bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of Phylogeny of Agrocybe Genus Based on Nucleotide Database in NCBI
Authors: Wang Long , Zhou Qingping , Li Lingli 
Published: July 2022

AbstractThe study of the phylogeny of species is a basic discipline for the effective protection, development, and utilization of their germplasm resources. Since this century, the fungi of the Agrocybe genus have become the most successful class of medium and high-grade edible and medicinal fungi that have been artificially domesticated and grown on a large scale, and have high commercial value. However, there are few reports on its germplasm resources. To clarify the genetic and developmental relationship at the genus level of the Agrocybe in the world. In this paper, based on the NCBI Nucleotide database(National Center for Biotechnology Information), taking the single gene ITS sequence as the research object, the T92 (Tamura 3-parameters) parameter model was used to calculate the genetic distance, and the neighbor joining method was used to construct the genus-level phylogenetic tree of the Agrocybe. The results showed that the phylogenetic tree constructed by 192 ITS single gene sequences of 43 species of the Agrocybe (including 31 known species and 12 undetermined species) in the NCBI Nucleotide database was roughly divided into 6 branches and belonged to different groups, and 17 undetermined species of the Agrocybe sp. was preliminarily identified. This study has a certain reference value for the genetic relationship among different species of Agrocybe all over the world, as well as the selection of the parent bank and the protection of germplasm resources of each species of the genus.
Impact of bilayer composition on the dimerization properties of the Slg1 stress sensor TMD from a multiscale analysis †
Authors: Keller Fabian , Alavizargar Azadeh , Wedlich-Söldner Roland , Heuer Andreas 
Published: July 2022

ABSTRACTMutual interactions between the transmembrane domains of membrane proteins and lipids on the bilayer properties has gained major interest. Most simulation studies of membranes rely on the Martini force field, which has proven extremely helpful in providing molecular insights into realistic systems. Accordingly, an evaluation of the accuracy of Martini is crucial to be able to correctly interpret the reported data. In this study, we combine atomistic and coarse-grained Martini simulations to investigate the properties of transmembrane domains (TMDs) in a model yeast membrane. The results show that the TMD binding state (monomeric, dimeric with positive or negative crossing angle) and the membrane composition significantly influence the properties around the TMDs and change TMD-TMD and TMD-lipid affinities. Furthermore, ergosterol (ERG) exhibits strong affinity to TMD dimers. Importantly, the right-handed TMD dimer configuration is stabilized via TMD-TMD contacts by addition of asymmetric anionic PS. The CG simulations corroborate many of these findings, with two notable exceptions: a systematic overestimation of TMD-ERG interaction and lack of stabilization of the right-handed TMD dimers with the addition of PS. Atomistic simulation results suggest that a meaningful comparison of dimer formation and experimentally-determined network factor may require to additionally take into account the precise conformation and thermodynamic relevance of multimeric TMD clusters.
Hypothalamic extraretinal photoreceptor Opsin3 regulates water balance, body temperature and motor activity
Authors: Bárez-López Soledad , Elsamad Ghadir , Bishop Paul , Searby Daniel , Kershaw Yvonne , Conway-Campbell Becky , Murphy David , Greenwood Michael P 
Published: July 2022

ABSTRACTOpsin 3 (Opn3) is a light-sensitive protein present throughout the mammalian brain, although its functions in this organ are currently unknown. SinceOpn3encoded mRNA increases in the supraoptic nucleus (SON) of the hypothalamus in response to hyperosmotic stimuli, we have explored the role of Opn3 in this nucleus. Byin situhybridization, we have demonstrated thatOpn3is expressed in neurones expressing both arginine vasopressin and oxytocin in the rat SON, suggesting that OPN3 functions in both neuronal types. Gene profiling analysis by RNA-seq suggested that neuropeptide production is impaired when knocking downOpn3in the rat SON, as confirmed by quantitative PCR and immunolabelling. Knocking down Opn3 in the rat SON altered physiological parameters including water intake, body temperature and motor activity. Altogether the data indicates that Opn3 in the SON is involved in the regulation of a number of neuropeptides and other proteins that participate in water homeostasis, body temperature and motor activity.
CAN OF SPINACH, a novel long non-coding RNA, affects iron deficiency responses in Arabidopsis thaliana
Authors: Bakirbas Ahmet , Walker Elsbeth L. 
Published: July 2022

