bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulation of cGAS activity through RNA-mediated phase separation
Authors: Chen Silian , Rong Miao , Lv Yun , Zhu Deyu , Xiang Ye 
Published: September 2020

AbstractCyclic GMP-AMP synthase (cGAS) is a double-stranded DNA (dsDNA) sensor that functions in the innate immune system. Upon binding dsDNA in the cytoplasm, cGAS and dsDNA form phase-separated aggregates in which cGAS catalyzes synthesis of 2’3’-cyclic GMP-AMP that subsequently triggers a STING-dependent, type I IFN response. Here, we showed that cytoplasmic RNAs, especially tRNAs, regulate cGAS activity. We discovered that RNAs did not activate cGAS but rather promoted phase separationin vitro. In cells, cGAS colocalized with RNAs and formed phase-separated granules even in the absence of cytoplasmic dsDNA. An Opti-prep gradient analysis of cell lysates showed that the endogenous cGAS was associated with cytoplasmic RNAs in an aggregative form. Furtherin vitroassays showed that RNAs compete for binding of cGAS with dsDNA and inhibit cGAS activity when the dsDNA concentration is high and promote the formation of phase separations and enhance cGAS activity when the dsDNA concentration is low. Thus, cytoplasmic RNAs regulate cGAS activity by interfering with formation of cGAS-containing aggregates.
Assessment of Risk Factors Correlated with Age-Adjusted Mortality by Region for Prostate Cancer in Japan: an epidemiological study
Authors: Nagano Takuya , Hoshi Akihiko 
Published: September 2020

AbstractIntroductionPrevious studies have suggested that smoking and drinking alcohol are prostate cancer risks. However, how regional unevenness of radiation oncologists/urologists in Japan or other risk factors including social background correlate with age-adjusted mortality of prostate cancer remain unknown.MethodsIn addition to known factors like smoking, we examined whether various other factors, such as the regional unevenness of radiotherapists/urologists, correlated with age-adjusted mortality rate (AAMR) for prostate cancer by prefecture. Statistical data were obtained from Annual Report of Hospital-Based Cancer Registries, Comprehensive Survey of Living Conditions and etc. We used the 10-year averages of AAMR from 2009 to 2018 in each prefecture to determine mortality rates.ResultsThere was no correlation between the number of radiation oncologists/urologists per 100,000 and the 10-year averages of AAMR by prefecture in Japan. On the other hand, smoking rates and drinking per capita were correlated, respectively (P = 0.0002 and 0.0008).ConclusionThe current study of statistics by prefecture in Japan also suggests that factors such as smoking and drinking alcohol are correlated with the risk of prostate cancer mortality. On the other hand, regional unevenness of radiation oncologists did not correlate. These results suggest that there is validity in this study design of analyzing factors of risk of prostate cancer mortality. And the study design was suggested to be useful for comparing various patient background factors.
Performance characteristics of the VIDAS® SARS-COV-2 IgM and IgG serological assays
Authors: Renard Nathalie , Daniel Soizic , Cayet Nadège , Pecquet Matthieu , Raymond Frédérique , Pons Sylvie , Lupo Julien , Tourneur Carole , Pretis Catherine , Gerez Guillaume , Blasco Patrick , Combe Maxime , Canova Imen , Lesénéchal Mylène , Berthier Franck 
Published: September 2020

