bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural characterization of antibody-responses from Zolgensma treatment provides the blueprint for the engineering of an AAV capsid suitable for redosing
Authors: Mietzsch Mario , Nelson Austin R. , Hsi Jane , Zachary Jon , Potts Lindsay , Chipman Paul , Ghanem Mohammad , Khandekar Neeta , Alexander Ian E. , Logan Grant J. , Huiskonen Juha T. , McKenna Robert 
Published: May 2024

AbstractMonoclonal antibodies (mAbs) are useful tools to dissect the neutralizing antibody response against the adeno-associated virus (AAV) capsids used as gene therapy delivery vectors. This study structurally characterizes the interactions of 21 human-derived antibodies from patients treated with the AAV9 vector, Zolgensma®, utilizing high-resolution cryo-electron microscopy. The majority of the bound antibodies do not conform to the icosahedral symmetry of the capsid, thus requiring localized reconstructions. These complex structures provide unprecedented details of the mAbs binding interfaces, with some antibodies inducing structural perturbations of the capsid upon binding. Key surface capsid amino acid residues were identified facilitating the design of capsid variants with an antibody escape phenotype, with the potential to expand the patient cohort treatable with AAV9 vectors to include those that were previously excluded due to their pre-existing neutralizing antibodies, and possibly also to those requiring redosing.
Non-invasive evidence for rhythmic interactions between the human brain, spinal cord, and muscle
Authors: Spedden Meaghan E. , O’Neill George C. , Timms Ryan C. , West Timothy O. , Mellor Stephanie , Tierney Tim M. , Alexander Nicholas A. , Seymour Robert , Farmer Simon F. , Bestmann Sven , Barnes Gareth R. 
Published: May 2024

AbstractVoluntary human movement relies on interactions between the spinal cord, brain, and sensory afferents. The integrative function of the spinal cord has proven particularly difficult to study directly and non-invasively in humans due to challenges in measuring spinal cord activity. Investigations of sensorimotor integration often rely on cortico-muscular coupling, which can capture interactions between the brain and muscle, but cannot reveal how the spinal cord mediates this communication. Here, we introduce a system for direct, non-invasive imaging of concurrent brain and cervical spinal cord activity in humans using optically-pumped magnetometers (OPMs). We used this system to study endogenous interactions between the brain, spinal cord, and muscle involved in sensorimotor control during simple maintained contraction. Participants (n=3) performed a hand contraction with real-time visual feedback while we recorded brain and spinal cord activity using OPMs and muscle activity using EMG. We first identify the part of the spinal cord exhibiting a peak in estimated current flow in the cervical region during contraction. We then demonstrate that rhythmic activity in the spinal cord exhibits significant coupling with both brain and muscle activity in the 5-35 Hz frequency range. These findings evidence the possibility of concurrent spatio-temporal imaging along the entire neuro-axis.
Single-Cell Transcriptomic Analysis of Kaposi Sarcoma
Authors: Rauch D. A. , Ramos P. Valiño , Khanfar M. , Harding J. , Joseph A. , Griffith O , Griffith M , Ratner L. 
Published: May 2024

