bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inactivating mutations and X-ray crystal structure of the tumor suppressor OPCML reveal cancer-associated functions
Authors: Birtley James R. , Alomary Mohammad , Zanini Elisa , Antony Jane , Maben Zachary , Weaver Grant C. , Von Arx Claudia , Mura Manuela , Marinho Aline T. , Lu Haonan , Morecroft Eloise V. N. , Karali Evdoxia , Chayen Naomi E. , Tate Edward W. , Jurewicz Mollie , Stern Lawrence J. , Recchi Chiara , Gabra Hani 
Published: July 2019

AbstractOPCML, a tumor suppressor gene, is frequently silenced epigenetically in ovarian and other cancers. Here we report, by analysis of databases of tumor sequences, the observation of OPCML somatic missense mutations from various tumor types and the impact of these mutations on OPCML function, by solving the X-ray crystal structure of this glycoprotein to 2.65 Å resolution. OPCML consists of an extended arrangement of three immunoglobulin-like domains and homodimerizes via a network of contacts between membrane-distal domains. We report the generation of a panel of OPCML variants with representative clinical mutations and demonstrate clear phenotypic effects in vitro and in vivo including changes to anchorage-independent growth, interaction with activated cognate receptor tyrosine kinases, cellular migration, invasion in vitro and tumor growth in vivo. Our results suggest that clinically occurring somatic missense mutations in OPCML have the potential to contribute to tumorigenesis in a variety of cancers.
Involvement of cigarette smoke-induced epithelial cell ferroptosis in COPD pathogenesis
Authors: Yoshida Masahiro , Minagawa Shunsuke , Araya Jun , Sakamoto Taro , Hara Hiromichi , Tsubouchi Kazuya , Hosaka Yusuke , Ichikawa Akihiro , Saito Nayuta , Kadota Tsukasa , Sato Nahoko , Kurita Yusuke , Kobayashi Kenji , Ito Saburo , Utsumi Hirohumi , Wakui Hiroshi , Numata Takanori , Kaneko Yumi , Mori Shohei , Asano Hisatoshi , Yamashita Makoto , Odaka Makoto , Morikawa Toshiaki , Nakayama Katsutoshi , Iwamoto Takeo , Imai Hirotaka , Kuwano Kazuyoshi 
Published: July 2019

AbstractFerroptosis is a necrotic form of regulated cell death (RCD) mediated by phospholipid peroxidation in association with free iron-mediated Fenton reactions. Disrupted iron homeostasis resulting in excessive oxidative stress has been implicated in the pathogenesis of chronic obstructive pulmonary disease (COPD). Here, we demonstrate the involvement of ferroptosis in COPD pathogenesis. Our in vivo and in vitro models show labile iron accumulation and enhanced lipid peroxidation with concomitant non-apoptotic cell death during cigarette smoke (CS) exposure, which are negatively regulated by GPx4 activity. Treatment with deferoxamine and ferrostatin-1, in addition to GPx4 knockdown, illuminate the role of ferroptosis in CS-treated lung epithelial cells. NCOA4-mediated ferritin selective autophagy (ferritinophagy) is initiated during ferritin degradation in response to CS treatment. CS exposure models, using both GPx4-deficient and overexpressing mice, clarify the pivotal role of GPx4-regulated cell death during COPD. These findings support a role for cigarette smoke-induced ferroptosis in the pathogenesis of COPD.
NASC-seq monitors RNA synthesis in single cells
Authors: Hendriks Gert-Jan , Jung Lisa A. , Larsson Anton J. M. , Lidschreiber Michael , Andersson Forsman Oscar , Lidschreiber Katja , Cramer Patrick , Sandberg Rickard 
Published: July 2019

