bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fluorescent Chiral Quantum Dots to Unveil Origin-Dependent Exosome Uptake and Cargo Release
Authors: Kim Gaeun , Zhu Runyao , Zhang Youwen , Jeon Hyunsu , Wang Yichun 
Published: December 2023

ABSTRACTExosomes are promising nanocarriers for drug delivery. Yet, it is challenging to apply exosomes in clinical use due to the limited understanding of their physiological functions. While cellular uptake of exosomes is generally known through endocytosis and/or membrane fusion, the mechanisms of origin-dependent cellular uptake and subsequent cargo release of exosomes into recipient cells are still unclear. Herein, we investigated the intricate mechanisms of exosome entry into recipient cells and the intracellular cargo release. In this study, we utilized chiral graphene quantum dots (GQDs) as representatives of exosomal cargo, taking advantage of the superior permeability of chiral GQDs into lipid membranes, as well as their excellent optical properties for tracking analysis. We observed a higher uptake rate of exosomes in their parental recipient cells. However, these exosomes were predominantly entrapped in lysosomes through endocytosis (intraspecies endocytic uptake). On the other hand, in non-parental recipient cells, exosomes exhibited a greater inclination for cellular uptake through membrane fusion, followed by direct cargo release into the cytosol (cross-species direct fusion uptake). We revealed the underlying mechanisms involved in the cellular uptake and the subsequent cargo release of exosomes depending on their cell-of-origin and recipient cell types. This study envisions valuable insights into further advancements in the effective drug delivery using exosomes, as well as a comprehensive understanding of cellular communication, including disease pathogenesis.
Neurotrophin NT-4/5 Promotes Structural Changes in Neurons of the Developing Visual Cortex
Authors: Antonini Antonella , Harris Sheri L. , Stryker Michael P. 
Published: December 2023

ABSTRACTCurrent hypotheses on the mechanisms underlying the development and plasticity of the ocular dominance system through competitive interactions between pathways serving the two eyes strongly suggest the involvement of neurotrophins and their high affinity receptors. In the cat, infusion of the tyrosine kinase B ligand (trkB), neurotrophin-4/5 (NT-4/5), abolishes ocular dominance plasticity that follows monocular deprivation (Gillespie et al., 2000), while tyrosine kinase A and C ligands (trkA and trkC) do not have this effect. One interpretation of this finding is that NT-4/5 causes overgrowth and sprouting of thalamocortical and/or corticocortical terminals, leading to promiscuous neuronal connections which override the experience-dependent fine tuning of connections based on correlated activity. The present study tested whether neurons in cortical regions infused with NT-4/5 showed anatomical changes compatible with this hypothesis. Cats at the peak of the critical period received chronic infusion NT-4/5 into visual cortical areas 17/18 via an osmotic minipump. Visual cortical neurons were labeled in fixed slices using the DiOlistics methods (Gan et al., 2000) and analyzed in confocal microsco-py. Infusion of NT-4/5 induced a significant increase of spine-like processes on primary dendrites and a distinctive sprouting of protuberances from neuronal somata in all layers. The increase of neuronal membrane was paralleled by an increase in density of the presynaptic marker synaptophysin in infused areas, suggesting an increase in the numbers of synapses. A contingent of these newly formed synapses may feed into inhibitory circuits, as suggested by an increase of GAD-65 immunostaining in NT-4/5 affected areas. These anatomical changes are consistent with the physiological changes in such animals, suggesting that excess trkB neurotrophin can stimulate the formation of promiscuous connections during the critical period.
Nucleosome wrapping state encodes principles of 3D genome organization
Authors: Wen Zengqi , Yu Xinqian , Fang Ruixin , Long Haizhen 
Published: December 2023

