bluuebunny/crossref_metadata_2025_split huggingface dataset:
Continuous Hypoxia Reduces Retinal Ganglion Cell Degeneration in a Mouse Model of Mitochondrial Optic Neuropathy
Authors: Warwick Alexander M. , Bomze Howard M. , Wang Luyu , Klingeborn Mikael , Hao Ying , Stinnett Sandra S. , Gospe Sidney M. 
Published: September 2022

ABSTRACTPurposeTo test whether continuous hypoxia is neuroprotective to retinal ganglion cells (RGCs) in a mouse model of mitochondrial optic neuropathy.MethodsRGC degeneration was assessed in genetically modified mice in which the floxed gene for the complex I subunit NDUFS4 is deleted from RGCs using Vlgut2-driven Cre recombinase. Beginning at postnatal day 25 (P25), Vglut2-Cre;ndufs4loxP/loxP mice and control littermates were housed under hypoxia (11% oxygen) or were kept under normoxia (21% oxygen). Survival of RGC somas and axons was assessed at P60 and P90 via histological analysis of retinal flat mounts and optic nerve cross sections, respectively. Retinal tissue was also assessed for neuroinflammation using Western blot and confocal microscopy.ResultsConsistent with our previous characterization of this model, at least one-third of RGCs had degenerated by P60 in Vglut2-Cre;ndufs4loxP/loxP mice remaining under normoxia. However, continuous hypoxia resulted in complete rescue of RGC somas and axons at this time point, with normal axonal myelination observed on electron microscopy. Though only partial, hypoxia-mediated rescue of complex I-deficient RGC somas and axons remained significant at P90. Hypoxia prevented reactive gliosis at P60, while the retinal accumulation of Iba1-positive mononuclear inflammatory cells was not substantially reduced.ConclusionsContinuous hypoxia achieved dramatic rescue of early RGC degeneration in mice with severe mitochondrial dysfunction. Although complete rescue was not durable to P90, our observations suggest that investigating the mechanisms underlying hypoxia-mediated neuroprotection of RGCs may identify useful therapeutic strategies for optic neuropathies resulting from less profound mitochondrial impairment, such as Leber Hereditary Optic Neuropathy.
Age-Associated B cells predict impaired humoral immunity after COVID-19 vaccination in patients receiving immune checkpoint blockade
Authors: Yam-Puc Juan Carlos , Hosseini Zhaleh , Horner Emily C. , Gerber Pehuén Pereyra , Beristain-Covarrubias Nonantzin , Hughes Robert , Lulla Aleksei , Rust Maria , Boston Rebecca H. , Ali Magda , Fischer Katrin , Simmons-Rosello Edward , O’Reilly Martin , Robson Harry , Booth Lucy H. , Kahanawita Lakmini , Correa-Noguera Andrea , Ceron-Gutierrez Lourdes , Keller Baerbel , Craxton Andrew , Anderson Georgina S.F. , Sun Xiao-Ming , Elmer Anne , Saunders Caroline , Bermperi Areti , Jose Sherly , Kingston Nathalie , Mulroney Thomas ,   CITIID-NIHR COVID-19 BioResource Collaboration, Chapman Mike , Grigoriadou Sofia , MacFarlane Marion , Willis Anne E. , Patil Kiran R. , Spencer Sarah , Staples Emily , Warnatz Klaus , Buckland Matthew S. , Hollfelder Florian , Hyvönen Marko , Döffinger Rainer , Parkinson Christine , Lear Sara , Matheson Nicholas J. , Thaventhiran James E. D. 
Published: September 2022

AbstractAge-associated B cells (ABCs) accumulate with age, as well as in individuals with a range of immunological dyscrasias. These include patients with cancer treated with immune checkpoint blockade and patients with inborn errors of immunity. In this study, we sought to determine whether ABCs found in all these conditions are similar, and whether they enhance or detract from the response to COVID-19 vaccination. We use single cell RNA sequencing to show that ABCs arising from distinct aetiologies have common transcriptional profiles and may be subdivided according to the expression of genes associated with different immune functions, such as the autoimmune regulator (AIRE). Next, we perform detailed longitudinal profiling of the COVID-19 vaccination response in patients and controls. We show that high pre-vaccination ABC frequency correlates with decreased levels of antigen-specific memory B cells, and reduced magnitude and longevity of neutralising capacity against SARS-CoV-2 virus. Potentially contributing to this, ABCs express high levels of the inhibitory FcγRIIB receptor and are distinctive in their ability to bind immune complexes. This could contribute to diminished vaccine responses either directly as result of inhibitory signalling or indirectly via enhanced clearance of immune complexed-antigen. Expansion of ABCs may therefore serve as a biomarker identifying individuals at risk of a suboptimal response to COVID-19 vaccination.
Presence of cells in the polyaneuploid cancer cell (PACC) state predicts risk of recurrence in prostate cancer
Authors: Trabzonlu Levent , Pienta Kenneth J. , Trock Bruce J. , De Marzo Angelo M. , Amend Sarah R. 
Published: September 2022

