bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-cell resolution genetic association analysis of heterogeneous bacterial communities by utilizing droplet digital PCR
Authors: Dutra Lara Ambrosio Leal , Jalasvuori Matti , Franz Ole , Nurminen Kimi , Salmi Pauliina , Tiirola Marja , Penttinen Reetta 
Published: September 2022

AbstractMicrobial communities often respond to various challenges, such as the presence of antibiotics, as a whole. Dissecting these community-level effects into separate acting entities requires the identification of organisms that carry functional genes for the observed feature. However, unculturable microbes abound in various environments, hence making the identification challenging. Here we present a cultivation-free technique that can be utilized to link functional genes with carrying bacterial species at single-cell resolution. The developed protocol is relatively simple to use, utilizes commercially available droplet microfluidics devices, does not require toxic reagents (as compared to some previous methods), eliminates invalid signals emerging from extracellular DNA, and allows simultaneous analysis of community diversity via 16S rRNA gene sequencing. The method can be customized for any given genetic trait to accurately identify its hosting subpopulation from a heterogeneous and potentially uncultivable bacterial community.
Nuclear translocation of spike mRNA and protein is a novel pathogenic feature of SARS-CoV-2
Authors: Sattar Sarah , Kabat Juraj , Jerome Kailey , Feldmann Friederike , Bailey Kristina , Mehedi Masfique 
Published: September 2022

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes severe pathophysiology in vulnerable older populations and appears to be highly pathogenic and more transmissible than SARS-CoV or MERS-CoV [1, 2]. The spike (S) protein appears to be a major pathogenic factor that contributes to the unique pathogenesis of SARS-CoV-2. Although the S protein is a surface transmembrane type 1 glycoprotein, it has been predicted to be translocated into the nucleus due to the novel nuclear localization signal (NLS) “PRRARSV”, which is absent from the S protein of other coronaviruses. Indeed, S proteins translocate into the nucleus in SARS-CoV-2-infected cells. To our surprise, S mRNAs also translocate into the nucleus. S mRNA colocalizes with S protein, aiding the nuclear translocation of S mRNA. While nuclear translocation of nucleoprotein (N) has been shown in many coronaviruses, the nuclear translocation of both S mRNA and S protein reveals a novel pathogenic feature of SARS-CoV-2.Author summaryOne of the novel sequence insertions resides at the S1/S2 boundary of Spike (S) protein and constitutes a functional nuclear localization signal (NLS) motif “PRRARSV”, which may supersede the importance of previously proposed polybasic furin cleavage site “RRAR”. Indeed, S protein’s NLS-driven nuclear translocation and its possible role in S mRNA’s nuclear translocation reveal a novel pathogenic feature of SARS-CoV-2.
Lineage-specific oncogenes drive growth of major forms of human cancer using common downstream mechanisms
Authors: Kauko Otto , Turunen Mikko , Pihlajamaa Päivi , Häkkinen Antti , Queiroz Rayner M. L. , Pääkkönen Mirva , Ventelä Sami , Gaetani Massimiliano , Lundström Susanna , Murgia Antonio , Sahu Biswajyoti , Routila Johannes , Irjala Heikki , Griffin Julian L. , Lilley Kathryn S. , Kivioja Teemu , Hautaniemi Sampsa , Taipale Jussi 
Published: September 2022