AbstractLong non-coding RNAs (lncRNAs) are RNA molecules with functions independent of any protein-coding potential. A whole transcriptome (RNA-seq) study of Arabidopsis shoots under iron sufficient and deficient conditions was carried out to determine the genes that are iron-regulated in the shoots. We identified two previously unannotated transcripts on chromosome 1 that are significantly iron-regulated. We have called this iron-regulated lncRNA, CAN OF SPINACH (COS). cos mutants have altered iron levels in leaves and seeds. Despite the low iron levels in the leaves, cos mutants have higher chlorophyll levels than WT plants. Moreover, cos mutants have abnormal development during iron deficiency. Roots of cos mutants are longer than those of WT plants, when grown on iron deficient medium. In addition, cos mutant plants accumulate singlet oxygen during iron deficiency. The mechanism through which COS affects iron deficiency responses is unclear, but small regions of sequence similarity to several genes involved in iron deficiency responses occur in COS, and small RNAs from these regions have been detected. We hypothesize that COS is required for normal adaptation to iron deficiency conditions.
Improved Nanopore full-length cDNA sequencing by PCR-suppression
Authors: Bayega Anthony , Oikonomopoulos Spyros , Wang Yu Chang , Ragoussis Jiannis 
Published: July 2022

AbstractFull-length transcript sequencing remains a main goal of RNA sequencing. However, even the application of long-read sequencing technologies such as Oxford Nanopore Technologies still fail to yield full-length transcript sequencing for a significant portion of sequenced reads. Since these technologies can sequence reads that are far longer than the longest known processed transcripts, the lack of efficiency to obtain full-length transcripts from good quality RNAs stems from library preparation inefficiency rather than the presence of degraded RNA molecules. It has previously been shown that addition of inverted terminal repeats in cDNA during reverse transcription followed by single-primer PCR creates a PCR suppression effect that prevents amplification of short molecules thus enriching the library for longer transcripts. We adapted this method for Nanopore cDNA library preparation and show that not only is PCR efficiency increased but gene body coverage is dramatically improved. The results show that implementation of this simple strategy will result in better quality full-length RNA sequencing data and make full-length transcript sequencing possible for most of sequenced reads.Contribution to the fieldLong-read RNA sequencing aims to sequence expressed transcripts in their entirety. However, this has remained a challenge, mainly due to inherent inefficiencies in cDNA library preparation. Herein, we provide a new Nanopore cDNA library preparation protocol, termed Panhandle, that improves the efficiency of cDNA PCR with yields 2 – 8 times the yields obtained with ordinary PCR. This is key, as this should in turn reflect in the possibility of lowering the number of PCR cycles needed to obtain ample sequencing material, which in turn could reduce PCR biases, PCR artifacts, turnaround time, reagents, and could increase general quality of the library. Further, transcripts generated using the Panhandle method show better gene body coverage and more accurate transcription start site mapping than regular methods. This represents an important step towards full-length cDNA sequencing by Nanopore.
Pathogen effector-associated nuclear-localization of RPW8.2 amplifies its expression to boost immunity in Arabidopsis
Authors: Zhao Jing-hao , Huang Yan-yan , Wang He , Yang Xue-mei , Fan Jing , Li Yan , Pu Mei , Zhou Shi-xin , Zhang Ji-wei , Zhao Zhi-xue , Li Guo-bang , Hassan Beenish , Hu Xiao-hong , Chen Xue-wei , Xiao Shunyuan , Wu Xian-jun , Wang Wen-ming 
Published: July 2022

