bluuebunny/crossref_metadata_2025 huggingface dataset:
DNA breaks-mediated cost reveals RNase HI as a new target for selectively eliminating antibiotic resistance
Authors: Balbontín Roberto , Frazão Nelson , Gordo Isabel
Published: September 2019

Antibiotic resistance often generates a fitness cost to bacteria in drug-free environments. Understanding the causes of the cost is considered the Holy Grail in the antibiotic resistance field, as it is the main determinant of the prevalence of resistances upon reducing antibiotics use. We show that DNA breaks can explain most of the variation in the cost of resistances common in pathogens. Here we demonstrate that targeting the RNase that degrades R-loops, which cause DNA breaks, exacerbates the cost of resistance. Consequently, lack of RNase HI function drives resistant clones to extinction in populations with high initial frequency of resistance, both in laboratory conditions and in a mouse model of gut colonization. Thus, RNase HI provides a target specific against resistant bacteria, which we validate using a repurposed drug. In summary, we revealed key mechanisms underlying the cost of antibiotic resistance that can be exploited to specifically eliminate resistant bacteria.
miR-206 Enforces a Slow Muscle Phenotype
Authors: Bjorkman Kristen K. , Guess Martin G. , Harrison Brooke C. , Polmear Michael M. , Peter Angela K. , Leinwand Leslie A.
Published: September 2019

Striated muscle is a highly specialized collection of tissues with contractile properties varying according to functional needs. Although muscle fiber types are established postnatally, lifelong plasticity facilitates stimulus-dependent adaptation. Functional adaptation requires molecular adaptation, partially provided by miRNA-mediated post-transcriptional regulation. miR-206 is a muscle-specific miRNA enriched in slow muscles. We investigated whether miR-206 drives the slow muscle phenotype or is merely an outcome. We found that miR-206 expression increases in both physiologic (including female sex and endurance exercise) and pathologic conditions that promote a slow phenotype. Consistent with that observation, the slow soleus muscle of male miR-206 knockout mice displays a faster phenotype than wild-type mice. Moreover, their left ventricles have a faster myosin profile accompanied by male-specific dilation and systolic dysfunction. Thus, miR-206 appears necessary to enforce a slow skeletal and cardiac muscle phenotype and to play a key role in muscle sexual dimorphisms.
Design and analysis of the 4-anilino-quin(az)oline kinase inhibition profiles of GAK/SLK/STK10 using quantitative structure activity relationships
Authors: Asquith Christopher R. M. , Laitinen Tuomo , Bennett James M. , Wells Carrow I. , Elkins Jonathan M. , Zuercher William J. , Tizzard Graham , Poso Antti
Published: September 2019

The 4-anilino-quinoline and 4-anilino-quinazoline ring systems have been the focus of significant efforts in prior kinase drug discovery programs, which have led to approved medicines. Broad kinome profiles of these compounds have now been assessed with the advent of advanced screening technologies. These ring systems while, originally designed for specific targets including epidermal growth factor receptor (EGFR), actually display a number of potent collateral kinase targets, some of which have been associated with negative clinical outcomes. We have designed and synthesized a series of 4-anilino-quin(az)olines in order to better understand the structure activity relationships of three main collateral kinase targets of quin(az)oline-based kinase inhibitors: cyclin G associated kinase (GAK), STE20-like serine/threonine-protein kinase (SLK) and Serine/threonine-protein kinase 10 (STK10) through a series of quantitative structure activity relationship (QSAR) analysis and water mapping of the kinase ATP binding sites.
A ‘comb’ algorithm for accurate detection of calcium transients and action potentials in regularly activating cardiac preparations
Authors: Tomek Jakub
Published: September 2019