ABSTRACTMutations in hundreds of genes have been associated with formation of human cancer, with different oncogenic lesions prevalent in different cancer types. Yet, the malignant phenotype is simple, characterized by unrestricted growth of cells that invade neighboring healthy tissue and in many cases metastasize to distant organs. One possible hypothesis explaining this dichotomy is that the cancer genes regulate a common set of target genes, which then function as master regulators of essential cancer phenotypes, such as growth, invasion and metastasis. To identify mechanisms that drive the most fundamental feature shared by all tumors – unrestricted cell proliferation – we used a multiomic approach to identify common transcriptional and posttranslational targets of major oncogenic pathways active in different cancer types, and combined this analysis with known regulators of the cell cycle. We identified translation and ribosome biogenesis as common targets of both transcriptional and posttranslational oncogenic pathways. By combining proteomic analysis of clinical samples with functional studies of cell cultures, we also establish NOLC1 as a key node whose convergent regulation both at transcriptional and posttranslational level is critical for tumor cell proliferation. Our results indicate that lineage-specific oncogenic pathways commonly regulate the same set of targets important for growth control, revealing novel key downstream nodes that could be targeted for cancer therapy or chemoprevention.
MTG-Link: leveraging barcode information from linked-reads to assemble specific loci
Authors: Guichard Anne , Legeai Fabrice , Tagu Denis , Lemaitre Claire 
Published: September 2022

AbstractBackgroundLocal assembly with short and long reads has proven to be very useful in many applications: reconstruction of the sequence of a locus of interest, gap-filling in draft assemblies, as well as alternative allele reconstruction of large insertion variants. Whereas linked-read technologies have a great potential to assemble specific loci as they provide long-range information while maintaining the power and accuracy of short-read sequencing, there is a lack of local assembly tools for linked-read data.ResultsWe present MTG-Link, a novel local assembly tool dedicated to linked-reads. The originality of the method lies in its read subsampling step which takes advantage of the barcode information contained in linked-reads mapped in flanking regions. We validated our approach on several datasets from different linked-read technologies. We show that MTG-Link is able to assemble successfully large sequences, up to dozens of Kb. We also demonstrate that the read subsampling step of MTG-Link considerably improves the local assembly of specific loci compared to other existing short-read local assembly tools. Furthermore, MTG-Link was able to fully characterize large insertion variants in a human genome and improved the contiguity of a 1.3 Mb locus of biological interest in several individual genomes of the mimetic butterfly (Heliconius numata).ConclusionsMTG-Link is an efficient local assembly tool designed for different linked-read sequencing technologies. MTG-Link source code is available at https://github.com/anne-gcd/MTG-Link and as a Bioconda package.Contactanne.guichard@irisa.fr
Non-destructive collection and metabarcoding of arthropod environmental DNA remained on a terrestrial plant
Authors: Yoneya Kinuyo , Ushio Masayuki , Miki Takeshi 
Published: September 2022

ABSTRACTFor the conservation and community ecology of arthropods and pest controls on terrestrial plants, survey of arthropods is a crucial step. However, efficient surveys are hindered by challenges in collecting small arthropods, and identifying the species. Environmental DNA (eDNA)-based techniques, such as eDNA metabarcording, help overcome these difficulties in aquatic systems. To apply eDNA metabarcording to terrestrial arthropods, we developed a non-destructive eDNA collection method. In this method, termed “plant flow collection,” we spray distilled or tap water, or use rainfall, which eventually flows over the surface of the plant, and is collected in a container that is set at the plant base. DNA is extracted from the filtered water samples and a DNA barcode region, such as cytochrome c oxidase subunit I (COI) gene, of the extracted DNA is amplified and sequenced using a high-throughput sequencer. We identified more than 38 taxonomic groups of arthropods at the family level, of which 7 were visually observed or artificially introduced species, whereas the other 31 groups of arthropods, including 18 species, were not observed in the visual survey. Put together, these results show that the developed method is effective for detecting the presence of arthropods in plants.
Light-induced nanoscale deformation in azobenzene thin film triggers rapid intracellular Ca2+increase via mechanosensitive cation channels
Authors: Peussa Heidi , Fedele Chiara , Tran Huy , Fadjukov Julia , Mäntylä Elina , Priimägi Arri , Nymark Soile , Ihalainen Teemu O. 
Published: September 2022

