bluuebunny/crossref_metadata_2025_split huggingface dataset:
Activation of FAM111A Protease Induces Defects in Nuclear Function that Likely Underlie its Roles in Disease and Viral Restriction
Authors: Nie Minghua , Oravcová Martina , Jami-Alahmadi Yasaman , Wohlschlegel James A. , Lazzerini-Denchi Eros , Boddy Michael N. 
Published: May 2020

AbstractMutations in the nuclear trypsin-like serine protease FAM111A cause Kenny-Caffey syndrome (KCS2) with hypoparathyroidism and skeletal dysplasia, or perinatally lethal osteocraniostenosis (OCS). In addition, FAM111A was identified as a restriction factor for certain host range mutants of the SV40 polyomavirus and VACV orthopoxvirus. However, because FAM111A function is poorly characterized, its roles in restricting viral replication and the etiology of KCS2 and OCS remain undefined. We find that the FAM111A KCS2 and OCS patient mutants are hyperactive, inducing apoptosis-like phenotypes in a protease-dependent manner. Similarly, in response to the attempted replication of SV40 host range mutants in restrictive cells, FAM111A activity induces the loss of nuclear barrier function and structure. Interestingly, pan-caspase inhibitors do not block FAM111A-dependent phenotypes such as nuclear “leakiness”, shrinkage and pore redistribution, implying it acts independently or upstream of caspases. In this regard, we identified nucleoporins and the associated GANP transcription factor as FAM111A interactors and candidate targets. Together our data provide key insight into how FAM111A activation can restrict viral replication, and how its deregulated activity could cause KCS2 and OCS.
Antagonistic control of DDK binding to licensed replication origins by Mcm2 and Rad53
Authors: Wahab Syafiq Abd , Remus Dirk 
Published: May 2020

ABSTRACTEukaryotic replication origins are licensed by the loading of the replicative DNA helicase, Mcm2-7, in inactive double hexameric form around DNA. Subsequent origin activation is under control of multiple protein kinases that either promote or inhibit origin activation, which is important for genome maintenance. Using the reconstituted budding yeast DNA replication system, we find that the flexible N-terminal tail of Mcm2 promotes the stable recruitment of Dbf4-dependent kinase (DDK) to Mcm2-7 double hexamers, which in turn promotes DDK phosphorylation of Mcm4 and -6 and subsequent origin activation. Conversely, we demonstrate that the checkpoint kinase, Rad53, inhibits DDK binding to Mcm2-7 double hexamers. Unexpectedly, this function is not dependent on Rad53 kinase activity, but requires Rad53 activation by trans-autophosphorylation, suggesting steric inhibition of DDK by activated Rad53. These findings identify critical determinants of the origin activation reaction and uncover a novel mechanism for checkpoint-dependent origin inhibition.
Chemically-informed Analyses of Metabolomics Mass Spectrometry Data with Qemistree
Authors: Tripathi Anupriya , Vázquez-Baeza Yoshiki , Gauglitz Julia M. , Wang Mingxun , Dührkop Kai , Nothias-Esposito Mélissa , Acharya Deepa D. , Ernst Madeleine , van der Hooft Justin J.J. , Zhu Qiyun , McDonald Daniel , Gonzalez Antonio , Handelsman Jo , Fleischauer Markus , Ludwig Marcus , Böcker Sebastian , Nothias Louis-Félix , Knight Rob , Dorrestein Pieter C. 
Published: May 2020

AbstractUntargeted mass spectrometry is employed to detect small molecules in complex biospecimens, generating data that are difficult to interpret. We developed Qemistree, a data exploration strategy based on hierarchical organization of molecular fingerprints predicted from fragmentation spectra, represented in the context of sample metadata and chemical ontologies. By expressing molecular relationships as a tree, we can apply ecological tools, designed around the relatedness of DNA sequences, to study chemical composition.
JavaDL: a Java-based Deep Learning Tool to Predict Drug Responses
Authors: Huang Beibei , Fong Lon W. R. , Chaudhari Rajan , Tan Zhi , Zhang Shuxing 
Published: May 2020