ABSTRACTThe COVID-19 pandemic, caused by the new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), continues to spread worldwide. Serological testing for SARS-CoV-2-specific antibodies plays an important role in understanding and controlling the pandemics, notably through epidemiological surveillance. Well validated and highly specific SARS-CoV-2 serological assays are urgently needed. We describe here the analytical and clinical performance of VIDAS® SARS-CoV-2 IgM and VIDAS® SARS-CoV-2 IgG, two CE-marked, EUA-authorized, automated, qualitative assays for the detection of SARS-CoV-2-specific IgM and IgG, respectively. Both assays showed high within-run and within-laboratory precision (coefficients of variation < 11.0%) and very low cross-reactivity towards sera of patients with a past common coronavirus or respiratory virus infection. Clinical specificity determined on up to 989 pre-pandemic healthy donors was ≥ 99% with a narrow 95% confidence interval for both IgM and IgG assays. Clinical sensitivity was determined on up to 232 samples from 130 RT-PCR-confirmed SARS-CoV-2 patients. The positive percent agreement (PPA) with SARS-CoV-2 PCR reached 100% at ≥ 16 days (VIDAS® SARS-CoV-2 IgM) and ≥ 32 days (VIDAS® SARS-CoV-2 IgG) of symptom onset. Combined IgM/IgG test results improved the PPA compared to each test alone. SARS-CoV-2 IgG seroconversion followed closely that of SARS-CoV-2 IgM and remained stable over time, while SARS-CoV-2 IgM levels rapidly declined. Interestingly, SARS-CoV-2-specific IgM and IgG responses were significantly higher in COVID-19 hospitalized vs. non-hospitalized patients. Altogether, the VIDAS® SARS-CoV-2 IgM and IgG assays are highly specific and sensitive serological tests suitable for the reliable monitoring of past SARS-CoV-2 infections and for seroepidemiology investigations.
A decoupled, modular and scriptable architecture for tools to curate data platforms
Authors: Langenstein Moritz , Hermjakob Henning , Llinares Manuel Bernal 
Published: September 2020

AbstractMotivationCuration is essential for any data platform to maintain the quality of the data it provides. Existing databases, which require maintenance, and the amount of newly published information that needs to be surveyed, are growing rapidly. More efficient curation is often vital to keep up with this growth, requiring modern curation tools. However, curation interfaces are often complex and difficult to further develop. Furthermore, opportunities for experimentation with curation workflows may be lost due to a lack of development resources, or a reluctance to change sensitive production systems.ResultsWe propose a decoupled, modular and scriptable architecture to build curation tools on top of existing platforms. Instead of modifying the existing infrastructure, our architecture treats the existing platform as a black box and relies only on its public APIs and web application. As a decoupled program, the tool’s architecture gives more freedom to developers and curators. This added flexibility allows for quickly prototyping new curation workflows as well as adding all kinds of analysis around the data platform. The tool can also streamline and enhance the curator’s interaction with the web interface of the platform. We have implemented this design in cmd-iaso, a command-line curation tool for the identifiers.org registry.AvailabilityThe cmd-iaso curation tool is implemented in Python 3.7+ and supports Linux, macOS and Windows. Its source code and documentation are freely available fromhttps://github.com/identifiers-org/cmd-iaso. It is also published as a Docker container athttps://hub.docker.com/r/identifiersorg/cmd-iaso.Contacthhe@ebi.ac.uk
GHB confers neuroprotection by stabilizing the CaMKIIα hub domain
Authors: Leurs Ulrike , Klein Anders B. , McSpadden Ethan D. , Griem-Krey Nane , Solbak Sara M. Ø. , Houlton Josh , Villumsen Inge S. , Vogensen Stine B. , Hamborg Louise , Gauger Stine J. , Palmelund Line B. , Larsen Anne Sofie G. , Shehata Mohamed A. , Kelstrup Christian D. , Olsen Jesper V. , Bach Anders , Burnie Robert O. , Kerr D. Steven , Gowing Emma K. , Teurlings Selina M. W. , Chi Chris C. , Gee Christine L. , Frølund Bente , Kornum Birgitte R. , van Woerden Geeske M. , Clausen Rasmus P. , Kuriyan John , Clarkson Andrew N. , Wellendorph Petrine 
Published: September 2020

