bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dual targeting ofSaccharomyces cerevisiaePso2 to mitochondria and the nucleus, and its functional relevance in the repair of DNA interstrand crosslinks
Authors: Somashekara Shravanahalli C. , Muniyappa Kalappa 
Published: March 2022

ABSTRACTRepair of DNA interstrand crosslinks (ICLs) involves a functional interplay among different DNA surveillance and repair pathways. Previous work has shown that ICL- inducing agents cause damage toSaccharomyces cerevisiaenuclear and mitochondrial DNA (mtDNA), and itspso2/snm1mutants exhibit a petite phenotype followed by loss of mtDNA integrity and copy number. Complex as it is, the cause and underlying molecular mechanisms remains elusive. Here, by combining a wide range of approaches within vitroandin vivoanalyses, we assessed the subcellular localization and function of Pso2. We found evidence that the nuclear-encoded Pso2 contains one mitochondrial targeting sequence (MTS) and two nuclear localization signals (NLS1 and NLS2), although NLS1 resides within the MTS. Further analysis revealed that Pso2 is a dual-localized ICL repair protein; it can be imported into both nucleus and mitochondria, and that genotoxic agents enhance its abundance in the latter. While MTS is essential for mitochondrial Pso2 import, either NLS1 or NLS2 is sufficient for its nuclear import; this implies that the two NLS motifs are functionally redundant. Ablation of MTS abrogated mitochondrial Pso2 import, and concomitantly, raised its levels in the nucleus. Strikingly, mutational disruption of both NLS motifs blocked the nuclear Pso2 import; at the same time, they enhanced its translocation into the mitochondria, consistent with the notion that the relationship between MTS and NLS motifs is competitive. However, the nuclease activity of import-deficient species of Pso2 was not impaired. The potential relevance of dual-targeting of Pso2 into two DNA-bearing organelles is discussed.
Long-term survival analysis of HIV patients on antiretroviral therapy in Congo: a 14 years retrospective cohort analysis, 2003-2017
Authors: Ndziessi Gilbert , Niama Ange Clauvel , Nkodia Arkadit Jeandria , Diafouka Merlin 
Published: March 2022

AbstractBackgroundThe long-term survival of patients on antiretroviral treatment in Congo remains less documented. Our study aimed to analyze the long-term survival of adults living with HIV on ART (Antiretroviral Therapy).MethodsWe conducted a historical cohort study on 2,309 adult PLHIV (People Living with HIV) followed between January 1, 2003 and December 31, 2017 whose viral load and date of initiation of ART were known. The Kaplan Meier method was used to estimate the probability of survival and the Cox regression model to identify factors associated with death.ResultsThe median age was 49 years; the female sex was predominant with 68.56%. The probability of survival at 14 years was 83%, (95% CI (Confidence Interval) [78-87]). On the other hand, when the lost to follow-up died, it was 66% (95% CI [62-70]) in the worst scenario. Stratified cox regression analysis showed that: being male, AHR (Adjusted Hazard Ratio) = 1.65 (95% CI [1.26-2.17]) was significantly associated with death, p-value <0.0001. Furthermore, having a viral load> 1000 copies / ml, AHR = 2.56 (95% CI [1.93-3.40]), be in the advanced WHO clinical stage, in particular: stage II, AHR = 4.07 (95% CI [2.36-7.01]); stage III, AHR = 13.49 (95% CI [8.99-20.27]) and stage IV, AHR = 34.45 (95% CI [23.74-50]) were also significantly associated with death; p-value <0.0001.ConclusionThe long-term survival of PLHIV is worrying despite the offer of ARVs.
Community-level characteristics of COVID-19 vaccine hesitancy in England: A nationwide cross-sectional study
Authors: Georges Bucyibaruta , Marta Blangiardo , Garyfallos Konstantinoudis 
Published: March 2022