Cardiac imaging and electrophysiological measurements yield vast amounts of data that typically need to be processed automatically. However, the detection and segmentation of calcium transients or action potentials is complicated by signal noise or signal drift, which may cause both false positive and negative segmentation. This article presents a simple but accurate ‘comb’ algorithm for detection of calcium transients and action potentials in such data where the pattern of activation is regular and its frequency is known. This corresponds either to cases where the cardiac preparation is paced externally, or where the preparation is beating in a stable rhythm. The prior knowledge of the heart rate is leveraged to overcome a broad range of artefacts and complications which arise in experimental data, such as different types of noise, signal drift, or alternans. The algorithm is simple to implement and has only a single free parameter, which is furthermore simple to set. A Matlab/Octave implementation of the comb algorithm is provided.
Unified inference of missense variant effects and gene constraints in the human genome
Authors: Huang Yi-Fei
Published: September 2019

A challenge in medical genomics is to identify variants and genes associated with severe genetic disorders. Based on the premise that severe, early-onset disorders often result in a reduction of evolutionary fitness, several statistical methods have been developed to predict pathogenic variants or constrained genes based on the signatures of negative selection in human populations. However, we currently lack a statistical framework to jointly predict deleterious variants and constrained genes from both variant-level features and gene-level selective constraints. Here we present such a unified approach, UNEECON, based on deep learning and population genetics. UNEECON treats the contributions of variant-level features and gene-level constraints as a variant-level fixed effect and a gene-level random effect, respectively. The sum of the fixed and random effects is then combined with an evolutionary model to infer the strength of negative selection at both variant and gene levels. Compared with previously published methods, UNEECON shows unmatched performance in predicting missense variants and protein-coding genes associated with autosomal dominant disorders, and feature importance analysis suggests that both gene-level selective constraints and variant-level predictors are important for accurate variant prioritization. Furthermore, based on UNEECON, we observe an unexpected low correlation between gene-level intolerance to missense mutations and that to loss-of-function mutations, which can be partially explained by the prevalence of disordered protein regions that are highly tolerant to missense mutations. Finally, we show that genes intolerant to both missense and loss-of-function mutations play key roles in the central nervous system and the autism spectrum disorders. Overall, UNEECON is a promising framework for both variant and gene prioritization.
Transcriptome of the parasitic flatwormSchistosoma mansoniduring intra-mammalian development
Authors: Wangwiwatsin Arporn , Protasio Anna V. , Wilson Shona , Owusu Christian , Holroyd Nancy E. , Sanders Mandy J. , Keane Jacqueline , Doenhoff Mike J. , Rinaldi Gabriel , Berriman Matthew
Published: September 2019

Schistosomes are parasitic blood flukes that survive for many years within the mammalian host vasculature. How the parasites establish a chronic infection in the hostile bloodstream environment, whilst evading the host immune response is poorly understood. The parasite develops morphologically and grows as it migrates to its preferred vascular niche, avoiding or repairing damage from the host immune system. In this study, we investigated temporal changes in gene expression during the intra-mammalian development ofSchistosoma mansoni. RNA-seq data were analysed from parasites developing in the lung through to egg-laying mature adult worms, providing a comprehensive picture ofin vivointra-mammalian development. Remarkably, genes involved in signalling pathways, developmental control, and adaptation to oxidative stress were up-regulated in the lung stage. The data also suggested a potential role in immune evasion for a previously uncharacterised gene. This study not only provides a large and comprehensive data resource for the research community, but also reveals new directions for further characterising host–parasite interactions that could ultimately lead to new control strategies for this neglected tropical disease pathogen.

Author Summary

The life cycle of the parasitic flatwormSchistosoma mansoniis split between snail and mammalian (often human) hosts. An infection can last for more than 10 years, during which time the parasite physically interacts with its mammalian host as it moves through the bloodstream, travelling through the lungs and liver, to eventually establish a chronic infection in the blood vessels around the host gut. Throughout this complex journey, the parasite develops from a relatively simple larval form into a more complex, sexually reproducing adult. To understand the molecular basis of parasite interactions with the host during this complex journey we have produced genome-wide expression data from developing parasites. The parasites were collected from experimentally-infected mice over its developmental time-course from the poorly studied lung stage, to the fully mature egg-laying adult worm. The data highlight many genes involved in processes known to be associated with key stages of the infection. In addition, the gene expression data provide a unique view of interactions between the parasite and the immune system in the lung, including novel players in host-parasite interactions. A detailed understanding of these processes may provide new opportunities to design intervention strategies, particularly those focussed on the early stages of the infection that are not targeted by current chemotherapy.
ROS function as a distinct mitochondrial retrograde response factor for appropriate cardiogenic specifications and cardiac function inDrosophilaembryos
Authors: Sharma Swati
Published: September 2019

