bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deciphering the role of brainstem glycinergic neurons during startle and prepulse inhibition
Authors: Huang Wanyun , Cano Jose C. , Fénelon Karine 
Published: May 2023

SUMMARYPrepulse inhibition (PPI) of the auditory startle response is the gold standard operational measure of sensorimotor gating. Affected by various neurological and neuropsychiatric illnesses, PPI also declines during aging. While PPI deficits are often associated with cognitive overload, attention impairments and motor dysfunctions, their reversal is routinely used in experimental systems for drug screening. Yet, the cellular and circuit-level mechanisms of PPI remain unclear, even under non-pathological conditions. Recent evidence shows that neurons located in the brainstem caudal pontine reticular nucleus (PnC) expressing the glycine transporter type 2 (GlyT2+) receive inputs from the central nucleus of the amygdala (CeA) and contribute to PPI via an uncharted pathway. Using tract-tracing and immunohistochemical analyses in GlyT2-eGFP mice, we reveal the neuroanatomical location of CeA glutamatergic neurons innervating GlyT2+neurons. Our precisein vitrooptogenetic manipulations coupled to field electrophysiological recordings demonstrate that CeA glutamatergic inputs do suppress auditory neurotransmission in PnC neurons but not via action on transmitter release from auditory afferents. Rather, our data is consistent with excitatory drive onto GlyT2+neurons. Indeed, our PPI experimentsin vivodemonstrate that optogenetic activation of GlyT2+PnC neurons increases PPI and is sufficient to induce PPI, clarifying the crucial role of these neurons in young GlyT2-Cre mice. In contrast, in older GlyT2-Cre mice, PPI is reduced and not further altered by optogenetic inhibition of GlyT2+neurons. We conclude that GlyT2+PnC neurons innervated by CeA glutamatergic inputs are crucial for PPI and we highlight their reduced activity during the age-dependent decline in PPI.SIGNIFICANCE STATEMENTSensorimotor gating is a pre-attentive mechanism that declines with age and that is affected by neuropsychiatric and neurological disorders. Prepulse inhibition (PPI) of startle commonly measures sensorimotor gating to assess cognitive and motor symptoms and to screen drug efficacy. Yet, the neuronal mechanisms underlying PPI are still unresolved, limiting therapeutic advances. Here, we identify brainstem glycinergic neurons essential for PPI using tract tracing,in vitroelectrophysiology and precisein vivooptogenetic manipulations during startle measurements in mice. Innervated by amygdala glutamatergic inputs, we show that these glycinergic neurons are essential and sufficient to induce PPI in young mice. In contrast, these neurons do not contribute to PPI in older mice. We provide new insights to the theoretical construct of PPI.
Effects of TP63 Mutations on Keratinocyte Adhesion and Migration
Authors: Salois Maddison N. , Gugger Jessica A. , Webb Saiphone , Sheldon Christina E. , Parraga Shirley P. , Lewitt G. Michael , Grange Dorothy K. , Koch Peter J. , Koster Maranke I. 
Published: May 2023

ABSTRACTThe goal of this study was to investigate the molecular mechanisms responsible for the formation of skin erosions in patients affected by Ankyloblepharon-ectodermal defects-cleft lip/palate syndrome (AEC). This ectodermal dysplasia is caused by mutations in theTP63gene, which encodes several transcription factors that control epidermal development and homeostasis. We generated induced pluripotent stem cells (iPSC) from AEC patients and corrected theTP63mutations using genome editing tools. Three pairs of the resulting conisogenic iPSC lines were differentiated into keratinocytes (iPSC-K). We identified a significant downregulation of key components of hemidesmosomes and focal adhesions in AEC iPSC-K compared to their gene-corrected counterparts. Further, we demonstrated reduced iPSC-K migration, suggesting the possibility that a process critical for cutaneous wound healing might be impaired in AEC patients. Next, we generated chimeric mice expressing aTP63-AECtransgene and confirmed a downregulation of these genes in transgene-expressing cellsin vivo. Finally, we also observed these abnormalities in AEC patient skin. Our findings suggest that integrin defects in AEC patients might weaken the adhesion of keratinocytes to the basement membrane. We propose that reduced expression of extracellular matrix adhesion receptors, potentially in conjunction with previously identified desmosomal protein defects, contribute to skin erosions in AEC.
Functional GPCR expression in eukaryotic LEXSY system
Authors: Luginina Aleksandra , Maslov Ivan , Khorn Polina , Volkov Oleksandr , Khnykin Andrey , Kuzmichev Pavel , Shevtsov Mikhail , Belousov Anatoliy , Dashevskii Dmitrii , Kornilov Daniil , Bestsennaia Ekaterina , Hofkens Johan , Hendrix Jelle , Gensch Thomas , Cherezov Vadim , Ivanovich Valentin , Mishin Alexey , Borshchevskiy Valentin 
Published: May 2023

