluating the activities of GLK1 target genes and GLK1 itself in vegetative leaves of natural Arabidopsis accessions grown under standard conditions, we uncovered a remarkable variation in the activity of GLK1 centered regulatory networks. This is linked with ecogeographic origin of the accessions, and can be associated with a complex genetic variation across loci acting in different functional pathways, including photosynthesis, ROS and brassinosteroid pathways. Our results identify candidate upstream regulators that contribute to GLK1 activity in rosette leaves. Indeed, accessions with higher GLK1 activity, arising from habitats with a high monthly variation in solar radiation levels, may show lower levels of photoinhibition at higher light intensities. Our results provide evidence for natural variation in GLK1 regulatory activities in vegetative leaves. This variation is associated with ecogeographic origin and can contribute to acclimation to high light conditions.
Diversity of RNA viruses in declining Mediterranean forests
Authors: Diez-Hermano Sergio , Pérez-Alonso Pedro Luis , Morell Wilson Acosta , Niño-Sanchez Jonatan , de la Peña Marcos , Diez Julio Javier 
Published: October 2023

AbstractGlobal change alters forestry habitats and facilitates the entry of new pathogens that don’t share a co-evolution history with the forest, leading them into a spiral of decline. As a result, relationships between forests’ organisms get disbalanced. Under this scenario, RNA viruses are of particular interest, as they participate in many of such relationships thanks to their ability to infect a wide range of hosts, even from different kingdoms of life. For this reason, the study of RNA viruses is essential to understand how viral flow across different hosts might occur, and to prevent possible outbreaks of diseases in the future. In this work the RNA virus diversity found in trees, arthropods and fungi from declining Mediterranean forests is described. To this extent, three habitats (Quercus ilex, Castanea sativaandPinus radiata) were sampled and RNAseq was performed on tree tissues, arthropods and fungi. 146 viral sequences were detected by searching for matches to conserved motifs of the RNA-dependent RNA polymerase (RdRP) using Palmscan. Up to 15 viral families were identified, with Botourmiaviridae (28.7%) and Partitiviridae (9.6%) being the most abundant. In terms of genome type, ssRNA(+) viruses were the most represented (83.5%), followed by dsRNA (15%) and two ssRNA(-) representatives. Viruses belonging to families with cross-kingdom capabilities such as Hypoviridae (1), Mitoviridae (6) and Narnaviridae (5) were also found. Distribution of viruses across ecosystems was:Q.ilex(57.5%),P.radiata(26.7%) andC.sativa(15.8%). Interestingly, two RdRP sequences had no matches in available viral databases. This work constitutes a starting point to gain insight into virus evolution and diversity occurring in forests affected by decline, as well as searching for novel viruses that might be participating in unknown infectious pathways.
Phenotypic complexities of rare heterozygous neurexin-1 deletions
Authors: Fernando Michael B. , Fan Yu , Zhang Yanchun , Tokolyi Alex , Murphy Aleta N. , Kammourh Sarah , Deans P.J. Michael , Ghorbani Sadaf , Onatzevitch Ryan , Pero Adriana , Padilla Christopher , Williams Sarah , Flaherty Erin K. , Prytkova Iya A. , Cao Lei , Knowles David A. , Fang Gang , Slesinger Paul A. , Brennand Kristen J. 
Published: October 2023

ABSTRACTGiven the large number of genes significantly associated with risk for neuropsychiatric disorders, a critical unanswered question is the extent to which diverse mutations --sometimes impacting the same gene--will require tailored therapeutic strategies. Here we consider this in the context of rare neuropsychiatric disorder-associated copy number variants (2p16.3) resulting in heterozygous deletions inNRXN1, a pre-synaptic cell adhesion protein that serves as a critical synaptic organizer in the brain. Complex patterns ofNRXN1alternative splicing are fundamental to establishing diverse neurocircuitry, vary between the cell types of the brain, and are differentially impacted by unique (non-recurrent) deletions. We contrast the cell-type-specific impact of patient-specific mutations inNRXN1using human induced pluripotent stem cells, finding that perturbations inNRXN1splicing result in divergent cell-type-specific synaptic outcomes. Via distinct loss-of-function (LOF) and gain-of-function (GOF) mechanisms,NRXN1+/-deletions cause decreased synaptic activity in glutamatergic neurons, yet increased synaptic activity in GABAergic neurons. Reciprocal isogenic manipulations causally demonstrate that aberrant splicing drives these changes in synaptic activity. ForNRXN1deletions, and perhaps more broadly, precision medicine will require stratifying patients based on whether their gene mutations act through LOF or GOF mechanisms, in order to achieve individualized restoration ofNRXN1isoform repertoires by increasing wildtype, or ablating mutant isoforms. Given the increasing number of mutations predicted to engender both LOF and GOF mechanisms in brain disorders, our findings add nuance to future considerations of precision medicine.
Delineation of the pathogenic presynaptic mechanisms of synaptotagmin-1 variants
Authors: Melland Holly , Venter Kyla , Leech Stephanie L. , Ferreira Amy , Arvell Elyas H. , Baker Kate , Gordon Sarah L. 
Published: October 2023

ABSTRACTMissense variants in the presynaptic calcium sensor synaptotagmin-1 (SYT1) are associated with an autosomal dominant neurodevelopmental disorder (NDD). These cause dominant-negative impairment of evoked neurotransmitter release in a mutation-specific manner; however, whether NDD-associated variants also perturb the auxiliary functions of SYT1 remains unknown. We investigated whether the expression of SYT1 variants in cultured hippocampal neurons altered either action potential-independent spontaneous synaptic vesicle exocytosis or synaptic vesicle endocytosis. SYT1 variants did not induce dominant-negative impairment of either process, confirming that defective evoked exocytosis is the major pathogenic mechanism of SYT1-associated NDD. To examine the differential impacts of human variants on evoked exocytosis, both NDD-associated and strategic mutations were used to explore the functional importance of two distinct Ca2+-binding residues in the C2B domain. We show that both the nature of the amino acid change and the specific residues targeted determine the severity of exocytic disturbance. Together, this work informs understanding of SYT1 function and further clarifies potential mechanistic targets for treating SYT1-associated NDD.