bluuebunny/crossref_metadata_2025_split huggingface dataset:
Utilizing Evolutionary Conservation to Detect Deleterious Mutations and Improve Genomic Prediction in Cassava
Authors: Long Evan M , Romay M. Cinta , Buckler Edward S. , Robbins Kelly R 
Published: September 2022

AbstractCassava (Manihot esculenta) is an annual root crop which provides the major source of calories for over half a billion people around the world. Since its domestication ∼10,000 years ago, cassava has been largely clonally propagated through stem cuttings. Minimal sexual recombination has led to an accumulation of deleterious mutations made evident by heavy inbreeding depression. To locate and characterize these deleterious mutations, and to measure selection pressure across the cassava genome, we aligned 52 related Euphorbiaceae and other related species representing millions of years of evolution. With single base-pair resolution of genetic conservation, we used protein structure models, amino acid impact, and evolutionary conservation across the Euphorbiaceae to estimate evolutionary constraint. With known deleterious mutations, we aimed to improve genomic evaluations of plant performance through genomic prediction. We first tested this hypothesis through simulation utilizing multi-kernel GBLUP to predict simulated phenotypes across separate populations of cassava. Simulations showed a sizable increase of prediction accuracy when incorporating functional variants in the model when the trait was determined by <100 quantitative trait loci (QTL). Utilizing deleterious mutations and functional weights informed through evolutionary conservation, we saw improvements in genomic prediction accuracy that were dependent on trait and prediction. We showed the potential for using evolutionary information to track functional variation across the genome, in order to improve whole genome trait prediction. We anticipate that continued work to improve genotype accuracy and deleterious mutation assessment will lead to improved genomic assessments of cassava clones.
A Coarse-Grained Molecular Dynamics Investigation on Spontaneous Binding of Aβ1-40Fibrils with Cholesterol-mixed DPPC Bilayers
Authors: Agrawal Nikhil , Skelton Adam A , Parisini Emilio 
Published: September 2022

AbstractAlzheimer’s disease is the most common form of dementia. Its aetiology is characterized by the misfolding and aggregation of amyloid-β (Aβ) peptides into β-sheet-rich Aβ oligomers/fibrils. Whereas experimental studies have suggested that Aβ oligomers/fibrils interact with the cell membranes and perturb their structures and dynamics, the molecular mechanism of this interaction is still not fully understood. In the present work, we have performed a total of 120 μs-long simulations to investigate the interaction between trimeric or hexameric Aβ1-40fibrils with either a 100% DPPC bilayer, a 70% DPPC-30% cholesterol bilayer or a 50% DPPC-50 % cholesterol bilayer. Our simulation data capture the spontaneous binding of the aqueous Aβ1-40fibrils with the membranes and show that the central hydrophobic amino acid cluster, the lysine residue adjacent to it and the C-terminal hydrophobic residues are all involved in the process. Moreover, our data show that while the Aβ1-40fibril does not bind to the 100% DPPC bilayer, its binding affinity for the membrane increases with the amount of cholesterol. Overall, our data suggest that two clusters of hydrophobic residues and one lysine help Aβ1-40fibrils establish stable interactions with a cholesterol-rich DPPC bilayer. These residues are likely to represent potential target regions for the design of inhibitors, thus opening new avenues in structure-based drug design against Aβ oligomer/fibril-membrane interaction.
Structural variation and eQTL analysis in two experimental populations of chickens divergently selected for feather pecking behavior
Authors: Falker-Gieske Clemens , Bennewitz Jörn , Tetens Jens 
Published: September 2022