AbstractNucleosome is the basic structural unit of the genome. During processes like DNA replication and gene transcription, the conformation of nucleosomes undergoes dynamic changes, including DNA unwrapping and rewrapping, as well as histone disassembly and assembly. However, the wrapping characteristics of nucleosomes across the entire genome, including region-specificity and their correlation with higher-order chromatin organization, remain to be studied. In this study, we investigated the wrapping length of DNA on nucleosomes across the whole genome using wrapping-seq. We discovered that the chromatin of mouse ES cells formsNucleosome WrappingDomains (NRDs), which is conserved in yeast and fly. We found that the degree of nucleosome wrapping decreases after DNA replication and is promoted by transcription. Furthermore, we observed that nucleosome wrapping states delineate 3D genome organization and DNA replication timing. In conclusion, we have revealed a novel principle of higher-order chromatin organization.
Dueling Endogenous Viral-Like Sequences Control Synaptic Plasticity
Authors: M’Angale P. Githure , Lemieux Adrienne , Liu Yumeng , Graslie Jasmine , Wang Shuhao , Simkin Alfred , Budnik Vivian , Kelch Brian A. , Thomson Travis 
Published: December 2023

ABSTRACTThe function of a large part of most genomes, generally called “junk DNA”, remains largely unknown. Much of this enigmatic DNA corresponds to transposons, which are considered genomic parasites. Here, we show the protein of the Ty1 retrotransposonCopiais enriched at theDrosophilaneuromuscular junction and is transported across synapses. Unexpectedly, disruptingCopiaexpression results in increases in both synapse development and structural synaptic plasticity. Plasticity is kept in balance asCopiaantagonizes theDrosophila Arc(activity-regulated cytoskeleton-associated protein) homolog, which is a transposon-derived gene. Our cryo-EM structure of theCopiacapsid shows a shell with large cargo capacity and leads to a hypothesis for mutual antagonism of Arc andCopiacapsid assembly. Our findings provide evidence that a fully functional transposon plays a role at synapses, suggesting that transposons and other types of ‘junk DNA’ are essential to developmental and cellular processes.
Fabry Cardiomyopathy: Myocardial Fibrosis, Inflammation and Down-Regulation of Mannose6Phosphate Receptors cause Low accessibility to Enzyme Replacement Therapy
Authors: Frustaci Andrea , Verardo Romina , Magnocavallo Michele , Frustaci Emanuela , Russo Matteo Antonio , Chimenti Cristina 
Published: December 2023

ABSTRACTBackgroundClinical impact of enzyme replacement therapy (ERT) on advanced Fabry disease cardiomyopathy (FDCM) appears limited. The pathologic mechanisms involved are still unclear.MethodsTen male patients with advanced FDCM (echocardiographic maximal wall thickness 19.3 ± 2.1 mm) underwent left ventricular endomyocardial biopsy before and 4 hours after beta-agalsidase infusion (1 mg/Kg). Comparative studies between pre and post infusion samples included: histology and electron microscopy; assessment of myocardial alpha-galactosidase A activity; immunohistochemistry for alpha-galactosidase A and semiquantitative evaluation (from 0 to 3) of its cardiomyocyte content; Ultrastructural immunogold analysis with anti-alpha-galactosidase A ab. Western Blot (WB) quantification of mannose-6-phosphate receptors (M6Pr). Controls were surgical left ventricular biopsies from patients with mitral stenosis.ResultsHistologic and Ultrastructural evaluation showed no removal of storage material while myocardial fibrosis was 9.8 ± 6.8 vs 3.8 ± 2.0 of controls and virus-negative lymphocytic inflammation was observed in 7 out of 10 patients. At Ultrastructural immunogold analysis, Myocardial alpha-galactosidase A activity increased in post infusion samples by overall 1.89-fold. Alpha-galactosidase A immunostaining in cardiomyocytes was absent at baseline in all patients and did not significantly improve in post-infusion samples. Immunogold particles increased by 1.33-fold(17.6 ± 3.6 pre infusion vs 21.5 ± 5.9 post)remaining far from normal controls (86.9 ± 6.6). Protein analysis showed M6Pr in advanced FDCM to be 81% lower than in normal heart.ConclusionsOur study shows a low accessibility to ERT of cardiomyocytes affected by advanced FDCM. It is sustained by myocardial fibrosis, inflammation and severe down-regulation of M6Pr.
Trends in antimicrobial resistance amongstSalmonellaTyphi in Bangladesh: a 24-year retrospective observational study (1999–2022)
Authors: Tanmoy Arif M , Hooda Yogesh , Sajib Mohammad S I , Rahman Hafizur , Sarkar Anik , Das Dipu , Islam Nazrul , Kanon Naito , Rahman Md. Asadur , Garrett Denise O , Endtz Hubert P , Luby Stephen P , Shahidullah Mohammod , Amin Md. Ruhul , Alam Jahangir , Hanif Mohammed , Saha Samir K , Saha Senjuti 
Published: December 2023

