bluuebunny/crossref_metadata_2025_split huggingface dataset:
GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data
Authors: Marini Federico , Ludt Annekathrin , Linke Jan , Strauch Konstantin 
Published: May 2021

AbstractBackgroundThe interpretation of results from transcriptome profiling experiments via RNA sequencing (RNA-seq) can be a complex task, where the essential information is distributed among different tabular and list formats - normalized expression values, results from differential expression analysis, and results from functional enrichment analyses. A number of tools and databases are widely used for the purpose of identification of relevant functional patterns, yet often their contextualization within the data and results at hand is not straightforward, especially if these analytic components are not combined together efficiently.ResultsWe developed the GeneTonic software package, which serves as a comprehensive toolkit for streamlining the interpretation of functional enrichment analyses, by fully leveraging the information of expression values in a differential expression context. GeneTonic is implemented in R and Shiny, leveraging packages that enable HTML-based interactive visualizations for executing drilldown tasks seamlessly, viewing the data at a level of increased detail. GeneTonic is integrated with the core classes of existing Bioconductor workflows, and can accept the output of many widely used tools for pathway analysis, making this approach applicable to a wide range of use cases. Users can effectively navigate interlinked components (otherwise available as flat text or spreadsheet tables), bookmark features of interest during the exploration sessions, and obtain at the end a tailored HTML report, thus combining the benefits of both interactivity and reproducibility.ConclusionGeneTonic is distributed as an R package in the Bioconductor project (https://bioconductor.org/packages/GeneTonic/) under the MIT license. Offering both bird’s-eye views of the components of transcriptome data analysis and the detailed inspection of single genes, individual signatures, and their relationships, GeneTonic aims at simplifying the process of interpretation of complex and compelling RNA-seq datasets for many researchers with different expertise profiles.
Targeting of Protein Kinase CK2 in Acute Myeloid Leukemia Cells Using the Clinical-Grade Synthetic-Peptide CIGB-300
Authors: Rosales Mauro , Pérez George V. , Ramón Ailyn C. , Cruz Yiliam , Rodríguez-Ulloa Arielis , Besada Vladimir , Ramos Yassel , Vázquez-Blomquist Dania , Caballero Evelin , Aguilar Daylen , González Luis J. , Zettl Katharina , Wiśniewski Jacek R. , Ke Yang , Perera Yasser , Perea Silvio E. 
Published: May 2021

AbstractProtein kinase CK2 has emerged as an attractive therapeutic target in acute myeloid leukemia (AML), advent that becomes particularly relevant since the treatment of this hematological neoplasia remains challenging. Here we explored for the first time the effect of the clinical-grade peptide-based CK2 inhibitor CIGB-300 on AML cells proliferation and viability. CIGB-300 internalization and subcellular distribution were also studied, and the role of B23/nucleophosmin 1 (NPM1), a major target for the peptide in solid tumors, was addressed by knock-down in model cell lines. Finally, pull-down experiments and phosphoproteomic analysis were performed to study CIGB-interacting proteins and identify the array of CK2 substrates differentially modulated after treatment with the peptide. Importantly, CIGB-300 elicited a potent anti-proliferative and proapoptotic effect in AML cells, with more than 80% of peptide transduced cells within three minutes. Unlike solid tumor cells, NPM1 did not appear to be a major target for CIGB-300 in AML cells. However, in vivo pull-down experiments and phosphoproteomic analysis evidenced that CIGB-300 targeted the CK2α catalytic subunit, different ribosomal proteins, and inhibited the phosphorylation of a common CK2 substrates array among both AML backgrounds. Remarkably, our results not only provide cellular and molecular insights unveiling the complexity of the CIGB-300 anti-leukemic effect in AML cells, but also reinforce the rationale behind the pharmacologic blockade of protein kinase CK2 for AML targeted therapy.
Single-dose AAV-based vaccine induces a high level of neutralizing antibodies against SARS-CoV-2 in rhesus macaques
Authors: Tong Dali , Zhang Mei , Yang Yunru , Xia Han , Tong Haiyang , Zhang Huajun , Zeng Weihong , Liu Muziying , Wu Yan , Ma Huan , Hu Xue , Liu Weiyong , Cai Yuan , Yao Yanfeng , Yao Yichuan , Liu Kunpeng , Shan Shifang , Li Yajuan , Gao Ge , Guo Weiwei , Peng Yun , Chen Shaohong , Rao Juhong , Zhao Jiaxuan , Min Juan , Zhu Qingjun , Zheng Yanmin , Liu Lianxin , Shan Chao , Zhong Kai , Qiu Zilong , Jin Tengchuan , Chiu Sandra , Yuan Zhiming , Xue Tian 
Published: May 2021

