bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hidden potential of the supporting scaffold as a structural module for plant cystatin design
Authors: Tremblay Jonathan , Goulet Marie-Claire , Goulet Charles , Michaud Dominique 
Published: March 2022

AbstractProtein engineering approaches have been proposed to improve the inhibitory properties of plant cystatins towards herbivorous pest digestive Cys proteases, typically involving sequence alterations in the inhibitory loops and/or N-terminal trunk of the protein interacting with specific amino acid residues of the target protease. In this study, we assessed whether the loops-supporting frame, or scaffold, would represent a valuable structural module for cystatin function improvement. Twenty hybrid cystatins were designed in silico, consisting of the N-terminal trunk and two inhibitory loops of a given donor cystatin grafted onto the scaffold of an alternative, recipient cystatin. Synthetic genes for the hybrids were expressed in E. coli, and the resulting proteins assessed for their potency to inhibit model Cys protease papain and the digestive Cys proteases of Colorado potato beetle (Leptinotarsa decemlineata) used as an insect pest model. In line with the occurrence of positively selected amino acids presumably influencing inhibitory activity in the scaffold region of plant cystatins, grafting the N-terminal trunk and inhibitory loops of a given cystatin onto the scaffold of an alternative cystatin generally had an effect on the inhibitory potency of these function-related elements against Cys proteases. For instance, hybrid cystatins including the three structural elements of model tomato cystatin SlCYS8 grafted on the scaffold of cystatins from other plant families showed Ki values altered by up to 3-fold for papain, and inhibitory efficiencies increased by up to 8-fold against L. decemlineata cathepsin L-like proteases, compared to wild-type SlCYS8 bearing the original scaffold. Our data point to a significant influence of the cystatin scaffold on the inhibitory activity of the N-terminal trunk and protease inhibitory loops. They also suggest the potential of this structural element as a module for plant cystatin design to generate functional variability against Cys proteases, including the digestive proteases of herbivorous pests.
Assessment of dynamics of global DNA methylation during the cryopreservation process of Pinus pinaster embryogenic lines
Authors: Mendoza-Poudereux Isabel , Cano María , Solís María Teresa , Esteve-Díaz Francisco , Testillano Pilar S. , Segura Juan , Sales Ester , Arrillaga Isabel 
Published: March 2022

AbstractLong-term in vitro maintenance of embryogenic lines of Pinus species has been associated with lower maturation capacity, because of this, cryopreservation protocols for the embryogenic lines are needed to maintain valuable genotypes. Since cryopreservation may induce epigenetic variations, we evaluate changes in DNA methylation levels through the course of the cryopreservation of maritime pine embryogenic lines, as compared to those lines maintained by repeated subcultures. Six maritime pine embryogenic lines were cryopreserved following a protocol that includes pre-treatments inducing osmotic stress in liquid media. The percentage of methylated cytosines (%5-mC) in total DNA was determined by using a colorimetric assay. Reactive oxygen species (ROS) accumulation in cell lines was also determined by quantifying dihydroethidium (DHE) fluorescence under a confocal laser-scanning microscope. In the first experiment, we found that global DNA methylation was significantly reduced during the cryopreservation protocol. Subsequently, we evaluated the methylation status of both cryopreserved and no cryopreserved lines (maintained by subcultures) and found differences among embryogenic lines but overall, cryopreservation did not alter %5-mC of the recovered lines while periodical subcultures increased methylation rates. In addition, maltose pretreatment did not increase significantly ROS production in embryogenic lines. Our results demonstrate that the genetic stability during cryopreservation highly depends on the embryogenic line studied, but the protocol allows maintaining methylation DNA rates in most of the recovered lines.
Development of Dry Powder Formulations of AS01Bcontaining vaccines using Thin-Film Freeze-Drying
Authors: AboulFotouh Khaled , Xu Haiyue , Williams Robert O. , Cui Zhengrong 
Published: March 2022