AbstractBackgroundRising antimicrobial resistance (AMR) inSalmonellaTyphi restricts typhoid treatment options, heightening concerns for pan-oral drug-resistant outbreaks. Bangladesh contemplates introducing typhoid conjugate vaccine (TCV) to address the typhoid burden and AMR. However, large-scale surveillance data on typhoid AMR in Bangladesh is scarce.ObjectiveThis study explores the AMR trends inSalmonellaTyphi isolates from Bangladesh, drawing comparisons with antibiotic consumption to optimize antibiotic stewardship strategies for the country.MethodsOur typhoid fever surveillance included two pediatric hospitals and three private clinics in Dhaka, Bangladesh, spanning 1999 to 2022. Blood cultures were performed at physicians’ discretion; cases were confirmed by microbiological culture, serological, and biochemical tests. Antimicrobial susceptibility was determined following CLSI guidelines. National antibiotic consumption data for cotrimoxazole, ciprofloxacin, and azithromycin was obtained from IQVIA-MIDAS database for comparison.ResultsOur 24-year surveillance, encompassing 12,435SalmonellaTyphi cases, revealed declining trends in first-line drugs (amoxicillin, chloramphenicol, cotrimoxazole) and multidrug resistance (MDR; 38% to 17%, 1999–2022). Cotrimoxazole consumption dropped, 0.8 to 0.1 DDD/1000/day (1999–2020). Ciprofloxacin non-susceptibility persisted (>90%) with unchanged consumption (1.1-1.3 DDD/1000/day, 2002–2020). Low ceftriaxone resistance (<1%) was observed, with rising MIC (0.03 to 0.12 mg/L, 1999–2019). Azithromycin consumption increased (0.1 to 3.8 DDD/1000/day, 1999–2020), but resistance remained ≤4%.ConclusionOur study highlights declining MDR amongstSalmonellaTyphi in Bangladesh, thus reintroducing first-line antimicrobials could work as an empirical treatment option for typhoid fever. Our analysis provides a baseline for monitoring the impact of future interventions, including the TCV, on typhoid burden and associated AMR.
Insights into the complex formation of a trimeric autotransporter adhesin with a peptidoglycan-binding periplasmic protein
Authors: Yoshimoto Shogo , Suzuki Atsuo , Kanie Junichi , Koiwai Kotaro , Lupas Andrei N. , Hori Katsutoshi 
Published: December 2023

AbstractTrimeric autotransporter adhesin (TAA) is an outer membrane (OM) protein that is widely distributed in gram-negative bacteria and is involved primarily in adhesion to biotic and abiotic surfaces, cell agglutination, and biofilm formation. TAAs are secreted onto the OM by the type Vc secretion system (SS). Because the interactions between TAAs and chaperones or special assistant proteins during secretion are short-lived, it is thought that TAAs reside on the OM without forming complexes with other proteins after secretion. In this study, we aimed to clarify the interactions between anAcinetobacterTAA, AtaA, and a peptidoglycan (PG)-binding periplasmic protein, TpgA, and to identify additional roles of TpgA based on these interactions. Pull-down assays using recombinant proteins identified the interacting domains. X-ray crystallography revealed the A3B3 heterohexameric complex structure of the N-terminal domain of TpgA with the transmembrane domain of AtaA and showed that both electrostatic and hydrophobic interactions contribute to stable complex formation. Bioinformatic analysis suggested that the TAA-TpgA complex is formed in a wide range of species that harbor thetaa-tpgAgene cassette in their genome. Furthermore, the absence of TpgA increased the release of AtaA from the cell surface, suggesting that TpgA prevents the release of TAA from the cell surface via its anchoring to the PG. We propose that the TAAs that form a complex with TpgA be assigned to type Vc2SS, a new subtype of type Vc SS.SignificanceGram-negative bacteria have specialized secretion systems (SSs) that translocate molecules from the cytoplasm to the extracellular space. This is the first report directly demonstrating that the transmembrane domain of a trimeric autotransporter adhesin (TAA), which is secreted by the type Vc SS, forms a stable complex with a peptidoglycan-binding periplasmic protein. This complex prevents the release of TAA from the cell surface. These results suggest that the secretion and architecture of some TAAs are more complex than was previously understood. Our work provides structural and functional insights into bacterial SSs that are important not only in microbiology but also for medical and bioengineering applications.
LLPS condensates of Fha initiate the inside-out assembly of the type VI secretion system
Authors: Pei Tong-Tong , An Ying , Wang Xing-Yu , Luo Han , Kan Yumin , Li Hao , Tang Ming-Xuan , Ye Zi-Yan , Liang Jia-Xin , Jian Tao , Zheng Hao-Yu , Wang Zeng-Hang , Liang Xiaoye , Zhang Mingjie , Liu Xiaotian , Dong Tao 
Published: December 2023