ABSTRACTCa2+/calmodulin-dependent protein kinase II alpha (CaMKIIα) is an abundant neuronal signaling protein involved in synaptic plasticity and memory formation1,2. The central hub domain regulates the activity of CaMKIIα by organizing the holoenzyme complex into functional oligomers3-6. Recent findings have suggested that the hub is also an allosteric determinant of kinase activity7, and is thus an emerging target for therapies to correct CaMKIIα dysregulation8,9. However, pharmacological modulation of the hub domain has never been demonstrated. Here we show that stabilization of the CaMKIIα hub domain confers neuroprotection. By combining photoaffinity labeling and chemical proteomics using small molecule analogs of the natural metabolite γ-hydroxybutyrate (GHB)10we reveal that CaMKIIα is the selective target for GHB. We further find that these GHB analogs bind to the hub interior by solving a 2.2 Å crystal structure of CaMKIIα with bound ligand. Using differential scanning fluorimetry, we show that binding of ligands to the hub interior increases the thermal stability of hub oligomers in a concentration-dependent manner. Moreover, we demonstrate the functional significance of this hub stabilization by showing substantial neuroprotective effects in cellular excitotoxicity assays and in a mouse model of cerebral ischemia. Together, our results reveal that CaMKIIα hub stabilization is the mechanism by which GHB provides endogenous neuroprotection and that small-molecule CaMKIIα-selective ligands have therapeutic potential.
Bipartite influence of abscisic acid on xylem differentiation trajectories is dependent on distinct VND transcription factors in Arabidopsis
Authors: Ramachandran Prashanth , Augstein Frauke , Mazumdar Shamik , Van Nguyen Thanh , Minina Elena A. , Melnyk Charles W. , Carlsbecker Annelie 
Published: September 2020

SummaryPlants display a remarkable ability to adjust their growth and development to changes in environmental conditions, such as reduction in water availability. This high degree of plasticity is apparent not only as altered root and shoot growth rates, but also as changes to tissue patterning and cell morphology [1,2]. We have previously shown thatArabidopsis thalianaroot xylem displays plastic developmental responses to limited water availability, mediated by non-cell autonomous action of abscisic acid, ABA [2]. Here, we show through analyses of ABA response reporters and tissue specific suppression of ABA signalling that xylem cells act as primary signalling centres for mediation of changes to both xylem cell fate and differentiation rate revealing a cell autonomous control of xylem development by ABA. Transcriptomic changes in response to ABA showed that members of the VASCULAR RELATED NAC DOMAIN (VND) transcription factor family are rapidly activated. Molecular and genetic analyses revealed that the two aspects of xylem developmental changes, cell fate and differentiation rate, are dependent on distinct members of this transcription factor family. Thus, this study provides insights into how different aspects of developmental plasticity can be interlinked, yet genetically independent of each other. Moreover, similarities in phenotypic and molecular responses to ABA in diverse species indicate an evolutionary conservation of the ABA-xylem development regulatory network among eudicots. Hence, this study gives molecular insights on how environmental stress promotes anatomical plasticity to key plant traits with potential relevance for water use optimization and adaptation to drought conditions.
Macrophages respond rapidly to ototoxic injury of lateral line hair cells but are not required for hair cell regeneration
Authors: Warchol Mark E. , Schrader Angela , Sheets Lavinia 
Published: September 2020

AbstractThe sensory organs of the inner ear contain resident populations of macrophages, which are recruited to sites of cellular injury. Such macrophages are known to phagocytose the debris of dying cells but the full role of macrophages in otic pathology is not understood. Lateral line neuromasts of zebrafish contain hair cells similar to those in the inner ear, and the optical clarity of larval zebrafish permits direct imaging of cellular interactions. In this study, we used larval zebrafish to characterize the response of macrophages to ototoxic injury of lateral line hair cells. Macrophages migrated into neuromasts within 20 min of exposure to the ototoxic antibiotic neomycin. The number of macrophages in close proximity of injured neuromasts was similar to that observed near uninjured neuromasts, suggesting that this early inflammatory response was mediated by ‘local’ macrophages. Upon entering injured neuromasts, macrophages actively phagocytosed hair cell debris. Such phagocytosis was significantly reduced by inhibiting Src-family kinases. Using chemical-genetic ablation of macrophages prior to ototoxic injury, we also examined whether macrophages were essential for the initiation of hair cell regeneration after neomycin exposure. Results revealed only minor differences in hair cell recovery in macrophage-depleted vs. control fish, suggesting that macrophages are not essential for the regeneration of lateral line hair cells.
Development of EphA2 siRNA-loaded lipid nanoparticles and combination with a small-molecule histone demethylase inhibitor in prostate cancer cells and tumor spheroids
Authors: Oner Ezgi , Kotmakci Mustafa , Baird Anne-Marie , Gray Steven G. , Butuner Bilge Debelec , Bozkurt Emir , Kantarci Ayse Gulten , Finn Stephen P. 
Published: September 2020

