bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA-binding protein Mub1 and the nuclear RNA exosome act to fine-tune environmental stress response
Authors: Birot Adrien , Kilchert Cornelia , Kus Krzysztof , Priest Emily , Alwash Ahmad Al , Castello Alfredo , Mohammed Shabaz , Vasiljeva Lidia 
Published: July 2020

ABSTRACTThe nuclear RNA exosome plays a key role in mediating degradation and processing of multiple cellular RNAs. Recognition of the specific RNA substrates by the exosome is mediated by the RNA-binding co-factors. Transient binding of co-factors either to the exosome or the substrate RNAs as well as their rapid decay make identification of the co-factors challenging. Here, we employ a comparative poly(A)+ RNA interactome capture approach in the fission yeast exosome mutants to identify proteins that interact with poly(A)+ RNA in an exosome-dependent manner. Our analyses identified multiple proteins whose occupancy on RNA is altered in the exosome mutants including zinc-finger protein Mub1. Mub1 is required to maintain the levels of a subset of the exosome RNA substrates including mRNAs encoding for stress-responsive proteins. Removal of the zinc finger domain leads to loss of RNA suppression under non-stressed conditions, altered expression of heat shock genes in response to stress, and reduced growth at elevated temperature. These findings highlight importance of exosome-dependent mRNA degradation in buffering gene expression networks to mediate cellular adaptation to stress.
Senescent cell death as an aging resistance mechanism in naked mole-rat
Authors: Kawamura Yoshimi , Oka Kaori , Takamori Mayuko , Sugiura Yuki , Oiwa Yuki , Fujioka Shusuke , Homma Sayuri , Miyawaki Shingo , Narita Minoru , Fukuda Takaichi , Suematsu Makoto , Bono Hidemasa , Okano Hideyuki , Miura Kyoko 
Published: July 2020

AbstractNaked mole-rats (NMRs) are the longest-lived rodents, showing minimal aging phenotypes. An unsolved paradox is that NMRs exhibit low intracellular anti-oxidant defence despite minimal aging. Here, we explained a link between these “contradicting” features by a phenomenon termed “senescent cell death (SCD)”—Senescence induced cell death in NMR cells due to their inherent vulnerability to reactive oxygen species and unique metabolic system. In NMR skin, we observed few senescent cells during aging or after ultraviolet irradiation, suggesting suppression of senescent cell accumulation in NMR tissue. We discovered that senescent NMR-fibroblasts induce SCD through retinoblastoma protein activation accompanied by autophagy dysregulation, increased oxidative damage and accelerated H2O2-releasing metabolic pathways. During senescence, NMR cells showed resistance to metabolic remodelling unlike mice. Our findings provide mechanistic insights into how extraordinary aging resistance is accomplished in NMR. This will contribute to the development of senolytic drugs to regulate age-related diseases.
Conserved conformational hierarchy across functionally divergent glycosyltransferases of the GT-B structural superfamily as determined from microsecond molecular dynamics
Authors: Ramirez-Mondragon Carlos A. , Nguyen Megin E. , Milicaj Jozafina , Tucci Frank J. , Muthyala Ramaiah , Taylor Erika A. , Sham Yuk Y. 
Published: July 2020

AbstractIt has long been understood that some proteins to undergo conformational transitions enroute to the Michaelis Complex to allow chemistry. Examination of crystal structures of glycosyltransferase enzymes in the GT-B structural class reveals that the presence of ligand in the active site is necessary for the protein to crystalize in the closed conformation. Herein we describe microsecond molecular dynamics simulations of two evolutionarily unrelated glycosytransferases, HepI and GtfA. Simulations were performed using these proteins in the open and closed conformations, (respectively,) and we sought to identify the major dynamical modes and communication networks which allow conformational transition between the open and closed structures. We provide the first reported evidence (within the scope of our experimental parameters) that conformational hierarchy/directionality of the interconversion between open and closed conformations is a conserved feature of enzymes of the same structural superfamily. Additionally, residues previously identified to be important for substrate binding in HepI were shown to have strong negative correlations with non-ionizable residues distal to the active site. Mutagenesis of these residues produced mutants with altered enzymatic efficiency exhibiting lower Kmvalues, while the kcatis effectively unchanged. The negatively correlated motions of these residues are important for substrate binding and forming the Michaelis complex, without impacting the activation barrier for catalysis. This suggests that in the bi-domain HepI, the enzyme dynamics did not impact the transition state stabilization or chemistry, but rather earlier steps along the reaction coordinate, leading to the reorganization of the active site electrostatic environment required for catalysis.
Reduced NCOR2 expression accelerates androgen deprivation therapy failure in prostate cancer
Authors: Long Mark D , Singh Prashant K , Llimos Gerard , Jacobi Justine J , Rowsam Aryn M , Rosario Spencer R , Kirk Jason , Affronti Hayley C , Campbell Moray J , Smiraglia Dominic J 
Published: July 2020