AbstractEpithelial cells are in continuous dynamic biochemical and physical interaction with their extracellular environment. Ultimately, this interplay guides fundamental physiological processes. In these interactions, cells generate fast local and global transients of Ca2+ions, which act as key intracellular messengers. However, the mechanical triggers initiating these responses have remained unclear. Light-responsive materials offer intriguing possibilities to dynamically modify the physical niche of the cells. Here, we use a light-sensitive azobenzene-based glassy material that can be micropatterned with visible light to undergo spatiotemporally controlled deformations. The material allows mechanical stimulation of single cells or multicellular assemblies, offering unique opportunities for experimental mechanobiology. Real-time monitoring of consequential rapid intracellular Ca2+signals reveal that Piezo1 is the key mechanosensitive ion channel generating the Ca2+transients after nanoscale mechanical deformation of the cell culture substrate. Furthermore, our studies indicate that Piezo1 preferably responds to lateral material movement at cell-material interphase rather than to absolute topographical change of the substrate. Finally, experimentally verified computational modeling of the signaling kinetics suggests that the lateral mechanical stimulus triggers multiplexed intercellular signaling that involves Na+, highlighting the complexity of mechanical signaling in multicellular systems. These results give mechanistic understanding on how cells respond to material dynamics and deformations.
Benchmarking strategies for cross-species integration of single-cell RNA sequencing data
Authors: Song Yuyao , Miao Zhichao , Brazma Alvis , Papatheodorou Irene 
Published: September 2022

AbstractThe growing number of available single cell gene expression datasets from different species creates opportunities to explore evolutionary relationships between cell types across species. Cross-species integration of single-cell RNA-sequencing data has been particularly informative in this context. However, in order to do so robustly it is essential to have rigorous benchmarking and appropriate guidelines to ensure that integration results truly reflect biology. We benchmarked 28 combinations of gene homology mapping methods and data integration algorithms in a variety of biological settings. We examined the capability of each strategy to perform species-mixing of known homologous cell types and to preserve biological heterogeneity using 9 established metrics. We also developed a new biology conservation metric to address the maintenance of cell type distinguishability. Overall, scANVI, scVI and SeuratV4 methods achieved a balance between species-mixing and biology conservation. For evolutionarily distant species, including in-paralogs was beneficial. SAMap outperformed when integrating whole-body atlases between species with challenging gene homology annotation. We provided our freely available cross-species integration and assessment pipeline to help analyse new data and develop new algorithms.
Developmental trajectories of the default mode, executive control, and salience networks from the third trimester through the newborn period
Authors: Scheinost Dustin , Chang Joseph , Brennan-Wydra Emma , Lacadie Cheryl , Constable R. Todd , Chawarska Katarzyna , Ment Laura R. 
Published: September 2022

ABSTRACTSocial cognition is critical to early learning. Functional imaging studies in adults and older children suggest the involvement of the default mode (DMN), executive control (ECN), and salience (SAL) networks in social cognition. These networks are vulnerable to environmental insults, and abnormalities of intra- and inter-network connectivity of the three are emerging as biomarkers of neurobehavioral disorders. However, the developmental trajectories of the DMN, ECN, and SAL across the third trimester of gestation and perinatal transition remain largely unknown. Employing resting-state functional MRI studies at 30-32, 34-36, and 40-44 weeks postmenstrual age (PMA), we tested the hypothesis that both intra- and inter-network functional connectivity in the DMN, ECN, and SAL develop across the 30-46 weeks PMA time interval in a longitudinal/cross-sectional sample of 84 fetuses and neonates. A secondary analysis addressed the impact of maternal mental health assessed at 28 weeks PMA on tri-network development from 30-46 weeks PMA. The DMN, ECN, and SAL develop across the third trimester of gestation and the first postnatal month. At the intra-network level, significant increases occurred between 36 to 44 weeks PMA for all three, with network strength values significantly different from 0 beginning at 40 weeks PMA for all. Functional connectivity increased less rapidly in the DMN than in the ECN and SAL networks, suggesting slower maturation of the network subserving social interactions. In contrast, significant inter-network DMN – ECN connectivity greater than 0 was found from 36 weeks PMA through the first postnatal month, suggesting the emergence of inter-network functional connectivity in the fetal brain. Finally, higher maternal mental health symptoms measured at the beginning of the third trimester negatively affected the developmental trajectory of the SAL network across the critical time interval of 30 weeks to 44 weeks PMA. Together, these data provide a framework to compare fetuses and neonates at risk for neurobehavioral disorders and assess the impact of the environment on the developing brain.
Pericytes control vascular stability and auditory spiral ganglion neuron survival
Authors: Zhang Yunpei , Neng Lingling , Sharma Kushal , Hou Zhiqiang , Johnson Anatasiya , Song Junha , Dabdoub Alain , Shi Xiaorui 
Published: September 2022