AbstractsiRNAs hold a great potential for cancer therapy, however, poor stability in body fluids and low cellular uptake limit their use in the clinic. To enhance the bioavailability of siRNAs in tumors, novel, safe, and effective carriers are needed. Here, we developed cationic solid lipid nanoparticles (cSLNs) to carry siRNAs targeting EphA2 receptor tyrosine kinase (siEphA2), which is overexpressed in many solid tumors including prostate cancer (PCa). Using DDAB cationic lipid instead of DOTMA reduced nanoparticle size and enhanced both cellular uptake and gene silencing in PCa cells. After verifying the efficacy of siEphA2-loaded nanoparticles, we further evaluated a potential combination with a histone lysine demethylase inhibitor, JIB-04. Silencing EphA2 by siEphA2-loaded DDAB-cSLN did not affect the viability (2D and 3D), migration, and clonogenicity of PC-3 cells alone. However, upon co-administration, there was a decrease in the aforementioned cellular responses due to JIB-04. Furthermore, JIB-04 decreased EphA2 expression, and thus, silencing efficiency of siEphA2-loaded nanoparticles was further increased with co-treatment. In conclusion, we have successfully developed a novel siRNA-loaded lipid nanoparticle for targeting EphA2. Moreover, detailed preliminary results of the effects of JIB-04, alone and in combination with siEphA2, on PCa cells and tumor spheroids were presented for the first time. Our delivery system provides high transfection efficiency and shows a great promise for targeting other genes and cancer types in furtherin vitroandin vivostudies.
DIA-based systems biology approach unveils novel E3-dependent responses to a metabolic shift
Authors: Karayel Ozge , Michaelis André C. , Mann Matthias , Schulman Brenda A. , Langlois Christine R. 
Published: September 2020

ABSTRACTYeastSaccharomyces cerevisiaeis a powerful model system for systems-wide biology screens and large-scale proteomics methods. Nearly complete proteomics coverage has been achieved owing to advances in mass spectrometry. However, it remains challenging to scale this technology for rapid and high-throughput analysis of the yeast proteome to investigate biological pathways on a global scale. Here we describe a systems biology workflow employing plate-based sample preparation and rapid, single-run data independent mass spectrometry analysis (DIA). Our approach is straightforward, easy to implement and enables quantitative profiling and comparisons of hundreds of nearly complete yeast proteomes in only a few days. We evaluate its capability by characterizing changes in the yeast proteome in response to environmental perturbations, identifying distinct responses to each of them, and providing a comprehensive resource of these responses. Apart from rapidly recapitulating previously observed responses, we characterized carbon source dependent regulation of the GID E3 ligase, an important regulator of cellular metabolism during the switch between gluconeogenic and glycolytic growth conditions. This unveiled new regulatory targets of the GID ligase during a metabolic switch. Our comprehensive yeast system read-out pinpointed effects of a single deletion or point mutation in the GID complex on the global proteome, allowing the identification and validation novel targets of the GID E3 ligase. Moreover, our approach allowed the identification of targets from multiple cellular pathways that display distinct patterns of regulation. Although developed in yeast, rapid whole proteome-based readouts can serve as comprehensive systems-level assay in all cellular systems.
Fluorescence-detection size-exclusion chromatography utilizing nanobody technology for expression screening of membrane proteins
Authors: Jin Fei , Wang Yao , Wang Mengqi , Sun Minxuan , Hattori Motoyuki 
Published: September 2020

