bluuebunny/crossref_metadata_2025_split huggingface dataset:
Laboratory Evolution Experiments Help Identify a Predominant Region of Constitutive Stable DNA Replication Initiation
Authors: Veetil Reshma T , Malhotra Nitish , Dubey Akshara , Seshasayee Aswin Sai Narain 
Published: September 2019

AbstractThe bacteriumE. colican initiate replication in the absence of the replication initiator protein DnaA and / or the canonical origin of replicationoriCin aΔrnhAbackground. This phenomenon, which can be primed by R-loops, is called constitutive stable DNA replication (cSDR). Whether DNA replication during cSDR initiates in a stochastic manner through the length of the chromosome or at specific sites, and howE. colican find adaptations to loss of fitness caused by cSDR remain inadequately answered. We use laboratory evolution experiments ofΔrnhA-ΔdnaAfollowed by deep sequencing to show that DNA replication preferentially initiates within a broad region located ∼0.4-0.7 Mb clockwise oforiC.This region includes many bisulfite-sensitive sites, which have been previously defined as R-loop forming regions; and includes a site containing sequence motifs that favour R-loop formation. Initiation from this region would result in head-on replication-transcription conflicts at rRNA loci. Inversions of these rRNA loci, which can partly resolve these conflicts, help the bacterium suppress the fitness defects of cSDR. These inversions partially restore the gene expression changes brought about by cSDR. The inversion however increases the possibility of conflicts at essential mRNA genes, which would utilise only a miniscule fraction of RNA polymerase molecules most of which transcribe rRNA genes. Whether subsequent adaptive strategies would attempt to resolve these conflicts remains an open question.ImportanceThe bacteriumE. colican replicate its DNA even in the absence of the molecules that are required for canonical replication initiation. This often requires the formation of RNA-DNA hybrid structures, and is referred to as constitutive stable DNA replication (cSDR). Where on the chromosome does cSDR initiate? We answer this question using laboratory evolution experiments and genomics, and show that selection favours cSDR initiation predominantly at a region ∼0.6 Mb clockwise oforiC.Initiation from this site will result in more head on collisions of DNA polymerase with RNA polymerase operating on rRNA loci. The bacterium adapts to this problem by inverting a region of the genome including several rRNA loci such that head-on collisions between the two polymerases are minimised. Understanding such evolutionary strategies in the context of cSDR can provide insights into the potential causes of resistance against antibiotics that target initiation of DNA replication.
Allele Specific Expression in Human – Genomic Makeup and Phenotypic Implications
Authors: Wainer-Katsir Kerem , Linial Michal 
Published: September 2019

AbstractThe allele-specific expression phenomenon refers to unbalanced expression from the two parental alleles in a tissue of a diploid organism. AlleleDB is a high-quality resource that reports on about 30,000 ASE variants (ASE-V) from hundreds of human samples. In this study, we present the genomic characteristics and phenotypic implications of ASE. We identified tens of segments with extreme density of ASE-V, many of them are located at the major histocompatibility complex (MHC) locus. Notably, at a resolution of 100 nucleotides, the likelihood of ASE-V increases with the density of polymorphic sites. Another dominant trend of ASE is a strong bias of the expression to the major allele. This observation relies on the known allele frequencies in the healthy human population. Overlap of ASE-V and GWAS associations was calculated for 48 phenotypes from the UK-Biobank. ASE-V were significantly associated with a risk for inflammation (e.g. asthma), autoimmunity (e.g., rheumatoid arthritis, multiple sclerosis, and type 1 diabetes) and several blood cell traits (e.g., red cell distribution width). At the level of the ASE-genes, we seek association with all traits and conditions reported in the GWAS catalog. The statistical significance of ASE-genes to GWAS catalog reveals association with the susceptibility to virus infection, autoimmunity, inflammation, allergies, blood cancer and more. We postulate that ASE determines phenotype diversity between individuals and the risk for a variety of immune-related conditions.
Integration of high-content fluorescence imaging into the metabolic flux assay reveals insights into mitochondrial properties and functions
Authors: Little Andrew C. , Kovalenko Ilya , Goo Laura E. , Hong Hanna S. , Kerk Samuel A. , Yates Joel A. , Purohit Vinee , Lombard David B. , Merajver Sofia D. , Lyssiotis Costas A. 
Published: September 2019