AbstractSequencing of newly synthesised RNA can monitor transcriptional dynamics with great sensitivity and high temporal resolution, but is currently restricted to populations of cells. Here, we develop new transcriptome alkylation-dependent single-cell RNA sequencing (NASC-seq), to monitor newly synthesised and pre-existing RNA simultaneously in single cells. We validate the method on pre-labelled RNA, and by demonstrating that more newly synthesised RNA was detected for genes with known high mRNA turnover. Monitoring RNA synthesis during Jurkat T-cell activation with NASC-seq reveals both rapidly up- and down-regulated genes, and that induced genes are almost exclusively detected as newly transcribed. Moreover, the newly synthesised and pre-existing transcriptomes after T-cell activation are distinct, confirming that NASC-seq simultaneously measures gene expression corresponding to two time points in single cells. Altogether, NASC-seq enables precise temporal monitoring of RNA synthesis at single-cell resolution during homoeostasis, perturbation responses and cellular differentiation.
SPRTN protease and checkpoint kinase 1 cross-activation loop safeguards DNA replication
Authors: Halder Swagata , Torrecilla Ignacio , Burkhalter Martin D. , Popović Marta , Fielden John , Vaz Bruno , Oehler Judith , Pilger Domenic , Lessel Davor , Wiseman Katherine , Singh Abhay Narayan , Vendrell Iolanda , Fischer Roman , Philipp Melanie , Ramadan Kristijan 
Published: July 2019

AbstractThe SPRTN metalloprotease is essential for DNA-protein crosslink (DPC) repair and DNA replication in vertebrate cells. Cells deficient in SPRTN protease exhibit DPC-induced replication stress and genome instability, manifesting as premature ageing and liver cancer. Here, we provide a body of evidence suggesting that SPRTN activates the ATR-CHK1 phosphorylation signalling cascade during physiological DNA replication by proteolysis-dependent eviction of CHK1 from replicative chromatin. During this process, SPRTN proteolyses the C-terminal/inhibitory part of CHK1, liberating N-terminal CHK1 kinase active fragments. Simultaneously, CHK1 full length and its N-terminal fragments phosphorylate SPRTN at the C-terminal regulatory domain, which stimulates SPRTN recruitment to chromatin to promote unperturbed DNA replication fork progression and DPC repair. Our data suggest that a SPRTN-CHK1 cross-activation loop plays a part in DNA replication and protection from DNA replication stress. Finally, our results with purified components of this pathway further support the proposed model of a SPRTN-CHK1 cross-activation loop.
Qualitative study of practices and challenges when making a diagnosis of asthma in primary care
Authors: Akindele Adeola , Daines Luke , Cavers Debbie , Pinnock Hilary , Sheikh Aziz 
Published: July 2019

AbstractMisdiagnosis (over-diagnosis and under-diagnosis) of asthma is common. Under-diagnosis can lead to avoidable morbidity and mortality, while over-diagnosis exposes patients to unnecessary side effects of treatment(s) and results in unnecessary healthcare expenditure. We explored diagnostic approaches and challenges faced by general practitioners (GPs) and practice nurses when making a diagnosis of asthma. Fifteen healthcare professionals (10 GPs and 5 nurses) of both sexes, different ages and varying years of experience who worked in NHS Lothian, Scotland were interviewed using in-depth, semi-structured qualitative interviews. Transcripts were analysed using a thematic approach. Clinical judgement of the probability of asthma was fundamental in the diagnostic process. Participants used heuristic approaches to assess the clinical probability of asthma and then decide what tests to do, selecting peak expiratory flow measurements, spirometry and/or a trial of treatment as appropriate for each patient. Challenges in the diagnostic process included time pressures, the variable nature of asthma, overlapping clinical features of asthma with other conditions such as respiratory viral illnesses in children and chronic obstructive pulmonary disease (COPD) in adults. To improve diagnostic decision-making, participants suggested regular educational opportunities and better diagnostic tools. In the future, standardising the clinical assessment made by healthcare practitioners should be supported by improved access to diagnostic services for additional investigation(s) and clarification of diagnostic uncertainty.
Quantifying two-dimensional and three-dimensional stereoscopic learning in anatomy using electroencephalography
Authors: Anderson Sarah J. , Jamniczky Heather A. , Krigolson Olave E. , Coderre Sylvain P. , Hecker Kent G. 
Published: July 2019