AbstractKaposi Sarcoma (KS) is a complex tumor caused by KS-associated herpesvirus 8 (KSHV). Histological analysis reveals a mixture of “spindle cells”, vascular-like spaces, extravasated erythrocytes, and immune cells. In order to elucidate the infected and uninfected cell types in KS tumors, we examined skin and blood samples from twelve subjects by single cell RNA sequence analyses. Two populations of KSHV-infected cells were identified, one of which represented a proliferative fraction of lymphatic endothelial cells, and the second represented an angiogenic population of vascular endothelial tip cells. Both infected clusters contained cells expressing lytic and latent KSHV genes. Novel cellular biomarkers were identified in the KSHV infected cells, including the sodium channel SCN9A. The number of KSHV positive tumor cells was found to be in the 6% range in HIV-associated KS, correlated inversely with tumor-infiltrating immune cells, and was reduced in biopsies from HIV-negative individuals. T-cell receptor clones were expanded in KS tumors and blood, although in differing magnitudes. Changes in cellular composition in KS tumors were identified in subjects treated with antiretroviral therapy alone, or immunotherapy. These studies demonstrate the feasibility of single cell analyses to identify prognostic and predictive biomarkers.Author SummaryKaposi sarcoma (KS) is a malignancy caused by the KS-associated herpesvirus (KSHV) that causes skin lesions, and may also be found in lymph nodes, lungs, gastrointestinal tract, and other organs in immunosuppressed individuals more commonly than immunocompetent subjects. The current study examined gene expression in single cells from the tumor and blood of these subjects, and identified the characteristics of the complex mixtures of cells in the tumor. This method also identified differences in KSHV gene expression in different cell types and associated cellular genes expressed in KSHV infected cells. In addition, changes in the cellular composition could be elucidated with therapeutic interventions.
Xanthomonas oryzaepv.oryzaetype-III effector TAL9b targets a broadly conserved disease susceptibility locus to promote pathogenesis in rice
Authors: Gokulan C.G. , Deb Sohini , Gaur Namami , Masade Apoorva , Gattu Niranjan , Rennya P.R. , Sao Nisha , James Donald , Sonti Ramesh V. , Patel Hitendra K. 
Published: May 2024

SUMMARYXanthomonas oryzaepv.oryzae(Xoo), the causal agent of bacterial blight of rice, translocates multiple Transcription Activator-Like Effectors (TALEs) into rice cells. The TALEs localize to the host cell nucleus, where they bind to the DNA in a sequence-specific manner and enhance gene expression to promote disease susceptibility. Xoo strain PXO99Aencodes nineteen TALEs, but the host targets of all these TALEs have not been defined. A meta-analysis of rice transcriptome profiles revealed a gene annotated as flavonol synthase/flavanone-3 hydroxylase (henceforthOsS5H/FNS-03g) to be highly induced upon Xoo infection. Further analyses revealed that this gene is induced by PXO99Ausing TAL9b, a broadly conserved TALE of Xoo. Disruption oftal9brendered PXO99Aless virulent. OsS5H/FNS-03g functionally complemented itsArabidopsishomologue AtDMR6, a well-studied disease susceptibility locus. Biochemical analyses suggested that OsS5H/FNS-03g is a bifunctional protein with Salicylic Acid 5’ Hydroxylase (S5H) and Flavone Synthase-I (FNS-I) activities. Further, an exogenous application of apigenin on rice leaves, the flavone that is enzymatically produced by OsS5H/FNS-03g, promoted virulence of PXO99Atal9b-. Overall, our study suggests that OsS5H/FNS-03g is a bifunctional enzyme and its product apigenin is potentially involved in promoting Xoo virulence.
Human tumor suppressor protein Pdcd4 binds at the mRNA entry channel in 40S small ribosomal subunit
Authors: Querido Jailson Brito , Sokabe Masaaki , Díaz-López Irene , Gordiyenko Yuliya , Zuber Philipp , Du Yifei , Albacete-Albacete Lucas , Ramakrishnan V. , Fraser Christopher S. 
Published: May 2024

AbstractTranslation is regulated mainly in the initiation step, and its dysregulation is implicated in many human diseases. Several proteins have been found to regulate translational initiation, including Pdcd4 (programmed cell death gene 4). Pdcd4 is a tumor suppressor protein that prevents cell growth, invasion, and metastasis. It is downregulated in most tumor cells, while global translation in the cell is upregulated. To understand the mechanisms underlying translational control by Pdcd4, we used single-particle cryo-electron microscopy to determine the structure of human Pdcd4 bound to 40S small ribosomal subunit, including Pdcd4-40S and Pdcd4-40S-eIF4A-eIF3-eIF1 complexes. The structures reveal the binding site of Pdcd4 at the mRNA entry site in the 40S, where the C-terminal domain (CTD) interacts with eIF4A at the mRNA entry site, while the N-terminal domain (NTD) is inserted into the mRNA channel and decoding site. The structures, together with quantitative binding andin vitrotranslation assays, shed light on the critical role of the NTD for the recruitment of Pdcd4 to the ribosomal complex and suggest a model whereby Pdcd4 blocks the eIF4F-independent role of eIF4A during recruitment and scanning of the 5′ UTR of mRNA.
A novel induced pluripotent stem cell model of Schwann cell differentiation revealsNF2- related gene regulatory networks of the extracellular matrix
Authors: Lazaro Olivia , Li Sihong , Carter William , Awosika Oluwamayowa , Robertson Sylvia , Hickey Brooke E. , Angus Steven P. , House Austin , Clapp Wade D. , Qadir Abdul S. , Johnson Travis S. , Rhodes Steven D. 
Published: May 2024

