bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome sequence and annotation ofPericonia digitata, a promising biocontrol agent of phytopathogenic oomycetes
Authors: Bovio Elena , Rancurel Corinne , Seassau Aurélie , Magliano Marc , Gislard Marie , Loisier Anaïs , Kuchly Claire , Ponchet Michel , Danchin Etienne G.J. , Van Ghelder Cyril 
Published: March 2023

AbstractThePericoniafungal genus belongs to the phylum Ascomycota, order Pleosporales, family Periconiaceae.Periconiaare found in many habitats but little is known about their ecology. Several species from this genus produce bioactive molecules.Periconia digitataextracts were shown to be deadly active against the pine wilt nematode. Furthermore,P. digitatawas shown to inhibit plant pathogenic oomycetePhytophthora parasitica. BecauseP. digitatahas great potential as a biocontrol agent and high quality genomic resources are still lacking in the Periconiaceae family, we generated long-read genomic data forP. digitata. Using the PacBio Hifi sequencing technology, we obtained a highly-contiguous genome assembled in 13 chromosomes and totalling ca. 39 Mb. In addition, we produced a reference transcriptome, based on 12 different culture conditions, and proteomic data to support the genome annotation. Besides representing a new reference genome within the Periconiaceae, this work will contribute to our better understanding of the Eukaryotic tree of life and opens new possibilities in terms of biotechnological applications.
Enveloped viruses pseudotyped with mammalian myogenic cell fusogens target skeletal muscle for gene delivery
Authors: Hindi Sajedah M. , Petrany Michael J. , Greenfeld Elena , Focke Leah C. , Cramer Alyssa A.W. , Whitt Michael A. , Prasad Vikram , Chamberlain Jeffrey S. , Podbilewicz Benjamin , Millay Douglas P. 
Published: March 2023

SummaryEntry of enveloped viruses into cells is mediated by fusogenic proteins that form a complex between membranes to drive rearrangements needed for fusion. Skeletal muscle development also requires membrane fusion events between progenitor cells to form multinucleated myofibers. Myomaker and Myomerger are muscle-specific cell fusogens, but do not structurally or functionally resemble classical viral fusogens. We asked if the muscle fusogens could functionally substitute for viral fusogens, despite their structural distinctiveness, and fuse viruses to cells. We report that engineering of Myomaker and Myomerger on the membrane of enveloped viruses leads to specific transduction of skeletal muscle. We also demonstrate that locally and systemically injected virions pseudotyped with the muscle fusogens can deliver micro-Dystrophin (μDys) to skeletal muscle of a mouse model of Duchenne muscular dystrophy. Through harnessing the intrinsic properties of myogenic membranes, we establish a platform for delivery of therapeutic material to skeletal muscle.
Spontaneous helping in pigs is mediated by helper’s social attention and distress signals of individuals in need
Authors: Moscovice Liza R. , Eggert Anja , Manteuffel Christian , Rault Jean-Loup 
Published: March 2023

AbstractHelping behaviour is of special interest for prosociality because it appears to be motivated by the needs of others. We developed a novel paradigm to investigate helping in pigs (Sus scrofa domesticus) and tested 75 individuals in eight groups in their home pens. Two identical compartments were attached to the pen, equipped with a window, and a door that could be opened from the outside by lifting a handle. Pigs in all groups spontaneously opened doors during a five-day familiarization. During testing, each pig was isolated once from its group and placed in one of the two compartments, in a counter-balanced order. In 85% of cases, pigs released a trapped group member from the test compartment within 20 minutes (median latency = 2.2 minutes). Pigs were more likely and quicker to open a door to free the trapped pig than to open a door to an empty compartment. Pigs who spent more time looking at the window of the test compartment were more likely to help. Distress signals by the trapped pig increased its probability of being helped. Responses are consistent with several criteria for identifying targeted helping, but results can also be explained by selfish motivations.
DNA storage in thermoresponsive microcapsules for repeated random multiplexed data access
Authors: Bögels Bas W.A. , Nguyen Bichlien H. , Ward David , Gascoigne Levena , Schrijver David P. , Pistikou Anna-Maria Makri , Joesaar Alex , Yang Shuo , Voets Ilja K. , Mulder Willem J.M. , Phillips Andrew , Mann Stephen , Seelig Georg , Strauss Karin , Chen Yuan-Jyue , de Greef Tom F. A. 
Published: March 2023