AbstractCoronavirus disease 2019 (COVID-19), which is triggered by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, continues to threaten global public health. Developing a vaccine that only requires single immunization but provides long-term protection for the prevention and control of COVID-19 is important. Here, we developed an adeno-associated virus (AAV)-based vaccine expressing a stable receptor-binding domain (SRBD) protein. The vaccine requires only a single shot but provides effective neutralizing antibodies (NAbs) over 598 days in rhesus macaques (Macaca mulatta). Importantly, our results showed that the NAbs were kept in high level and long lasting against authentic wild-type SARS-CoV-2, Beta, Delta and Omicron variants using plaque reduction neutralization test. Of note, although we detected pre-existing AAV2/9 antibodies before immunization, the vaccine still induced high and effective NAbs against COVID-19 in rhesus macaques. AAV-SRBD immune serum also efficiently inhibited the binding of ACE2 with RBD in the SARS-CoV-2 B.1.1.7 (Alpha), B.1.351 (Beta), P.1/P.2 (Gamma), B.1.617.2 (Delta), B.1.617.1/3(Kappa), and C.37 (Lambda) variants. Thus, these data suggest that the vaccine has great potential to prevent the spread of SARS-CoV-2.
Ankrd26 is critical for cell differentiation and cancer-linked mutations affect its key properties
Authors: Hofbrucker-MacKenzie Sarah A. , Englisch A. Sofie , Izadi Maryam , Metzner Klara , Kessels Michael M. , Qualmann Britta 
Published: May 2021

AbstractDerailed signaling originating from the plasma membrane is associated with many types of cancer. Different human cancers and thrombocytopenia are linked toANKRD26mutations. We unveil that Ankrd26 is a plasma membrane-localized protein forming nanoclusters and that Ankrd26 is critical for retinoic acid/BDNF-induced neuroblastoma differentiation. An N-terminal amphipathic structure lacking in an AML-associated Ankrd26 mutant is indispensable for membrane binding and bending by partial membrane insertion and renders Ankrd26 inactive in both gain-of-function and loss-of- function/rescue studies addressing cellular differentiation. In a papillary thyroid carcinoma-linked mutant, truncated Ankrd26 is fused with the kinase domain of the protooncogene RET. Our data show that the Ankrd26 part of this fusion mutant mediates anchoring of the RET kinase domain to the plasma membrane and self-association by the coiled coil domain of Ankrd26. Ankrd26-RET fusion led to massively increased ERK1/2 activity and RET autophosphorylation at both Y905 and Y1015, i.e. caused aberrant RET signaling. Our results highlight the importance and molecular details of Ankrd26-mediated organizational platforms for cellular differentiation and signaling pathways from the plasma membrane, which, if derailed, lead to cancer-associated pathomechanisms involving the unveiled Ankrd26 properties.
Metformin Is Associated with Favorable Outcomes in Patients with COVID-19 and Type 2 Diabetes Mellitus
Authors: Ma Zhiyuan , Patel Nishit , Vemparala Pranathi , Krishnamurthy Mahesh 
Published: May 2021

AbstractAimCoronavirus disease 2019 (COVID-19) is a new pandemic the entire world is facing since December of 2019. In this retrospective study, we aim to address whether metformin use offers a low mortality on patients with COVID-19 and pre-existing type 2 diabetes mellitus (T2DM).Materials and MethodsA cohort of 1356 hospitalized patients with COVID-19 and pre-existing T2DM was analyzed by multivariate regression. Covariates that potentially confound the association were further adjusted using propensity score matching or inverse probability of treatment weighting. A meta-analysis of the present study along with 5 published studies with metformin use prior to admission in patients with COVID-19 and T2DM was carried out.ResultsWe found that metformin therapy prior to admission in patients with COVID-19 and T2DM was significantly associated with less primary outcome events including in-hospital mortality and hospice care enrollment with an odds ratio (OR) of 0.25 (95% CI, 0.06-0.74) and less in-hospital length of stay, compared to non-metformin group. There were no statistical differences between the metformin group and non-metformin group for all three inflammatory markers (ferritin, CRP, and IL-6) on admission or peak levels during hospitalization. Furthermore, meta-analysis demonstrated that metformin use was significantly correlated with reduced mortality with an OR of 0.73 (95% CI, 0.65-0.82) in the fixed effect model and 0.58 (95% CI, 0.42-0.80) for the random effect model.ConclusionsOur results provide supporting evidence that metformin may confer increased survival in patients with COVID-19 and T2DM treated with Metformin prior to hospitalization.
Association of Microalbuminuria with High HbA1C levels in Melanesian Adults with Diabetes of at-least 1 Year Duration
Authors: Billy Ian , Aglua Izzard 
Published: May 2021