AbstractG protein-coupled receptors (GPCRs) represent an important class of drug targets, and their structural studies facilitate rational drug discovery. However, atomic structures of only about 20% of human GPCRs have been solved to date. Recombinant production of GPCRs for structural studies at a large scale is challenging due to their low expression levels and stability. Here we tested the eukaryotic system LEXSY (Leishmania tarentolae) for GPCR production. We expressed the human A2Aadenosine receptor (A2AAR) in LEXSY, purified it, and compared with the same receptor produced in insect cells, which is the most popular expression system for structural studies of GPCRs. The A2AAR purified from both expression systems showed similar purity, stability, ligand-induced conformational changes and structural dynamics, with a remarkably higher protein yield in the case of LEXSY expression.
Rapamycin-sensitive mechanisms confine the growth of fission yeast below the temperatures detrimental to cell physiology
Authors: Morozumi Yuichi , Mahayot Fontip , Nakase Yukiko , Soong Jia Xin , Yamawaki Sayaka , Sofyantoro Fajar , Imabata Yuki , Oda Arisa H. , Tamura Miki , Kofuji Shunsuke , Akikusa Yutaka , Ohta Kunihiro , Shiozaki Kazuhiro 
Published: May 2023

AbstractCells cease to proliferate above their growth-permissible temperatures, a ubiquitous phenomenon generally attributed to protein denaturing and heat damage to other cellular macromolecules. We here report that, in the presence of the macrolide compound rapamycin, the fission yeastSchizosaccharomyces pombecan proliferate at high temperatures that normally arrest its growth. Rapamycin is a potent inhibitor of the protein kinase complex TOR Complex 1 (TORC1), and consistently, mutations to the TORC1 subunit RAPTOR/Mip1 and the TORC1 substrate Sck1 significantly improve cellular heat resistance. These results suggest that TORC1, a well-established growth promoter, restricts the high-temperature growth of fission yeast and that compromised TORC1 signaling allows cell proliferation at higher temperatures. Aiming for a more comprehensive understanding of the negative regulation of high-temperature growth, we conducted genome-wide screens inS. pombe, which identified Sck1 and additional factors that appear to suppress cell proliferation at high temperatures. Our study has uncovered unexpected mechanisms of growth restraint even below the temperatures deleterious to cell physiology. Thus, growth arrest at high temperatures may not directly result from heat damage to cellular components essential for proliferation and viability.Significance StatementThe immunosuppressant rapamycin is a specific inhibitor of the protein kinase Target Of Rapamycin (TOR), and the drug is known to extend the lifespan of diverse eukaryotic organisms. In this study, we have found that rapamycin confers heat resistance on fission yeast, allowing its proliferation above the normal permissive temperatures. This unexpected observation suggests that TOR, which is known as a growth-promoting kinase, is inhibitory to cell proliferation at high temperatures. Our genome-wide screens have identified additional genes whose deletion leads to improved growth under heat stress. Thus, cells may have mechanisms that restrict proliferation even below the temperatures deleterious to their physiology.
MskAge - An Epigenetic Biomarker of Musculoskeletal Age Derived from a Genetic Algorithm Islands Model
Authors: Green Daniel Charles , Reynard Louise , Henstock James , Reppe Sjur , Gutvik Kaare , Peffers Mandy , Shanley Daryl , Clegg Peter , Canty-Laird Elizabeth 
Published: May 2023