AbstractBackgroundThe non-proliferating polyaneuploid cancer cell (PACC) state is associated with therapeutic resistance in cancer. A subset of cancer cells enters the PACC state by polyploidization and acts as cancer stem cells by undergoing depolyploidization and repopulating the tumor cell population after the therapeutic stress is relieved. Our aim was to systematically assess the presence and importance of this entity in men who underwent radical prostatectomy with curative intent to treat their presumed localized PCa.Materials and MethodsMen with NCCN intermediate- or high-risk PCa who underwent radical prostatectomy l from 2007-2015 and who did not receive neoadjuvant treatment were included. From the cohort of 2159 patients, the analysis focused on a subcohort of 209 patients was selected, and 38 cases. Prostate tissue microarrays (TMAs) were prepared from formalin-fixed paraffin-embedded blocks of the radical prostatectomy specimens. A total of 2807 tissue samples of matched normal/benign and cancer were arrayed in 9 TMA blocks. The presence of PACCs and the number of PACCs on each core were noted.ResultsThe total number of PACCs and the total number of cores with PACCs were significantly correlated with increasing Gleason score (p=0.0004) and increasing CAPRA-S (p=0.004), but no other variables. In univariate proportional hazards models of metastasis-free survival, year of surgery, Gleason score (9-10 vs. 7-8), pathology stage, CAPRA-S, total PACCs, and cores positive for PACCs were all statistically significant. The multivariable models with PACCs that gave the best fit included CAPRA-S. Adding either total PACCs or cores positive for PACCs to CAPRA-S both significantly improved model fit compared to CAPRA-S alone.ConclusionOur findings show that the number of PACCs and the number of cores positive for PACCs are statistically significant prognostic factors for metastasis-free survival, after adjusting for CAPRA-S, in a case-cohort of intermediate- or high-risk men who underwent radical prostatectomy. In addition, despite the small number of men with complete data to evaluate time to mCRPC, the total number of PACCs was a statistically significant predictor of mCRPC in univariate analysis, and suggested a prognostic effect even after adjusting for CAPRA-S.
APOE ε4 gene dose effect on imaging and blood biomarkers of glial reactivity and β-amyloid pathology
Authors: Snellman Anniina , Ekblad Laura L. , Tuisku Jouni , Koivumäki Mikko , Ashton Nicholas J. , Lantero-Rodriguez Juan , Karikari Thomas K. , Helin Semi , Bucci Marco , Löyttyniemi Eliisa , Parkkola Riitta , Karrasch Mira , Schöll Michael , Zetterberg Henrik , Blennow Kaj , Rinne Juha O. 
Published: September 2022

AbstractIncreased reactivity of microglia and astrocytes is known to be present at various stages of the Alzheimer’s continuum but their relationship with core Alzheimer’s disease pathology in the preclinical stages is less clear. We investigated glial reactivity and β-amyloid pathology in cognitively unimpaired APOE ε4 homozygotes, heterozygotes and non-carriers using 11C-PK11195 PET (targeting 18-kDa translocator protein), 11C-PiB PET (targeting β-amyloid), brain MRI, and a preclinical cognitive composite (APCC). Plasma glial fibrillary acidic protein (GFAP) by and plasma Aβ1-42/1-40 were measured using single molecule array and immunoprecipitation combined with mass spectrometry, respectively. We observed that (i)11C-PiB-binding was significantly higher in APOE ε4 homozygotes compared with non-carriers in all evaluated regions, (ii) regional 11C-PK11195-binding did not differ between the APOE ε4 gene doses or between Aβ-positive and -negative individuals, and (iii) higher 11C-PK11195-binding and plasma GFAP were associated with lower hippocampal volume, and elevated 11C-PiB-binding and plasma GFAP concentration with lower APCC scores. Increased glial reactivity might emerge in later stages of preclinical Alzheimer’s disease in parallel with early neurodegenerative changes.
Inferring causal genes at type 2 diabetes GWAS loci through chromosome interactions in islet cells
Authors: Torres Jason M. , Sun Han , Nylander Vibe , Downes Damien J. , van de Bunt Martijn , McCarthy Mark I. , Hughes Jim R. , Gloyn Anna L. 
Published: September 2022

