bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fine-scale congruence in bacterial community structure from marine sediments sequenced by short-reads on Illumina and long-reads on Nanopore
Authors: Lemoinne Alice , Dirberg Guillaume , Georges Myriam , Robinet Tony 
Published: June 2023

AbstractFollowing the development of high-throughput sequencers, environmental prokaryotic communities are usually described by metabarcoding with genetic markers on the 16S domain. However, short-read sequencing encounters a limitation in phylogenetic coverage and taxonomic resolution, due to the primers choice and read length. On these critical points, nanopore sequencing, a rising technology, suitable for long-read metabarcoding, was much undervalued because of its relatively higher error rate per read. Here we compared the prokaryotic community structure in a mock community and 52 sediment samples from two contrasted mangrove sites, described by short-reads on 16SV4-V5 marker (ca. 0.4kpb) analyzed by Illumina sequencing (MiSeq, V3), with those described by long-reads on bacterial nearly complete 16S (ca. 1.5 kpb) analyzed by Oxford Nanopore (MinION, R9.2). Short- and long-reads retrieved all the bacterial genera from the mock, although both showing similar deviations from the awaited proportions. From the sediment samples, with a coverage-based rarefaction of reads and after singletons filtering, co-inertia and Procrustean tests showed that bacterial community structures inferred from short- and long-reads were significantly similar, showing both a comparable contrast between sites and a coherent sea-land orientation within sites. In our dataset, 84.7 and 98.8% of the short-reads were assigned strictly to the same species and genus, respectively, than those detected by long-reads. Primer specificities of long-16S allowed it to detect 92.2% of the 309 families and 87.7% of the 448 genera that were detected by the short 16SV4-V5. Long-reads recorded 973 additional taxa not detected by short-reads, among which 91.7% were identified to the genus rank, some belonging to 11 exclusive phyla, albeit accounting for only 0.2% of total long-reads.
Translational approach to social isolation during a global pandemic: Hippocampal somatic mutation
Authors: Lee Bomee , Seo Yuri , Jung Sohee , Im Soojung , Choi Hyung Jun , Bae Jae Nam , Kim Yangsik 
Published: June 2023

AbstractThe coronavirus disease 2019 (COVID-19) pandemic has attributed to stress not only by the infection itself but also by social isolation owing to self-quarantine and social distancing. Stress has adverse effects on the mental health and chronic medical diseases; the potential of stress-induced somatic mutations in the brain to cause psychiatric disorders is being studied. Here we conducted behavioral studies, protein expression studies, single-nucleus sequencing (snRNAseq), and whole-genome sequencing (WGS) of the hippocampus of mice that underwent early maternal separation and social isolation, and a demographic study of community populations who had been self-quarantined owing to COVID-19 exposure to investigate the link between somatic mutations and stress due to social isolation. The demographic study demonstrated more negative mental health findings among individuals who live alone or are single. Mice subjected to early maternal separation and social isolation demonstrated increased anxiety-like behaviors and stress-related corticotropin-releasing hormone receptor 1, and neurogenesis-related sex-determining region Y-box 2 and doublecortin expression. In snRNA-seq, differences, such as transthyretin increase, were observed in the maternal separation group, and somatic mutations, including insertion in the intron site of Tmem267, were observed in the social isolation group on WGS. The results of this study suggest that stress, such as social isolation, can cause changes at the genetic level, as well as behavioral and brain protein changes.
The proprotein convertase BLI-4 promotes collagen secretion during assembly of theCaenorhabditis eleganscuticle
Authors: Birnbaum Susanna K. , Cohen Jennifer D. , Belfi Alexandra , Murray John I. , Adams Jennifer R.G. , Chisholm Andrew D. , Sundaram Meera V. 
Published: June 2023