AbstractFeather pecking (FP) is a damaging non-aggressive behavior in laying hens with a heritable component. Its occurrence has been linked to the immune system, the circadian clock, and foraging behavior. Furthermore, dysregulation of miRNA biogenesis, disturbance of the gamma-aminobutyric acid (GABAergic) system, as well as neurodevelopmental deficiencies are currently under debate as factors influencing the propensity for FP behavior. Past studies, which focused on the dissection of the genetic factors involved in FP, relied on single nucleotide polymorphisms (SNPs) and short insertions and deletions < 50 bp (InDels). These variant classes only represent a certain fraction of the genetic variation of an organism. Hence, we re-analyzed whole genome sequencing data from two experimental populations, which have been divergently selected for FP behavior for over more than 15 generations, and performed variant calling for structural variants (SVs) as well as tandem repeats (TRs) and jointly analyzed the data with SNPs and InDels. Genotype imputation and subsequent genome-wide association studies in combination with expression quantitative trait loci analysis led to the discovery of multiple variants influencing the GABAergic system. These include a significantly associated TR downstream of the GABA receptor subunit beta-3 (GABRB3) gene, two micro RNAs targeting several GABA receptor genes, and dystrophin (DMD), a direct regulator of GABA receptor clustering. Furthermore, we found the transcription factor ETV1 to be associated with differential expression of 23 genes, which points towards a role of ETV1, together with SMAD4 and KLF14, in the disturbed neurodevelopment of high feather pecking chickens.
Leishmania mexicana Centrin Knock out Parasites Promote M1-polarizing Metabolic Changes
Authors: Volpedo Greta , Oljuskin Timur , Azodi Nazli , Hamano Shinjiro , Matlashewski Greg , Gannavaram Sreenivas , Nakhasi Hira L. , Satoskar Abhay R. 
Published: September 2022

ABSTRACTLeishmaniasis is a tropical disease present in more than 90 countries. Presently, there is no approved vaccine for human use. We have previously developed live attenuated L. mexicana Cen−/− (LmexCen−/−) as a vaccine candidate that showed excellent efficacy that was characterized by reduced activation of Th2 responses and enhanced Th1 responses, contrary to wild type L. mexicana (LmexWT) infection. Towards understanding the interplay between immune mechanisms of protection and metabolic reprogramming, we applied untargeted mass spectrometric analysis to LmexCen−/− and compared them with LmexWT infection. Data showed that enriched pentose phosphate pathway (PPP) in ears immunized with LmexCen−/− parasites, compared to naïve and LmexWT-infected ears. This pathway is known to promote an M1 phenotype in macrophages, suggesting a switch to a pro-inflammatory phenotype following LmexCen−/− inoculation. Accordingly, inhibition of the PPP in macrophages cultured with LmexCen−/− parasites led to diminished production of nitric oxide, IL-12, and IL-1β, hallmarks of classical activation. Overall, our study revealed novel immune regulatory mechanisms that may be critical for the induction of protective immunity.
Formation of the active Hermes transpososome is driven by asymmetric DNA binding of BED domains
Authors: Lannes Laurie , Furman Christopher M. , Hickman Alison B. , Dyda Fred 
Published: September 2022

AbstractThe cut-and-paste Hermes DNA transposase stands out among the transposases that have been biochemically or structurally characterized so far. Many transposases function as dimers, but the Hermes transposase forms a tetramer of dimers to achieve its active form in vivo. Intriguingly, the transposition complex, or transpososome, relies on only one dimer to perform the enzymatic reactions necessary to the mobilization of its transposon. Our investigation combining biochemical and structural approaches shows that the Hermes octamer extensively interacts with its transposon left-end (LE) engaging the BED domains of three Hermes protomers belonging to three dimers. By contrast, the right-end (RE) is entirely deprived of such interaction inside the transpososome. Our work suggests that formation of the Hermes synaptic complex is sequential and relies on the considerable difference of affinity of the transposase towards its transposon ends. Thus, we propose that Hermes dimers multimerize to gather enough BED domains to find the LE among the abundant genomic DNA, facilitating the subsequent interaction with the RE, most likely solely based on recognition of its terminal inverted repeat.
Pathway elucidation and microbial synthesis of proaporphine and bis-benzylisoquinoline alkaloids from sacred lotus (Nelumbo nucifera)
Authors: Pyne Michael E. , Gold Nicholas D. , Martin Vincent J. J. 
Published: September 2022