AbstractOne year after the start of the COVID-19 vaccination programme in England, more than 43 million people older than 12 years old had received at least a first dose. Nevertheless, geographical differences persist, and vaccine hesitancy is still a major public health concern; understanding its determinants is crucial to managing the COVID-19 pandemic and preparing for future ones. In this cross-sectional population-based study we used cumulative data on the first dose of vaccine received by 01-01-2022 at Middle Super Output Area level in England. We used Bayesian hierarchical spatial models and investigated if the geographical differences in vaccination uptake can be explained by a range of community-level characteristics covering socio-demographics, political view, COVID-19 health risk awareness and targeting of high risk groups and accessibility. Deprivation is the covariate most strongly associated with vaccine uptake (Odds Ratio 0.55, 95%CI 0.54-0.57; most versus least deprived areas). The most ethnically diverse areas have a 38% (95%CI 36-40%) lower odds of vaccine uptake compared with those least diverse. Areas with the highest proportion of population between 12 and 24 years old had lower odds of vaccination (0.87, 95%CI 0.85-0.89). Finally increase in vaccine accessibility is associated with higher COVID-19 uptake (OR 1.07, 95%CI 1.03-1.12). Our results suggest that one year after the start of the vaccination programme, there is still evidence of inequalities in uptake, affecting particularly minorities and marginalised groups. Strategies including prioritising active outreach across communities and removing practical barriers and factors that make vaccines less accessible are needed to level up the differences.
Plasma alkaline phosphatase is associated to mortality risk in aortic valve stenosis patients
Authors: Nunes José Pedro L. 
Published: March 2022

AbstractBackgroundaortic valve stenosis is an important clinical condition, with a significant mortality rate in the elderly. Plasma values of alkaline phosphatase (ALP) have been shown to act as a marker of prognosis in different clinical conditions and in the general population.MethodsPlasma levels of alkaline phosphatase were studied in a cohort of patients with aortic valve stenosis, and a five-year survival evaluation was carried out.Results24 patients were under study, of which 12 were dead at 5-year follow-up. The median age at baseline evaluation was 79 years (interquartile range, 72-85 years), and 11 patients were of the female sex (13 were male). The median value of ALP, of 83 IU/L, was used to separate patients into two groups; 2 patients died in the group with low ALP values versus 10 patients who died in the group with high ALP values. Using ALP with the same cut-off level, Kaplan Meyer study with log-rank analysis showed a significance level <0.01. Cox regression analysis showed an overall significant result, with a significant level for plasma ALP (significance level 0.03), but not for age, sex or transvalvular gradient (assessed by echocardiography).ConclusionsElevated plasma ALP is associated to increased mortality risk in aortic valve stenosis patients. This finding may merit evaluation in studies with a larger number of patients.
High Dimensional Mediation Analysis: a new method applied to maternal smoking, placental DNA methylation and birth outcomes
Authors: Jumentier Basile , Barrot Claire-Cécile , Estavoyer Maxime , Tost Jorg , Heude Barbara , François Olivier , Lepeule Johanna 
Published: March 2022

AbstractBackgroundHigh-dimensional mediation analysis is an extension of unidimensional mediation analysis that includes multiple mediators, and is increasingly used to evaluate the indirect omics-layer effects of environmental exposures on health outcomes. Analyses involving high-dimensional mediators raise several statistical issues. While many methods have recently been developed, no consensus has been reached about the optimal combination of approaches to high-dimensional mediation analyses.ObjectivesWe developed and validated a method for high-dimensional mediation analysis (HDMAX2) and applied it to evaluate the causal role of placental DNA methylation in the pathway between exposure to maternal smoking (MS) during pregnancy and gestational age (GA) and weight (BW) of the baby at birth.MethodsHDMAX2 combines latent factor regression models for epigenome-wide association studies with max-squared tests for mediation, and considers CpGs and aggregated mediator regions (AMR). HDMAX2 was carefully evaluated on simulated data, and compared to state-of-the-art multi-dimensional epigenetic mediation methods. Then HDMAX2 was applied on data from 470 women of the EDEN cohort.ResultsHDMAX2 demonstrated increased power compared to state-of-the-art multi-dimensional mediation methods, and identified several AMRs not identified in previous mediation analyses of exposure to MS on BW and GA. The results provided evidence for a polygenic architecture of the mediation pathway with an overall indirect effect of CpGs and AMRs of 44.5 g lower BW (32.1% of the total effect). HDMAX2 also identified AMRs having simultaneous effects both on GA and on BW. Among the top hits of both GA and BW analyses, regions located inCOASY, BLCAPandESRP2also mediated the relationship between GA on BW, suggesting a reverse causality in the relationship between GA and the methylome.DiscussionHDMAX2 outperformed existing approaches and revealed an unsuspected complexity of the causal relationships between exposure to MS and BW at the epigenome-wide level. HDMAX2 is applicable to a wide range of tissues and omic layers.
IgG N-glycans are associated with prevalent and incident complications of type 2 diabetes
Authors: Memarian Elham , Heijmans Ralph , Slieker Roderick C. , Sierra Adriana , Gornik Olga , Beulens Joline WJ , Hanic Maja , Elders Petra , Pascual Julio , Sijbrands Eric , Lauc Gordan , Dotz Viktoria , Barrios Clara , M’t Hart Leen , Wuhrer Manfred , van Hoek Mandy 
Published: March 2022