AbstractMotivationAccurate prediction of drug response in each patient is the holy grail in personalized medicine. Recently, deep learning techniques have been witnessed with revival in a variety of areas such as image processing and genomic data analysis, and they will be useful for the coming age of big data analysis in pharmaceutical research and chemogenomic applications. This provides us an impetus to develop a novel deep learning platform to accurately and reliably predict the response of cancer to different drug treatments.ResultsIn this study, we describe a Java-based implementation of deep neural network (DNN) method, termed JavaDL, to predict cancer responses to drugs solely based on their chemical features. To this end, we devised a novel cost function by adding a regularization term which suppresses overfitting. We also adopted an “early stopping” strategy to further reduce overfit and improve the accuracy and robustness of our models. Currently the software has been integrated with a genetic algorithm-based variable selection approach and implemented as part of our JavaDL package. To evaluate our program, we compared it with several machine learning programs including SVM and kNN. We observed that JavaDL either significantly outperforms other methods in model building and prediction or obtains better results in handling big data analysis. Finally, JavaDL was employed to predict drug responses of several highly aggressive triple-negative breast cancer cell lines, and the results showed robust and accurate predictions with r2as high as 0.80.AvailabilityThe program is freely available athttps://imdlab.mdanderson.org/JavaDL/JavaDL.php.
PrimeDesign software for rapid and simplified design of prime editing guide RNAs
Authors: Hsu Jonathan Y. , Anzalone Andrew V. , Grünewald Julian , Lam Kin Chung , Shen Max W. , Liu David R. , Joung J. Keith , Pinello Luca 
Published: May 2020

AbstractPrime editing (PE) is a versatile genome editing technology, but design of the required guide RNAs is more complex than for standard CRISPR-based nucleases or base editors. Here we describe PrimeDesign, a user-friendly, end-to-end web application and command-line tool for the design of PE experiments. PrimeDesign can be used for single and combination editing applications, as well as genome-wide and saturation mutagenesis screens. Using PrimeDesign, we also constructed PrimeVar, the first comprehensive and searchable database for prime editing guide RNA (pegRNA) and nicking sgRNA (ngRNA) combinations to install or correct >68,500 pathogenic human genetic variants from the ClinVar database.
Stable gene expression for normalisation and single-sample scoring
Authors: Bhuva Dharmesh D. , Cursons Joseph , Davis Melissa J. 
Published: May 2020

AbstractBackgroundTranscriptomic signatures are useful in defining the molecular phenotypes of cells, tissues, and patient samples. Their most successful and widespread clinical application is the stratification of breast cancer patients into molecular (PAM50) subtypes. In most cases, gene expression signatures are developed using transcriptome-wide measurements, thus methods that match signatures to samples typically require a similar degree of measurements. The cost and relatively large amounts of fresh starting material required for whole-transcriptome sequencing has limited clinical applications, and accordingly thousands of existing gene signatures are unexplored in a clinical context.ResultsGenes in a molecular signature can provide information about molecular phenotypes and their underlying transcriptional programs from tissue samples, however determining the transcriptional state of these genes typically requires the measurement of all genes across multiple samples to allow for comparison. An efficient assay and scoring method should quantify the relative abundance of signature genes with a minimal number of additional measurements. We identified genes with stable expression across a range of abundances, and with a preserved relative ordering across large numbers (thousands) of samples, allowing signature scoring, and supporting general data normalisation for transcriptomic data. Based on singscore, we have developed a new method,stingscore, which quantifies and summarises relative expression levels of signature genes from individual samples through the inclusion of these “stably-expressed genes”.ConclusionWe show that our proposed list of stable genes has better stability across cancer and normal tissue data than previously proposed stable or housekeeping genes. Additionally, we show that signature scores computed from whole-transcriptome data are comparable to those calculated using only values for signature genes and our panel of stable genes. This new approach to gene expression signature analysis may facilitate the development of panel-type tests for gene expression signatures, thus supporting clinical translation of the powerful insights gained from cancer transcriptomic studies.
Improved growth and morphological plasticity ofHaloferax volcanii
Authors: de Silva Roshali T. , Abdul-Halim Mohd F. , Pittrich Dorothea A. , Brown Hannah J. , Pohlschroder Mechthild , Duggin Iain G. 
Published: May 2020