AbstractThe type VI secretion system (T6SS) is one of the most powerful nanomachines employed by Gram-negative pathogens for penetrating diverse cell envelopes, including bacteria and fungi, to deliver potent effectors into target cells. While the membrane-anchored contractile tubular structure of the T6SS is well characterized, the assembly process remains poorly understood. The prevailing model suggests that the assembly of T6SS initiates from its outer-membrane component. Here, we report a distinct model that the cytoplasmic protein Fha initiates T6SS assembly inAcidovorax citrulli, an important plant pathogen. Fha dictates the formation of the inner-membrane complex and the baseplate, and directly interacts with these key components. Importantly, imaging and biochemical assays reveal that Fha undergoes liquid-liquid phase separation (LLPS), forming condensates that selectively recruit essential T6SS proteins, which are otherwise dispersed in cells. Fha also exhibited conserved functions in human pathogensVibrio choleraeandPseudomonas aeruginosa. These findings unveil an inside-first LLPS-driven model for T6SS assembly and suggest LLPS might be broadly involved in mediating the assembly of bacterial macromolecular complexes and facilitating interspecies interactions and pathogenesis.Significance statementThe T6SS plays a pivotal role in interspecies competition and host-microbe interactions by delivering toxins to various prokaryotes and eukaryotes. Its crucial function relies on a membrane-anchored macromolecular structure comprising at least 13 conserved components. However, the mechanisms governing the efficient assembly of its diverse cytosolic and membrane-bound components remain elusive. Here, we identify Fha, a conserved cytosolic protein, as a key initiator of T6SS assembly. Fha recruits multiple structural and effector components, forming LLPS condensates. Fha homologs of plant and human pathogens exhibit conserved functions. Our findings not only unveil an inside-first assembly model for the T6SS, initiating from inner-membrane and baseplate components, but also suggest LLPS may have a broader impact on bacterial physiology beyond intracellular activities.
Humoral immune responses to the monovalent XBB.1.5-adapted BNT162b2 mRNA booster
Authors: Marking Ulrika , Bladh Oscar , Aguilera Katherina , Yang Yiqiu , Norin Nina Greilert , Blom Kim , Hober Sophia , Klingström Jonas , Havervall Sebastian , Åberg Mikael , Sheward Daniel J. , Thålin Charlotte 
Published: December 2023

AbstractContinued SARS-CoV-2 evolution and immune escape necessitated the development of updated vaccines, and a monovalent vaccine incorporating the XBB.1.5 variant spike protein is currently being rolled out. Amidst the emergence of the highly mutated BA.2.86 lineage and against the backdrop of pronounced immune imprinting, it is important to characterize the antibody responses following vaccination, particularly in the elderly.Here, we show that the monovalent XBB.1.5-adapted booster vaccination substantially enhanced both binding and neutralising antibody responses against a panel of variants, including BA.2.86, in an older population with four or more previous vaccine doses. Furthermore, neutralizing antibody titers to XBB.1.5 and BA.2.86 were boosted more strongly than titers to historical variants were.Our findings thereby suggest increased vaccine induced protection against both antigenically matched variants, as well as the more distant BA.2.86 variant, and support current vaccine policies recommending a monovalent XBB.1.5 booster dose to older individuals.
Structural implications of BK polyomavirus sequence variations in the major viral capsid protein Vp1 and large T-antigen: a computational study
Authors: Durairaj Janani , Follonier Océane M. , Leuzinger Karoline , Alexander Leila T , Wilhelm Maud , Pereira Joana , Hillenbrand Caroline A. , Weissbach Fabian H. , Schwede Torsten , Hirsch Hans H. 
Published: December 2023