AbstractAdvances in computer visualization enabling both 2D and 3D representation have generated tools to aid perception of spatial relationships and provide a new forum for instructional design. A key knowledge gap is the lack of understanding of how the brain neurobiologically processes and learns from spatially presented content, and new quantitative variables are required to address this gap. The objective of this study was to apply quantitative neural measures derived from electroencephalography (EEG) to examine stereopsis in anatomy learning by comparing mean amplitude changes in N250 (related to object recognition) and reward positivity (related to responding to feedback) event related to potential components using a reinforcement-based learning paradigm. Health sciences students (n = 61) learned to identify and localize neuroanatomical structures using 2D, 3D, or a combination of models while EEG and behavioral (accuracy) data were recorded. Participants learning using 3D models had a greater object recognition (N250 amplitude) compared to those who learned from 2D models. Based on neurological results, interleaved learning incorporating both 2D and 3D models provided an advantage in learning, retention, and transfer activities represented by decreased reward positivity amplitude. Behavioral data did not have the same sensitivity as neural data for distinguishing differences in learning with and without stereopsis in these learning activities. Measuring neural activity reveals new insights in applied settings for educators to consider when incorporating stereoscopic models in the design of learning interventions.
Insights into the transcriptomic response of the plant engineering bacterium Ensifer adhaerens OV14 during transformation
Authors: Zuniga-Soto Evelyn , Fitzpatrick David A. , Doohan Fiona M. , Mullins Ewen 
Published: July 2019

AbstractThe ability to engineer plant genomes has been primarily driven by the soil bacterium Agrobacterium tumefaciens but recently the potential of alternative rhizobia such as Rhizobium etli and Ensifer adhaerens OV14, the latter of which supports Ensifer Mediated Transformation (EMT) has been reported. Surprisingly, a knowledge deficit exists in regards to understanding the whole genome processes underway in plant transforming bacteria, irrespective of the species. To begin to address the issue, we undertook a temporal RNAseq-based profiling study of E. adhaerens OV14 in the presence/absence of Arabidopsis thaliana tissues. Following co-cultivation with root tissues, 2333 differentially expressed genes (DEGs) were noted. Meta-analysis of the RNAseq data sets identified a clear shift from plasmid-derived gene expression to chromosomal-based transcription within the early stages of bacterium-plant co-cultivation. During this time, the number of differentially expressed prokaryotic genes increased steadily out to 7 days co-cultivation, a time at which optimum rates of transformation were observed. Gene ontology evaluations indicated a role for both chromosomal and plasmid-based gene families linked specifically with quorum sensing, flagellin production and biofilm formation in the process of EMT. Transcriptional evaluation of vir genes, housed on the pCAMBIA 5105 plasmid in E. adhaerens OV14 confirmed the ability of E. adhaerens OV14 to perceive and activate its transcriptome in response to the presence of 200 µM of acetosyringone. Significantly, this is the first study to characterise the whole transcriptomic response of a plant engineering bacterium in the presence of plant tissues and provides a novel insight into prokaryotic genetic processes that support T-DNA transfer.
Cloud-driven modulations of Greenland ice sheet surface melt
Authors: Niwano Masashi , Hashimoto Akihiro , Aoki Teruo 
Published: July 2019

AbstractClouds have been recognized to enhance surface melt on the Greenland Ice Sheet (GrIS). However, quantitative estimates of the effects of clouds on the GrIS melt area and ice-sheet-wide surface mass balance are still lacking. Here we assess the effects of clouds with a state-of-the-art regional climate model, conducting a numerical sensitivity test in which adiabatic atmospheric conditions as well as zero cloud water/ice amounts are assumed (i.e., clear-sky conditions), although the precipitation rate is the same as in the control all-sky simulation. By including or excluding clouds, we quantify time-integrated feedbacks for the first time. We find that clouds were responsible for a 3.1%, 0.3%, and 0.7% increase in surface melt extent (of the total GrIS area) in 2012, 2013, and 2014, respectively. During the same periods, clouds reduced solar heating and thus daily runoff by 1.6, 0.8, and 1.0 Gt day−1, respectively: clouds did not enhance surface mass loss. In the ablation areas, the presence of clouds results in a reduction of downward latent heat flux at the snow/ice surface so that much less energy is available for surface melt, which highlights the importance of indirect time-integrated feedbacks of cloud radiative effects.
Molecular contrast on phase-contrast microscope
Authors: Toda Keiichiro , Tamamitsu Miu , Nagashima Yu , Horisaki Ryoichi , Ideguchi Takuro 
Published: July 2019