AbstractAS01Bis a liposomal formulation of two immunostimulants namely 3-O-desacyl-4’-monophosphoryl lipid A (MPL) and QS-21. The liposomal formulation of AS01Breduces the endotoxicity of MPL and the lytic activity of QS-21; however, it renders the adjuvant sensitive to accidental slow freezing. The liposomal formulation also represents a major challenge towards the formulation of dry powders of vaccines containing AS01B. In the present study, we tested the feasibility of applying thin-film freeze-drying (TFFD) to engineer dry powders of the AS01Bliposomal adjuvant alone or vaccines containing AS01Bas an adjuvant. Initially, we showed that after the AS01Bliposomal adjuvant was subjected to TFFD using sucrose as a stabilizer at 4%w/v, the particle size distribution of AS01Bliposomes reconstituted from the dry powder was identical to the liquid adjuvant before drying. We then showed using ovalbumin (OVA) as a model antigen adjuvanted with AS01B(AS01B/OVA) that subjecting the AS01B/OVA vaccine to TFFD and subsequent reconstitution did not negatively affect the AS01Bliposome integrity, nor the immunogenicity of the vaccine. Importantly, the thin-film freeze-dried vaccine was not sensitive to repeated freezing-and-thawing. Finally, the feasibility of using TFFD to prepare dry powders of AS01B-adjuvanted vaccines was further confirmed using AS01B-adjuvanted Fluzone Quadrivalent and Shingrix, which contains AS01B. It is concluded that the TFFD technology can enable the formulation of AS01B-adjuvanted vaccines as freezing-insensitive dry powders in single-vial presentation.
Blood-brain barrier permeability to enrofloxacin in Pengze crucian carp (Carassius auratus var. Pengze)
Authors: Zhang Fan , Wang Runping , Huang Jianzhen , Zhang Haixin , Wang Long , Zhong Zhiwei , Ruan Jiming , Liu Huazhong 
Published: March 2022

AbstractTo explore the permeability of blood-brain barrier (BBB) to enrofloxacin (ENR) and the role of brain injury markers in the evaluation of brain damage, crucian carp (Carassius auratus var. Pengze) was employed in this work as the research object treated by a single oral administration of the antibiotic. Results showed that ENR residues could be detected in brain of crucian carp exposed to both half lethal dose (LD50) and safe dose (SD) of ENR throughout the trial period, indicating that ENR had an ability of permeating the BBB of crucian carp. Evans blue (EB) dispersively distributed in brain tissue of fish exposed to SD ENR, but not in the vehicle-treated fish brain, which suggested structural failure of BBB by ENR. Expression levels of BBB-related molecules, occludin and P-glycoprotein (P-gp), were significantly down-regulated by ENR. Brain injury markers, NSE, S100B and GFAP were improved that were demonstrated by elevated contents of proteins in brain and serum. According to the data of correlation analysis, it was observed that ENR residue was closely related to S100B and GFAP, indicating that S100B and GFAP could be used as evaluation indicators for brain injury of crucian carp. All findings mentioned above suggest that ENR may cause structural change of BBB, resulting in biological brain damage in crucian carp.
Acinetobase: the comprehensive database and repository of Acinetobacter strains
Authors: Valcek Adam , Collier James , Botzki Alexander , Van der Henst Charles 
Published: March 2022

AbstractBackgroundAcinetobacter baumannii is one of the most problematic nosocomial pathogens that can efficiently thrive within hospital settings, mainly due to resistances towards antibiotics, desiccation, disinfectants, human serum and oxidative stress. Recently, increased resistance against last resort antibiotics earns this bacterium the highest priority concern classified by the CDC and the WHO. An obvious hallmark of this bacterium is the high heterogeneity observed amongst A. baumannii isolates, with a limited core genome. This feature complexifies the study of A. baumannii bacteria as an entity, subsequently reflected in a diversity of phenotypes of not only antimicrobial and environmental resistance but also virulence.Main bodyHigh degree of genome plasticity, along with the use of a limited subset of established reference strains, can lead to strain-specific observations, decreasing the global understanding of this pathogenic agent. Phenotypic variability of A. baumannii strains is easily observable such as with the macrocolony morphologies, in vitro and in vivo virulence, natural competence level, production of different capsular polysaccharide structures and cellular densities. Some strains encode an extensive amount of virulence factors while other, including the reference strains, lack several key ones. The lack/excess of genes or specific physiological processes might interfere with in vivo and in vitro experiments, thus providing limited impact on the global understanding of Acinetobacter bacteria as a whole.ConclusionAs an answer to the high heterogeneity amongst A. baumannii strains, we propose a first comprehensive database that includes the bacterial strains and the associated phenotypic and genetic data. This new repository, freely accessible to the entire scientific community, allow selecting the best bacterial isolate(s) related to any biological question, using an efficient and fast exchange platform.
The nuclear receptor NR4A1 restrains neutrophil granulocyte mediated brain damage in cerebral ischemia
Authors: Strecker Jan-Kolja , Liebmann Marie , Revenstorff Julian , Beuker Carolin , Schmidt-Pogoda Antje , Hucke Stephanie , Vogl Thomas , Roth Johannes , Thomas Christian , Kuhlmann Tanja , Wiendl Heinz , Klotz Luisa , Minnerup Jens 
Published: March 2022