AbstractBackgroundEvidence suggest a potential relationship between high or variable HbA1C levels and presence or rate of change of microalbuminuria. Disruption of the vascular endothelial glycocalyx has been linked to chronic hyperglycemia and microalbuminuria, suggesting a possible shared pathophysiological mechanism.AimTo 1) explore potential association between microalbuminuria and high HbA1C levels in Melanesian adults with diabetes mellitus, and 2) asses predictive value of a high HbA1C reading as an indicator of the presence or progression of microalbuminuria.MethodA cross-sectional study on 190 patients with either type 1 or 2 diabetes of at least 1-year duration done at a provincial hospital in Papua New Guinea in 2017.ResultA significant [P=0.0221], though weak [R2=0.028 <0.70], correlation between UACR and HbA1C [95% statistical confidence] was observed in univariate regression, which was marginally significant [P=0.056] after controlling for weight, systolic hypertension, duration of diabetes, gender and age in multivariate regression.ConclusionA significant [p=0.022], though weak, correlation between UACR and HbA1C levels was observed, which may support usefulness of HbA1C as a predictor for microalbuminuria and diabetic kidney disease. In settings without microalbuminuria testing, high HbA1c levels can be used as a proxy to indicate presence or progression of microalbuminuria, thus prompting timely interventions to prevent further progression of diabetic nephropathy.
Growth and eGFP-production of CHO-K1 suspension cells cultivated from single-cell to lab-scale
Authors: Schmitz Julian , Hertel Oliver , Yermakov Boris , Noll Thomas , Grünberger Alexander 
Published: May 2021

AbstractScaling down bioproduction processes became a major driving force for more accelerated and efficient process development over the last decades. Especially expensive and time-consuming processes like the production of biopharmaceuticals with mammalian cell lines benefit clearly from miniaturisation, due to higher parallelisation and increased insights while at the same time decreasing experimental time and costs. Lately, novel microfluidic methods have been developed, especially microfluidic single-cell cultivation (MSCC) devices proofed to be valuable to miniaturise the cultivation of mammalian cells. So far growth characteristics of microfluidic cultivated cell lines were not systematically compared to larger cultivation scales, however validation of a miniaturisation tool against initial cultivation scales is mandatory to proof its applicability for bioprocess development. Here, we systematically investigate growth, morphology, and eGFP-production of CHO-K1 cells in different cultivation scales including microfluidic chip (230 nL), shake flask (60 mL), and lab-scale bioreactor (1.5 L). Our study shows a high comparability regarding growth rates, cellular diameters, and eGFP production which proofs the feasibility of MSCC as miniaturised cultivation tool for mammalian cell culture. In addition, we demonstrate that MSCC allows insights into cellular heterogeneity and single-cell dynamics concerning growth and production behaviour which, when occurring in bioproduction processes, might severely affect process robustness. Eventually, by providing insights into cellular heterogeneity, MSCC has the potential to be applied as a novel and powerful tool in the context of cell line development and bioprocesses implementation.
Differential interferon-α subtype immune signatures suppress SARS-CoV-2 infection
Authors: Schuhenn J. , Meister T.L. , Todt D. , Bracht T. , Schork K. , Billaud J.-N. , Elsner C. , Heinen N , Karakoese Z. , Haid S. , Kumar S. , Brunotte L. , Eisenacher M. , Chen J. , Yuan Z , Pietschmann T. , Wiegmann B. , Beckert H. , Taube C. , Le-Trilling VTK. , Trilling M. , Krawczyk A. , Ludwig S. , Sitek B. , Steinmann E. , Dittmer U. , Sutter K. , Pfaender S. 
Published: May 2021