SUMMARYMetabolic flux technology with the Seahorse bioanalyzer has emerged as a standard technique in cellular metabolism studies, allowing for simultaneous kinetic measurements of respiration and glycolysis. Methods to extend the utility and versatility of the metabolic flux assay would undoubtedly have immediate and wide-reaching impacts. Herein, we describe a platform that couples the metabolic flux assay with high-content fluorescence imaging to simultaneously enhance normalization of respiration data with cell number; analyze cell cycle progression; quantify mitochondrial content, fragmentation state, membrane potential, and mitochondrial reactive oxygen species. Integration of fluorescent dyes directly into the metabolic flux assay generates a more complete data set of mitochondrial features in a single assay. Moreover, application of this integrated strategy revealed insights into mitochondrial function following PGC1a and PRC1 inhibition in pancreatic cancer and demonstrated how the Rho-GTPases impact mitochondrial dynamics in breast cancer.
Contrasting approaches to genome-wide association studies impact the detection of resistance mechanisms in Staphylococcus aureus
Authors: Wheeler Nicole E. , Reuter Sandra , Chewapreecha Claire , Lees John A. , Blane Beth , Horner Carolyne , Enoch David , Brown Nicholas M. , Estée Török M. , Aanensen David M. , Parkhill Julian , Peacock Sharon J. 
Published: September 2019

AbstractRapid detection of antibiotic resistance using whole-genome sequencing (WGS) could improve clinical outcomes and limit the spread of resistance. For this to succeed, we need an accurate way of linking genotype to phenotype, that identifies new resistance mechanisms as they appear. To assess how close we are to this goal, we characterized antimicrobial resistance determinants in >4,000 Staphylococcus aureus genomes of isolates associated with bloodstream infection in the United Kingdom and Ireland. We sought to answer three questions: 1) how well did known resistance mechanisms explain phenotypic resistance in our collection, 2) how many previously identified resistance mechanisms appeared in our collection, and 3) how many of these were detectable using four contrasting genome-wide association study (GWAS) methods. Resistance prediction based on the detection of known resistance determinants was 98.8% accurate. We identified challenges in correcting for population structure, clustering orthologous genes, and identifying causal mechanisms in rare or common phenotypes, which reduced the recovery of known mechanisms. Limited sensitivity and specificity of these methods made prediction using GWAS-discovered hits alone less accurate than using literature-derived genetic determinants. However, GWAS methods identified novel mutations associated with resistance, including five mutations in rpsJ, which improved tetracycline resistance prediction for 28 isolates, and a T118I substitution in fusA which resulted in better fusidic acid resistance prediction for 5 isolates. Thus, GWAS approaches in conjunction with phenotypic testing data can support the development of comprehensive databases to enable real-time use of WGS for patient management.
Multi-trait genome-wide analyses of the brain imaging phenotypes in UK Biobank
Authors: Wu Chong 
Published: September 2019

AbstractMany genetic variants identified in genome-wide association studies (GWAS) are associated with multiple, sometimes seemingly unrelated traits. This motivates multi-trait association analyses, which have successfully identified novel associated loci for many complex diseases. While appealing, most existing methods focus on analyzing a relatively small number of traits and may yield inflated Type I error rates when a large number of traits need to be analyzed jointly. As deep phenotyping data are becoming rapidly available, we develop a novel method, referred to as aMAT (adaptive multi-trait association test), for multi-trait analysis of any number of traits. We applied aMAT to GWAS summary statistics for a set of 58 volumetric imaging derived phenotypes from the UK Biobank. aMAT had a genomic inflation factor of 1.04, indicating the Type I error rates were well controlled. More important, aMAT identified 24 distinct risk loci, 13 of which were ignored by standard GWAS. In comparison, the competing methods either had a suspicious genomic inflation factor or identified much fewer risk loci. Finally, four additional sets of traits have been analyzed and provided similar conclusions.
Multiplexed Non-invasive in vivo Imaging to Assess Metabolism and Receptor Engagement in Tumor Xenografts
Authors: Rudkouskaya Alena , Sinsuebphon Nattawut , Ochoa Marien , Mazurkiewicz Joe E. , Intes Xavier , Barroso Margarida 
Published: September 2019