AbstractMembrane proteins play numerous physiological roles and are thus of tremendous interest in pharmacology. Nevertheless, stable and homogeneous sample preparation is one of the bottlenecks in biophysical and pharmacological studies of membrane proteins because membrane proteins are typically unstable and poorly expressed. To overcome such obstacles, GFP fusion-based Fluorescence-detection Size-Exclusion Chromatography (FSEC) has been widely employed for membrane protein expression screening for over a decade. However, fused GFP itself may occasionally affect the expression and/or stability of the targeted membrane protein, leading to both false-positive and false-negative results in expression screening. Furthermore, GFP fusion technology is not well suited for some membrane proteins depending on their membrane topology. Here, we developed an FSEC assay utilizing nanobody (Nb) technology, named FSEC-Nb, in which targeted membrane proteins are fused to a small peptide tag and recombinantly expressed. The whole-cell extracts are solubilized, mixed with anti-peptide Nb fused to GFP and applied to a size-exclusion chromatography column attached to a fluorescence detector for FSEC analysis. FSEC-Nb enables one to evaluate the expression, monodispersity and thermostability of membrane proteins without the need of purification by utilizing the benefits of the GFP fusion-based FSEC method, but does not require direct GFP fusion to targeted proteins. We applied FSEC-Nb to screen zinc-activated ion channel (ZAC) family proteins in the Cys-loop superfamily and membrane proteins from SARS-CoV-2 as examples of the practical application of FSEC-Nb. We successfully identified a ZAC ortholog with high monodispersity but moderate expression levels that could not be identified with the previously developed GFP fusion-free FSEC method. Consistent with the results of FSEC-Nb screening, the purified ZAC ortholog showed monodispersed particles by both negative staining EM and cryo-EM. Furthermore, we identified two membrane proteins from SARS-CoV-2 with high monodispersity and expression level by FSEC-Nb, which may facilitate structural and functional studies of SARS-CoV-2. Overall, our results show FSEC-Nb as a powerful tool for membrane protein expression screening that can provide further opportunity to prepare well-behaved membrane proteins for structural and functional studies.
Measuring effects of trainee professional development on research productivity: A cross-institutional meta-analysis
Authors: Brandt Patrick D. , Varvayanis Susi Sturzenegger , Baas Tracey , Bolgioni Amanda F. , Alder Janet , Petrie Kimberly A. , Dominguez Isabel , Brown Abigail M. , Abigail Stayart C. , Singh Harinder , Wart Audra Van , Chow Christine S. , Mathur Ambika , Schreiber Barbara M. , Fruman David A. , Bowden Brent , Holmquist Chris E. , Arneman Daniel , Hall Joshua D. , Hyman Linda E. , Gould Kathleen L. , Chalkley Roger , Brennwald Patrick J. , Layton Rebekah L. 
Published: September 2020

AbstractPhD-trained scientists are essential contributors to the workforce in diverse employment sectors that include academia, industry, government, and non-profit organizations. Hence, best practices for training the future biomedical workforce are of national concern. Complementing coursework and laboratory research training, many institutions now offer professional training that enables career exploration and develops a broad set of skills critical to various career paths. The National Institutes of Health funded academic institutions to design innovative programming to enable this professional development through a mechanism known as Broadening Experiences in Scientific Training (BEST). Programming at the BEST awardee institutions included career panels, skill-building workshops, job-searching workshops, site visits, and internships. An initial concern was since doctoral training is lengthy and requires focused attention on dissertation research, having students participate in additional complementary training activities might lengthen time to degree and hamper student research productivity. To address this concern, using time to degree and publication records as measures of efficiency and productivity, metrics were analyzed from ten BEST awardee institutions. Comparing doctoral students who participated to those who did not, results revealed that across these diverse academic institutions, there were no differences in time to degree or manuscript output. Furthermore, a few institutions even demonstrated a positive correlation between participation in career and professional development activities and productivity. Our findings suggest that doctoral students should be encouraged to participate in career and professional development opportunities to ensure their preparedness for a variety of diverse and important careers in the workforce.Significance StatementOur study is unique in that it compiled doctoral degree durations at ten different universities, recorded individual participation in career and professional development activities in terms of dosage, and tracked individual engagement in real-time rather than relying on surveys sent to trainees after graduation. Participation in career and professional development activities, including internships, did not decrease efficiency or productivity. Our findings suggest that doctoral students should be encouraged to participate in career and professional development opportunities to ensure their preparedness for a variety of diverse and important careers in the workforce.