AbstractRESISTANCE TO POWDERY MILDEW 8 (RPW8) defines a unique N-terminal coiled-coil domain of nucleotide-binding and leucine-rich repeat immune receptors required for immune signaling in plants. Arabidopsis RPW8.2 is specifically induced by the powdery mildew (PM) fungus (Golovinomyces cichoracearum) in the infected epidermal cells to activate immunity. The mechanism of RPW8.2-induction is not well understood. Here, we identify aG. cichoracearumfactor delivered to the nucleus of the host cell, named Gc-RPW8.2 interacting protein 1 (GcR8IP1). Ectopic expression of GcR8IP1 in Arabidopsis orNicotiana benthamianasuppressed host immune responses and enhanced susceptibility to PM. Host-induced gene silencing ofGcR8IP1compromised PM infectivity in susceptible Arabidopsis plants. Co-expression of GcR8IP1 with RPW8.2 increased nuclear localization of RPW8.2, which in turn, promoted transcriptional amplification ofRPW8.2. Thus, RPW8.2-dependent defense strengthening is due to altered partitioning of RPW8.2 by an effector of a PM fungus, which exemplifies an atypical form of effector-triggered immunity.
PHYTOMap: Multiplexed single-cell 3D spatial gene expression analysis in plant tissue
Authors: Nobori Tatsuya , Oliva Marina , Lister Ryan , Ecker Joseph R. 
Published: July 2022

AbstractRetrieving the complex responses of individual cells in the native three-dimensional tissue context is crucial for a complete understanding of tissue functions. Here, we present PHYTOMap (Plant HYbridization-based Targeted Observation of gene expression Map), a multiplexed fluorescence in situ hybridization method that enables single-cell and spatial analysis of gene expression in whole-mount plant tissue in a transgene-free manner and at low cost. We applied PHYTOMap to simultaneously analyze 28 cell type marker genes in Arabidopsis roots and successfully identified major cell types, demonstrating that our method can substantially accelerate the spatial mapping of marker genes defined in single-cell RNA-seq datasets in complex plant tissue.
The porcine cGAS-STING pathway exerts an unusual antiviral function independent of IFN and autophagy
Authors: Jiang Sen , Xia Nengwen , Luo Jia , Zhang Youwen , Cao Qi , Zhang Jiajia , Wang Yuening , Zheng Wanglong , Chen Nanhua , Meurens François , Zhu Jianzhong 
Published: July 2022

AbstractThe innate immune DNA sensing cGAS-STING pathway exerts strong antiviral activity through the downstream interferon (IFN) production; however, it has been recently recognized that IFN independent activity of STING also plays an important role in antiviral functions. Nevertheless, the IFN independent antiviral activity of STING is not fully understood. In this study, we showed that porcine STING (pSTING) played a critical role in anti-HSV1 and anti-VSV infections, and IFN defective mutants including pSTING pLxIS sub, S365A and ΔCTT all exhibited similar antiviral functions to wild type (WT) pSTING. Further, all these IFN defective pSTING mutants possessed a comparable autophagy activity relative to WT pSTING as expected. From pSTING WT, S365A and ΔCTT, the residues responsible for autophagy were mutated, which included L333A/R334A, Y167A/L170A and Y245A/L248A, respectively. Surprisingly, all these autophagy defective pSTING mutants still resisted from the two viral infections, demonstrating the pSTING antiviral function independent of IFN as well as autophagy. On the other hand, all the autophagy defective pSTING mutants triggered cell apoptosis, which was associated with the antiviral functions. Additionally, pSTING lost its antiviral activity in TBK1-/- and IRF3-/- porcine macrophages, indicating the involvement of TBK1 and IRF3 in other STING activity such as apoptosis. Collectively, our results revealed that STING exerts both IFN and autophagy independent antiviral activity, and also suggested that STING triggered cell apoptosis might resist from virus infections.
Identification of Mycobacterium abscessus subspecies by MALDI-TOF Mass Spectrometry and Machine Learning
Authors: Rodríguez-Temporal David , Herrera Laura , Alcaide Fernando , Domingo Diego , Vila Neus , Arroyo Manuel J. , Méndez Gema , Muñoz Patricia , Mancera Luis , Ruiz-Serrano María Jesús , Rodríguez-Sánchez Belén 
Published: July 2022