AbstractAims/hypothesisInflammation is important in development of type 2 diabetes complications. The N-glycosylation of IgG influences its role in inflammation. Until now, the association of IgG N-glycosylation with type 2 diabetes complications has not been extensively investigated. We hypothesized that N-glycosylation of IgG may be related to development of complications of type 2 diabetes.MethodsIn three independent type 2 diabetes cohorts, IgG N-glycosylation was measured by UPLC (DiaGene n=1815, GenodiabMar n=640) and mass spectrometry (DCS n=1266). We investigated the associations of IgG N-glycosylation (fucosylation, galactosylation, sialylation and bisection) with incident and prevalent nephropathy, retinopathy and macrovascular disease using Cox- and logistic regression, followed by meta-analyses. The models were adjusted for age, sex and additionally for clinical risk factors.ResultsIgG galactosylation was negatively associated with prevalent and incident nephropathy after adjustment for clinical risk factors. Sialylation was negatively associated with incident diabetic nephropathy. For retinopathy, similar associations were found for galactosylation in the basic model. For macrovascular complications, negative associations with galactosylation and sialylation were confined to the cross-sectional analyses.ConclusionsWe showed that IgG N-glycosylation traits are associated with higher prevalence and future development of nephropathy, after correction for clinical risk factors. For other complications, IgG N-glycosylation was associated with their prevalence only, possibly reflecting ongoing vascular inflammation. These findings indicate the predictive potential of IgG N-glycosylation in nephropathy.
“Integration of multimodal data in the developing tooth reveals candidate dental disease genes”
Authors: Winchester Emma Wentworth , Hardy Alexis , Cotney Justin 
Published: March 2022

AbstractDental malformations range from rare syndromes to common nonsyndromic phenotypes. These malformations can predispose individuals to dental disease, which can in turn affect systemic health. While many dental phenotypes are heritable, most cases have not been linked to deleterious mutations in single genes. We demonstrate that human and conserved mouse craniofacial enhancers show enrichment of dental phenotype-associated variants. Given these findings in bulk craniofacial tissues, we looked to determine the role of tooth enhancers in this phenomenon. We used ChIP-seq and machine learning to identify enhancers of E13.5 mouse incisors. Multi-tissue comparisons of human and mouse enhancers revealed that putative tooth enhancers had the strongest enrichment of dental phenotype-associated variants, suggesting a role for dysregulation of tooth development in dental phenotypes. To uncover novel dental phenotype-driving genes in the developing tooth we performed coexpression analysis and annotated the contributing cell types of gene modules using scRNAseq. Through integration of chromatin state, bulk gene coexpression, and cell type resolved gene expression we prioritized a list of candidate novel dental disease genes for future investigations in mouse models and human studies.
Metabolite interactions in the bacterial Calvin cycle and implications for flux regulation
Authors: Sporre Emil , Karlsen Jan , Schriever Karen , Samuelsson Johannes Asplund , Janasch Markus , Strandberg Linnéa , Kotol David , Zeckey Luise , Piazza Ilaria , Syrén Per-Olof , Edfors Fredrik , Hudson Elton P. 
Published: March 2022