This manuscript has been withdrawn by the author as it was submitted and made public without the full consent of all the authors. Therefore, the author does not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Disruption to NKCC1 impairs the response of myelinating Schwann cells to neuronal activity and leads to severe peripheral nerve pathology
Authors: Kegel Linde , Marshall-Phelps Katy LH , Baraban Marion , Almeida Rafael G , Rubio-Brotons Maria , Klingseisen Anna , Benito-Kwiecinski Silvia , Early Jason J , Bin Jenea , Livesey Matthew R , Poole Richard J , Lyons David A
Published: September 2019

Myelinating Schwann cells of the peripheral nervous system (PNS) express numerous ion channels and transporters, and have the capacity to respond to neuronal activity. However, it remains unknown how the response of Schwann cells to neuronal activity affects peripheral nerve formation, health or function in vivo. Through a genetic screen in zebrafish, we identified a mutant,ue58, with severe disruption to the morphology of myelin along peripheral nerves and associated nerve oedema. Molecular analyses indicated that this phenotype was caused by the loss of function of a previously uncharacterized gene,slc12a2b, which encodes a zebrafish paralog of the solute carrier NKCC1. NKCC1 is a co-transporter of Na+, K+, and Cl−ions and water, typically from the extracellular space into cells. Upon impairingslc12a2bfunction, constitutively, or specifically in neurons or myelinating Schwann cells, we observed disruption to myelin and nerve oedema. Strikingly, we found that treatment ofslc12a2bmutants with TTX completely prevented the emergence of these pathologies. Furthermore, TTX treatment rescued pathology in animals with cell-type specific loss ofslc12a2bfrom myelinating Schwann cells. Together our data indicate that NKCC1 regulates ion homeostasis following neuronal activity and that this is required to maintain myelinated axon and peripheral nerve integrity.
Loss of Cdc13 causes genome instability by a deficiency in replication-dependent telomere capping
Authors: Langston Rachel E , Palazzola Dominic , Bonnell Erin , Wellinger Raymund J. , Weinert Ted
Published: September 2019

In budding yeast, Cdc13, Stn1, and Ten1 form a telomere binding heterotrimer dubbed CST. Here we investigate the role of Cdc13/CST in maintaining genome stability, using a Chr VII disome system that can generate recombinants, loss, and enigmatic unstable chromosomes. In cells expressing a temperature sensitiveCDC13allele,cdc13F684S, unstable chromosomes frequently arise due to problems in or near a telomere. Hence, when Cdc13 is defective, passage through S phase causes Exo1-dependent ssDNA and unstable chromosomes, which then are the source for whole chromosome instability events (e.g. recombinants, chromosome truncations, dicentrics, and/or loss). Specifically, genome instability arises from a defect in Cdc13’s replication-dependent telomere capping function, not Cdc13s putative post-replication telomere capping function. Furthermore, the unstable chromosomes form without involvement of homologous recombination nor non-homologous end joining. Our data suggest that a Cdc13/CST defect in semi-conservative replication near the telomere leads to ssDNA and unstable chromosomes, which then are lost or subject to complex rearrangements. This system defines a links between replication-dependent chromosome capping and genome stability in the form of unstable chromosomes.
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

The 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.

Importance

The 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

The 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

Metabolic 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

Rapid 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

Many 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

Following 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

Background

Treatment 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.

Methods

Using 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).

Results

Altering 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.

Conclusions

Our 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 SUMMARY

Currently, 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

Heat-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.

The 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

Sumoylation 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

Rapid 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.