AbstractThe inner ear has a rich population of pericytes, a multi-functional mural cell essential for sensory hair cell heath and normal hearing. However, the mechanics of how pericytes contribute to the homeostasis of the auditory vascular-neuronal complex in the spiral ganglion is not yet known. In this study, using an inducible and conditional pericyte depletion mouse (PdgfrbCreERT2+/-;ROSA26iDTR+/-) model, we demonstrate, for the first time, that pericyte depletion causes loss of vascular volume and spiral ganglion neurons (SGNs) and adversely affects hearing sensitivity. Using anin vitrotrans-well co-culture system, we show pericytes markedly promote neurite and vascular branch growth in neonatal SGN explants and adult SGNs. The pericyte-controlled neural growth is strongly mediated by pericyte-released exosomes containing vascular endothelial growth factor-A (VEGF-A). Treatment of neonatal SGN explants or adult SGNs with pericyte-derived exosomes significantly enhances angiogenesis, SGN survival, and neurite growth, all of which were inhibited by a selective blocker of the VEGF receptor 2 (Flk1). Our study demonstrates that pericytes in the adult ear are critical for vascular stability and SGN health. Cross-talk between pericytes and SGNs via exosomes is essential for neuronal and vascular health and normal hearing.
Testing the evolutionary drivers of nitrogen-fixing symbioses in challenging soil environments
Authors: Siniscalchi Carolina M. , Kates Heather R. , Soltis Pamela S. , Soltis Douglas E. , Guralnick Robert P. , Folk Ryan A. 
Published: September 2022

SummaryWhile the importance of root nodular symbioses (RNS) in plants has long been recognized, the ecological and evolutionary factors maintaining RNS remain obscure. RNS is associated with environmental stressors such as aridity and nitrogen-poor soils; the ability to tolerate harsh environments may provide ecological opportunities for diversification, yet, nodulators are also diverse outside these environments.We test several environmental determinants of increased survival and enhanced diversification of RNS species, using an explicitly phylogenetic approach for the first time. We assembled the largest phylogeny of the nitrogen-fixing clade to date and a comprehensive set of abiotic niche estimates and nodulation data. We used comparative phylogenetic tools to test environmental and diversification associations.We found that RNS is associated with warm, arid, and nitrogen-poor habitats. However, RNS was gained long before lineages entered these habitats. RNS is associated with accelerated diversification, but diversification rates are heterogeneous among nodulators, and non-legume nodulators do not show elevated diversification.Our findings undermine the interpretation that RNS directly drove the invasion of challenging habitats, and do not support a direct relationship between soil or climate and the diversity of nodulators. Still, RNS may have been an important exaptation allowing further niche evolution.
Cyclitol secondary metabolism is a central feature ofBurkholderialeaf symbionts
Authors: Danneels Bram , Blignaut Monique , Marti Guillaume , Sieber Simon , Vandamme Peter , Meyer Marion , Carlier Aurélien 
Published: September 2022