BackgroundAge is a significant risk factor for functional decline and disease of the musculoskeletal system, yet few biomarkers exist to facilitate ageing research in musculoskeletal tissues. Multivariate models based on DNA methylation, termed epigenetic clocks, have shown promise as markers of biological age. However, the accuracy of existing epigenetic clocks in musculoskeletal tissues are no more, and often less accurate than a randomly sampled baseline model.ResultsWe developed a highly accurate epigenetic clock, Msk-Age, that is specific to tissues and cells of the musculoskeletal system. MskAge was built using a penalised genetic algorithm islands model that addresses multi-tissue clock bias. The final model was trained on the transformed principal components of CpGs selected by the genetic algorithm, which are significantly enriched for pathways terms related to the skeletal system and mesenchyme development. We show that MskAge tracks epigenetic ageingex vivoandin vitro. Epigenetic age estimates are rejuvenated to zero with cellular reprogramming and are accelerated at a rate of 0.45 years per population doubling. Remarkably, MskAge explains more variance associated within vitroageing of fibroblasts than the purpose-developed skin and blood clock.ConclusionThe precision of MskAge and its ability to capture perturbations in biological ageing make it a promising research tool for musculoskeletal and ageing biologists.
Method for cycle detection in sparse, irregularly sampled, long-term neuro-behavioral timeseries: Basis pursuit denoising with polynomial detrending of long-term, inter-ictal epileptiform activity
Authors: Balzekas Irena , Trzasko Joshua , Yu Grace , Richner Thomas J. , Mivalt Filip , Sladky Vladimir , Gregg Nicholas M. , Gompel Jamie Van , Miller Kai , Croarkin Paul E. , Kremen Vaclav , Worrell Gregory A. 
Published: May 2023

AbstractNumerous physiological processes are cyclical, but sampling these processes densely enough to perform frequency decomposition and subsequent analyses can be challenging. Mathematical approaches for decomposition and reconstruction of sparsely and irregularly sampled signals are well established but have been under-utilized in physiological applications. We developed a basis pursuit denoising with polynomial detrending (BPWP) model that recovers oscillations and trends from sparse and irregularly sampled timeseries. We validated this model on a unique dataset of long-term inter-ictal epileptiform discharge (IED) rates from human hippocampus recorded with a novel investigational device with continuous local field potential sensing. IED rates have well established circadian and multiday cycles related to sleep, wakefulness, and seizure clusters. Given sparse and irregular samples of IED rates from multi-month intracranial EEG recordings from ambulatory humans, we used BPWP to compute narrowband spectral power and polynomial trend coefficients and identify IED rate cycles in three subjects. In select cases, we propose that random and irregular sampling may be leveraged for frequency decomposition of physiological signals.Author SummaryCircadian and multiday cycles are an important part of many long-term neuro-behavioral phenomena such as pathological inter-ictal epileptiform discharges (IEDs) in epilepsy. Long-term, ambulatory, neuro-behavioral monitoring in human patients involves complex recording systems that can be subject to intermittent, irregular data loss and storage limitations, resulting in sparse, irregularly sampled data. Cycle identification in sparse data or irregular data using traditional frequency decomposition techniques typically requires interpolation to create a regular timeseries. Using unique, long-term recordings of pathological brain activity in patients with epilepsy implanted with an investigational device, we developed a method to identify cycles in sparse, irregular neuro-behavioral data without interpolation. We anticipate this approach will enable retrospective cycle identification in sparse neuro-behavioral timeseries and support prospective sparse sampling in monitoring systems to enable long-term monitoring of patients and to extend storage capacity in a variety of ambulatory monitoring applications.
Draft genome sequence of Microbacterium fakhimisp. nov., a novel bacterium associated with the algaChlamydomonas reinhardtii
Authors: Fakhimi Neda , Torres María Jesus , Delgado-Luque Jesús , Fernandez Emilio , Galván Aurora , Dubini Alexandra , González-Ballester David 
Published: May 2023