AbstractMetabolite-level regulation of enzyme activity is important for microbes to cope with environmental shifts. Knowledge of such regulations can also guide strain engineering to improve industrial phenotypes. Recently developed chemoproteomics workflows allow for genome-wide detection of metabolite-protein interactions that may regulate pathway activity. We applied limited proteolysis small molecule mapping (LiP-SMap) to identify and compare metabolite-protein interactions in the proteomes of two cyanobacteria and two lithoautotrophic bacteria that fix CO2using the Calvin cycle. Clustering analysis of the hundreds of detected interactions showed that some metabolites interacted in a species-specific manner, such as interactions of glucose-6-phosphate inCupriavidus necatorand of glyoxylate inSynechocystis spPCC 6803. These are interpreted in light of the different central carbon conversion pathways present. Metabolites interacting with the Calvin cycle enzymes fructose-1,6/sedoheptulose-1,7-bisphosphatase (F/SBPase) and transketolase were tested for effects on catalytic activityin vitro. The Calvin cycle intermediate glyceraldehyde-3-phosphate activated bothSynechocystisandCupriavidusF/SBPase, which suggests a feed-forward activation of the cycle in both photoautotrophs and chemolithoautotrophs. In contrast to the stimulating effect in reduced conditions, glyceraldehyde-3-phosphate inactivated theSynechocystisF/SBPase in oxidized conditions by accelerating protein aggregation. Thus, metabolite-level regulation of the Calvin cycle is more prevalent than previously appreciated and may act in addition to redox regulation.
Tripartite extended amygdala - basal ganglia CRH circuit drives arousal and avoidance behaviour
Authors: Chang Simon , Fermani Federica , Lao Chu-Lan , Huang Lianyun , Jakovcevski Mira , Giaimo Rossella Di , Gagliardi Miriam , Menegaz Danusa , Hennrich Alexander Adrian , Ziller Michael , Eder Matthias , Klein Rüdiger , Cai Na , Deussing Jan M. 
Published: March 2022

AbstractAn adaptive stress response involves various mediators and circuits orchestrating a complex interplay of physiological, emotional and behavioural adjustments. We identified a population of corticotropin-releasing hormone (CRH) neurons in the lateral part of the interstitial nucleus of the anterior commissure (IPACL) – a subdivision of the extended amygdala, which exclusively innervate the substantia nigra (SN). Specific stimulation of this circuit elicits arousal and avoidance behaviour contingent on CRH receptor 1 (CRHR1) located at axon terminals in the SN, which originate from external globus pallidus (GPe) neurons. The neuronal activity prompting the observed behaviour is shaped by IPACLCRH and GPeCRHR1 neurons coalescing in the SN. These results delineate a novel tripartite CRH circuit functionally connecting extended amygdala and basal ganglia nuclei to drive arousal and avoidance behaviour.One-Sentence SummaryBrain centres involved in emotional and motor control are connected through a stress peptide promoting arousal and avoidance behaviour
Corticotropin-releasing hormone signaling from prefrontal cortex to lateral septum supports social novelty preference
Authors: de León Reyes Noelia Sofia , Díaz Paula Sierra , Nogueira Ramon , Ruiz-Pino Antonia , Nomura Yuki , de Solis Christopher , Schulkin Jay , Asok Arun , Leroy Félix 
Published: March 2022

AbstractSocial preference, the decision to interact with one member of the same species over another, is a key feature of optimizing social interactions. In rodents, social preference relies on both extrinsic factors, such as sex, strain and kinship, and intrinsic ones, such as the memory of previous encounters, which favors interactions with novel compared to familiar animals (social novelty preference). At present, it is unclear which neuronal circuits guide social preferences and whether such circuits promote social interactions with the preferred individuals or suppress interactions with the non-preferred ones. Although both the infra-limbic area of the pre-frontal cortex (ILA) and the lateral septum (LS) have been shown to support social novelty preference, the neuronal circuits and molecular mechanisms by which these brain regions interact to regulate social interactions are unknown. Here, we identify a population of inhibitory neurons in ILA that express the neuropeptide corticotropin releasing hormone (CRH) and project to the rostro-dorsal region of LS (rdLS). Release of CRH from ILA in rdLS during interactions with familiar mice disinhibits rdLS neurons, thereby suppressing interactions with familiar mice and contributing to social novelty preference. We further demonstrate how the maturation of CRH expression during the first two post-natal weeks enables the developmental shift from a preference for littermates in juveniles to a preference for novel mice in adults.
Induction of cortical Par complex polarity by designed proteins causes cytoskeletal symmetry breaking in unpolarized mammalian cells
Authors: Watson Joseph L. , Ben-Sasson Ariel J. , Bittleston Alice , Manton James D. , Baker David , Derivery Emmanuel 
Published: March 2022