AbstractImmigration and activation of immune cells play a significant role in damage progression after ischemic stroke. It has been shown that the nuclear receptor NR4A1 exerts a crucial role within the inflammatory response of various immune diseases via regulating immune cell activation. In this study, we investigated the role of NR4A1 on the activation and recruitment of brain resident and peripheral immune cells after cerebral ischemia. Here, we show that NR4A1 mediates an anti-inflammatory and damage limiting effect after ischemic stroke through immigrating neutrophil granulocytes. Importantly, NR4A1-activation with its ligand Cytosporone-B improves functional outcome and diminishes brain damage. Therefore, modulation of NR4A1 is a promising therapeutic target in the treatment of stroke.
Mettl3-mediated m6A modification of Fgf16 restricts cardiomyocyte proliferation during heart regeneration
Authors: Jiang Fu-Qing , Chen Jia-Xuan , Chen Wu-Yun , Zhao Wan-Ling , Song Guo-Hua , Liang Chi-Qian , Zhou Yi-Min , Huang Huan-Lei , Huang Rui-Jin , Zhao Hui , Park Kyu-Sang , Ju Zhen-Yu , Cai Dong-Qing , Qi Xu-Feng 
Published: March 2022

AbstractCardiovascular disease is the leading cause of death worldwide due to the inability of adult heart to regenerate after injury. N6-methyladenosine (m6A) methylation catalyzed by the enzyme methyltransferase-like 3 (Mettl3) plays important roles in various physiological and pathological bioprocesses. However, the role of m6A in heart regeneration remains largely unclear. To study m6A function in heart regeneration, we modulated Mettl3 expression in vitro and in vivo. Knockdown of Mettl3 significantly increased the proliferation of cardiomyocytes and accelerated heart regeneration following heart injury in neonatal and adult mice. However, Mettl3 overexpression decreased cardiomyocyte proliferation and suppressed heart regeneration in postnatal mice. Conjoint analysis of methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA-seq identified Fgf16 as a downstream target of Mettl3-mediated m6A modification during postnatal heart regeneration. RIP-qPCR and luciferase reporter assays revealed that Mettl3 negatively regulates Fgf16 mRNA expression in an m6A-Ythdf2-dependent manner. The silencing of Fgf16 suppressed the proliferation of cardiomyocytes. However, the overexpression of ΔFgf16, in which the m6A consensus sequence was mutated, significantly increased cardiomyocyte proliferation and accelerated heart regeneration in postnatal mice compared with wild-type Fgf16. Our data demonstrate that Mettl3 post-transcriptionally reduces Fgf16 mRNA levels through an m6A-Ythdf2-dependen pathway, thereby controlling cardiomyocyte proliferation and heart regeneration.
A clinically annotated post-mortem approach to study multi-organ somatic mutational clonality in histologically healthy tissues
Authors: Luijts Tom , Elliott Kerryn , Siaw Joachim T. , Van de Velde Joris , Beyls Elien , Claeys Arne , Lammens Tim , Larsson Erik , Willaert Wouter , Vral Anne , Van den Eynden Jimmy 
Published: March 2022