Shear 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

The 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

Prions 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
Charting the native architecture of thylakoid membranes with single-molecule precision
Authors: Wietrzynski Wojciech , Schaffer Miroslava , Tegunov Dimitry , Albert Sahradha , Kanazawa Atsuko , Plitzko Jürgen M. , Baumeister Wolfgang , Engel Benjamin D.
Published: September 2019

Thylakoid membranes scaffold an assortment of large protein complexes that work together to harness the energy of light to produce oxygen, NADPH, and ATP. It has been a longstanding challenge to visualize how the intricate thylakoid network organizes these protein complexes to finely tune the photosynthetic reactions. Using cryo-electron tomography to analyze membrane surface topology, we have mapped the native molecular landscape of thylakoid membranes within green algae cells. Our tomograms provide insights into the molecular forces that drive thylakoid stacking and reveal that photosystems I and II are strictly segregated at the borders between appressed and non-appressed membrane domains. This new approach to charting thylakoid topology lays the foundation for dissecting photosynthetic regulation at the level of single protein complexes within the cell.
Zic2 abrogates an alternative Wnt signaling pathway to convert axon attraction into repulsion
Authors: Morenilla-Palao Cruz , López-Cascales Maria Teresa , López-Atalaya José P. , Baeza Diana , Calvo-Diaz Luis , Giner de Gracia Aida , Barco Angel , Herrera Eloísa
Published: September 2019

Wnt signaling is involved in axon pathfinding during brain wiring but it is unknown how Wnt ligands promote attraction or repulsion. In addition, the participation of the canonical (βcatenin-dependent transcription) versus non-canonical (βcatenin-independent) Wnt pathways in this process remains controversial. Here we show that Wnt5a is expressed at the optic chiasm midline and promotes axon crossing by triggering an alternative Wnt pathway that depends on polarized accumulation of βcatenin at the axon terminal but does not activate the canonical pathway. Remarkably, this alternative pathway is silenced by the transcription factor Zic2 in the small subset of ipsilaterally projecting neurons. Zic2 directly regulates genes related to Wnt and Eph signaling that lead to global accumulation of βcatenin but triggers its asymmetric phosphorylation to facilitate the steering of the growth cone. This alternative Wnt pathway found in contralateral axons and its Zic2-mediated abrogation in ipsilateral neurons is likely operating in many other contexts requiring a two-way response to Wnt ligands.
Regulation of histone methylation by automethylation of PRC2
Authors: Wang Xueyin , Long Yicheng , Paucek Richard D. , Gooding Anne R. , Lee Thomas , Burdorf Rachel M. , Cech Thomas R.
Published: September 2019

Polycomb-repressive complex 2 (PRC2) is a histone methyltransferase that is critical for regulating transcriptional repression in mammals. Its catalytic subunit, EZH2, is responsible for the trimethylation of H3K27 and also undergoes automethylation. Using mass spectrometry analysis of recombinant human PRC2, we identified three methylated lysine residues (K510, K514, and K515) on a disordered but highly conserved loop of EZH2. Methylation of these lysines increases PRC2 histone methyltransferase activity, whereas their mutation decreases activity in vitro. De novo histone methylation in an EZH2 knockout cell line is greatly impeded by mutation of the automethylation lysines. EZH2 automethylation occurs intramolecularly (in cis) by methylation of a pseudosubstrate sequence on a flexible loop. This posttranslational modification and cis regulation of PRC2 are analogous to the activation of many protein kinases by autophosphorylation. We propose that EZH2 automethylation allows PRC2 to modulate its histone methyltransferase activity by sensing histone H3 tails, SAM concentration, and perhaps other effectors.
Business model analytics: technically review business model research domain
Authors: Hajiheydari Nastaran , Talafidaryani Mojtaba , Khabiri SeyedHossein , Salehi Masoud
Published: September 2019

Purpose

Although the business model field of study has been a focus of attention for both researchers and practitioners within the past two decades, it still suffers from concern about its identity. Accordingly, this paper aims to clarify the intellectual structure of business model through identifying the research clusters and their sub-clusters, the prominent relations and the dominant research trends.

Design/methodology/approach

This paper uses some common text mining methods including co-word analysis, burst analysis, timeline analysis and topic modeling to analyze and mine the title, abstract and keywords of 14,081 research documents related to the domain of business model.