AbstractSchwann cells are vital to development and maintenance of the peripheral nervous system and their dysfunction has been implicated in a range of neurological and neoplastic disorders, includingNF2-related schwannomatosis. We developed a novel human induced pluripotent stem cell (hiPSC) model to study Schwann cell differentiation in health and disease. We performed transcriptomic, immunofluorescence, and morphological analysis of hiPSC derived Schwann cell precursors (SPCs) and terminally differentiated Schwann cells (SCs) representing distinct stages of development. To validate our findings, we performed integrated, cross-species analyses across multiple external datasets at bulk and single cell resolution. Our hiPSC model of Schwann cell development shared overlapping gene expression signatures with human amniotic mesenchymal stem cell (hAMSCs) derived SCs andin vivomouse models, but also revealed unique features that may reflect species-specific aspects of Schwann cell biology. Moreover, we identified gene co-expression modules that are dynamically regulated during hiPSC to SC differentiation associated with ear and neural development, cell fate determination, theNF2gene, and extracellular matrix (ECM) organization. By cross-referencing results between multiple datasets, we identified new genes potentially associated withNF2expression. Our hiPSC model further provides a tractable platform for studying Schwann cell development in the context of human disease.
CetZ1-dependent polar assembly of the motility machinery in haloarchaea
Authors: Brown Hannah J. , Islam Md Imtiazul , Ruan Juanfang , Baker Matthew A. B. , Ithurbide Solenne , Duggin Iain G. 
Published: May 2024

AbstractArchaeal CetZ cytoskeletal proteins are a major group of the tubulin superfamily involved in the development of motile rod-shaped cells. In the model archaeonHaloferax volcanii, it has been unknown whether CetZs contribute to motility solely through the effects of rod cell shape on swimming speed, or in other ways too. Here, we used cryo-electron and fluorescence microscopy to observe cell surface filaments and the assembly of the motility machinery in cells carryingcetZ1orcetZ2deletion, overexpression, or dominant GTPase-deficient mutations. CetZ1 was found to play important roles in the polar assembly of motility marker proteins, including ArlD1, a constituent of the archaellum base, the chemotaxis sensory array adapter CheW1, and signal transducer CheY. Notably, overexpression ofcetZ1reduced motility and the assembly of the motility machinery markers but did not affect the rod shape of motile cells. Dual protein localization studies further suggested that CetZ1 is not a direct stoichiometric component of the motility machineries but promotes their assembly via a significant role in organisation or structure of the cell poles.SignificanceThis study demonstrates that cytoskeletal proteins (CetZs) can contribute to assembly of the motility machinery in archaea. In the model organism,H. volcanii, this function is expected to contribute significantly to the overall impact of CetZ1 on swimming motility, in addition to its established role in rod cell formation generating a streamlined shape. Our study also provides the first evidence that archaeal CetZ tubulin superfamily proteins can have structural or organisational roles for the assembly of protein complexes on the cell surface and cell poles. The multiple functions and subcellular locations of CetZ1 during motile cell development are reminiscent of eukaryotic cytoskeletal proteins and the roles of tubulin in basal bodies during the development of the eukaryotic flagellum.
Pore engineering as a general strategy to improve protein-based enzyme nanoreactor performance
Authors: Kwon Seokmu , Andreas Michael P. , Giessen Tobias W. 
Published: May 2024