ABSTRACTMycobacterium abscessus complex is one of the most common and pathogenic nontuberculous mycobacteria (NTM) isolated in clinical laboratories. It consists of three subspecies: M. abscessus subsp. abscessus, M. abscessus subsp. bolletii and M. abscessus subsp. massiliense. Due to their different antibiotic susceptibility pattern, a rapid and accurate identification method is necessary for their differentiation. Although matrix assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) has proven useful for NTM identification, the differentiation of M. abscessus subspecies is challenging. In this study, a collection of 244 clinical isolates of M. abscessus complex was used for MALDI-TOF MS analysis and for the development of machine learning predictive models. Overall, using a Random Forest model with several confidence criteria (samples by triplicate and similarity values >60%), a total of 95.8% of isolates were correctly identified at subspecies level. In addition, differences in culture media, colony morphology and geographic origin of the strains were evaluated, showing that the latter most affected the mass spectra of isolates. Finally, after studying all protein peaks previously reported for this complex, two novel peaks with potential for subspecies differentiation were found. Therefore, machine learning methodology has proven to be a promising approach for rapid and accurate identification of subspecies of the M. abscessus complex using MALDI-TOF MS.
Enveloped viruses show increased propensity to cross-species transmission and zoonosis
Authors: Valero-Rello Ana , Sanjuán Rafael 
Published: July 2022

ABSTRACTThe transmission of viruses between different host species is a major source of emerging diseases and is of particular concern in the case of zoonotic transmission from mammals to humans. Several zoonosis risk factors have been identified, but it is currently unclear which viral traits primarily influence this process, as previous work has focused on a few hundred viruses that are not representative of the actual viral diversity. Here we investigate fundamental virological traits that influence cross-species transmissibility and zoonotic propensity by interrogating a database of over 12,000 mammalian virus-host associations, obtained mainly from recent viral metagenomics projects. Our analysis reveals that enveloped viruses tend to infect more host species and are more likely to infect humans than non-enveloped viruses, while other viral traits such as genome composition, structure, size or the viral replication compartment play a minor role. This contrasts with the previous notion that viral envelopes did not significantly impact or even reduced zoonotic risk, and should help better prioritize outbreak prevention efforts. We suggest several mechanisms by which viral envelopes could promote cross-species transmissibility, including structural flexibility and evasion of viral entry barriers.
Microbiota colonization tunes the antigen threshold of microbiota-specific T cell activation in the gut
Authors: Hoces Daniel , Corak Basak , Estrada Brull Anna , Berent Sara , Faccin Erica , Moresi Claudia , Keys Tim , Joller Nicole , Slack Emma 
Published: July 2022

ABSTRACTHarnessing the potential of commensal bacteria for immunomodulatory therapy in the gut requires the identification of conditions that modulate immune activation towards incoming colonizing bacteria. In this study, we used the commensal Bacteroides thetaiotaomicron (B.theta) and combined it with B.theta-specific transgenic T cells, in the context of defined colonization of gnotobiotic and immunodeficiency mouse models, to probe the factors modulating bacteria-specific T cell activation against newly colonizing bacteria. After colonizing germ-free (GF) and conventionally raised (SPF) mice with B.theta, we only observed proliferation of B.theta-specific T cells in GF mice. Using simple gnotobiotic communities we could further demonstrate that T-cell activation against newly colonizing gut bacteria is restricted by previous bacteria colonization in GF mice. However, this restriction requires a functional adaptive immune system as Rag1-/- allowed B.theta-specific T cell proliferation even after previous colonization. Interestingly, this phenomenon seems to be dependent on the type of TCR-transgenic model used. B.theta-specific transgenic T cells also proliferated after gut colonization with an E.coli strain carrying the B.theta-specific epitope. However, this was not the case for the SM-1 transgenic T cells as they did not proliferate after similar gut colonization with an E.coli strain expressing the cognate epitope. In summary, we found that activation of T cells towards incoming bacteria in the gut is modulated by the influence of colonizing bacteria on the adaptive immune system of the host.
Development and optimization of biologically contained Marburg virus for high-throughput antiviral screening
Authors: Vanmechelen Bert , Stroobants Joren , Chiu Winston , Naesens Lieve , Schepers Joost , Vermeire Kurt , Maes Piet 
Published: July 2022