AbstractNCOR2 is frequently and significantly mutated in late stage androgen deprivation therapy resistant prostate cancer (ADT-RPCa). NCOR2 has been characterized as a transcriptional corepressor and has mechanistic links to DNA methylation, but its global functions and overall contributions to PCa progression remain enigmatic. In the current study, we utilize immunohistochemical staining of samples from over 700 PCa patients and reveal associations of reduced NCOR2 expression with correlates of aggressive primary PCa and recurrence in patients who received adjuvant androgen deprivation therapy. We mapped the dihydrotestosterone (DHT) dependent and independent effects of NCOR2 on the transcriptome, cistrome and DNA methylome in androgen sensitive (AS) and ADT-RPCa cells using the isogenic LNCaP and LNCaP-C4-2 (C4-2) cell models. Transcriptional profiling identified androgen dependent and independent regulatory roles of NCOR2, the latter of which was enhanced in the ADT-RPCa state and included neuronal differentiation. Interestingly, reduced expression of NCOR2 resulted in a striking global DNA hypermethylation pattern that significantly enriched at enhancer regions. ChIP-seq revealed that NCOR2 was more clearly associated with promoters in AS LNCaP cells, which was modestly enhanced by DHT treatment. However, in ADT-RPCa C4-2 cells, the NCOR2 cistrome was larger and more distal. Motif analyses and integration of large-scale public cistrome data revealed strong enrichment for FOXA1 in mediating NCOR2 binding, and included additional factors such as AR, E2F, TET2, MED1 and MBD2. Utilizing the CWR22 xenograft model, we demonstrate a direct role for NCOR2 in PCa progression as reduced NCOR2 expression attenuated the impact of ADT, and significantly accelerated recurrence of disease. Transcriptomic analyses in recurrent CWR22 tumors indicated NCOR2-dependent gene expression profiles during ADT that were enriched for neuroendocrine associated genes and also associated with worse survival in human patients with ADT-RPCa. DNA methylation profiles in CWR22 tumors with reduced NCOR2 expression recapitulated the hypermethylation observedin vitro, and further revealed that hypermethylation patterns are commonly associated with ADT-RPCa disease, which was also confirmed in human samples. These studies reveal robust roles for NCOR2 in regulating the PCa transcriptome and epigenome and underscore recent mutational studies linking NCOR2 loss of function to PCa disease progression.
HIF-stabilization prevents delayed fracture healing
Authors: Lang Annemarie , Helfmeier Sarah , Stefanowski Jonathan , Kuppe Aditi , Sunkara Vikram , Pfeiffenberger Moritz , Wolter Angelique , Damerau Alexandra , Hemmati-Sadeghi Shabnam , Ringe Jochen , Haag Rainer , Hauser Anja E. , Löhning Max , Perka Carsten , Duda Georg N. , Hoff Paula , Schmidt-Bleek Katharina , Gaber Timo , Buttgereit Frank 
Published: July 2020

AbstractThe initial phase of fracture healing decides on success of bone regeneration and is characterized by an inflammatory milieu and low oxygen tension (hypoxia). Negative interference with or prolongation of this fine-tuned initiation phase will ultimately lead to a delayed or incomplete healing such as non-unions which then requires an effective and gentle therapeutic intervention. Common reasons include a dysregulated immune response, immunosuppression or a failure in cellular adaptation to the inflammatory hypoxic milieu of the fracture gap and a reduction in vascularizing capacity by environmental noxious agents (e.g. rheumatoid arthritis, smoking). The hypoxia-inducible factor (HIF)-1α is responsible for the cellular adaptation to hypoxia, activating angiogenesis and supporting cell attraction and migration to the fracture gap. Here, we hypothesized that stabilizing HIF-1α could be a cost-effective and low-risk prevention strategy of fracture healing disorders. Therefore, we combined a well-known HIF-stabilizer – deferoxamine (DFO) – and a less known HIF-enhancer – macrophage migration inhibitory factor (MIF) – to synergistically induce improved fracture healing. Stabilization of HIF-1α enhanced calcification and osteogenic differentiation of MSCsin vitro.In vivo, the application of DFO with or without MIF during the initial healing phase accelerated callus mineralization and vessel formation in a clinically relevant mouse-osteotomy-model in a compromised healing setting. Our findings provide support for a promising preventive strategy towards bone healing disorders in patients with a higher risk due to e.g. delayed neovascularization by accelerating fracture healing using DFO and MIF to stabilize HIF-1α.
Unpacking the eagle collision risk model: practical guidance for wind energy
Authors: Evans Michael J. , Sporer Misti , Erickson Wally , Page Joy 
Published: July 2020