SummaryResolving causal genes for type 2 diabetes at loci implicated by genome-wide association studies (GWAS) requires integrating functional genomic data from relevant cell types. Chromatin features in endocrine cells of the pancreatic islet are particularly informative and recent studies leveraging chromosome conformation capture (3C) with Hi-C based methods have elucidated regulatory mechanisms in human islets. However, these genome-wide approaches are less sensitive and afford lower resolution than methods that target specific loci. To gauge the extent to which targeted 3C further resolves chromatin-mediated regulatory mechanisms at GWAS loci, we generated interaction profiles at 23 loci using next-generation (NG) Capture-C in a human beta cell model (EndoC-βH1) and contrasted these maps with Hi-C maps in EndoC-βH1 cells and human islets and a promoter capture Hi-C map in human islets. We found improvements in assay sensitivity of up to 33-fold and resolved 4.8X more chromatin interactions. At a subset of 18 loci with 25 co-localised GWAS and eQTL signals, NG Capture-C interactions implicated effector transcripts at five additional genetic signals relative to promoter capture Hi-C through physical contact with gene promoters. Therefore, high resolution chromatin interaction profiles at selectively targeted loci can complement genome- and promoter-wide maps.
TLK1-mediated RAD54 phosphorylation spatio-temporally regulates Homologous Recombination Repair
Authors: Ghosh Ishita , Kwon Youngho , Shabestari Aida Badamchi , Chikhale Rupesh , Chen Jing , Wiese Claudia , Sung Patrick , Benedetti Arrigo De 
Published: September 2022

AbstractEnvironmental agents like ionizing radiation (IR) and chemotherapeutic drugs can cause severe damage to the DNA, often in the form of double-strand breaks (DSBs). Remaining unrepaired, DSBs can lead to chromosomal rearrangements, and cell death. One major error-free pathway to repair DSBs is homologous recombination repair (HRR). Tousled-like kinase 1 (TLK1), a Ser/Thr kinase that regulates the DNA damage checkpoint, has been found to interact with RAD54, a central DNA translocase in HRR. To determine how TLK1 regulates RAD54, we inhibited or depleted TLK1 and tested how this impacts HRR in human cells using a ISce-I-GR-DsRed fused reporter endonuclease. Our results show that TLK1 phosphorylates RAD54 at three threonines (T41, T59, and T700), two of which are located within its N-terminal domain (NTD) and one is located within its C-terminal domain (CTD). Phosphorylation at both T41 and T59 supports HRR and protects cells from DNA DSB damage. In contrast, phosphorylation of T700 leads to impaired HRR and engenders no protection to cells from cytotoxicity and rather results in repair delay. Further, our work enlightens the effect of RAD54-T700 (RAD54-CTD) phosphorylation by TLK1 in mammalian system and reveals a new site of interaction with RAD51.
Cryo-EM of prion strains from the same genotype of host identifies conformational determinants
Authors: Hoyt Forrest , Alam Parvez , Artikis Efrosini , Schwartz Cindi L. , Hughson Andrew G. , Race Brent , Baune Chase , Raymond Gregory J. , Baron Gerald S. , Kraus Allison , Caughey Byron 
Published: September 2022

ABSTRACTPrion strains in a given type of mammalian host are distinguished by differences in clinical presentation, neuropathological lesions, survival time, and characteristics of the infecting prion protein (PrP) assemblies. Near-atomic structures of prions from two host species with different PrP sequences have been determined but comparisons of distinct prion strains of the same amino acid sequence are needed to identify purely conformational determinants of prion strain characteristics. Here we report a 3.2 Å resolution cryogenic electron microscopy-based structure of the 22L prion strain purified from the brains of mice engineered to express only PrP lacking glycophosphatidylinositol anchors (a22L). Comparison of this near-atomic structure to our recently determined structure of the aRML strain propagated in the same inbred mouse reveals that these two mouse prion strains have distinct conformational templates for growth via incorporation of PrP molecules of the same sequence. Both a22L and aRML are assembled as stacks of PrP molecules forming parallel in-register intermolecular β-sheets and intervening loops, with single monomers spanning the ordered fibril core. Each monomer shares an N-terminal steric zipper, three major β-arches, and an overall V-shape, but the details of these and other conformational features differ markedly. Thus, variations in shared conformational motifs within a parallel in-register β-stack fibril architecture provide a structural basis for prion strain differentiation within a single host genotype.
RNA processing/modifying enzymes play key roles in the response to thermospermine in Arabidopsis thaliana
Authors: Tanaka Takahiro , Koyama Daiki , Saraumi Mitsuru , Motose Hiroyasu , Takahashi Taku 
Published: September 2022