AbstractFollowing an ever-increased focus on personalized medicine, there is a continuing need to develop preclinical molecular imaging modalities to guide the development and optimization of targeted therapies. To date, non-invasive quantitative imaging modalities that can comprehensively assess simultaneous cellular drug delivery efficacy and therapeutic response are lacking. In this regard, Near-Infrared (NIR) Macroscopic Fluorescence Lifetime Förster Resonance Energy Transfer (MFLI-FRET) imaging offers a unique method to robustly quantify receptor-ligand engagement in vivo and subsequent intracellular internalization, which is critical to assess the delivery efficacy of targeted therapeutics. However, implementation of multiplexing optical imaging with FRET in vivo is challenging to achieve due to spectral crowding and cross-contamination. Herein, we report on a strategy that relies on a dark quencher that enables simultaneous assessment of receptor-ligand engagement and tumor metabolism in intact live mice. First, we establish that IRDye QC-1 (QC-1) is an effective NIR dark acceptor for the FRET-induced quenching of donor Alexa Fluor 700 (AF700) using in vitro NIR FLI microscopy and in vivo wide-field MFLI imaging. Second, we report on simultaneous in vivo imaging of the metabolic probe IRDye 800CW 2-deoxyglucose (2-DG) and MFLI-FRET imaging of NIR-labeled transferrin FRET pair (Tf-AF700/Tf-QC-1) uptake in tumors. Such multiplexed imaging revealed an inverse relationship between 2-DG uptake and Tf intracellular delivery, suggesting that 2-DG signal may predict the efficacy of intracellular targeted delivery. Overall, our methodology enables for the first time simultaneous non-invasive monitoring of intracellular drug delivery and metabolic response in preclinical studies.
In silicohippocampal modeling for multi-target pharmacotherapy in schizophrenia
Authors: Sherif Mohamed A , Neymotin Samuel A , Lytton William W 
Published: September 2019

AbstractBackgroundTreatment of schizophrenia has had limited success in treating core cognitive symptoms. The evidence of multi-gene involvement suggests that multi-target therapy may be needed. Meanwhile, the complexity of schizophrenia pathophysiology and psychopathology, coupled with the species-specificity of much of the symptomatology, places limits on analysis via animal models,in vitroassays, and patient assessment. Multiscale computer modeling complements these traditional modes of study.MethodsUsing a hippocampal CA3 computer model with 1200 neurons, we examined the effects of alterations in NMDAR, HCN (Ihcurrent), and GABAAR on information flow (measured with normalized transfer entropy), and in gamma activity in local field potential (LFP).ResultsAltering NMDARs, GABAAR,Ih, individually or in combination, modified information flow in an inverted-U shape manner, with information flow reduced at low and high levels of these parameters. The strong information flow seen at the peaks were associated with an intermediate level of synchrony, seen as an intermediate level of gamma activity in the LFP, and an intermediate level of pyramidal cell excitability.ConclusionsOur results are consistent with the idea that overly low or high gamma power is associated with pathological information flow and information processing. These data suggest the need for careful titration of schizophrenia pharmacotherapy to avoid extremes that alter information flow in different ways. These results also identify gamma power as a potential biomarker for monitoring pathology and multi-target pharmacotherapy.AUTHOR SUMMARYCurrently, there are no good treatments for the cognitive symptoms of schizophrenia. We used a biophysically realistic computational model of hippocampal CA3 to investigate the effect of potential pharmacotherapeutic targets on the dynamics of CA3 activity and information processing to predict multi-target drug treatments for schizophrenia. We found an inverted-U shaped relationship between information flow and drug target manipulations, as well as between information flow and gamma power. Our study suggests that neuronal excitability and synchrony may be tuned between extremes to enhance information flow and information processing. It further predicts the need for careful titration of schizophrenia drugs, whether used individually or in drug cocktails.
Proteomic analysis reveals the recruitment of intrinsically disordered regions to stress granules
Authors: Zhu Mang , Kuechler Erich R. , Zhang Joyce , Matalon Or , Dubreuil Benjamin , Hofmann Analise , Loewen Chris , Levy Emmanuel D. , Gsponer Joerg , Mayor Thibault 
Published: September 2019