SummaryType I interferons (IFN-I) exert pleiotropic biological effects during viral infections, balancing virus control versus immune-mediated pathologies and have been successfully employed for the treatment of viral diseases. Humans express twelve IFN-alpha (α) subtypes, which activate downstream signalling cascades and result in distinct patterns of immune responses and differential antiviral responses. Inborn errors in type I IFN immunity and the presence of anti-IFN autoantibodies account for very severe courses of COVID-19, therefore, early administration of type I IFNs may be protective against life-threatening disease. Here we comprehensively analysed the antiviral activity of all IFNα subtypes against SARS-CoV-2 to identify the underlying immune signatures and explore their therapeutic potential. Prophylaxis of primary human airway epithelial cells (hAEC) with different IFNα subtypes during SARS-CoV-2 infection uncovered distinct functional classes with high, intermediate and low antiviral IFNs. In particular IFNα5 showed superior antiviral activity against SARS-CoV-2 infection. Dose-dependency studies further displayed additive effects upon co-administered with the broad antiviral drug remdesivir in cell culture. Transcriptomics of IFN-treated hAEC revealed different transcriptional signatures, uncovering distinct, intersecting and prototypical genes of individual IFNα subtypes. Global proteomic analyses systematically assessed the abundance of specific antiviral key effector molecules which are involved in type I IFN signalling pathways, negative regulation of viral processes and immune effector processes for the potent antiviral IFNα5. Taken together, our data provide a systemic, multi-modular definition of antiviral host responses mediated by defined type I IFNs. This knowledge shall support the development of novel therapeutic approaches against SARS-CoV-2.
Development of a Bayesian network for probabilistic risk assessment of pesticides
Authors: Mentzel Sophie , Grung Merete , Tollefsen Knut Erik , Stenrød Marianne , Petersen Karina , Moe S. Jannicke 
Published: May 2021

AbstractConventional environmental risk assessment of chemicals is based on a calculated risk quotient, representing the ratio of exposure to effects of the chemical, in combination with assessment factors to account for uncertainty. Probabilistic risk assessment approaches can offer more transparency, by using probability distributions for exposure and/or effects to account for variability and uncertainty. In this study, a probabilistic approach using Bayesian network (BN) modelling is explored as an alternative to traditional risk calculation. BNs can serve as meta-models that link information from several sources and offer a transparent way of incorporating the required characterization of uncertainty for environmental risk assessment. To this end, a BN has been developed and parameterised for the pesticides azoxystrobin, metribuzin, and imidacloprid. We illustrate the development from deterministic (traditional) risk calculation, via intermediate versions, to fully probabilistic risk characterisation using azoxystrobin as an example. We also demonstrate seasonal risk calculation for the three pesticides.
The gatekeeper of Yersinia type III secretion is under RNA thermometer control
Authors: Pienkoß Stephan , Javadi Soheila , Chaoprasid Paweena , Nolte Thomas , Twittenhoff Christian , Dersch Petra , Narberhaus Franz 
Published: May 2021