AbstractOwing to its longevity and extremely high information density, DNA has emerged as an attractive medium for archival data storage. Scalable parallel random access of information is a desirable property of any storage system. For DNA-based storage systems, however, this yet has to be robustly established. Here we develop thermoconfined PCR, a novel method that enables multiplexed, repeated random access of compartmentalized DNA files. Our strategy is based on stable localization of biotin-functionalized oligonucleotides inside microcapsules with temperature-dependent membrane permeability. At low temperatures, microcapsules are permeable to enzymes, primers, and amplified products, while at high temperatures membrane collapse prevents molecular crosstalk during amplification. We demonstrate that our platform outperforms non-compartmentalized DNA storage with respect to repeated random access and reducing amplification bias during multiplex PCR. Using fluorescent sorting, we additionally demonstrate sample pooling and data retrieval by barcoding of microcapsules. Our thermoresponsive microcapsule technology offers a scalable, sequence-agnostic approach for repeated random access of archival DNA files.
Many Families of Lids for TonB-dependent Transporters inBacteroides
Authors: Price Morgan N. , Deutschbauer Adam M. , Arkin Adam P. 
Published: March 2023

AbstractMost TonB-dependent transporters inBacteroidesbelong to the SusC family and work with an outer-membrane lipoprotein from the SusD family that functions like a lid. But the best-studied strain,B. thetaiotaomicronVPI-5482, also contains 18 TonB-dependent transporters that are not from the SusC family. We identified six families of putative lids for these transporters. The putative lids are lipoproteins that are encoded next to TonB-dependent transporters, but they are not homologous to SusD. AlphaFold-Multimer predicts that the putative lids bind the outer faces of the corresponding TonB-dependent receptors. Genetic data suggests that members of four of these families are required for the activity of the corresponding TonB-dependent receptors. Overall, of the 18 TonB-dependent receptors that do not belong to the SusC family, we identified alternate lids for nine.
Multidimensional specialization and generalization are pervasive in soil prokaryotes with generalists dominating communities and specialists more central in networks
Authors: Hernandez Damian J. , Kiesewetter Kasey N. , Almeida Brianna K. , Revillini Daniel , Afkhami Michelle E. 
Published: March 2023

AbstractHabitat specialization underpins biological processes from species distributions to speciation. However, organisms are often described as specialists or generalists based on a single niche axis, despite facing complex, multidimensional environments. Here, we analyzed 236 prokaryotic communities across the United States demonstrating for the first time that 90% of >1,200 prokaryotes followed one of two trajectories: specialization on all niche axes (multidimensional specialization) or generalization on all axes (multidimensional generalization). We then documented that this pervasive multidimensional specialization/generalization had a wide range of ecological and evolutionary consequences. First, multidimensional specialization and generalization are highly conserved with very few transitions between these two trajectories. Second, multidimensional generalists dominated communities because they were 73 times more abundant than specialists. Lastly, multidimensional specialists played important roles in community structure with ∼220% more connections in microbiome networks. These results indicate that multidimensional generalization and specialization are evolutionarily stable with multidimensional generalists supporting larger populations and multidimensional specialists playing important roles within communities likely stemming from their overrepresentation among pollutant detoxifiers and nutrient cyclers. Taken together, we demonstrate that the vast majority of soil prokaryotes are restricted to one of two multidimensional niche trajectories, multidimensional specialization or multidimensional generalization, which then has far-reaching consequences for evolutionary transitions, microbial dominance, and community roles.One-Sentence SummaryPervasive multidimensional specialization and generalization impacts evolutionary trajectories, microbial dominance, and community roles.
Mitochondrial Sodium/Calcium Exchanger (NCLX) Regulates Basal and Starvation-Induced Autophagy Through Calcium Signaling
Authors: de Miranda Ramos Vitor , Serna Julian D.C. , Vilas-Boas Eloisa A. , Cabral-Costa João Victor , da Cunha Fernanda M. , Kataura Tetsushi , Korolchuk Viktor I. , Kowaltowski Alicia J. 
Published: March 2023