ABSTRACTSacred lotus (Nelumbo nucifera) has been utilized as a food, medicine, and spiritual symbol for nearly 3,000 years. The medicinal properties of lotus are largely attributed to its unique profile of benzylisoquinoline alkaloids (BIAs), which includes potential anti-cancer, anti-malarial and anti-arrhythmic compounds. BIA biosynthesis in sacred lotus differs markedly from that of opium poppy and other members of the Ranunculales, most notably in an abundance of BIAs possessing the (R)-stereochemical configuration and the absence of reticuline, a major branchpoint intermediate in most BIA producers. Owing to these unique metabolic features and the pharmacological potential of lotus, we set out to elucidate the BIA biosynthesis network inN. nucifera. Here we show that lotus CYP80G (NnCYP80G) and a superior ortholog from Peruvian nutmeg (Laurelia sempervirens;LsCYP80G) stereospecifically convert (R)-N-methylcoclaurine to the proaporphine alkaloid glaziovine, which is subsequently methylated to pronuciferine, the presumed precursor to nuciferine. While sacred lotus employs a dedicated (R)-route to aporphine alkaloids from (R)-norcoclaurine, we implemented an artificial stereochemical inversion approach to flip the stereochemistry of the core BIA pathway. Exploiting the unique substrate specificity of dehydroreticuline synthase from common poppy (Papaver rhoeas) and pairing it with dehydroreticuline reductase enabledde novosynthesis of (R)-N-methylcoclaurine from (S)- norcoclaurine and its subsequent conversion to pronuciferine. We leveraged our stereochemical inversion approach to also elucidate the role ofNnCYP80A in sacred lotus metabolism, which we show catalyzes the stereospecific formation of the bis-BIA nelumboferine. Screening our collection of 66 plantO-methyltransferases enabled conversion of nelumboferine to liensinine, a potential anti-cancer bis-BIA from sacred lotus. Our work highlights the unique benzylisoquinoline metabolism ofN. nuciferaand enables the targeted overproduction of potential lotus pharmaceuticals using engineered microbial systems.
Factors associated with misdiagnosis of hospitalised patients in general hospitals of Central Uganda
Authors: Katongole Simon Peter , Akweongo Patricia , Anguyo DDMO Robert , Kasozi Daniel Evans , Adoma Afari Augustine 
Published: September 2022

AbstractMisdiagnosis of inpatients is a major public health issue whose scope and causes are unknown in Sub-Saharan African countries. The purpose of this cross-sectional study, which was conducted in five hospitals in central Uganda, was to identify the factors associated with inpatient misdiagnosis in general hospitals in Central Uganda. Records of 2,431 patients admitted between July 1st, 2019 and June 30th, 2020 were specifically reviewed to obtain data on variables thought to be associated with misdiagnosis. The admission diagnosis assigned at the emergency or outpatient department was compared to the discharge diagnosis assigned immediately after the patient’s admission, with any difference considered a misdiagnosis. The disease, patient, health system, and environmental factors associated with misdiagnosis were identified using multivariable logistic regression analysis.Misdiagnosis was found in the records of 223/2431 (9.2%) of the admitted patients. A patient admitted to Nakaseke hospital [aOR=1.95, 95% CI=1.17-3.25, p=0.01], being admitted at night [aOR=3, 95% CI=1.81-5.02, p0.01], male patient [aOR=1.89, 95% CI=1.35-2.64, p0.01], patient’s age groups 10-19 [AOR=2.3, 95% CI=2.3-9.25, p0.01]; 20-29 [AOR=8.15, 95% CI=4.18-15.89], p<0.01; 30-39; and 40-49;; AOR=8.12, 95% CI=3.99-16.54, p<0.01; AOR=7.88, 95% CI=3.71-16.73, p<0.01; and AOR=12.14, 95% CI=6.41-23.01, p<0.0]. Misdiagnosis was also associated with multimorbidity (aOR=4.71, 95% CI=1.91-11.65, p0.01) and patients treated for uncommon diseases (aOR=2.57, 95% CI=1.28-5.18, p0.01). Patients without underlying diseases [aOR=0.63; 95% CI=0.43-0.91, p=0.015] and those who were not referred [aOR=0.51; 95% CI=0.31-0.86, p=0] .011] were less likely to be related to misdiagnosis.To improve diagnostic accuracy, hospitals should reorganize patient admission processes, conducted targeted training, develop policy or guidelines targeting factors predisposing to misdiagnosis, and the adopt a diagnostic error prevention culture.
An updated evolutionary and structural study of TBK1 reveals highly conserved motifs as potential pharmacological targets in neurodegenerative diseases
Authors: Papageorgiou Louis , Mangana Eleni , Papakonstantinou Eleni , Diakou Io , Pierouli Katerina , Dragoumani Konstantina , Bacopoulou Flora , Chrousos George P , Exarchos Themis P , Vlamos Panagiotis , Eliopoulos Elias , Vlachakis Dimitrios 
Published: September 2022