Findings

The results revealed that the business model field of study consists of three main research areas including electronic business model, business model innovation and sustainable business model, each of which has some sub-areas and has been more evident in some particular industries. Additionally, from the time perspective, research issues in the domain of sustainable development are considered as the hot and emerging topics in this field. In addition, the results confirmed that information technology has been one of the most important drivers, influencing the appearance of different study topics in the various periods.

Originality/value

The contribution of this study is to quantitatively uncover the dominant knowledge structure and prominent research trends in the business model field of study, considering a broad range of scholarly publications and using some promising and reliable text mining techniques.
The impact of R&D tax incentive programs on the performance of innovative companies
Authors: Makeeva Elena , Murashkina Ilona , Mikhaleva Irina
Published: September 2019

Purpose

This study aims to explore the influence of corporate taxation on the performance of innovative companies under various research and development (R&D) tax incentive programs.

Design/methodology/approach

The empirical model is based on the data of 520 companies for period 2007-2016. This model includes return on assets as the main proxy for performance and effective tax rate as a main explanatory variable. Controlling for other known determinants, the authors divide the sample into the subsamples to control for the various R&D tax incentive programs. The fact that the model includes the lagged explanatory variable of performance the Blundell –Bond model was applied.

Findings

The authors found evidence that corporate taxation has a significant impact on performance, but the direction could be ambiguous. Impact of the corporate tax rate on performance in general sample is significantly negative, which is consistent with results obtained by authors for the non-innovative companies. However, for further examination, the authors use subsamples of companies with different R&D tax incentive programs. The effect of corporate tax becomes positive under the patent box program only. Moreover, under various R&D tax incentive program, the impact of main control variables has changed. Therefore, the authors conclude that not only corporate taxation but also R&D tax incentive programs significantly influence the performance of innovative companies.

Research limitations/implications

The data are limited due to fragmented information disclosure about the R&D tax incentive program used. Thus, a different data set might reveal new information and correlation between variable on the same topic. Moreover, the authors do not cover all R&D tax incentive programs, which are specified for companies and countries. However, the study fills the gap between corporate taxation, performance and innovative companies. As the significant result was found the further research is important. The study contributes not only in the field of research but also a practical one. The choice of R&D tax incentive program influences main indicators of companies’ performance so it may change the behavior of the investors and decision-making managers of the companies.

Originality/value

Given the increasing interest in the topic of innovative companies, this study fills the gap between corporate taxation in innovative companies and performance. In addition, the importance of R&D tax incentive programs as a feature of innovative companies was found.
Intellectual capital and resilience in torn societies
Authors: Daou Alain , Joseph Jay , Yousif Dalia Sabah , Fathallah Ramzi , Reyes Gerald
Published: September 2019

Purpose

The purpose of this paper is to explore the association between intellectual capital (IC) and resilience in torn societies while proposing an integrative framework. Due to adversities faced by entrepreneurs in such contexts, an understanding of the role of resilience along with IC has become crucial for businesses to succeed and survive.

Design/methodology/approach

This study takes an in-depth look at the three components of IC – human, organizational and external capital and their association with resilience. In order to do so, a qualitative study on 17 Iraqi micro, small and medium enterprises (MSMEs) was conducted using data collected through semi-structured interviews with the founders. The interviews were translated and coded by native speakers.

Findings

The results suggest that IC and resilience are interrelated concepts where IC components contribute to the resilience capabilities of entrepreneurs to survive and continue their businesses during turbulent times.

Practical implications

Implications for managers and policymakers are presented; in brief, strategies and policies are required to support entrepreneurial success in the Iraqi context.

Originality/value

The study contributes to the literature on IC for entrepreneurs. So far, few studies have dealt with the association between IC and resilience, and less so in torn societies. This paper contributes to research on enterprise development and survival under conflict zones; it highlights some of the factors that could form resilience of a MSME in the face of uncertainty; and it contributes to the literature on IC as it helps us understand certain capacities that build up and/or support MSME resilience in such a context.