AbstractMitochondria shape intracellular Ca2+signaling through the concerted activity of Ca2+uptake via mitochondrial calcium uniporter, and efflux from by Na+/Ca2+exchangers (NCLX). Here, we describe a novel relationship between NCLX, intracellular Ca2+, and autophagic activity. Conditions that stimulate autophagyin vivoandin vitro,such as caloric restriction and nutrient deprivation, upregulate NCLX expression in hepatic tissue and cells. Conversely, knockdown of NCLX impairs basal and starvation-induced autophagy. Similarly, acute inhibition of NCLX activity by CGP 37157 affects bulk and endoplasmic reticulum autophagy (ER-phagy) without significant impacts on mitophagy. Mechanistically, CGP 37157 inhibited the formation of FIP200 puncta and downstream autophagosome biogenesis. Inhibition of NCLX caused decreased cytosolic Ca2+levels, and intracellular Ca2+chelation similarly suppressed autophagy. Furthermore, chelation did not exhibit an additive effect on NCLX inhibition of autophagy, demonstrating that mitochondrial Ca2+efflux regulates autophagy through the modulation of Ca2+signaling. Collectively, our results show that the mitochondrial Ca2+extrusion pathway through NCLX is an important regulatory node linking nutrient restriction and autophagy regulation.
Three-dimensional reconstructions of mechanosensory end organs suggest a unifying mechanism underlying dynamic, light touch
Authors: Handler Annie , Zhang Qiyu , Pang Song , Nguyen Tri M. , Iskols Michael , Nolan-Tamariz Michael , Cattel Stuart , Plumb Rebecca , Sanchez Brianna , Ashjian Karyl , Shotland Aria , Brown Bartianna , Kabeer Madiha , Turecek Josef , Rankin Genelle , Xiang Wangchu , Pavarino Elisa C. , Africawala Nusrat , Santiago Celine , Lee Wei-Chung Allen , Shan Xu C. , Ginty David D. 
Published: March 2023

ABSTRACTSpecialized mechanosensory end organs within mammalian skin—hair follicle-associated lanceolate complexes, Meissner corpuscles, and Pacinian corpuscles—enable our perception of light, dynamic touch1. In each of these end organs, fast-conducting mechanically sensitive neurons, called Aβ low-threshold mechanoreceptors (Aβ LTMRs), associate with resident glial cells, known as terminal Schwann cells (TSCs) or lamellar cells, to form complex axon ending structures. Lanceolate-forming and corpuscle-innervating Aβ LTMRs share a low threshold for mechanical activation, a rapidly adapting (RA) response to force indentation, and high sensitivity to dynamic stimuli1–6. How mechanical stimuli lead to activation of the requisite mechanotransduction channel Piezo27–15and Aβ RA-LTMR excitation across the morphologically dissimilar mechanosensory end organ structures is not understood. Here, we report the precise subcellular distribution of Piezo2 and high-resolution, isotropic 3D reconstructions of all three end organs formed by Aβ RA-LTMRs determined by large volume enhanced Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) imaging. We found that within each end organ, Piezo2 is enriched along the sensory axon membrane and is minimally or not expressed in TSCs and lamellar cells. We also observed a large number of small cytoplasmic protrusions enriched along the Aβ RA-LTMR axon terminals associated with hair follicles, Meissner corpuscles, and Pacinian corpuscles. These axon protrusions reside within close proximity to axonal Piezo2, occasionally contain the channel, and often form adherens junctions with nearby non-neuronal cells. Our findings support a unified model for Aβ RA-LTMR activation in which axon protrusions anchor Aβ RA-LTMR axon terminals to specialized end organ cells, enabling mechanical stimuli to stretch the axon in hundreds to thousands of sites across an individual end organ and leading to activation of proximal Piezo2 channels and excitation of the neuron.
Modular small RNA drives pathogen emergence
Authors: Balasubramanian Deepak , Almagro-Moreno Salvador 
Published: March 2023