AbstractSome types of collagens, including transmembrane MACIT collagens andC. eleganscuticle collagens, are N-terminally cleaved at a dibasic site that resembles the consensus for furin or other proprotein convertases of the subtilisin/kexin (PCSK) family. Such cleavage may release transmembrane collagens from the plasma membrane and affect extracellular matrix assembly or structure. However, the functional consequences of such cleavage are unclear and evidence for the role of specific PCSKs is lacking. Here, we used endogenous collagen fusions to fluorescent proteins to visualize the secretion and assembly of the first collagen-based cuticle inC. elegansand then tested the role of the PCSK BLI-4 in these processes. Unexpectedly, we found that cuticle collagens SQT-3 and DPY-17 are secreted into the extraembryonic space several hours before cuticle matrix assembly. Furthermore, this early secretion depends on BLI-4/PCSK; inbli-4and cleavage-site mutants, SQT-3 and DPY-17 are not efficiently secreted and instead form large intracellular aggregates. Their later assembly into cuticle matrix is reduced but not entirely blocked. These data reveal a role for collagen N-terminal processing in intracellular trafficking and in the spatial and temporal restriction of matrix assemblyin vivo. Our observations also prompt a revision of the classic model forC. eleganscuticle matrix assembly and the pre-cuticle-to-cuticle transition, suggesting that cuticle layer assembly proceeds via a series of regulated steps and not simply by sequential secretion and deposition.
Disentangling plant- and environment-mediated drivers of active rhizosphere bacterial community dynamics during short-term drought
Authors: Bandopadhyay Sreejata , Li Xingxing , Bowsher Alan W. , Last Robert L. , Shade Ashley 
Published: June 2023

AbstractBackgroundMitigating the effects of climate stress on crops is important for global food security. The microbiome associated with plant roots, henceforth, the rhizobiome, can harbor beneficial microbes that alleviate stress impacts. However, the factors influencing the recruitment of the rhizobiome during stress are unclear. We conducted an experiment to understand bacterial rhizobiome responses to short-term drought for two crop species: switchgrass and common bean. We used 16S rRNA and 16S rRNA gene sequencing to investigate the impact of drought severity on the recruitment of active bacterial rhizobiome members. We included planted and unplanted conditions to distinguish the environment-versus plant-mediated drivers of the active rhizobiome.ResultsThough each crop had a distinct rhizobiome, there were differences in the active microbiome structure between drought and watered and between planted and unplanted treatments. Despite their different community structures, the drought rhizobiome dynamics were similar across the two crops. However, the presence of a plant more strongly explained the rhizobiome variation in bean (17%) than in switchgrass (3%), with a small effect of plant mediation during drought only observed for the bean rhizobiome. The switchgrass rhizobiome was stable despite differences in the rhizosphere metabolite profiles between planted and unplanted treatments. Specifically, steroidal saponins and diterpennoids were enriched in drought, planted switchgrass soils.ConclusionsWe conclude that rhizobiome benefits to resist short-term drought are crop-specific, with the possibility of decoupling of plant exudation and rhizobiome responses, as we observed in switchgrass. We propose bacterial taxa uniquely associated with common bean plants during the short-term drought, which could be further evaluated to determine any plant benefit during drought.
Multiscale modeling of HBV infection integrating intra- and intercellular viral propagation for analyzing extracellular viral markers
Authors: Kitagawa Kosaku , Kim Kwang Su , Iwamoto Masashi , Hayashi Sanae , Park Hyeongki , Nishiyama Takara , Nakamura Naotoshi , Fujita Yasuhisa , Nakaoka Shinji , Aihara Kazuyuki , Perelson Alan S. , Allweiss Lena , Dandri Maura , Watashi Koichi , Tanaka Yasuhito , Iwami Shingo 
Published: June 2023

AbstractChronic infection of hepatitis B virus (HBV) is caused by the persistence of closed circular DNA (cccDNA) in the nucleus of infected hepatocytes. Despite available therapeutic anti-HBV agents, eliminating the cccDNA remains challenging. The quantifying and understanding dynamics of cccDNA are essential for developing effective treatment strategies and new drugs. However, it requires a liver biopsy to measure the intrahepatic cccDNA, which is basically not accepted because of the ethical aspect. We here aimed to develop a non-invasive method for quantifying cccDNA in the liver using surrogate markers present in peripheral blood. We constructed a multiscale mathematical model that explicitly incorporates both intracellular and intercellular HBV infection processes. The model, based on age-structured partial differential equations (PDEs), integrates experimental data from in vitro and in vivo investigations. By applying this model, we successfully predicted the amount and dynamics of intrahepatic cccDNA using specific viral markers in serum samples, including HBV DNA, HBsAg, HBeAg, and HBcrAg. Our study represents a significant step towards advancing the understanding of chronic HBV infection. The non-invasive quantification of cccDNA using our proposed methodology holds promise for improving clinical analyses and treatment strategies. By comprehensively describing the interactions of all components involved in HBV infection, our multiscale mathematical model provides a valuable framework for further research and the development of targeted interventions.
Structural insights into the initiation of free radical formation in the Class Ib ribonucleotide reductases
Authors: Yadav Lumbini R. , Mande Shekhar C. 
Published: June 2023