ABSTRACTMicrobacterium fakhimisp. nov. has been isolated from a contaminated algal culture (Chlamydomonas reinhardtii). Its genome has been fully sequenced (3,753,259 base pairs) and a tentative annotation is provided (3,704 genes). Both, genome information and growth tests suggest thatM. fakhimisp. nov. is auxotroph for biotin and thiamine and unable to use sulfate as sulfur (S) source. S-reduced forms, such as methionine and cysteine can supportM. fakhimisp. nov. growth. The potential biotechnological interest of this bacteria is discussed here and in a related research paper (Fakhimi et al., 2023b).
Phosphorylation of 53BP1 by ATM enforce neurodevelopmental programs in cortical organoids
Authors: Lim Bitna , Djekidel Mohamed Nadhir , Matsui Yurika , Jung Seunghyun , Yuan Zuo-Fei , Wang Xusheng , Yang Xiaoyang , Pilehroud Abbas Shirinifard , Pan Haitao , Wang Fang , Pruett-Miller Shondra , Kavdia Kanisha , Pagala Vishwajeeth , Fan Yiping , Peng Junmin , Xu Beisi , Peng Jamy C. 
Published: May 2023

ABSTRACT53BP1 is a well-established DNA damage repair factor recently shown to regulate gene expression and critically influence tumor suppression and neural development. For gene regulation, how 53BP1 is regulated remains unclear. Here, we showed that 53BP1-serine 25 phosphorylation by ATM is required for neural progenitor cell proliferation and neuronal differentiation in cortical organoids. 53BP1-serine 25 phosphorylation dynamics controls 53BP1 target genes for neuronal differentiation and function, cellular response to stress, and apoptosis. Beyond 53BP1, ATM is required for phosphorylation of factors in neuronal differentiation, cytoskeleton, p53 regulation, and ATM, BNDF, and WNT signaling pathways for cortical organoid differentiation. Overall, our data suggest that 53BP1 and ATM control key genetic programs required for human cortical development.
Image-based identification and isolation of micronucleated cells to dissect cellular consequences
Authors: DiPeso Lucian , Pendyala Sriram , Huang Heather Z , Fowler Douglas M , Hatch Emily M 
Published: May 2023

AbstractRecent advances in isolating cells based on visual phenotypes have transformed our ability to identify the mechanisms and consequences of complex traits. Micronucleus (MN) formation is a frequent outcome of genome instability, triggers extensive disease-associated changes in genome structure and signaling coincident with MN rupture, and is almost exclusively defined by visual analysis. Automated MN detection in microscopy images has proved extremely challenging, limiting unbiased discovery of the mechanisms and consequences of MN formation and rupture. In this study we describe two new MN segmentation modules: a rapid model for classifying micronucleated cells and their rupture status (VCS MN), and a robust model for accurate MN segmentation (MNFinder) from a broad range of fluorescence microscopy images. As a proof-of- concept, we define the transcriptome of non-transformed human cells with intact or ruptured MN after inducing chromosome missegregation by combining VCS MN with photoactivation-based cell isolation and RNASeq. Surprisingly, we find that neither MN formation nor rupture triggers a strong unique transcriptional response. Instead, transcriptional changes appear correlated with small increases in aneuploidy in these cell classes. Our MN segmentation modules overcome a significant challenge with reproducible MN quantification, and, joined with visual cell sorting, enable the application of powerful functional genomics assays, including pooled CRISPR screens and time-resolved analyses of cellular and genetic consequences, to a wide-range of questions in MN biology.
DeepPhe-CR: Natural Language Processing Software Services for Cancer Registrar Case Abstraction
Authors: Hochheiser Harry , Finan Sean , Yuan Zhou , Durbin Eric B. , Jeong Jong Cheol , Hands Isaac , Rust David , Kavuluru Ramakanth , Wu Xiao-Cheng , Warner Jeremy L. , Savova Guergana 
Published: May 2023