ABSTRACTPathogen emergence is a poorly understood complex phenomenon. To date, the molecular mechanisms that allow strains within a bacterial population to emerge as human pathogens remain mostly enigmatic. We recently uncovered that toxigenicVibrio choleraeencode preadaptations to host colonization, what we term virulence adaptive polymorphisms (VAPs), however, the molecular mechanisms driving them are not known.ompUis a VAP-encoding gene that is associated with the production of the major outer membrane porin OmpU. Here, we show that theompUORF also encodes a modular small RNA overlapping its 3’ terminus that plays a major role inV. choleraephysiology. We determined that the OmpU-encoded sRNA (OueS) strongly suppresses biofilm formation, a phenotype that is essential for host intestinal colonization, via repression of iron uptake. OueS controls over 84% of the genes regulated by ToxR, a major virulence regulator, and plays an integral role during the infection process. We demonstrate that OueS is critical for intestinal colonization and its bimodular nature dictates the virulence potential ofV. cholerae. Overall, our study reveals specific molecular mechanisms leading to the emergence of pathogenic traits in bacteria unveiling the hidden genetics associated with this process. We propose a scenario where a limited number of modular genes could explain the emergence of novel phenotypic traits in biological systems.
Understanding the neural mechanisms of emotion-cognition interaction via high resolution mapping in space, time, frequency, and information transfer
Authors: Dietrich Anya , Pinzuti Edoardo , Cabral-Calderin Yuranny , Müller-Dahlhaus Florian , Wibral Michael , Tüscher Oliver 
Published: March 2023

AbstractHuman behaviour is inextricably linked to the interaction of emotion and cognition. For decades, emotion and cognition were perceived as separable processes, yet with mutual interactions. Recently, this differen-tiation has been challenged by more integrative approaches, but without addressing the exact neurophysiological basis of their interaction. Here, we aimed to uncover neurophysiological mechanisms of emotion-cognition interaction. We used an emotional Flanker task paired with EEG/FEM beamforming in a large cohort (N=121) of healthy human participants, obtaining high temporal and fMRI-equivalent spatial resolution. Spatially, emotion and cognition processing overlapped in the right inferior frontal gyrus (rIFG), specifically inpars triangularis. Temporally, emotion and cognition processing overlapped during the transition from emotional to cognitive processing, with a stronger interaction inβ-band power leading to worse behavioral performance. Despite functionally segregated subdivisions in rIFG, frequency-specific information flowed extensively within IFG and top-down to visual areas (V2, Precuneus) – explaining the behavioral interference effect. Thus, for the first time we here show the neural mechanisms of emotion-cognition interaction in space, time, frequency and information transfer with high temporal and spatial resolution, revealing a central role forβ-band activity in rIFG. Our results support the idea that rIFG plays a broad role in both inhibitory control and emotional interference inhibition as it is a site of convergence in both processes. Furthermore, our results have potential clinical implications for understanding dysfunctional emotion-cognition interaction and emotional interference inhibition in psychiatric disor-ders, e.g. major depression and substance use disorder, in which patients have difficulties in regulating emotions and executing inhibitory control.
A sex-specific switch in a single glial cell patterns the apical extracellular matrix
Authors: Fung Wendy , Tan Taralyn M. , Kolotuev Irina , Heiman Maxwell G. 
Published: March 2023

ABSTRACTApical extracellular matrix (aECM) constitutes the interface between every tissue and the outside world. It is patterned into diverse tissue-specific structures through unknown mechanisms. Here, we show that a male-specific genetic switch in a singleC. elegansglial cell patterns the aECM into a ∼200 nm pore, allowing a male sensory neuron to access the environment. We find that this glial sex difference is controlled by factors shared with neurons (mab-3, lep-2, lep-5) as well as previously unidentified regulators whose effects may be glia-specific (nfya-1, bed-3, jmjd-3.1). The switch results in male-specific expression of a Hedgehog-related protein, GRL-18, that we discover localizes to transient nanoscale rings at sites of aECM pore formation. Blocking male-specific gene expression in glia prevents pore formation, whereas forcing male-specific expression induces an ectopic pore. Thus, a switch in gene expression in a single cell is necessary and sufficient to pattern aECM into a specific structure.
The skate spiracular organ develops from a unique neurogenic placode, distinct from lateral line placodes
Authors: Gillis J. Andrew , Criswell Katharine E. , Baker Clare V. H. 
Published: March 2023