AbstractThe symbioses between plants of the Rubiaceae and Primulaceae families withBurkholderiabacteria represent unique and intimate plant-bacterial relationships. Many of these interactions have been identified through PCR-dependent typing methods, but there is little information available about their functional and ecological roles. We assembled seventeen new endophyte genomes representing endophytes from thirteen plant species, including those of two previously unknown associations. Genomes of leaf endophytes belonging toBurkholderia s.l. show extensive signs of genome reduction, albeit to varying degrees. Except for one endophyte, none of the bacterial symbionts could be isolated on standard microbiological media. Despite their taxonomic diversity, all endophyte genomes contained gene clusters linked to the production of specialized metabolites, including genes linked to cyclitol sugar analog metabolism and in one instance non-ribosomal peptide synthesis. These genes and gene clusters are unique withinBurkholderia s.l. and are likely horizontally acquired. We propose that the acquisition of secondary metabolite gene clusters through horizontal gene transfer is a prerequisite for the evolution of a stable association between these endophytes and their hosts.
Vesicles driven by dynein and kinesin exhibit directional reversals without external regulators
Authors: D’Souza Ashwin I. , Grover Rahul , Monzon Gina A. , Santen Ludger , Diez Stefan 
Published: September 2022

AbstractIntracellular transport along cytoskeletal filaments propelled by molecular motors ensures the targeted delivery of cargoes to their destinations. Such transport is rarely unidirectional but rather bidirectional, including intermittent pauses and directional reversals owing to the simultaneous presence of opposite-polarity motors. It has been unclear whether such a complex motility pattern results from the sole mechanical interplay between opposite-polarity motors or requires external regulators. Here, we addressed this outstanding question by reconstituting cargo motility along microtubules in vitro by attaching purified Dynein-Dynactin-BICD2 (DDB) and kinesin-3 (KIF16B) to large unilamellar vesicles. Strikingly, we found that this minimal system is sufficient to recapitulate runs, pauses and reversals similar to in vivo cargo motility. In our experiments, reversals were always preceded by vesicle pausing and the transport directionality could be tuned by the relative numbers of opposite-polarity motors on the vesicles. Unexpectedly, during all runs the vesicle velocity was not influenced by the presence of the opposing motors. To gain mechanistic insight into bidirectional transport, we developed a mathematical model which predicts that low numbers of engaged motors are critical to transition between runs and pauses. Taken together, our results suggest that motors diffusively anchored to membranous cargo transiently engage in a tug-of-war during pauses where stochastic motor attachment and detachment events can lead to directional reversals without the necessity of external regulators.
α2-ADRENERGIC MODULATION OF Ih IN ADULT-BORN GRANULE CELLS IN THE OLFACTORY BULB
Authors: Hu Ruilong , Shankar Janam , Dong Grant Z. , Villar Pablo S. , Araneda Ricardo C. 
Published: September 2022

ABSTRACTIn the olfactory bulb (OB), a large population of axon-less inhibitory interneurons, the granule cells (GCs), coordinate network activity and tune the output of principal neurons, the mitral and tufted cells (MCs), through dendrodendritic interactions. Furthermore, GCs undergo neurogenesis throughout life, providing a source of plasticity to the neural network of the OB. The function and integration of GCs in the OB is regulated by several afferent neuromodulatory signals, including noradrenaline (NA), a state-dependent neuromodulator that plays a crucial role in the regulation of cortical function and task-specific decision processes. However, the mechanisms by which NA regulates GC function are not fully understood. Here, we show that NA modulates hyperpolarization-activated currents (Ih) via the activation of α2-adrenergic receptors in adult-born GCs (abGCs), thus directly acting on channels that play essential roles in regulating neuronal excitability and network oscillations in the brain. This modulation affects the dendrodendritic output of GCs leading to an enhancement of lateral inhibition onto the MCs. Furthermore, we show that NA modulates subthreshold resonance in GCs, which could affect the temporal integration of abGCs. Together, these results provide a novel mechanism by which a state-dependent neuromodulator acting on Ih can regulate GC function in the bulb.