AbstractEnzyme nanoreactors are nanoscale compartments consisting of encapsulated enzymes and a selectively permeable barrier. Sequestration and co-localization of enzymes can increase catalytic activity, stability, and longevity, highly desirable features for many biotechnological and biomedical applications of enzyme catalysts. One promising strategy to construct enzyme nanoreactors is to repurpose protein nanocages found in nature. However, protein-based enzyme nanoreactors often exhibit decreased catalytic activity, partially caused by a mismatch of protein shell selectivity and the substrate requirements of encapsulated enzymes. No broadly applicable and modular protein-based nanoreactor platform is currently available. Here, we introduce a pore-engineered universal enzyme nanoreactor platform based on encapsulins – microbial self-assembling protein nanocompartments with programmable and selective enzyme packaging capabilities. We structurally characterize our protein shell designs via cryo-electron microscopy and highlight their polymorphic nature. Through fluorescence polarization assays, we show their improved molecular flux behavior and highlight their expanded substrate range via a number of proof-of-concept enzyme nanoreactor designs. This work lays the foundation for utilizing our encapsulin-based nanoreactor platform for future biotechnological and biomedical applications.
Perceptual consequences of retinal stabilization with a high-frequency LCD display
Authors: Li Yuanhao H. , Rucci Michele 
Published: May 2024

AbstractSeveral recent studies have shown decreased sensitivity when stimuli are immobilized on the retina, a procedure known as retinal stabilization. Because of the technical challenges inherent in this procedure, studies have either used fast-phosphor CRT displays or directly updated the stimulus on the retina by means of adaptive optics scanning laser ophthalmoscopes. Both display systems provide brief pulses to the retina, raising the question of whether this flicker contributed to perceptual effects. Here we report the results of retinal stabilization experiments conducted with LCD monitors at high refresh rates. Results replicate previous findings of high-frequency impairments under retinal stabilization. These data provide further support for a functional role of small eye movements during visual fixation.
IL-2 enhances effector function but suppresses follicular localization of CD8+T cells in chronic infection
Authors: Chen Yaping , Zhou Pengcheng , Gubser Patrick Marc , Leong Yew Ann , He Jing , Wei Yunbo , Makota Fadzai Victor , Pazhouhandeh Mehrdad , Zheng Ting , Yunis Joseph , Li Zhanguo , Kallies Axel , Yu Di 
Published: May 2024

SummaryCytotoxic CD8+T cells, essential in combating viral infections and cancer, become dysfunctional from prolonged antigen exposure. Precursors of exhausted T (TPEX) cells are pivotal in sustaining immune responses in chronic diseases and mediating immunotherapy efficacy. They also control viral infection within B-cell follicles, facilitated by CXCR5 expression. How cytokines regulate TPEXcell fate and follicular entry is not well understood. We reveal that IL-2 treatment enhances CD8+T cell effector functions in chronic LCMV infection but hinders CXCR5+TPEXcell formation and infection control within B-cell follicles. Mechanistically, IL-2 suppresses TPEXcell differentiation in a STAT5 and BLIMP1-dependent manner. Using an IL-2 fusion protein targeting CD122, we shifted the differentiation towards CX3CR1+T cells with increased effector function. Clinical observations with low-dose IL-2 in autoimmune disease confirmed IL-2’s inhibitory effect on CXCR5+TPEXcells, underscoring IL-2’s crucial regulatory role and therapeutic potential in modulating TPEXand effector T cell generation.
Pitfalls and recommendations for large-scale SNP genotyping in a non-model endangered species: the southern damselflies (Coenagrion mercuriale) as a case study
Authors: Lévêque Agathe , Arnaud Jean-François , Vignon Vincent , Mazoyer Clément , Godé Cécile , Duputié Anne 
Published: May 2024

AbstractGenomic markers are essential tools for studying species of conservation concern, yet non-model species often lack a genome reference. Here we describe a methodology for identifying and genotyping thousands of SNP loci in the southern damselfly (Coenagrion mercuriale), a bioindicator of freshwater stream quality classified as near-threatened, with locally declining populations. We used a hybrid approach combining reduced representation sequencing and target enrichment. First, we identified putative SNP loci using ddRADseq andde novoassembly. Then, single primer enrichment technology targeted 6,000 of these SNPs across 1,920 individuals. Challenges encountered included sequence recapture failure, coverage depth discrepancies, and aberrantFISvalues. We provide recommendations to address such issues. After multiple filtering, we retained 2,092 SNPs. We used them to characterise rear-edge populations of the southern damselfly in Northern France, a region where populations are sparsely distributed. Previous surveys utilising microsatellite markers allowed comparison of genetic diversity and differentiation estimates. Consistent with prior findings, genetic diversity estimates were similar across the studied populations that showed no sign of inbreeding. SNP markers exhibited greater resolution in detecting fine-scaled genetic structure, identifying two putative hybrids in adjacent populations, a feat unattainable with microsatellite loci. Altogether, this study highlighted the ongoing challenge of large-scale SNP genotyping using target sequencing techniques in non-model species to set conservation guidelines. Nonetheless, these new markers showed greater statistical power in identifying conservation units and offered the promise of greater precision in the identification of admixture events or the estimation of key population parameters such as effective population size.
Spontaneous HFO Sequences Reveal Propagation Pathways for Precise Delineation of Epileptogenic Networks
Authors: Cai Zhengxiang , Jiang Xiyuan , Bagić Anto , Worrell Gregory A. , Richardson Mark , He Bin 
Published: May 2024