AbstractSome microbes display pleomorphism, showing variable cell shapes in a single culture, whereas others differentiate to adapt to changed environmental conditions. The pleomorphic archaeonHaloferax volcaniicommonly forms discoid-shaped (‘plate’) cells in culture, but may also be present as rods, and can develop into motile rods in soft agar, or longer filaments in certain biofilms. Here we report improvement ofH. volcaniigrowth in both semi-defined and complex media by supplementing with eight trace-element micronutrients. With these supplemented media, transient development of plate cells into uniformly-shaped rods was clearly observed during the early log phase of growth; cells then reverted to plates for the late log and stationary phases. In media prepared with high-purity water and reagents, without supplemental trace elements, rods and other complex elongated morphologies (‘pleomorphic rods’) were observed at all growth stages of the culture; the highly-elongated cells sometimes displayed a substantial tubule at one or less frequently both poles, as well as unusual tapered and highly-curved forms. Polar tubules were observed forming by initial mid-cell narrowing or tubulation, causing a dumbbell-like shape, followed by cell division towards one end. Formation of the uniform early-log rods, as well as the pleomorphic rods and tubules were dependent on the function of the tubulin-like cytoskeletal protein, CetZ1. Our results have revealed the remarkable morphological plasticity ofH. volcaniicells in response to multiple culture conditions, and should facilitate the use of this species in further studies of archaeal biology.
Prm2deficiency triggers a Reactive Oxygen Species (ROS)-mediated destruction cascade during epididymal sperm maturation in mice
Authors: Schneider Simon , Shakeri Farhad , Trötschel Christian , Arévalo Lena , Kruse Alexander , Buness Andreas , Poetsch Ansgar , Steger Klaus , Schorle Hubert 
Published: May 2020

AbstractProtamines are the safeguards of the paternal sperm genome. They replace most of the histones during spermiogenesis, resulting in DNA hypercondensation, thereby protecting its genome from environmental noxa. Impaired protamination has been linked to male infertility in mice and humans in many studies. Apart from impaired DNA integrity, protamine-deficient human and murine sperm show multiple secondary effects, including decreased motility and aberrant head morphology. In this study, we use aPrm2-deficient mouse model in combination with label-free quantitative proteomics to decipher the underlying molecular processes of these effects. We show that loss of the sperm’s antioxidant capacity, indicated by downregulation of key proteins like SOD1 and PRDX5, ultimately initiates an oxidative stress-mediated destruction cascade during epididymal sperm maturation. This is confirmed by an increased level of 8-OHdG in epididymal sperm, a biomarker for oxidative stress-mediated DNA damage.Prm2-deficient testicular sperm are not affected and initiate the proper development of blastocyst stage preimplantation embryosin vitroupon intracytoplasmic sperm injection (ICSI) into oocytes. Our results provide new insight into the role ofPrm2and its downstream molecular effects on sperm function and present an important contribution to the investigation of new treatment regimens for infertile men with impaired protamination.Significance statementSexual reproduction requires the successful fertilization of female eggs by male sperm. The generation of functional sperm is a complex, multi-step differentiation process known as spermatogenesis that takes places in the male testis. One important step for physiological sperm function is the incorporation of small proteins, known as protamines into the DNA. Defects within this process are common causes of male infertility. However, the underlying molecular mechanisms still remain largely unknown, thus preventing targeted therapies. Here, we identify the molecular cascade being initiated in protamine-deficient murine sperm that ultimately impedes fertilization. Our findings have broad implications for the development of new treatment options for infertile men with faulty protamination that seek medical advice.
Brain/MINDS Beyond Human Brain MRI Project: A Protocol for Multi-Site Harmonization across Brain Disorders Throughout the Lifespan
Authors: Koike Shinsuke , Tanaka Saori C , Okada Tomohisa , Aso Toshihiko , Asano Michiko , Maikusa Norihide , Morita Kentaro , Okada Naohiro , Fukunaga Masaki , Uematsu Akiko , Togo Hiroki , Miyazaki Atsushi , Murata Katsutoshi , Urushibata Yuta , Autio Joonas , Ose Takayuki , Yoshimoto Junichiro , Araki Toshiyuki , Glasser Matthew F , Van Essen David C , Maruyama Megumi , Sadato Norihiro , Kawato Mitsuo , Kasai Kiyoto , Okamoto Yasumasa , Hanakawa Takashi , Hayashi Takuya ,   Brain/MINDS Beyond Human Brain MRI Group
Published: May 2020