AbstractClass I ribonucleotide reductases consisting of R1 and R2 subunits convert ribonucleoside diphosphates to deoxyribonucleoside diphosphates involving an intricate free radical mechanism. The generation of free radicals in the Class Ib ribonucleotide reductases is mediated by reaction involving di-manganese ions in the R2 subunits and is externally assisted by flavodoxin-like NrdI subunit. This is unlike Class Ia ribonucleotide reductases, where the free radical generation is initiated at its di-iron centre in the R2 subunits with no external support from another subunit. Despite much work on the R2 subunits of Class Ib ribonucleotide reductases, also referred as NrdF, and its partner NrdI, the structural details of free radical generation remain largely unknown. In this study we have determined the crystal structures of Mycobacterial NrdI in oxidized and reduced forms, and similarly those of NrdF2: NrdI complex (NrdF2I). These structures provide the first atomic view of the mechanism of free radical generation in the R2 subunit. We propose that oxygen molecule accesses FMN through a well-formed channel in NrdI, seen clearly in the crystal structure, and upon electron transfer is converted to a superoxide ion. Similarly, a path for superoxide radical transfer between NrdI and NrdF2 is also observed. A delocalised Mn ion in the R2 subunit is seen in the electron density, which attacks Tyr 110 to produce a Tyr• free radical. Finally, a solvent channel to the dimanganese-binding site is observed to complete the cycle. The study therefore provides important structural clues on the initiation of free radical generation in the R2 subunit of the ribonucleotide reductase complex.Significance statementRibonucleotide reductases generate the deoxyribonucleotide pool in the cell for DNA replication and repair. The enzymes utilise free radical mechanism, where the mechanism of radical formation defines different classes of ribonucleotide reductases. Class Ib ribonucleotide reductases generate the free radical though di-manganese chemistry, assisted externally by NrdI. We describe here structural features required to achieve this mechanism. The structures clearly show a tunnel for oxygen access to the FMN site, tunnel to transport the consequent superoxide radical that is formed, a dislocated activated Mn, which appears to coordinate with a Tyrosine residue to form Tyr• radical and a water channel to complete the reaction cycle, thus enhancing our understanding of the steps of free radical generation.
Transgenic expression of Arabidopsis ELONGATION FACTOR-TU RECEPTOR (AtEFR) gene in banana enhances resistance to Banana Xanthomonas Wilt disease
Authors: Adero Mark Ochieng , Tripathi Jaindra Nath , Oduor Richard Okoth , Zipfel Cyril , Tripathi Leena 
Published: June 2023

AbstractBanana Xanthomonas wilt (BXW) caused byXanthomonas campestrispv. musacearum(Xcm) is a severe bacterial disease devastating banana production in East and Central Africa, where banana is cultivated as a staple crop. Classical breeding of banana is challenging because the crop is clonally propagated and has limited genetic diversity. Thus, genetic engineering serves as a viable alternative for banana improvement. Several studies have shown that interfamily transfer of theelongation factor Tu receptorgene (AtEFR) fromArabidopsis thalianato other plant families can increase broad-spectrum resistance against bacterial diseases. In this study, transgenic events of banana cultivar dwarf Cavendish expressing theAtEFRgene were generated and evaluated for resistance against Xcm under greenhouse conditions. The transgenic banana events were responsive to the EF-Tu-derived elf18 peptide and exhibited enhanced resistance to BXW disease compared to non-transgenic control plants. This study suggests that the functionality ofAtEFRis retained in banana with the potential of enhancing resistance to BXW disease under field conditions.
GLUT4 dynamic subcellular localization is controlled by AMP kinase activation as revealed by proximal proteome mapping in human muscle cells
Authors: Ray Anuttoma , Wen Jennifer , Yammine Lucie , Culver Jeff , Garren Jeonifer , Xue Liang , Hales Katherine , Xiang Qing , Birnbaum Morris J. , Zhang Bei B. , Monetti Mara , McGraw T.E. 
Published: June 2023