AbstractThe spiracular organ is an epithelial pouch or tube lined with mechanosensory hair cells, found embedded in the wall of the spiracle/spiracular chamber (remnant of the first pharyngeal cleft) in many non-teleost jawed fishes. It is innervated via a branch of the anterior lateral line nerve and usually considered a specialised lateral line organ, although it most likely functions as a proprioceptor for jaw movement. It is homologous to the paratympanic organ: a hair cell-lined epithelial pouch embedded in the wall of the middle ear (which evolved from the spiracular chamber) of birds, alligators andSphenodon. A previous fate-mapping study showed that the chicken paratympanic organ and its afferent neurons originate from a molecularly distinct placode immediately dorsal to the geniculate (first epibranchial) placode. Here, DiI fate-mapping in a cartilaginous fish (little skate,Leucoraja erinacea) shows that the spiracular organ derives from a previously unrecognised neurogenic placode immediately dorsal to the geniculate placode and molecularly distinct from lateral line placodes. These findings further support the developmental and evolutionary independence of this unique jawed-vertebrate mechanosensory organ from the lateral line system.Summary statementFate-mapping in a cartilaginous fish supports the developmental independence from the lateral line system of the mechanosensory spiracular organ, consistent with its homology with the amniote paratympanic organ.
AspFlex: molecular tools to study gene expression and regulation inAcinetobacter baumannii
Authors: Brychcy Merlin , Kokodynski Alexis , Lloyd Devin , Godoy Veronica G. 
Published: March 2023

AbstractAcinetobacter baumanniiis a gram negative nosocomial opportunistic pathogen frequently found in hospital settings, causing high incidence of in-hospital infections. It belongs to the ESKAPE group of pathogens (the “A” stands forA. baumannii) that is known to easily develop antibiotic resistances. It is crucial to create a molecular toolkit to investigate its basic biology, such as gene regulation. DespiteA. baumanniibeing a threat for almost two decades, an efficient and high-throughput plasmid system that can replicate inA. baumanniihas not yet been developed. This study adapts an existing toolkit forEscherichia colito meetA. baumannii’sunique requirements and expands it by constructing a mobile CRISPR interference (CRISPRi) system that can produce gene knockdowns inA. baumannii.
Single-Soma Deep RNA Sequencing of Human Dorsal Root Ganglion Neurons Reveals Novel Molecular and Cellular Mechanisms Underlying Somatosensation
Authors: Yu Huasheng , Usoskin Dmitry , Nagi Saad S. , Hu Yizhou , Kupari Jussi , Bouchatta Otmane , Cranfill Suna Li , Gautam Mayank , Su Yijing , Lu You , Wymer James , Glanz Max , Albrecht Phillip , Song Hongjun , Ming Guo-Li , Prouty Stephen , Seykora John , Wu Hao , Ma Minghong , Rice Frank L , Olausson Håkan , Ernfors Patrik , Luo Wenqin 
Published: March 2023

AbstractThe versatility of somatosensation arises from heterogeneous dorsal root ganglion (DRG) neurons. However, soma transcriptomes of individual human DRG (hDRG) neurons – critical information to decipher their functions – are lacking due to technical difficulties. Here, we developed a novel approach to isolate individual hDRG neuron somas for deep RNA sequencing (RNA-seq). On average, >9,000 unique genes per neuron were detected, and 16 neuronal types were identified. Cross-species analyses revealed remarkable divergence among pain-sensing neurons and the existence of human-specific nociceptor types. Our deep RNA-seq dataset was especially powerful for providing insight into the molecular mechanisms underlying human somatosensation and identifying high potential novel drug targets. Our dataset also guided the selection of molecular markers to visualize different types of human afferents and the discovery of novel functional properties using single-cellin vivoelectrophysiological recordings. In summary, by employing a novel soma sequencing method, we generated an unprecedented hDRG neuron atlas, providing new insights into human somatosensation, establishing a critical foundation for translational work, and clarifying human species-specific properties.