ABSTRACTClimate change is one of the greatest threats facing biodiversity, and solutions to reduce carbon emissions are needed to conserve species. Renewable energies are a prominent means to achieve this goal, but the potential for direct harm to wildlife has raised concerns as these technologies proliferate. To protect biodiversity, approaches that facilitate renewable energy development while protecting species are needed. In the United States wind energy developers must obtain a permit for any Bald or Golden eagles that might be killed at a facility. The U.S. Fish & Wildlife Service estimates fatalities using a Bayesian modeling framework, which combines pre-construction eagle surveys with prior information. The ways in which prior information is incorporated and how pre-construction monitoring affects model outcomes can be unclear to regulated entities and other stakeholders, creating uncertainty in the permitting process and retarding both the build-out of renewable energy and conservation measures for eagles. We conducted a simulation study quantifying the differences in predicted eagle fatalities obtained by incorporating prior information and using only site-specific survey data across a range of scenarios, evaluating the impact of survey effort on the magnitude of this effect. We identified predictable relationships between survey effort, eagle activity, facility size and discrepancies between estimates. We also translated these patterns into real-world financial costs, illustrating the interaction between pre-construction surveys, fatality estimates, and compensatory mitigation obligations in determining permit timing and expense.
Reduced Type-A Carbohydrate-Binding Module Interactions to Cellulose Leads to Improved Endocellulase Activity
Authors: Nemmaru Bhargava , Ramirez Nicholas , Farino Cindy J. , Yarbrough John M. , Kravchenko Nicholas , Chundawat Shishir P.S. 
Published: July 2020

AbstractDissociation of non-productively bound cellulolytic enzymes from cellulose is hypothesized to be a key rate-limiting factor impeding cost-effective biomass conversion to fermentable sugars. However, the role of carbohydrate-binding modules (CBMs) in enabling non-productive enzyme binding is not well understood. Here, we examine the subtle interplay of CBM binding and cellulose hydrolysis activity for three model Type-A CBMs (families 1, 3a, and 64) tethered to a multifunctional endoglucanase (CelE) on two distinct cellulose allomorphs (i.e., cellulose I and III). We generated a small-library of mutant CBMs with varying cellulose affinity, as determined by equilibrium binding assays, followed by monitoring cellulose hydrolysis activity of CelE-CBM fusion constructs. Finally, kinetic binding assays using quartz crystal microbalance with dissipation (QCM-D) were employed to measure CBM adsorption and desorption rate constantsKonandKoff, respectively, towards nanocrystalline cellulose derived from both allomorphs. Overall, our results indicate that reduced CBM equilibrium binding affinity towards cellulose I alone, resulting from increased desorption rates (Koff) and reduced effective adsorption rates (nKon), is correlated to overall improved endocellulase activity. Future studies could employ similar approaches to unravel the role of CBMs in non-productive enzyme binding and develop improved cellulolytic enzymes for industrial applications.
Inhibitors of the Bub1 spindle assembly checkpoint kinase: Synthesis of BAY-320 and comparison with 2OH-BNPP1
Authors: Amalina Ilma , Bennett Ailsa , Whalley Helen , Perera David , McGrail Joanne C. , Tighe Anthony , Procter David J , Taylor Stephen S. 
Published: July 2020