AbstractRegulation of glucose transport into muscle and adipocytes, central for control of whole-body metabolism, is determined by the amount of GLUT4 glucose transporter in the plasma membrane (PM). Physiologic signals (activated insulin receptor or AMP kinase [AMPK]), acutely increase PM GLUT4 to enhance glucose uptake. Here we show in kinetic studies that intracellular GLUT4 is in equilibrium with the PM in unstimulated cultured human skeletal muscle cells, and that AMPK promotes GLUT4 redistribution to the PM by regulating both exocytosis and endocytosis. AMPK-stimulation of exocytosis requires Rab10 and Rab GTPase activating protein TBC1D4, requirements shared with insulin control of GLUT4 in adipocytes. Using APEX2 proximity mapping, we identify, at high-density and high-resolution, the GLUT4 proximal proteome, revealing GLUT4 traverses both PM proximal and distal compartments in unstimulated muscle cells. These data support intracellular retention of GLUT4 in unstimulated muscle cells by a dynamic mechanism dependent on the rates of internalization and recycling. AMPK promoted GLUT4 translocation to the PM involves redistribution of GLUT4 among the same compartments traversed in unstimulated cells, with a significant redistribution of GLUT4 from the PM distal Trans Golgi Network Golgi compartments. The comprehensive proximal protein mapping provides an integrated, whole cell accounting of GLUT4’s localization at a resolution of ∼20 nm, a structural framework for understanding the molecular mechanisms regulating GLUT4 trafficking downstream of different signaling inputs in physiologically relevant cell type and as such, sheds new light on novel key pathways and molecular components as potential therapeutic approaches to modulate muscle glucose uptake.
E3 ubiquitin ligase Deltex facilitates the expansion of Wingless gradient and antagonizes Wingless signaling through a conserved mechanism of transcriptional effector Armadillo/β-catenin degradation
Authors: Sharma Vartika , Sachan Nalani , Sarkar Bappi , Mutsuddi Mousumi , Mukherjee Ashim 
Published: June 2023

ABSTRACTThe Wnt/Wg pathway controls myriads of biological phenomena throughout the development and adult life of all organisms across the phyla. Thus, an aberrant Wnt signaling is associated with a wide range of pathologies in humans. Tight regulation of Wnt/Wg signaling is required to maintain proper cellular homeostasis. Here we report a novel role of E3 ubiquitin ligase Deltex in Wg signaling regulation.Drosophila dxgenetically interacts withwg and its pathway components. Further, Dx LOF results in a reduced spreading of Wg while its over-expression expands the diffusion gradient of the morphogen. We attribute this change in Wg gradient to the endocytosis of Wg through Dx which directly affects the short and long-range Wg targets. We also demonstrate the role of Dx in regulating Wg effector Armadillo where Dx down-regulates Arm through proteasomal degradation. We also showed the conservation of Dx function in the mammalian system where DTX1 is shown to bind with β-catenin and facilitates its proteolytic degradation, spotlighting a novel step that potentially modulates Wnt/Wg signaling cascade.
MYC is essential for induction of major ZGA and subsequent preimplantation development
Authors: Yamamoto Takuto , Wang Haoxue , Sato Hana , Honda Shinnosuke , Ikeda Shuntaro , Minami Naojiro 
Published: June 2023