AbstractRecent research on histologically healthy human tissues identified omnipresent mutational microclones, driven by somatic mutations known to be responsible for carcinogenesis (e.g., in TP53 or NOTCH1). These new insights are fundamentally changing current tumour evolution models, with broad oncological implications. Most studies are based on surgical remnant tissues, which are not available for many organs and rarely in a pan-organ setting (multiple organs from the same individual). Here, we describe an approach based on clinically annotated post-mortem tissues, derived from whole-body donors that are routinely used for educational purposes at human anatomy units. We validated this post-mortem approach using UV-exposed and unexposed epidermal skin tissues and confirm the presence of positively selected NOTCH1/2-, TP53- and FAT1-driven clones. No selection signals were detected in a set of immune genes or housekeeping genes. Additionally, we provide the first evidence for smoking-induced clonal changes in oral epithelia, likely underlying the origin of head and neck carcinogenesis. In conclusion, the whole-body donor-based approach provides a nearly unlimited healthy tissue resource to study mutational clonality and gain fundamental mutagenic insights in the presumed earliest stages of tumour evolution.
microRNA-1 represses signaling pathway components to impact embryonic structures derived from all three germ layers
Authors: Sampilo Nina Faye , Song Jia L. 
Published: March 2022

AbstractmicroRNAs are evolutionarily conserved non-coding RNAs that direct post-transcriptional regulation of target transcripts. We use the sea urchin embryo to achieve a comprehensive understanding of miR-1’s function in a developing embryo. Results indicate that miR-1 regulates gut contractions, specification, and positioning of serotonergic neurons, as well as mesodermally-derived muscles, pigment cells, and skeletogenic cells. Gain-of-function of miR-1 generally leads to more severe developmental defects than its loss-of-function. We identified that miR-1 directly suppresses Ets1/2, Tbr, and VegfR7 of the skeletogenic gene regulatory network, and Notch, Nodal, and Wnt1 signaling components. We found that miR-1’s direct suppression of Nodal may indirectly regulate FoxQ2 to impact serotonergic neurons. Excess miR-1 may lead to decreased Nodal and Notch that result in decreased circumpharnygeal muscle fibers and the number of pigment cells. The striking ectopic skeletal branching induced by miR-1 mimic injections may be explained by miR-1’s direct suppression of Nodal that leads to expression changes of Vegf3, and Fgfa that mediate skeletogenesis. This work demonstrates that miR-1 plays a diverse regulatory role that impacts tissues derived from all germ layers.Summary statementThis study identifies wide-ranging regulatory roles and regulatory mechanisms of miR-1 that impact structures derived from all three germ layers during embryonic development.
Greenscreen decreases Type I Errors and increases true peak detection in genomic datasets including ChIP-seq
Authors: Klasfeld Sammy , Wagner Doris 
Published: March 2022

AbstractChromatin immunoprecipitation followed by sequencing (ChIP-seq) is used widely to identify both factor binding to genomic DNA and chromatin modifications. Analysis of ChIP-seq data is impacted by regions of the genome which generate ultra-high artifactual signals. To remove these signals from ChIP-seq data, ENCODE developed blacklists, comprehensive sets of regions defined by low mappability and ultra-high signals for human, mouse, worm, and flies. Currently, blacklists are not available for many model and non-model species. Here we describe an alternative approach for removing false-positive peaks we called “greenscreen”. Greenscreen is facile to implement, requires few input samples, and uses analysis tools frequently employed for ChIP-seq. We show that greenscreen removes artifact signal as effectively as blacklists in Arabidopsis and human ChIP-seq datasets while covering less of the genome, dramatically improving ChIP-seq data quality. Greenscreen filtering reveals true factor binding overlap and of occupancy changes in different genetic backgrounds or tissues. Because it is effective with as few as three inputs, greenscreen is readily adaptable for use in any species or genome build. Although developed for ChIP-seq, greenscreen also identifies artifact signals from other genomic datasets including CUT&RUN. Finally, we present an improved ChIP-seq pipeline which incorporates greenscreen, that detects more true peaks than published methods.One Sentence SummaryA facile method for removing artifact signal from ChIP-seq that improves downstream analyses
BayesRB: a markov chain Monte Carlo-based polygenic genetic risk score algorithm for dichotomous traits
Authors: Shan Ying , Weeks Daniel E. 
Published: March 2022