SummaryBub1 is a serine/threonine kinase proposed to function centrally in both mitotic chromosome alignment and the spindle assembly checkpoint (SAC), however its role remains controversial. Although it is well documented that Bub1 phosphorylation of Histone 2A at T120 (H2ApT120) recruits Sgo1/2 to kinetochores, the requirement of its kinase activity for chromosome alignment and the SAC is debated. As small-molecule inhibitors can be invaluable tools for investigation of kinase function, we decided to evaluate the relative potential of two agents (2OH-BNPPI and BAY-320) as Bub1 inhibitors. After confirming that both agents inhibit Bub1in vitro, we developed a cell based-assay to specifically measure Bub1 inhibitionin vivo. For this assay we overexpressed a fusion of Histone 2B and the Bub1 kinase region (Bub1C) tethering it in close proximity to H2A, which generated a strong ectopic H2ApT120 signal along chromosome arms. The ectopic signal generated from Bub1C activity was effectively inhibited by BAY-320, but not 2OH-BNPP1. In addition, only BAY-320 was able to inhibit endogenous Bub1-mediated Sgo1 localisation. Preliminary experiments using BAY-320 suggested a minor role for Bub1 kinase activity in chromosome alignment and the SAC, however results suggest that BAY-320 may exhibit off-target effects at the concentration required to demonstrate these outcomes. In conclusion, 2OH-BNPP1 may not be an effective Bub1 inhibitorin vivo, and while BAY-320 is able to inhibit Bub1in vivo, the high concentrations required and potential for off-target effects highlight the ongoing need for improved Bub1 inhibitors.
Authentic field experiences for STEM teachers: Collecting Florida fossils
Authors: MacFadden Bruce J. , Pirlo Jeanette , Abramowitz Brian , Killingsworth Stephanie , Ziegler Michael 
Published: July 2020

AbstractThe extensive sedimentary sequence of Florida preserves evidence of prehistoric life spanning some 40 million years into the past. This paper describes the results of a three-pronged professional development (PD) program conducted in November 2019 in which Florida teachers from eight counties gained knowledge and experience about the process and content of paleontology at an active field research site in northern Florida. Working alongside scientists, 15 elementary, middle, and high school teachers collected 5-million-year-old fossil vertebrates and made scientifically important discoveries that advance understanding of Florida’s prehistoric life. The PD included three components: (1) a pre-trip webinar; (2) a morning tour of our museum exhibits to scaffold teacher’s understanding of the kinds of fossils they would find; and (3) the actual day-long field experience collecting fossils. A post-PD evaluation revealed gains in knowledge about, and experience with, fossils and paleontology. We also found that overall satisfaction with the PD underscored the importance of each of the three components supporting one-another—resulting in a more informative and rewarding learning experience for the participants. Fossils and the science of paleontology are a gateway for STEM learning and this subject and its extensions are applicable to existing standards in earth and life sciences at many grade levels.
Single adeno-associated virus-based multiplexed CRISPR-Cas9 system to nullify core components of the mammalian molecular clock
Authors: Kim Boil , Kim Jihoon , Chun Minjeong , Park Inah , Choi Mijung , Kim Kyungjin , Choe Han Kyoung 
Published: July 2020

ABSTRACTThe mammalian molecular clock is based on a transcription-translation feedback loop (TTFL) containing Period1, 2 (Per1, 2), Cryptochrome1, 2 (Cry1, 2), and Brain and Muscle ARNT-Like 1 (Bmal1). TTFL robustness is endowed by genetic complementation between these components; therefore, multiple genes must be knocked out to physiologically investigate the molecular clock, which requires extensive research resources. To facilitate molecular clock disruption, we developed a CRISPR-Cas9-based single adeno-associated viral (AAV) system targeting the circadian clock (CSAC) forPers, Crys, orBmal1. First, we designed single guide RNAs (sgRNAs) targeting individual clock genes using anin silicoapproach and validated their efficiency in Neuro2a cells. To target multiple genes, multiplex sgRNA plasmids were constructed using Golden Gate assembly and expressed in viral vectors. CSAC efficiency was demonstrated by decreased protein expressionin vitroand ablated molecular oscillationex vivo. We also measured locomotor activity and body temperature in Cas9-expressing mice injected with CSAC at the suprachiasmatic nucleus. Circadian rhythm disruption was observed under free-running conditions, indicating that CSAC can efficiently and robustly disrupt molecular circadian clock. Thus, CSAC is a simple and powerful tool for investigating the physiological role of the molecular clockin vivo.
Genetic ancestry changes in Stone to Bronze Age transition in the East European plain
Authors: Saag Lehti , Vasilyev Sergey V. , Varul Liivi , Kosorukova Natalia V. , Gerasimov Dmitri V. , Oshibkina Svetlana V. , Griffith Samuel J. , Solnik Anu , Saag Lauri , D’Atanasio Eugenia , Metspalu Ene , Reidla Maere , Rootsi Siiri , Kivisild Toomas , Scheib Christiana Lyn , Tambets Kristiina , Kriiska Aivar , Metspalu Mait 
Published: July 2020