AbstractAn optical microscope enables image-based findings and diagnosis on microscopic targets, which is indispensable in many scientific, industrial and medical settings. A standard benchtop microscope platform, equipped with e.g., bright-field and phase-contrast modes, is of importance and convenience for various users because the wide-field and label-free properties allow for morphological imaging without the need for specific sample preparation. However, these microscopes never have capability of acquiring molecular contrast in a label-free manner. Here, we develop a simple add-on optical unit, comprising of an amplitude-modulated mid-infrared semiconductor laser, that is attached to a standard microscope platform to deliver the additional molecular contrast of the specimen on top of its conventional microscopic image, based on the principle of photothermal effect. We attach this unit, termed molecular-contrast unit, to a standard phase-contrast microscope, and demonstrate high-speed label-free molecular-contrast phase-contrast imaging of silica-polystyrene microbeads mixture and molecular-vibrational spectroscopic imaging of HeLa cells. Our simple molecular-contrast unit can empower existing standard microscopes and deliver a convenient accessibility to the molecular world.
Gas6 is a reciprocal regulator of mitophagy during mammalian oocyte maturation
Authors: Kim Kyeoung-Hwa , Kim Eun-Young , Ko Jung-Jae , Lee Kyung-Ah 
Published: July 2019

AbstractPreviously, we found that the silencing of growth arrest-specific gene 6 (Gas6) expression in oocytes impairs cytoplasmic maturation through mitochondrial overactivation with concurrent failure of pronuclear formation after fertilization. In this study, we report that Gas6 regulates mitophagy and safeguards mitochondrial activity by regulating mitophagy-related genes essential to the complete competency of oocytes. Based on RNA-Seq and RT-PCR analysis, in Gas6-silenced MII oocytes, expressions of mitophagy-related genes were decreased in Gas6-silenced MII oocytes, while mitochondrial proteins and Ptpn11, the downstream target of Gas6, was increased. Interestingly, GAS6 depletion induced remarkable MTOR activation. Gas6-depleted MII oocytes exhibited mitochondrial accumulation and aggregation caused by mitophagy inhibition. Gas6-depleted MII oocytes had a markedly lower mtDNA copy number. Rapamycin treatment rescued mitophagy, blocked the increase in MTOR and phosphorylated-MTOR, and increased the mitophagy-related gene expression in Gas6-depleted MII oocytes. After treatment with Mdivi-1, a mitochondrial division/mitophagy inhibitor, all oocytes matured and these MII oocytes showed mitochondrial accumulation but reduced Gas6 expression and failure of fertilization, showing phenomena very similar to the direct targeting of Gas6 by RNAi. Taken together, we conclude that the Gas6 signaling plays a crucial role in control of oocytes cytoplasmic maturation by modulating the dynamics and activity of oocyte mitochondria.
Intrinsic dynamic behavior of enzyme:substrate complexes govern the catalytic action of β-galactosidases across clan GH-A
Authors: Kumar Rajender , Henrissat Bernard , Coutinho Pedro M. 
Published: July 2019

AbstractThe conformational itineraries taken by carbohydrate residues in the catalytic subsite of retaining glycoside hydrolases (GHs), harness the link between substrate conformation and reactivity. GHs’ active sites may be described as a combination of subsites dedicated to the binding of individual sugar residues and to catalysis. The three-dimensional structure of GH:carbohydrate complexes has demonstrated that carbohydrate ring conformation changes in an ordered manner during catalysis. Here we demonstratein silicothat a link exists between subsite binding dynamics and substrate specificity for β-galactosidases from clan GH-A families GH1, GH2, GH35, GH42 and GH59. Different oligosaccharides were docked in the active site of reference β-galactosidase structures using Vina-Carb. Subsequent molecular dynamics (MD) simulations revealed that these enzymes favor a high degree of flexibility and ring distortion of the substrate the lytic subsite −1. Although the β-galactosidase families examined are structurally and mechanistically related, distinct patterns of ring distortion were unveiled for the different families. For β-galactosidases, three different family-dependent reaction itineraries (1S3 → 4H3‡ → 4C1,1,4B → 4H3/ 4E‡ → 4C1, and1S5 → 4E/ 4H5‡ → 4C1) were identified, all compatible with the antiperiplanar lone pair hypothesis (ALPH) for the hydrolysis of β-glycosides. This comparative study reveals the fuzzy character of the changes in carbohydrate ring geometry prior to carbohydrate hydrolysis.
SerpinA3 in the Early Recognition of Acute Kidney Injury to Chronic Kidney Disease (CKD) transition in the rat and its Potentiality in the Recognition of Patients with CKD
Authors: Sánchez-Navarro Andrea , Mejía-Vilet Juan M. , Pérez-Villalva Rosalba , Carrillo-Pérez Diego L. , Marquina-Castillo Brenda , Gamba Gerardo , Bobadilla Norma A. 
Published: July 2019