AbstractHeat-stress triggers the formation of condensates known as stress granules (SGs), which store non-translating mRNA and stalled translation initiation complexes. To gain a better understanding of SGs, we identified yeast proteins that sediment after heat-shock by mass spectrometry. Heat-regulated proteins are biased toward a subset of abundant proteins that are significantly enriched in intrinsically disordered regions (IDRs). SG localization of over 80 heat-regulated proteins was confirmed using microscopy, including 32 proteins that were not known previously to localize to SGs. We find that several IDRs are sufficient to mediate SG recruitment. Moreover, the diffusive exchange of IDRs within SGs, observed via FRAP, can be highly dynamic while other components remain immobile. Lastly, we showed that the IDR of the Ubp3 deubiquitinase is critical for SG formation. This work confirms that IDRs play an important role in cellular compartmentalization upon stress, can be sufficient for SG incorporation, can remain dynamic in vitrified SGs, and play a vital role during heat-stress.SummaryThe authors provide an in-depth proteomic study of yeast heat stress granule (SG) proteins. They identified intrinsic disordered regions (IDRs) as one of the main features shared by these proteins and demonstrated IDRs can be sufficient for SG recruitment.
Ethanol stress stimulates sumoylation of transcription factor Cst6 which restricts expression of its target genes
Authors: Theivakadadcham Veroni S. Sri , Rosonina Emanuel 
Published: September 2019

ABSTRACTSumoylation is an essential post-translational modification that functions in multiple cellular processes, including transcriptional regulation. Indeed, transcription factors represent one of the largest groups of proteins that are modified by the SUMO peptide. Multiple roles have been identified for sumoylation of transcription factors, including regulation of their activity, interaction with chromatin, and binding site selection. Here, we examine how Cst6, a bZIP-containing sequence-specific transcription factor in Saccharomyces cerevisiae, is regulated by sumoylation. Cst6 is required for survival during ethanol stress and has roles in the utilization of carbon sources other than glucose. We find that Cst6 is sumoylated to appreciable levels in normally growing yeast at Lys residues 139, 461 and 547, and that its sumoylation level increases in ethanol and oxidative stress conditions, but decreases if ethanol is used as the sole carbon source. To understand the role of Cst6 sumoylation during ethanol stress, we generated a yeast strain that expresses a non-sumoylatable mutant form of Cst6. Cellular levels of the mutant protein are moderately reduced compared to the wild-type form, implying that sumoylation promotes Cst6 stability. Although the mutant can bind DNA, chromatin immunoprecipitation (ChIP) analysis shows that its occupancy level is significantly reduced on promoters of some ethanol stress-regulated genes, suggesting that Cst6 recruitment is attenuated or delayed if it can not be sumoylated. Furthermore, impaired Cst6 sumoylation in the mutant strain correlates with elevated expression of some target genes, either constitutively or during induction by ethanol stress. This is most striking for RPS3, which shows dramatically increased expression in the mutant strain. Together, our results suggest that sumoylation controls multiple properties of Cst6 to limit the expression of its target genes.
Mechanical activation of TWIK-related potassium channel by nanoscopic movement and rapid second messenger signaling
Authors: Nicholas Petersen E. , Pavel Mahmud Arif , Hansen Samuel S. , Gudheti Manasa , Wang Hao , Yuan Zixuan , Murphy Keith R. , Ja William W. , Ferris Heather A , Jorgensen Erik M. , Hansen Scott B. 
Published: September 2019