ABSTRACTObjectiveThe manual extraction of case details from patient records for cancer surveillance efforts is a resource-intensive task. Natural Language Processing (NLP) techniques have been proposed for automating the identification of key details in clinical notes. Our goal was to develop NLP application programming interfaces (APIs) for integration into cancer registry data abstraction tools in a computer-assisted abstraction setting.MethodsWe used cancer registry manual abstraction processes to guide the design of DeepPhe-CR, a web-based NLP service API. The coding of key variables was done through NLP methods validated using established workflows. A container-based implementation including the NLP wasdeveloped. Existing registry data abstraction software was modified to include results from DeepPhe-CR. An initial usability study with data registrars provided early validation of the feasibility of the DeepPhe-CR tools.ResultsAPI calls support submission of single documents and summarization of cases across multiple documents. The container-based implementation uses a REST router to handle requests and support a graph database for storing results. NLP modules extract topography, histology, behavior, laterality, and grade at 0.79-1.00 F1 across common and rare cancer types (breast, prostate, lung, colorectal, ovary and pediatric brain) on data from two cancer registries. Usability study participants were able to use the tool effectively and expressed interest in adopting the tool.DiscussionOur DeepPhe-CR system provides a flexible architecture for building cancer-specific NLP tools directly into registrar workflows in a computer-assisted abstraction setting. Improving user interactions in client tools, may be needed to realize the potential of these approaches. DeepPhe-CR:https://deepphe.github.io/.
Gender influence on changes of Coagulation factors in cryoprecipitate plasma at Kisii Teaching and Referral Hospital
Authors: Ogolla Collince Odiwuor , Nyanchongi Benson , Momanyi Chrisphine 
Published: May 2023

AbstractBackgroundCryoprecipitate is used without knowing the concentration of coagulation factors it contains which poses danger of circulatory overload with no any improvement if several bags with low factor levels are transfused when the levels changes or drastically reduce.ObjectiveThe objective was to evaluate gender influence on changes of Coagulation factors in cryoprecipitate plasma at Kisii Teaching and Referral Hospital.MethodsThe study involved time series analysis design involving analysis of cryoprecipitate during storage at -18°C for 5 weeks. Blood collected from the Kisii satellite blood transfusion center was received at Hematology laboratory where factor assays were performed on Erba Mannheim ECL 105 semi-automated coagulation analyzer. Thawing for subsequent coagulation factor analysis and serial testing was done using Stericox Plasma Thawing Bath at 37°C, for 45 mins. Data were entered into Excel and analyzed by SPSS version 25.ResultsThe mean rank for cryoprecipitate from week one to week five was in a decreasing trend with 3.00, 1.99 and 1.01 respectively. This confirms a steady statistical significant difference in mean ranks for the time period. The coagulation factors in cryoprecipitate plasma in the donated blood were not affected by the gender of the blood donor.ConclusionThe gender of the donor has no effect on the coagulation factors in cryoprecipitate plasma
Telomere-to-Telomere Assembly Improves Host Reads Removal in Metagenomic High-Throughput Sequencing of Human Samples
Authors: Wang Lei , Xing Guoning 
Published: May 2023

ABSTRACTMetagenomic high-throughput sequencing brings revolution to the study of human microbiome, clinical pathogen detection, discovery and infection diagnosis, but clinical samples often contain abundant human nucleic acids, leading to a high proportion of host reads. A high-quality human reference genome is essential for removing host reads to make downstream analyses faster and more accurate. The recently published complete human genome, Telomere-to-Telomere CHM13 assembly (T2T), though achieved great success immediately, has yet to be tested for metagenomic sequencing. In this study, we demonstrated the innovation that T2T brings to the field, using a diverse set of samples containing 4.97 billion reads sequenced from 165 libraries, on short- and long-read platforms. To exclude the effect of algorithms in comparison of the genomes, we benchmarked the per-read performance of state-of-the-art algorithms. For short reads, bwa mem was the best-performing algorithm, with positive median of differences (MD) and adjusted p-values <0.001 for all comparisons, while no consistent difference in overall performance was found for long reads algorithms. T2T, when compared to current reference genomes hg38 and YH, significantly improved the per-read sensitivity (MD: 0.1443 to 0.7238 percentage point, all adjusted p-values < 0.001) in removing host reads for all sequencers, and the per-read Mathew’s correlation coefficient (MCC) with T2T was also higher (MD: 1.063 to 16.41 percentage point, all adjusted p-values <0.001). Genomic location of reads exclusively mappable to T2T concentrated mainly in newly added regions. Misclassified reads generally resulted from low complexity sequences, contaminations in reference genomes and sequencing abnormalities. In downstream microbe detection procedures, T2T did not affect true positive calls but greatly reduced false positive calls. The improvement in the ability to correctly remove host reads foretells the success of T2T to serve as the next prevailing reference genome in metagenomic sequencing of samples containing human nucleic acids.