AbstractPsychiatric and neurological disorders are afflictions of the brain that can affect individuals throughout their lifespan. Many brain magnetic resonance imaging (MRI) studies have been conducted; however, imaging-based biomarkers are not yet well established for diagnostic and therapeutic use. This article describes an outline of the planned study, the Brain/MINDS Beyond human brain MRI project (FY2018 ∼ FY2023), which aims to establish clinically-relevant imaging biomarkers with multi-site harmonization by collecting data from healthy traveling subjects (TS) at 13 research sites. Collection of data in psychiatric and neurological disorders across the lifespan is also scheduled at 13 sites, whereas designing measurement procedures, developing and analyzing neuroimaging protocols, and databasing are done at three research sites. The Harmonization protocol (HARP) was established for five high-quality 3T scanners to obtain multimodal brain images including T1 and T2-weighted, resting state and task functional and diffusion-weighted MRI. Data are preprocessed and analyzed using approaches developed by the Human Connectome Project. Preliminary results in 30 TS demonstrated cortical thickness, myelin, functional connectivity measures are comparable across 5 scanners, providing high reproducibility and sensitivity to subject-specific connectome. A total of 75 TS, as well as patients with various psychiatric and neurological disorders, are scheduled to participate in the project, allowing a mixed model statistical harmonization. The HARP protocols are publicly available online, and all the imaging, demographic and clinical information, harmonizing database will also be made available by 2024. To the best of our knowledge, this is the first project to implement a rigorous, prospective harmonization protocol with multi-site TS data. It explores intractable brain disorders across the lifespan and may help to identify the disease-specific pathophysiology and imaging biomarkers for clinical practice.
Individuals with autism have no detectable deficit in neural markers of prediction error when presented with auditory rhythms of varied temporal complexity
Authors: Knight Emily J. , Oakes Leona A. , Hyman Susan L. , Freedman Edward G. , Foxe John J. 
Published: May 2020

ABSTRACTThe brain’s ability to encode temporal patterns and predict upcoming events is critical for speech perception and other aspects of social communication. Deficits in predictive coding may contribute to difficulties with social communication and overreliance on repetitive predictable environments in individuals with autism spectrum disorder (ASD). Using a mismatch negativity (MMN) task involving rhythmic tone sequences of varying complexity, we tested the hypotheses that 1) individuals with ASD have reduced MMN response to auditory stimuli that deviate in presentation timing from expected patterns, particularly as pattern complexity increases and 2) amplitude of MMN signal is inversely correlated with level of impairment in social communication and repetitive behaviors. Electroencephalography was acquired as individuals (age 6-21years) listened to repeated five-rhythm tones that varied in the Shannon entropy of the rhythm across three conditions (zero, medium-1 bit) and high-2 bit entropy). The majority of the tones conformed to the established rhythm (standard tones); occasionally the 4thtone was temporally shifted relative to its expected time of occurrence (deviant tones). Social communication and repetitive behaviors were measured using the Social Responsiveness Scale and Repetitive Behavior Scale-Revised. Both neurotypical controls (n=19) and individuals with ASD (n=21) show stepwise decreases in MMN as a function of increasing entropy. Contrary to the result forecasted by a predictive coding hypothesis, individuals with ASD do not differ from controls in these neural mechanisms of prediction error to auditory rhythms of varied temporal complexity, and there is no relationship between these signals and social communication or repetitive behavior measures.Lay SummaryWe tested the idea that the brain’s ability to use previous experience to influence processing of sounds is weaker in individuals with autism spectrum disorder (ASD) than in neurotypical individuals. We found no difference between individuals with ASD and neurotypical controls in brain wave responses to sounds that occurred earlier than expected in either simple or complex rhythms. There was also no relationship between these brain waves and social communication or repetitive behavior scores.
Clusterin secretion is attenuated by pro-inflammatory cytokines in culture models of cartilage degradation
Authors: Matta Csaba , Fellows Christopher R. , Quasnichka Helen , Williams Adam , Jeremiasse Bernadette , Allaway David , Mobasheri Ali 
Published: May 2020