AbstractTransition from the Stone to the Bronze Age in Central and Western Europe was a period of major population movements originating from the Ponto-Caspian Steppe. Here, we report new genome-wide sequence data from 28 individuals from the territory north of this source area – from the under-studied Western part of present-day Russia, including Stone Age hunter-gatherers (10,800–4,250 cal BC) and Bronze Age farmers from the Corded Ware complex called Fatyanovo Culture (2,900–2,050 cal BC). We show that Eastern hunter-gatherer ancestry was present in Northwestern Russia already from around 10,000 BC. Furthermore, we see a clear change in ancestry with the arrival of farming – the Fatyanovo Culture individuals were genetically similar to other Corded Ware cultures, carrying a mixture of Steppe and European early farmer ancestry and thus likely originating from a fast migration towards the northeast from somewhere in the vicinity of modern-day Ukraine, which is the closest area where these ancestries coexisted from around 3,000 BC.
MORONET: Multi-omics Integration via Graph Convolutional Networks for Biomedical Data Classification
Authors: Wang Tongxin , Shao Wei , Huang Zhi , Tang Haixu , Zhang Jie , Ding Zhengming , Huang Kun 
Published: July 2020

ABSTRACTTo fully utilize the advances in omics technologies and achieve a more comprehensive understanding of human diseases, novel computational methods are required for integrative analysis for multiple types of omics data. We present a novel multi-omics integrative method named Multi-Omics gRaph cOnvolutional NETworks (MORONET) for biomedical classification. MORONET jointly explores omics-specific learning and cross-omics correlation learning for effective multi-omics data classification. We demonstrate that MORONET outperforms other state-of-the-art supervised multi-omics integrative analysis approaches from a wide range of biomedical classification applications using mRNA expression data, DNA methylation data, and miRNA expression data. Furthermore, MORONET is able to identify important biomarkers from different omics data types that are related with the investigated diseases.
Explainable AI reveals changes in skin microbiome composition linked to phenotypic differences
Authors: Carrieri Anna Paola , Haiminen Niina , Maudsley-Barton Sean , Gardiner Laura-Jayne , Murphy Barry , Mayes Andrew , Paterson Sarah , Grimshaw Sally , Winn Martyn , Shand Cameron , Rowe Will , Hawkins Stacy , MacGuire-Flanagan Ashley , Tazzioli Jane , Kenny John , Parida Laxmi , Hoptroff Michael , Pyzer-Knapp Edward O. 
Published: July 2020

AbstractAlterations in the human microbiome have been observed in a variety of conditions such has asthma, gingivitis, dermatitis and cancer, and much remains to be learned about the links between the microbiome and human health. The fusion of artificial intelligence with rich microbiome datasets can offer an improved understanding of the microbiome’s role in our health. To gain actionable insights it is essential to consider both the predictive power and the transparency of the models by providing explanations for the predictions.We combine the effort of collecting a corpus of leg skin microbiome samples of two healthy cohorts of women with the development of anexplainable artificial intelligence (EAI)approach that provides accurate predictions of phenotypes and explanations. The explanations are expressed in terms of variations in the abundance of key microbes that drive the predictions.We predict skin hydration, subject’s age, pre/post-menopausal status and smoking status from the leg skin microbiome. The key changes in microbial composition linked to skin hydration can accelerate the development of personalised treatments for healthy skin, while those associated with age may offer insights into the skin aging process. The leg microbiome signatures associated with smoking and menopausal status are consistent with previous findings from oral/respiratory tract microbiomes and vaginal microbiomes respectively. This suggests that easily accessible microbiome samples could be used to investigate health-related phenotypes, offering potential for non-invasive diagnosis and condition monitoring.Our EAI approach sets the stage for new work focused on understanding the complex relationships between microbial communities and phenotypes. Our approach can be applied to predict any conditions from microbiome samples and has the potential to accelerate the development of microbiome-based personalised therapeutics and non-invasive diagnostics.