AbstractEpilepsy, a neurological disorder affecting millions worldwide, poses great challenges in precisely delineating the epileptogenic zone – the brain region generating seizures – for effective treatment. High-frequency oscillations (HFOs) are emerging as promising biomarkers; however, the clinical utility is hindered by the difficulties in distinguishing pathological HFOs from non- epileptiform activities at single electrode and single patient resolution and understanding their dynamic role in epileptic networks. Here, we introduce an HFO-sequencing approach to analyze spontaneous HFOs traversing cortical regions in 40 drug-resistant epilepsy patients. This data- driven method automatically detected over 8.9 million HFOs, pinpointing pathological HFO- networks, and unveiled intricate millisecond-scale spatiotemporal dynamics, stability, and functional connectivity of HFOs in prolonged intracranial EEG recordings. These HFO sequences demonstrated a significant improvement in localization of epileptic tissue, with an 818.47% increase in concordance with seizure-onset zone (mean error: 2.92 mm), compared to conventional benchmarks. They also accurately predicted seizure outcomes for 90% AUC based on pre-surgical information using generalized linear models. Importantly, this mapping remained reliable even with short recordings (mean standard deviation: 3.23 mm for 30-minute segments). Furthermore, HFO sequences exhibited distinct yet highly repetitive spatiotemporal patterns, characterized by pronounced synchrony and predominant inward information flow from periphery towards areas involved in propagation, suggesting a crucial role for excitation-inhibition balance in HFO initiation and progression. Together, these findings shed light on the intricate organization of epileptic network and highlight the potential of HFO-sequencing as a translational tool for improved diagnosis, surgical targeting, and ultimately, better outcomes for vulnerable patients with drug-resistant epilepsy.One Sentence SummaryPathological fast brain oscillations travel like traffic along varied routes, outlining recurrently visited neural sites emerging as critical hotspots in epilepsy network.
Optimized AAV capsids for diseases of the basal ganglia show robust potency and distribution in adult nonhuman primates
Authors: Leib DE , Chen YH , Tecedor L , Ranum PT , Keiser MS , Lewandowski BC , Carrell EM , Arora S , Huerta-Ocampo I , Liu X , Davidson BL 
Published: May 2024

AbstractHuntington’s disease and other disorders of the basal ganglia create challenges for biomolecule-based medicines given the poor accessibility of these deep brain structures following intracerebral or intravascular delivery. Additionally, for adeno-associated viruses (AAVs) intravascular delivery exposes peripheral tissues to the vast majority of the therapy, increasing the risk of immune responses and the quantity and associated cost of goods required for therapeutically relevant brain penetration levels. Here, we found that low dose, low volume delivery of unbiased AAV libraries into a focused brain region allowed recovery of novel capsids capable of broad access to key deep brain and cortical structures relevant for human therapies at doses orders of magnitude lower than used in current clinical trials. One such capsid, AAV-DB-3, provided transduction of up to 45% of medium spiny neurons in the adult NHP striatum, along with substantial transduction of relevant deep layer neurons in the cortex. Notably, AAV-DB-3 behaved similarly in mice as in NHPs and also potently transduced human neurons derived from induced pluripotent stem cells. Thus, AAV-DB-3 provides a unique AAV for network level brain gene therapies that translates up and down the evolutionary scale for preclinical studies and eventual clinical use.