AbstractRecognizing patients at early phases of chronic kidney disease (CKD) is difficult, and it is even more challenging to predict acute kidney injury (AKI) and its transition to CKD. The gold standard to timely identify renal fibrosis is the kidney biopsy, an invasive procedure not usually performed for this purpose in clinical practice. SerpinA3 was identified by high-resolution-mass-spectrometry in urines from animals with CKD. An early and progressive elevation of urinary SerpinA3 (uSerpinA3) was observed during the AKI to CKD transition together with SerpinA3 relocation from the cytoplasm to the apical tubular membrane in the rat kidney. uSerpinA3/alpha-1-antichymotrypsin was significantly increased in patients with CKD secondary to focal and segmental glomerulosclerosis (FSGS), ANCA associated vasculitis (AAV) and proliferative class III and IV lupus nephritis (LN). uSerpinA3 levels were independently and positively associated with renal fibrosis. In patients with class V LN, uSerpinA3 levels were not different from healthy volunteers. uSerpinA3 was not found in patients with systemic inflammatory diseases without renal dysfunction. Our observations suggest that uSerpinA3 can detect renal fibrosis and inflammation, with a particular potential for the early detection of AKI to CKD transition and for the differentiation among lupus nephritis classes III/IV and V.
Gene Expression Analyses in Non Muscle Invasive Bladder Cancer Reveals a Role for Alternative Splicing and Tp53 Status
Authors: Dueñas Marta , Pérez-Figueroa Andrés , Oliveira Carla , Suárez-Cabrera Cristian , Sousa Abel , Oliveira Patricia , Villacampa Felipe , Paramio Jesús M. , Martínez-Fernández Mónica 
Published: July 2019

AbstractNon-muscle invasive bladder cancer (NMIBC) represents a crucial problem for the national health care systems due to its high rates of recurrence and the consequent need of frequent follow-ups. Here, gene expression analyses in patients diagnosed as NMIBC were performed to determine those molecular pathways involved in tumor initiation, finding that both MYC and E2F are up regulated and helps to tumor initiation and progression. Our results also support an important involvement of alternative splicing events, modifying key pathways to favour bladder tumor evolution. Finally, since MDM2 showed differential exon usage, mutations in TP53 and its protein expression have been also studied in the same patients. Our data support that recurrence is epigenetically mediated and favoured by an increase protein expression of TP53, which appears more frequently mutated in advanced stages and grades, being associated to a worse prognosis. Therefore, TP53 mutational status could be used as a potential biomarker in the first stages of NMIBC to predict recurrence and prognosis.
Paired RNA Radiocarbon and Sequencing Analyses Indicate the Importance of Autotrophy in a Shallow Alluvial Aquifer
Authors: Mailloux Brian J. , Kim Carol , Kichuk Tess , Nguyen Khue , Precht Chandler , Wang Shi , Jewell Talia N. M. , Karaoz Ulas , Brodie Eoin L. , Williams Kenneth H. , Beller Harry R. , Buchholz Bruce A. 
Published: July 2019

AbstractDetermining the carbon sources for active microbial populations in the subsurface is a challenging but highly informative component of subsurface microbial ecology. This work developed a method to provide ecological insights into groundwater microbial communities by characterizing community RNA through its radiocarbon and ribosomal RNA (rRNA) signatures. RNA was chosen as the biomolecule of interest because rRNA constitutes the majority of RNA in prokaryotes, represents recently active organisms, and yields detailed taxonomic information. The method was applied to a groundwater filter collected from a shallow alluvial aquifer in Colorado. RNA was extracted, radiometrically dated, and the 16S rRNA was analyzed by RNA-Seq. The RNA had a radiocarbon signature (Δ14C) of −193.4 ± 5.6‰. Comparison of the RNA radiocarbon signature to those of potential carbon pools in the aquifer indicated that at least 51% of the RNA was derived from autotrophy, in close agreement with the RNA-Seq data, which documented the prevalence of autotrophic taxa, such as Thiobacillus and Gallionellaceae. Overall, this hybrid method for RNA analysis provided cultivation-independent information on the in-situ carbon sources of active subsurface microbes and reinforced the importance of autotrophy and the preferential utilization of dissolved over sedimentary organic matter in alluvial aquifers.