ABSTRACTProteomic studies have implicated clusterin as a potential biomarker of osteoarthritis (OA). However, there are two isoforms of clusterin with opposing functions, and their roles in OA have not previously been clarified. The secreted form of clusterin (sCLU) is a cytoprotective extracellular chaperone which prevents protein aggregation and enhances cell proliferation and viability, whereas nuclear clusterin (nCLU) acts as a pro-death signal. In this study, we focused on the role of sCLU and used established, pathophysiologically relevant,in vitroculture models to validate this potential biomarker of cartilage degradation. The secretome of equine cartilage explants, osteochondral biopsies and chondrocytes was analysed by western blotting for released sCLU, cartilage oligomeric protein (COMP) and matrix metalloproteinases (MMP) 3 and 13, following treatment with or without pro-inflammatory cytokines interleukin-1β (IL-1β) and tumour necrosis factor-α (TNF-α). The amount of sulphated glycosaminoglycans (sGAG) released into the medium was determined by dimethylmethylene blue (DMMB) analysis. Clusterin mRNA expression was quantified by real-time PCR. MMP-3, MMP-13, COMP and sGAG released from explants and osteochondral biopsies was elevated with cytokine treatment, confirming cartilage degradation in these models. Release of sCLU was attenuated with cytokine treatment in all threein vitromodels. Expression of clusterin mRNA in cartilage explants and chondrocytes was down-regulated 7-days post cytokine stimulation. Cytokine stimulation attenuated expression and secretion of sCLU, therefore potentially limiting the cytoprotection which sCLU provides. These observations further implicate sCLU as having a role in OA, and diagnostic value as a potential biomarker for cartilage degradation.
Differential levels of dermatan sulfate generate distinct Collagen I gel architectures
Authors: M Jyothsna K , Sarkar Purba , Jha Keshav Kumar , Raghunathan Varun , Bhat Ramray 
Published: May 2020

ABSTRACTCollagen I is the most abundant extracellular matrix (ECM) protein in vertebrate tissues. As an endogenously synthesized fibrillar biopolymer or as a synthetic hydrogel, it provides mechanical durability to tissue microenvironments and regulates cell function. Predominant regulators of its fibrillogenesis are dermatan sulfate proteoglycans (DSPGs), proteins conjugated with iduronic acid containing DS glycosaminoglycans (GAGs). Although DS is known to regulate tissue function through its modulation of Collagen I architecture, a precise quantifiable understanding of the latter remains elusive. We investigate this problem by visualizing the pattern of structural elements within fixed Collagen I gels polymerized in the presence of varying concentrations of DS (50-, 200- and 400- μg/mL) using second harmonic generation microscopy (SHG). Measuring four independent imaging parameters: fibril density, mean SHG signal (which estimates the ordering of the fibrils), surface occupancy (which estimates the space occupied by fibrils), and the fibril width allows us to construct an informative model of the effects of DS on Collagen I element architecture. Supported by confocal microscopy, our observations indicate that the effect on collagen fibril pattern of DS is contextual upon its concentrations. Lower levels of DS result in more numerous disorganized fibrils; higher levels restore organization, but at lower fibril densities. Such Collagen I gel pattern-tuning of DS is likely of relevance for understanding its functions in disease progression and biomaterial applications.
Social recognition in rats and mice requires integration of olfactory, somatosensory and auditory cues
Authors: de la Zerda Shani Haskal , Netser Shai , Magalnik Hen , Briller Mayan , Marzan Dan , Glatt Sigal , Wagner Shlomo 
Published: May 2020

AbstractIn humans, discrimination between individuals, also termed social recognition, can rely on a single sensory modality, such as vision. By analogy, social recognition in rodents is thought to be based upon olfaction. Here, we hypothesized that social recognition in rodents relies upon integration of olfactory, auditory and somatosensory cues, hence requiring active behavior of social stimuli. Using distinct social recognition tests, we demonstrated that adult male rats and mice do not recognize familiar stimuli or learn the identity of novel stimuli that are inactive due to anesthesia. We further revealed that impairing the olfactory, somatosensory or auditory systems prevents recognition of familiar stimuli. Finally, we found that familiar and novel stimuli generate distinct movement patterns during social discrimination and that subjects react differentially to the movement of these stimuli. Thus, unlike what occurs in humans, social recognition in rats and mice relies on integration of information from several sensory modalities.