AbstractThermospermine acts in negative regulation of xylem differentiation through enhancing mRNA translation of the members of the SAC51 gene family in Arabidopsis. These mRNAs contain conserved upstream open-reading-frames (uORFs) that are inhibitory to the main ORF translation. To address the mode of action of thermospermine in this process, we have isolated mutants that are insensitive to thermospermine, named its. We show here that four genes responsible for the mutants, its1 to its4, encode a homologue of SPOUT RNA methyl transferase, an rRNA pseudouridine synthase CBF5/NAP57, a putative spliceosome disassembly factor STIPL1/NTR1, and a plant-specific RNA-binding protein PHIP1, respectively. While these mutants except its1 are almost normal in appearance, they enhance the dwarf phenotype of a mutant of ACL5 defective in thermospermine biosynthesis, resulting in tiny-sized plants reminiscent of a double knockout of ACL5 and SACL3, a member of the SAC51 family. We confirmed that the GUS reporter activity from the SAC51 5’-GUS fusion transcript was severely reduced in all of these mutants. These results unveil the importance of RNA processing and modification for the translation of transcripts containing regulatory uORFs.
Accurate Detection of Proteins in Cryo-Electron Tomograms from Sparse Labels
Authors: Huang Qinwen , Zhou Ye , Liu Hsuan-Fu , Bartesaghi Alberto 
Published: September 2022

AbstractCryo-electron tomography (CET) combined with sub-volume averaging (SVA), is currently the only imaging technique capable of determining the structure of proteins imaged inside cells at molecular resolution. To obtain high-resolution reconstructions, sub-volumes containing randomly distributed copies of the protein of interest need be identified, extracted and subjected to SVA, making accurate particle detection a critical step in the CET processing pipeline. Classical template-based methods have high false-positive rates due to the very low signal-to-noise ratios (SNR) typical of CET volumes, while more recent neural-network based detection algorithms require extensive labeling, are very slow to train and can take days to run. To address these issues, we propose a novel particle detection framework that uses positive-unlabeled learning and exploits the unique properties of 3D tomograms to improve detection performance. Our end-to-end framework is able to identify particles within minutes when trained using a single partially labeled tomogram. We conducted extensive validation experiments on two challenging CET datasets representing different experimental conditions, and observed more than 10% improvement in mAP and F1 scores compared to existing particle picking methods used in CET. Ultimately, the proposed framework will facilitate the structural analysis of challenging biomedical targets imaged within the native environment of cells.
T cell-specific P2RX7 favors lung parenchymal CD4+ T cell accumulation in response to severe lung infections
Authors: Santiago-Carvalho Igor , Almeida-Santos Gislane , Macedo Bruna Gois , Barbosa-Bomfim Caio Cesar , Almeida Fabricio Moreira , Cione Marcos Vinícios Pinheiro , Vardam-Kaur Trupti , Masuda Mia , Van Dijk Sarah , Melo Bruno Marcel , do Nascimento Rogério Silva , Souza Rebeka da Conceição , Peixoto-Rangel Alba Lucínia , Coutinho-Silva Robson , Hirata Mario H. , Alves-Filho José Carlos , Álvarez José Maria , Lassounskaia Elena , da Silva Henrique Borges , D’Império-Lima Maria Regina 
Published: September 2022

ABSTRACTCD4+ T cells are key components of the immune response during lung infections and can mediate protection against tuberculosis (TB) or influenza. However, CD4+ T cells can also promote lung pathology during these infections, making it unclear how these cells control such discrepant effects. Using mouse models of hypervirulent TB and influenza, we observed that exaggerated accumulation of parenchymal CD4+ T cells promotes lung damage. Low numbers of lung CD4+ T cells, in contrast, are sufficient to protect against hypervirulent TB. In both situations, lung CD4+ T cell accumulation is mediated by CD4+ T cell-specific expression of the extracellular ATP (eATP) receptor P2RX7. P2RX7 upregulation in lung CD4+ T cells promotes expression of the chemokine receptor CXCR3 and favors in situ proliferation. Our findings suggest that direct sensing of lung eATP by CD4+ T cells is critical to induce tissue CD4+ T cell accumulation and pathology during lung infections.GRAPHICAL ABSTRACT
Evaluation of mouse behavioral responses to nutritive versus nonnutritive sugar using a deep learning-based 3D real-time pose estimation system
Authors: Kim Jineun , Kim Dae-gun , Jung Wongyo , Suh Greg S. B. 
Published: September 2022