AbstractTANK binding kinase 1 protein (TBK1) is a kinase that belongs to the IκB (IKK) family. TBK1, also known as T2K, FTDALS4, NAK, IIAE8 and NF-κB, is responsible for the phosphorylation of the amino acid residues Serine and Threonine. This enzyme is involved in various key biological processes, including interferon activation and production, homeostasis, cell growth, autophagy, insulin production and the regulation of TNF-α, IFN-β and IL-6. Mutations in the TBK1 gene alter the protein’s normal function and may lead to an array of pathological conditions, including disorders of the Central Nervous System. The present study sought to elucidate the role of the TBK1 protein in Amyotrophic Lateral Sclerosis (ALS), a human neurodegenerative disorder. A broad evolutionary and phylogenetic analysis of TBK1 was performed across numerous organisms to distinguish conserved regions important for the protein’s function. Subsequently, mutations and SNPs were explored and their potential effect on the enzyme’s function was investigated. These analytical steps, in combination with the study of the secondary, tertiary, and quaternary structure of TBK1, enabled the identification of conserved motifs, which can function as novel pharmacological targets and inform therapeutic strategies for Amyotrophic Lateral Sclerosis.
A genomic study of the Japanese population focusing on the glucocorticoid receptor interactome highlights distinct genetic characteristics associated with stress response
Authors: Mitsis Thanasis , Papageorgiou Louis , Papakonstantinou Eleni , Diakou Io , Pierouli Katerina , Dragoumani Konstantina , Bacopoulou Flora , Kino Tomoshige , Chrousos George P , Eliopoulos Elias , Vlachakis Dimitrios 
Published: September 2022

AbstractAll living organisms have been programmed to maintain a complex inner equilibrium called homeostasis, despite numerous adversities during their lifespan. Any threatening or perceived as such stimuli for homeostasis is termed a stressor, and a highly conserved response system called the stress response system has been developed to cope with these stimuli and maintain or reinstate homeostasis. The glucocorticoid receptor, a transcription factor belonging to the nuclear receptors protein superfamily, has a major role in the stress response system, and research on its’ interactome may provide novel information regarding the mechanisms underlying homeostasis maintenance. A list of 149 autosomal genes which have an essential role in GR function or are prime examples of GRE-containing genes was composed in order to gain a comprehensive view of the GR interactome. A search for SNPs on those particular genes was conducted on a dataset of 3.554 Japanese individuals, with mentioned polymorphisms being annotated with relevant information from the ClinVar, LitVar, and dbSNP databases. Forty-two SNPs of interest and their genomic locations were identified. These SNPs have been associated with drug metabolism and neuropsychiatric, metabolic, and immune system disorders, while most of them were located in intronic regions. The frequencies of those SNPs were later compared with a dataset consisting of 1465 Korean individuals in order to find population-specific characteristics based on some of the identified SNPs of interest. The results highlighted that rs1043618 frequencies were different in the two populations, with mentioned polymorphism having a potential role in chronic obstructive pulmonary disease in response to environmental stressors. This SNP is located in the HSPA1A gene which codes for an essential GR co-chaperone, and such information showcases that similar gene may be novel genomic targets for managing or combatting stress-related pathologies.
Rnf20 shapes the endothelial control of heart morphogenesis and function
Authors: Kessler Linda , Gao Rui , Tetik-Elsherbiny Nalan , Lityagina Olga , Zhailauova Azhar , Ren Yonggang , Trogisch Felix A. , Cordero Julio , Dou Yanliang , Wang Yinuo , Chichelnitskiy Evgeny , Kraske Joscha Alexander , Schäfer Patricia Laura , Wu Chi-Chung , Barreto Guillermo , Potente Michael , Wieland Thomas , Ola Roxana , Heineke Joerg , Dobreva Gergana 
Published: September 2022

SummaryDuring embryogenesis, distinct cardiac cell types form, which shape the structural and functional properties of the heart. How their activity is coordinated is largely unknown. Here we show that Rnf20 is a multifaceted regulator of cardiac morphogenesis and function. On the one hand, Rnf20 controls extracellular matrix dynamics and endothelial-cardiomyocyte crosstalk essential for second heart field development. On the other hand, it safeguards endothelial cell identity and function by maintaining physiological angiocrine signaling and preventing endothelial-to-mesenchymal transition. Endothelial-specific deletion of Rnf20 led to ventricular septal defects, myocardial thinning and cardiac dysfunction as a result of aberrant signaling and excessive extracellular matrix deposition that induced precocious cardiomyocyte binucleation and irregular contractility. Furthermore, we uncovered upstream factors (e.g. Sox9) and multiple angiocrine and extracellular matrix molecules that alter cardiomyocyte functionality upon endothelial Rnf20 loss. In summary, our work identifies a novel, endothelial-specific role of Rnf20 in regulating cardiac morphogenesis and function.
Screening under infection-relevant conditions reveals chemical sensitivity in multidrug resistant invasive non-typhoidal Salmonella (iNTS)
Authors: Tsai Caressa N. , Massicotte Marie-Ange , MacNair Craig R. , Perry Jordyn N. , Brown Eric D. , Coombes Brian K 
Published: September 2022