AbstractIn mouse preimplantation development, zygotic genome activation (ZGA), which synthesizes new transcripts from the embryos, begins in the S phase of the one-cell stage, with major ZGA occurring especially at the late two-cell stage.Mycis a transcription factor expressed in parallel with ZGA, but its direct association with the major ZGA has not been clarified. In this study, we found that developmental arrest occurs at the two-cell stage when mouse embryos were treated with antisense oligos targetingMycor inhibitors specific for MYC from the one-cell stage. In order to identify when MYC inhibition affected development, we applied time-limited inhibitor treatment, and found that inhibition of MYC at the two-cell, four-cell, and morula stages had no effect on preimplantation development, whereas treatment with the inhibitor at the early two-cell stage arrested development at the two-cell stage. Furthermore, transcriptome analysis revealed that when MYC function was inhibited, genes expressed in the major ZGA phase were suppressed. These results suggest that Myc is essential for the induction of major ZGA and its subsequent development. Revealing the function ofMycin preimplantation development is expected to contribute to advances in assisted reproductive technology.
Salmonella entericaserovar Typhi uses two type 3 secretion systems to replicate in human macrophages and to colonize humanized mice
Authors: Hamblin Meagan , Schade Ruth , Narasimhan Ramya , Monack Denise M. 
Published: June 2023

AbstractSalmonella entericaserovar Typhi (S.Typhi) is a human-restricted pathogen that replicates in macrophages. In this study, we investigated the roles of theS.Typhi Type 3 secretion systems (T3SSs) encoded onSalmonellaPathogenicity Islands (SPI) -1 (T3SS-1) and -2 (T3SS-2) during human macrophage infection. We found that mutants ofS. Typhi deficient for both T3SSs were defective for intramacrophage replication as measured by flow cytometry, viable bacterial counts, and live time-lapse microscopy. T3SS-secreted proteins PipB2 and SifA contributed toS.Typhi replication and were translocated into the cytosol of human macrophages through both T3SS-1 and -2, demonstrating functional redundancy for these secretion systems. Importantly, anS. Typhi mutant strain that is deficient for both T3SS-1 and -2 was severely attenuated in the ability to colonize systemic tissues in a humanized mouse model of typhoid fever. Overall, this study establishes a critical role forS.Typhi T3SSs during its replication within human macrophages and during systemic infection of humanized mice.ImportanceSalmonella entericaserovar Typhi is a human-restricted pathogen that causes typhoid fever. Understanding the key virulence mechanisms that facilitateS.Typhi replication in human phagocytes will enable rational vaccine and antibiotic development to limit spread of this pathogen. WhileS.Typhimurium replication in murine models has been studied extensively, there is limited information available aboutS.Typhi replication in human macrophages, some of which directly conflicts with findings fromS.Typhimurium murine models. This study establishes that both ofS.Typhi’s two Type 3 Secretion Systems (T3SS-1 and -2) contribute to intramacrophage replication and virulence.
Spontaneous human CD8 T cell and EAE-inducible human CD4/CD8 T cell lesions in the brain and spinal cord of HLA-DRB1*15-positive multiple sclerosis PBMC humanized mice
Authors: Papazian Irini , Kourouvani Maria , Dagkonaki Anastasia , Gouzouasis Vasileios , Dimitrakopoulou Lila , Markoglou Nikolaos , Badounas Fotis , Tselios Theodore , Anagnostouli Maria , Probert Lesley 
Published: June 2023

SummaryAutoimmune diseases of the central nervous system (CNS) such as multiple sclerosis (MS) are only partially represented in current experimental models and the development of humanized immune mice is crucial for better understanding of immunopathogenesis and testing of therapeutics. We describe a humanized mouse model with several key features of MS. Severely immunodeficient B2m-NOG mice were transplanted with peripheral blood mononuclear cells (PBMC) from HLA-DRB1-typed MS and healthy (HI) donors and showed rapid engraftment by human T and B lymphocytes. Mice receiving cells from MS patients with recent/ongoing Epstein-Barr virus (EBV) reactivation showed high B cell engraftment capacity. Both HLA-DRB1*15 (DR15) MS and DR15 HI mice, not HLA-DRB1*13 MS mice, developed human T cell infiltration of CNS borders and parenchyma. DR15 MS mice uniquely developed inflammatory lesions in brain and spinal cord grey matter, with spontaneous, hCD8 T cell lesions, and mixed hCD8/hCD4 T cell lesions in EAE immunized mice, with variation in localization and severity between different patient donors. Main limitations of this model for further development are poor monocyte engraftment and lack of demyelination, lymph node organization and IgG responses. These results show that PBMC humanized mice represent promising research tools for investigating MS immunopathology in a patient-specific approach.