AbstractAnimals are able to detect the nutritional content of sugar independently of taste. When given a choice between nutritive sugar and nonnutritive sugar, animals develop a preference for nutritive sugar over nonnutritive sugar during a period of food deprivation1-5. To quantify behavioral features during an episode of licking nutritive versus nonnutritive sugar, we implemented a multi-vision, deep learning-based 3D pose estimation system, termed the AI Vision Analysis for Three-dimensional Action in Real-Time (AVATAR)6. Using this method, we found that mice exhibit significantly different approach behavioral responses toward nutritive sugar versus nonnutritive sugar even before licking a sugar solution. Notably, the behavioral sequences during approach toward nutritive versus nonnutritive sugar became significantly different over time. These results suggest that the nutritional value of sugar not only promotes its consumption, but also elicits distinct repertoires of feeding behavior in deprived mice.
Development of an Agrobacterium-delivered codon-optimized CRISPR/Cas9 system for chickpea genome editing
Authors: Gupta Santosh Kumar , Vishwakarma Niraj Kumar , Malakar Paheli , Vanaspati Poonam , Sharma Nilesh Kumar , Chattopadhyay Debasis 
Published: September 2022

AbstractChickpea is considered recalcitrant to in vitro tissue culture. The Clustered, Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9 (CRISPR/Cas9) based genome editing in chickpea can remove the bottleneck of limited genetic variation in this cash crop rich in nutrients and protein. However, the generation of stable mutant lines using CRISPR/Cas9 requires efficient and highly reproducible transformation approaches. We modified a binary vector pPZP200 by introducing a codon-optimized Cas9 gene for chickpea and the promoters of Medicago truncatula U6 snRNA for expressing guide RNA targeted to the Phytoene Desaturase (PDS) gene. The dissected single cotyledons with half embryo of chickpea were used as explants for genetic transformation. A single gRNA was found sufficient to achieve high efficiency (42%) editing with the generation of PDS mutants with albino phenotypes. A simple, rapid, highly reproducible, stable transformation and CRISPR/Cas9-based genome editing system for chickpea was established. For the first time, this study aimed to demonstrate this system’s applicability by performing a gene knockout of the chickpea phytoene desaturase gene (CaPDS) in stable shoots using an improved chickpea transformation protocol.
A STIM dependent dopamine-insulin axis maintains the larval drive to feed and grow in Drosophila
Authors: Kasturacharya Nandashree , Dhall Jasmine Kaur , Hasan Gaiti 
Published: September 2022

AbstractAppropriate nutritional intake is essential for organismal survival. In holometabolous insects such asDrosophila melanogaster, the quality and quantity of food ingested as larvae determines adult size and fecundity. Here we have identified a subset of dopaminergic neurons (THD’) that maintain the larval motivation to feed. Dopamine release from these neurons requires the ER Ca2+sensor STIM. Larvae with loss of STIM stop feeding and growing, whereas expression of STIM in THD’ neurons rescues feeding, growth and viability of STIM null mutants. Moreover STIM is essential for maintaining excitability and release of dopamine from THD’ neurons. Optogenetic stimulation of THD’ neurons activated neuropeptidergic cells, including median neuro secretory cells that secrete insulin-like peptides. Loss of STIM in THD’ cells alters the developmental profile of specific insulin-like peptides including ilp3. Loss of ilp3 partially rescues STIM null mutants and inappropriate expression of ilp3 in larvae affects development and growth. In summary we have identified a novel STIM-dependent function of dopamine neurons that modulates developmental changes in larval feeding behaviour and growth.Author summaryThe ability to feed appropriately when hungry is an essential feature for organismal survival and is under complex neuronal control. An array of neurotransmitters and neuropeptides integrate external and internal signalling cues to initiate, maintain and terminate feeding. In adult vertebrates and invertebrates dopamine serves as a reward cue for motor actions, including feeding. Larvae of holometabolous insects, includingDrosophila melanogaster, feed and grow constantly followed by gradual cessation of feeding, once sufficient growth is achieved for transition to the next stages of development. Here we identified a subset of larval dopaminergic neurons inDrosophila melanogaster, activity in which maintains continuous feeding in larvae. By analysis of a null mutant we show that these neurons require the Stromal Interaction Molecule (STIM) an ER Ca2+sensor, to maintain excitability. In turn they modulate activity of certain neuropeptidergic cells. Among these are the median neurosecretory cells (MNSc) that synthesize and secrete insulin-like peptides including ilp3. The identified dopaminergic neurons dysregulate the normal pattern of larval ilp3 expression leading to premature cessation of feeding and growth. Overall, our study identified a simple dopamine modulated mechanism for feeding and growth whose manipulation could be useful for model organism studies related to feeding disorders, obesity and diabetes.