ABSTRACTBloodstream infections caused by invasive, non-typhoidal salmonellae (iNTS) are a major global health concern. These infections are especially problematic in sub-Saharan Africa, where the sequence type (ST) 313 of invasive non-typhoidal Salmonella Typhimurium (iNTS) is dominant. Unlike S. Typhimurium strains that cause mild gastroenteritis, iNTS strains are resistant to multiple first-line antibiotics and have higher extraintestinal invasiveness, limiting current treatment options. Here, we performed multiple small molecule screens under infection-relevant conditions to reveal chemical sensitivities in ST313 as entry points to drug discovery to combat the clinical burden of iNTS. By screening the invasive ST313 sequence type under host-mimicking conditions, we identified the antimicrobial activity of the nucleoside analog 3’-azido-3’-deoxythymidine, which required bacterial thymidine kinase activity for its antimicrobial activity. In a parallel macrophage-based screening platform, we also identified three host-directed compounds (amodiaquine, berbamine, and indatraline) that significantly restricted intracellular replication of ST313 in macrophages without directly impacting bacterial viability. This work provides evidence that despite elevated invasiveness and multidrug resistance, iNTS S. Typhimurium remains susceptible to unconventional drug discovery approaches.
Identification of a self-renewing muscle satellite cell state by single-cell chromatin accessibility profiling
Authors: Okafor Arinze E. , Lin Xin , Situ Chenghao , Wei Xiaolin , Wei Xiuqing , Wu Zhenguo , Diao Yarui 
Published: September 2022

ABSTRACTA balance between self-renewal and differentiation is critical for the regenerative capacity of tissue-resident stem cells. In skeletal muscle, successful regeneration requires the orchestrated activation, proliferation, and differentiation of muscle satellite cells (MuSCs) that are normally quiescent. A subset of MuSCs undergoes self-renewal to replenish the stem cell pool, but the features that identify and define self-renewing MuSCs remain to be elucidate. Here, through single-cell chromatin accessibility analysis, we reveal the self-renewal versus differentiation trajectories of MuSCs over the course of regeneration in vivo. We identify TGFBR3 as a unique marker of self-renewing MuSCs that can be purified and efficiently contribute to regeneration after transplantation; and we show that SMAD4 and its downstream genes are genetically required for self-renewal in vivo by restricting differentiation. Our study unveils the identity and mechanisms of self-renewing MuSCs, while providing a key resource for comprehensive analysis of muscle regeneration.
Somatic nuclear blebbing may indicate proliferating germ cells but does not indicate organismal aging in Caenorhabditis elegans
Authors: Fan Qiang , Li Xue-Mei , Zhai Chao , Li Shang-Tong , Dong Meng-Qiu 
Published: September 2022

AbstractAbnormal nuclear morphology is suggested to be a hallmark of aging. One type of such abnormalities is nuclear blebbing, but little is known about whether and how nuclear blebbing participates in animal aging. What regulates nuclear blebbing is also unknown. In this study, we show that the frequency of nuclear blebbing in the hypodermis increases during aging in wild-type C. elegans. These nuclear blebs are enveloped by the nuclear lamina, the inner and the outer nuclear membrane, and 42% of them contain chromatin. Detachment of a bleb from the nucleus is rare but does happen, thereby generating cytoplasmic chromatin. Cytoplasmic chromatin-containing lysosomes juxtaposing the nucleus are detected in old worms. Therefore, nuclear blebbing contributes to the age-associated chromatin loss. However, the frequency of nuclear blebbing does not correlate with the rate of aging in C. elegans. Old age does not necessarily induce nuclear blebbing, neither does starvation, heat stress, or oxidative stress. Intriguingly, we find that proliferation of germ cells promotes nuclear blebbing.HighlightsNuclear blebs accumulate in the hypodermis during C. elegans agingNuclear blebbing contributes to chromatin lossThe frequency of nuclear blebbing does not correlate with the rate of agingProliferating germ cells promote nuclear blebbing in the hypodermis