AbstractIdentifying high-risk individuals with diseases through reliable prediction models guides screening and preventive treatment. Most complex diseases have a genetic basis influenced by multiple genes and so disease risk can be estimated using polygenic risk score (PRS) algorithms. Many PRS algorithms have been developed so far. Among them, BayesR shows good characteristics of unbiasedness, accuracy, sparseness, and robustness. It detects the associated SNPs, estimates the SNP effects, and makes prediction of disease risks based on all SNPs simultaneously. However, this method assumes that the phenotypes follow a Gaussian distribution, which cannot be met in case-control studies. Here, we made an extension of the BayesR method, called BayesRB, by adding auxiliary variables to the BayesR model. We explored the characteristics, efficacy, and accuracy of BayesRB when estimating SNP effects and predicting disease risks compared with three traditional algorithms under different conditions using both simulated data and real data from the Welcome Trust Case Control Consortium (WTCCC). For SNP effect estimation, BayesRB shows unbiasedness and sparseness for big and small effect SNPs, respectively. For disease risk prediction, BayesRB had the best performance among the methods. This study provides a theoretical basis for complex disease risk prediction and disease prevention
An Alzheimer’s disease pathway uncovered by functional omics: the risk gene CELF1 regulates KLC1 splice variant E expression, which drives Aβ pathology
Authors: Kikuchi Masataka , Viet Justine , Nagata Kenichi , Sato Masahiro , David Géraldine , Audic Yann , Silverman Michael A. , Yamamoto Mitsuko , Akatsu Hiroyasu , Hashizume Yoshio , Chiba Kyoko , Takeda Shuko , Akamine Shoshin , Miyamoto Tesshin , Uozumi Ryota , Gotoh Shiho , Mori Kohji , Ikeda Manabu , Paillard Luc , Morihara Takashi 
Published: March 2022

AbstractIn an era when numerous disease-associated genes have been identified, determining the molecular mechanisms of complex diseases is still difficult. The CELF1 region was identified by genome-wide association studies as an Alzheimer’s disease (AD) risk locus. Using transcriptomics and cross-linking and immunoprecipitation sequencing (CLIP-seq), we found that CELF1, an RNA-binding protein, binds to KLC1 RNA and regulates its splicing. Analysis of two brain banks revealed that CELF1 expression is correlated with inclusion of KLC1 exons downstream of the CELF1-binding region identified by CLIP-seq. In AD, low CELF1 levels result in high levels of KLC1 splice variant E (KLC1_vE), an amyloid-β (Aβ) pathology-driving gene product. Cell culture experiments confirmed regulation of KLC1_vE by CELF1. Analysis of mouse strains with different propensities for Aβ accumulation confirmed that Klc1_vE drives Aβ pathology. Using omics methods, we revealedthe molecular pathway of a complex disease supported by human and mouse genetics.
Seroincidence of Enteric Fever in Juba, South Sudan
Authors: Aiemjoy Kristen , Rumunu John , Hassen Juma John , Wiens Kirsten E. , Garrett Denise , Kamenskaya Polina , Harris Jason B. , Azman Andrew S. , Teunis Peter , Seidman Jessica , Wamala Joseph F. , Andrews Jason R. , Charles Richelle C. 
Published: March 2022

ABSTRACTWe apply a new serosurveillance tool to estimate typhoidal Salmonella burden from dried blood spots in Juba, South Sudan, finding a seroincidence rate of 35 per 100 person-years and cumulative incidence of 78% over four years.
Risk Factors and Pivotal Periods: Marital Status over 28 Years for Parents of Individuals with Autism
Authors: Bahri Niki , Sterrett Kyle , Lord Catherine 
Published: March 2022

AbstractLongitudinal, prospective analyses of marital status in parents of individuals with autism are needed. We describe the timing of divorce, and the factors that contribute to divorce in a longitudinal sample of families of individuals with autism. Participants included parents of 219 children, initially referred for autism and other developmental delays, followed to age 30 years. Approximately 36% of individuals with autism in our sample experienced a parental divorce by age 30. Higher rates of divorce were associated with maternal education, race and age at child’s birth, as well as autism symptom severity and diagnosis. Divorces were most common in early years (under age 5) and also in the teenage years and beyond (over age 15). After age 15, higher risk was associated with higher cognitive ability and daily living skills, and being a multiplex family. Results suggest that divorce risk in families of children with autism remains high through childhood into early adulthood. Understanding factors related to changes in marital status may help us better support families across time.