AbstractMany bacterial pathogens use a type III secretion system (T3SS) as molecular syringe to inject effector proteins into the host cell. In the foodborne pathogen Yersinia pseudotuberculosis, delivery of the secreted effector protein cocktail through the T3SS depends on YopN, a molecular gatekeeper that controls access to the secretion channel from the bacterial cytoplasm. Here, we show that several checkpoints adjust yopN expression to virulence conditions. A dominant cue is the host body temperature. A temperature of 37 °C is known to induce the RNA thermometer (RNAT)-dependent synthesis of LcrF, a transcription factor that activates expression of the entire T3SS regulon. Here, we uncovered a second layer of temperature control. We show that another RNAT silences translation of the yopN mRNA at low environmental temperatures. The long and short 5’-untranslated region of both cellular yopN isoforms fold into a similar secondary structure that blocks ribosome binding. The hairpin structure with an internal loop melts at 37 °C and thereby permits formation of the translation initiation complex as shown by mutational analysis, in vitro structure probing and toeprinting methods. Importantly, we demonstrate the physiological relevance of the RNAT in the faithful control of type III secretion by using a point-mutated thermostable RNAT variant with a trapped SD sequence. Abrogated YopN production in this strain led to unrestricted effector protein secretion into the medium, bacterial growth arrest and delayed translocation into eukaryotic host cells. Cumulatively, our results show that substrate delivery by the Yersinia T3SS is under hierarchical surveillance of two RNATs.Author summaryTemperature serves as reliable external cue for pathogenic bacteria to recognize the entry into or exit from a warm-blooded host. At the molecular level, a temperature of 37 °C induces various virulence-related processes that manipulate host cell physiology. Here, we demonstrate the temperature-dependent synthesis of the secretion regulator YopN in the foodborne pathogen Yersinia pseudotuberculosis, a close relative of Yersinia pestis. YopN blocks secretion of effector proteins through the type III secretion system unless host cell contact is established. Temperature-specific regulation relies on an RNA structure in the 5’-untranslated region of the yopN mRNA, referred to as RNA thermometer, which allows ribosome binding and thus translation initiation only at an infection-relevant temperature of 37 °C. A mutated variant of the thermosensor resulting in a closed conformation prevented synthesis of the molecular gatekeeper YopN and led to permanent secretion and defective translocation of virulence factors into host cells. We suggest that the RNA thermometer plays a critical role in adjusting the optimal cellular concentration of a surveillance factor that maintains the controlled translocation of virulence factors.
Fluorescence signatures of SARS-CoV-2 spike S1 proteins and an human ACE-2: excitation-emission maps and fluorescence lifetimes
Authors: Grzesiak Jonas , Fellner Lea , Grünewald Karin , Kölbl Christoph , Walter Arne , Horlacher Reinhold , Duschek Frank 
Published: May 2021

AbstractSignificanceFast and reliable detection of infectious SARS-CoV-2 virus loads is an important issue. Fluorescence spectroscopy is a sensitive tool to do so in clean environments. This presumes a comprehensive knowledge of fluorescence data.AimThis work aims at providing fully featured information on wavelength and time-dependent data of the fluorescence of the SARS-CoV-2 spike protein S1 subunit, its receptor binding domain (RBD) and the human angiotensinconverting enzyme 2 (hACE2), especially with respect to possible optical detection schemes.ApproachSpectrally resolved excitation-emission maps of the involved proteins and measurements of fluorescence lifetimes were recorded for excitations from 220 to 295 nm. The fluorescence decay times were extracted by using a bi-exponential kinetic approach. The binding process in the SARS-CoV-2 RBD was likewise examined for spectroscopic changes.ResultsDistinct spectral features for each protein are pointed out in relevant spectra extracted from the excitation emission maps. We also identify minor spectroscopic changes under the binding process. The decay times in the bi-exponential model are found to be (2.0± 0.1) ns and (8.0 ±1.0) ns.ConclusionsSpecific material data serve as important background information for the design of optical detection and testing methods for SARS-CoV-2 loaded media.
Predictive and motivational factors influencing anticipatory contrast: A comparison of contextual and gustatory predictors in food restricted and free-fed rats
Authors: Hayes Jessica , Garau Celia , Chiacchierini Giulia , Urcelay Gonzalo P. , McCutcheon James E. , Apergis-Schoute John 
Published: May 2021

AbstractIn anticipation of palatable food, rats can learn to restrict consumption of a less rewarding food type resulting in a binge on the preferred food when it is made available. This construct is known as anticipatory negative contrast (ANC) and can help elucidate the processes that underlie binge-like behavior as well as self-control in rodent motivation models. In the current investigation we aimed to shed light on the ability of distinct predictors of a preferred food choice to generate contrast effects and the motivational processes that underlie this behavior. Using a novel set of rewarding solutions, we directly compared contextual and gustatory ANC predictors in both food restricted and free-fed Sprague-Dawley rats. Our results indicate that, despite being food restricted, rats are selective in their eating behavior and show strong contextually-driven ANC and do so after fewer training sessions than free-fed animals. These differences mirrored changes in palatability for the less preferred solution across the different sessions as measured by lick microstructure analysis. Moreover, in contrast to previous research, gustatory cues in both food restricted and free-fed rats were sufficient for ANC to develop although this flavor-driven ANC did not relate to a corresponding change in lick patterning. These differences in the lick microstructure between context- and flavor-driven ANC indicate that the motivational processes underlying ANC generated by the two predictor types are distinct.