AbstractPolarized cells rely on a polarized cytoskeleton for polarized trafficking, oriented migration and spindle orientation during asymmetric cell division. While cytoskeleton remodeling machineries have been extensively characterized at the molecular level, how polarity signaling at the cortex controls remodeling of the cytoskeleton in the cytosol remains elusive. In particular, how the Par complex, the conserved mastermind of polarity during asymmetric cell division, gets assembled and functions is not understood at the molecular level. Here, we dissected the logic of the Par complex pathway by capitalizing on designed proteins able to induce spontaneous symmetry breaking of the cortex in populations of naïve, unpolarized cells. We found that the primary kinetic barrier to Par complex assembly is the relief of Par6 autoinhibition, and that inducing Par complex cortical polarity was sufficient to induce two key hallmarks of asymmetric cell division in unpolarized cells: spindle orientation and central spindle asymmetry. These two outputs of the Par complex are separately controlled: spindle orientation is determined by Par3 and does not require the kinase activity of aPKC, while central spindle asymmetry solely depends on an asymmetric activity of aPKC at the cortex. Our work shows how polarity information flows between the cortex and the cytosol despite its diffusive nature, and paves the way towards induction of asymmetric cell division in cultured cells.
Expressed therapeutic protein yields are predicted by transiently transfected mammalian cell population
Authors: Porosk Ly , Nebogatova Jekaterina , Härk Heleri Heike , Vunk Birgit , Arukuusk Piret , Toots Urve , Ustav Mart , Langel Ülo , Kurrikoff Kaido 
Published: March 2022

AbstractTherapeutic proteins are currently at the hotspot of innovation in the pharmaceutical medicine. However, their industrial production is technically challenging and improved methods for transcriptional manipulation of mammalian industrial cell cultures are needed. In this work we show that some of the most frequently used lab scale transfection efficacy assays fail to predict performance in the protein production settings. We compare the efficacies of a number of transfection reagents using adherent and suspension mammalian cell cultures and assessment based on several assays that utilize reporter protein quantitation, transfected cell population and post-transfection viability of cells. We validate reporter assays for assessing transfection methods in the lab that predict protein production in industrial settings. We also demonstrate that cell penetrating peptide-based transfection achieve significantly higher protein yields compared to PEI and lipoplex methods in both CHO and HEK293 producer cell lines. Availability of fast lab scale screening methods allows future development of improved transfection methods for protein production. One such potentially effective transient transfection method is the CPP-based approach presented currently.
Targeting A-Kinase Anchoring Protein 12 Phosphorylation in Hepatic Stellate Cells Regulates Liver Injury and Fibrosis in Mouse Models
Authors: Ramani Komal , Mavila Nirmala , Abeynayake Aushinie , Tomasi Maria Lauda , Wang Jiaohong , Matsuda Mitchitaka , Seki Ekihiro 
Published: March 2022

AbstractTrans-differentiation of hepatic stellate cells (HSCs) to activated state potentiates liver fibrosis through release of extracellular matrix (ECM) components, distorting the liver architecture. Since limited antifibrotics are available, pharmacological intervention targeting activated HSCs may be considered for therapy. A-kinase anchoring protein 12 (AKAP12) is a scaffolding protein that directs protein kinases A/C (PKA/PKC) and cyclins to specific locations spatiotemporally controlling their biological effects. It has been shown that AKAP12’s scaffolding functions are altered by phosphorylation. In previously published work, observed an association between AKAP12 phosphorylation and HSC activation. In this work we demonstrate that AKAP12’s scaffolding activity towards the endoplasmic reticulum (ER)-resident collagen chaperone, heat-shock protein 47 (HSP47) is strongly inhibited by AKAP12’s site-specific phosphorylation in activated HSCs. CRISPR-directed gene editing of AKAP12’s phospho- sites restores its scaffolding towards HSP47, inhibiting HSP47’s collagen maturation functions and HSC activation. AKAP12 phospho-editing dramatically inhibits fibrosis, ER stress response, HSC inflammatory signaling and liver injury in mice. Our overall findings suggest a pro-fibrogenic role of AKAP12 phosphorylation that may be targeted for therapeutic intervention in liver fibrosis.