AbstractComparable to the related Ebola virus, Marburg virus is an emerging zoonotic pathogen that causes hemorrhagic fever with a high mortality rate. Therefore, handling of Ebola virus and Marburg virus is limited to biosafety level 4 facilities, of which only a limited number exists worldwide. However, researchers have developed several virus alternatives that are safe to handle in lower biosafety settings. One particularly interesting approach is the engineering of biologically contained Ebola virus by removing an essential gene from the virus genome and providing this missing gene in trans in a specific cell line. Because the virus is confined to this specific cell line, this results in a system that is safe to handle. So far, Ebola virus is the only virus for which biological containment has been reported. Here, we describe the first successful rescue of biologically contained Marburg virus and demonstrate that biological containment is also feasible for other filoviruses. Specifically, we describe the development of containment cell lines for Marburg virus through lentiviral transduction and show the growth and safety characteristics of eGFP-expressing, biologically contained Marburg virus in these cell lines. Additionally, we exploited this newly established Marburg virus system to screen over 500 compounds from available libraries. Lastly, we also validated the applicability of our biologically contained Marburg virus system in a 384-well format, to further illustrate the usefulness of this novel system as an alternative for high-throughput MARV screening of compound libraries.
Establishing Physalis as a new Solanaceae model system enables genetic reevaluation of the inflated calyx syndrome
Authors: He Jia , Alonge Michael , Ramakrishnan Srividya , Benoit Matthias , Soyk Sebastian , Reem Nathan T. , Hendelman Anat , Eck Joyce Van , Schatz Michael C. , Lippman Zachary B. 
Published: July 2022

ABSTRACTThe highly diverse Solanaceae family contains several widely studied model and crop species. Fully exploring, appreciating, and exploiting this diversity requires additional model systems. Particularly promising are orphan fruit crops in the genus Physalis, which occupy a key evolutionary position in the Solanaceae and capture understudied variation in traits such as inflorescence complexity, fruit ripening and metabolites, disease and insect resistance, self-compatibility, and most notable, the striking Inflated Calyx Syndrome (ICS), an evolutionary novelty found across angiosperms where sepals grow exceptionally large to encapsulate fruits in a protective husk. We recently developed transformation and genome editing in Physalis grisea (groundcherry). However, to systematically explore and unlock the potential of this and related Physalis as genetic systems, high-quality genome assemblies are needed. Here, we present chromosome-scale references for P. grisea and its close relative P. pruinosa and use these resources to study natural and engineered variation in floral traits. We first rapidly identified a natural structural variant in a bHLH gene that causes petal color variation. Further, and against expectations, we found that CRISPR-Cas9 targeted mutagenesis of 11 MADS-box genes, including purported essential regulators of ICS, had no effect on inflation. In a forward genetics screen, we identified huskless, which lacks ICS due to mutation of an AP2-like gene that causes sepals and petals to merge into a single whorl of mixed identity. These resources and findings elevate Physalis to a new Solanaceae model system, and establish a new paradigm for the search of factors driving ICS.
A characterization of the neural representation of confidence during probabilistic learning
Authors: Bounmy Tiffany , Eger Evelyn , Meyniel Florent 
Published: July 2022

AbstractLearning in a stochastic and changing environment is a difficult task. Models of learning typically postulate that observations that deviate from the learned predictions are surprising and used to update those predictions. Bayesian accounts further posit the existence of a confidence-weighting mechanism: learning should be modulated by the confidence level that accompanies those predictions. However, the neural bases of this confidence are much less known than the ones of surprise. Here, we used a dynamic probability learning task and high-field MRI to identify putative cortical regions involved in the representation of confidence about predictions during human learning. We devised a stringent test based on the conjunction of four criteria. We localized several regions in parietal and frontal cortices whose activity is sensitive to the confidence of an ideal observer, specifically so with respect to potential confounds (surprise and predictability), and in a way that is invariant to which item is predicted. We also tested for functionality in two ways. First, we localized regions whose activity patterns at the subject level showed an effect of both confidence and surprise in qualitative agreement with the confidence-weighting principle. Second, we found neural representations of ideal confidence that also accounted for subjective confidence. Taken together, those results identify a set of cortical regions potentially implicated in the confidence-weighting of learning.