ABSTRACTBK polyomavirus (BKPyV) is a double-stranded DNA virus causing nephropathy, hemorrhagic cystitis, and urothelial cancer in transplant patients. The BKPyV-encoded capsid protein Vp1 and large T-antigen (LTag) are key targets of neutralizing antibodies and cytotoxic T-cells, respectively. Our single-center data suggested that variability in Vp1 and LTag may contribute to failing BKPyV-specific immune control, and impact vaccine design. We therefore analyzed all available entries in GenBank (1516VP1; 742LTAG)and explored potential structural effects using computational approaches. BKPyV-genotype (gt)1 was found in 71.18% of entries, followed by BKPyV-gt4 (19.26%), BKPyV-gt2 (8.11%) and BKPyV-gt3 (1.45%), but rates differed according to country and specimen type. Vp1-mutations matched a serotype different than the assigned one or were serotype-independent in 43%, 18% affected more than one amino acid. Notable Vp1-mutations altered antibody-binding domains, interactions with sialic acid receptors, or were predicted to change conformation. LTag-sequences were more conserved, with only 16 mutations detectable in more than one entry and without significant effects on LTag-structure or interaction domains. However, LTag changes were predicted to affect HLA-class I presentation of immunodominant 9mers to cytotoxic T-cells. These global data strengthen single center observations and specifically our earlier findings revealing mutant 9mer epitopes conferring immune escape from HLA-I cytotoxic T cells. We conclude that variability of BKPyV-Vp1 and LTag may have important implications for diagnostic assays assessing BKPyV-specific immune control and for vaccine design.IMPORTANCEType and rate of amino acid variations in BKPyV may provide important insights into BKPyV diversity in human populations and an important step towards defining determinants of BKPyV-specific immunity needed to protect vulnerable patients from BKPyV diseases. Our analysis of BKPyV sequences obtained from human specimens reveals an unexpectedly high genetic variability for this double-stranded DNA virus that strongly relies on host cell DNA replication machinery with its proof reading and error correction mechanisms. BKPyV variability and immune escape should be taken into account when designing further approaches to antivirals, monoclonal antibodies and vaccines for patients at risk of BKPyV diseases.
The multiscale topological organization of the functional brain network in adolescent PTSD
Authors: Corredor David , Segobin Shailendra , Hinault Thomas , Eustache Francis , Dayan Jacques , Guillery-Girard Bérengère , Naveau Mikaël 
Published: December 2023

AbstractThe experience of an extremely aversive event can produce enduring deleterious behavioral and neural consequences, among which posttraumatic stress disorder (PTSD) is a representative example. In this work, we aim to study the whole-cortex functional organization of adolescents with PTSD without thea prioriselection of specific regions of interest or functional networks. To do so, we built on the network neuroscience framework and specifically on multisubject community analysis to study the functional connectivity of the brain. We show, across different topological scales (the number of communities composing the cortex), an increased coupling between regions belonging to unimodal (sensory) regions and a reduced coupling between transmodal (association) regions in the adolescent PTSD group. These results open up an intriguing possibility concerning an altered large-scale cortical organization in adolescent PTSD.Significance StatementThe understanding of brain responses following the experience of a traumatic event and the eventual apparition of posttraumatic stress disorder (PTSD) symptoms during youth remains an active topic of research in clinical neuroscience. We adapted a multisubject community detection algorithm to study the functional brain organization of PTSD from a whole cortex and multiscale topological perspective, thereby taking into account the complex (network) organization of the brain. PTSD patients and control subjects presented a different whole cortex functional organization that remained present across topological scales. PTSD patients showed a decreased interaction in transmodal cortices and, inversely, an enhanced interaction in unimodal cortices. This investigation highlights the importance of studying the brain from a complex and whole cortex perspective.