AbstractRapid conversion of force into a biological signal enables living cells to respond to mechanical forces in their environment. The force is believed to initially affect the plasma membrane and then alter the behavior of membrane proteins. Phospholipase D2 (PLD2) is a mechanosensitive enzyme that is regulated by a structured membrane-lipid site comprised of cholesterol and saturated ganglioside (GM1). Here we show stretch activation of TWIK-related K+channel (TREK-1) is mechanically evoked by PLD2 and spatial patterning involving ordered GM1 and 4,5-bisphosphate (PIP2) clusters. First, mechanical force deforms the ordered lipids, which lowers membrane cholesterol, disrupts the interaction of PLD2 with the GM1 lipids, and allows a complex of TREK-1 and PLD2 to associate with PIP2clusters. The association with PIP2activates the enzyme, which produces the second messenger phosphatidic acid (PA) that gates the channel. Co-expression of catalytically inactive PLD2 inhibits TREK-1 stretch currents in a biological membrane. Cellular uptake of cholesterol inhibits TREK-1 currents in culture and depletion of cholesterol from astrocytes releases TREK-1 from GM1 lipids in mouse brain. Depletion of the PLD2 ortholog in flies results in hypersensitivity to mechanical force. We conclude PLD2 mechanosensitivity combines with TREK-1 ion permeability to elicit a mechanically evoked response.SummaryShear thinning activates TREK-1 through a second messenger.
Multi-epitope Peptide Vaccine Prediction for Candida albicans targeting Pyruvate Kinase Protein; an Immunoinformatics Approach
Authors: Sati Anfal Osama Mohamed , Abdelmoneim Hamza Abdelrahman Hamza , Dawoud Enas Dawoud Khairi , Abbas Tebyan Ameer Abdelhameed , Abdelrahman Fatima Abdelrahman Bshier , Saad Khalid Abbas Hassan , Abduallah Rouaa Babikir Ahmed , Mustafa Marwa Mohamed Elhag Saeed , Sidahmed Tamador abdelrahman , Elhassan Reham M. , Hassan Mohamed A. 
Published: September 2019

AbstractThe fungusCandida albicansis an opportunistic pathogen that causes a wide range of infections. It’s the primary cause of candidiasis and the fourth most common cause of nosocomial infection. In addition, disseminated invasive candidiasis which is a major complication of the disease has an estimated mortality rate of 40%-60% even with the use of antifungal drugs. Over the last decades, several different anti-Candida vaccines have been suggested with different strategies for immunization against candidiasis such as, live-attenuated fungi, recombinant proteins, and glycoconjugates but none has been approved by the FDA, yet. This study aims to introduce a new possible vaccine forC. albicansthrough analyzing peptides of its pyruvate kinase (PK) protein as an immunogenic stimulant computationally.A total number of 28C. albicans, pyruvate kinase proteins were obtained from NCBI on the 9thof February 2019 and were subjected to multiple sequence alignment using Bioedit for conservancy. The main analytical tool was IEDB, Chimera for homology modelling, and MOE for docking.Among the tested peptides, fifteen promising T-cell peptides were predicted. Five peptides were more important than the others (HMIFASFIR, YRGVYPFIY, AVAAVSAAY, LRWAVSEAV, and IFASFIRTA) They show high Binding Affinity to MHC molecules, low binding energy required indicating more stable bonds, and their ideal length of nine peptides. (PTRAEVSDV) peptide is the most promising linear B-cell peptide due to its physiochemical parameters and optimal length (nine amino acids). It’s highly recommended to have these five strong candidates in future in vivo and in vitro analysis studies.
Conformation-dependent influences of hydrophobic amino acids in two in-register parallel β-sheet amyloids, an α-synuclein amyloid and a local structural model of PrPSc
Authors: Otaki Hiroki , Taguchi Yuzuru , Nishida Noriyuki 
Published: September 2019

AbstractPrions are unconventional pathogens that encode the pathogenic information in conformations of the constituent abnormal isoform of prion protein (PrPSc), independently of the nucleotide genome. Therefore, conformational diversity of PrPSc underlies the existence of many prion strains and species barriers of prions, although the conformational information is extremely limited. Interestingly, differences between polymorphic or species-specific residues responsible for the species/strain barriers are often caused by conservative replacements between hydrophobic amino acids. This implies that subtle differences among hydrophobic amino acids are significant for PrPSc structures. Here, we analyzed the influence of different hydrophobic residues on the structures of an in-register parallel β-sheet amyloid of α-synuclein (αSyn) using molecular dynamics (MD) simulation, and applied the knowledge from the αSyn amyloid to modeling a local structure of human PrPSc encompassing residues 107–143. We found that mutations equivalent to polymorphisms that cause transmission barriers substantially affect the stabilities; for example, the G127V mutation, which makes the host resistant to various human prion diseases, greatly destabilized the model amyloid. Our study demonstrates specifically how and in what structures hydrophobic residues can exert unique effects on in-register parallel β-sheet amyloids and provides insights into the molecular mechanism of the strain diversity of prions and other pathogenic amyloids.For Table of Contents Only