bluuebunny/crossref_metadata_2025_split huggingface dataset:
Large-scale, dynamin-like motions of the human guanylate binding protein 1 revealed by multi-resolution simulations
Authors: Barz Bogdan , Loschwitz Jennifer , Strodel Birgit 
Published: June 2019

AbstractGuanylate binding proteins (GBPs) belong to the dynamin-related superfamily and exhibit various functions in the fight against infections. The functions of the human guanylate binding protein 1 (hGBP1) are tightly coupled to GTP hydrolysis and dimerization. Despite known crystal structures of the hGBP1 monomer and GTPase domain dimer, little is known about the dynamics of hGBP1. To gain a mechanistic understanding of hGBP1, we performed sub-millisecond multi-resolution molecular dynamics simulations of both the hGBP1 monomer and dimer. We found that hGBP1 is a highly flexible protein that undergoes a hinge motion similar to the movements observed for other dynamin-like proteins. Another large-scale motion was observed for the C-terminal helixα13, providing a molecular view for theα13–α13 distances previously reported for the hGBP1 dimer. Most of the loops of the GTPase domain were found to be flexible, disclosing why GTP binding is needed for hGBP1 dimerization to occur.Author summaryGunaylate binding proteins are key fighters against microbial and viral pathogens. In the human body there are seven types of such proteins, among which is the guanylate binding protein 1 (hGBP1). This protein is able to perform its function only once it is activated by binding and converting guanosinetriphosphat (GTP) to guanosinediphosphat and guanosinemonophosphat via hydrolysis. In concert with the conversion of GTP the dimerization of hGBP1 occurs, which can further interact with the lipid membrane of the pathogen and disrupt it. While the crystal structure of the protein is known, the activation and dimerization steps are not well understood at molecular level as studying them experimentally is difficult. An alternative approach is given by molecular simulations, allowing us to elucidate the protein dynamics closely connected to these steps. From our simulations applied to both the hGBP1 monomer and dimer we identified large-scale motions taking place in hGBP1 that had not been reported before. We discuss the relevance of these motions in terms of their biological function, such as possible membrane damage caused by one of the motions or locking the protein in the dimer state.
Probing the Subcellular Distribution of Phosphatidylinositol Reveals a Surprising Lack at the Plasma Membrane
Authors: Zewe James P. , Miller April , Sangappa Sahana , Wills Rachel C. , Goulden Brady D. , Hammond Gerald R. V. 
Published: June 2019

AbstractThe polyphosphoinositides (PPIn) are central regulatory lipids that direct membrane function in eukaryotic cells. Understanding how their synthesis is regulated is crucial to revealing these lipids’ role in health and disease. PPIn are derived from the major structural lipid, phosphatidylinositol (PI). However, although the distribution of most PPIn have been characterized, the subcellular localization of PI available for PPIn synthesis is not known. Here, we have used several orthogonal approaches to map the subcellular distribution of PI, including localizing exogenous fluorescent PI, as well as detecting lipid conversion products of endogenous PI after acute chemogenetic activation of PI-specific phospholipase and 4-kinase. We report that PI is broadly distributed throughout intracellular membrane compartments. However, there is a surprising lack of PI in the plasma membrane compared to the PPIn. These experiments implicate regulation of PI supply to the plasma membrane, as opposed to regulation of PPIn-kinases, as crucial to the control of PPIn synthesis and function at the PM.SummaryZewe et al develop approaches to map the subcellular distribution of the major phospholipid, phosphatidylinositol (PI), revealing that the lipid is present in most membranes except for plasma membrane, where it is mainly found as PI4P and PI(4,5)P2.
Depletion of Ric-8B leads to reduced mTORC2 activity
Authors: Nagai Maíra H. , Gutiyama Luciana M. , Xavier Victor P. S. , Machado Cleiton F. , Reis Alice H. , Donnard Elisa R. , Galante Pedro A. F. , Abreu Jose G. , Festuccia William T. , Malnic Bettina 
Published: June 2019

AbstractmTOR, a serine/threonine protein kinase that is involved in a series of critical cellular processes, can be found in two functionally distinct complexes, mTORC1 and mTORC2. In contrast to mTORC1, little is known about the mechanisms that regulate mTORC2. Here we show that mTORC2 activity is reduced in mice with a hypomorphic mutation of the Ric-8B gene. Ric-8B is a highly conserved protein that acts as a non-canonical guanine nucleotide exchange factor (GEF) for heterotrimeric Gαs/olf type subunits. We found that Ric-8B hypomorph embryos are smaller than their wild type littermates, fail to close the neural tube in the cephalic region and die during mid-embryogenesis. Comparative transcriptome analysis revealed that signaling pathways involving GPCRs and G proteins are dysregulated in the Ric-8B mutant embryos. Interestingly, this analysis also revealed an unexpected impairment of the mTOR signaling pathway.Phosphorylation of Akt at Ser 473 is downregulated in the Ric-8B mutant embryos, indicating a decreased activity of mTORC2. In contrast, phosphorylation of S6, a downstream target of mTORC1, is unaltered. Knockdown of the endogenous Ric-8B gene in HEK293T cells leads to reduced phosphorylation levels of Akt at Ser 473, but not of S6, further supporting the selective involvement of Ric-8B in mTORC2 activity. Our results reveal a crucial role for Ric-8B in development and provide novel insights into the signals that regulate mTORC2 activity.Author SummaryGene inactivation in mice can be used to identify genes that are involved in important biological processes and that may contribute to disease. By using this approach, we found that the Ric-8B gene is essential for embryogenesis and for the normal development of the nervous system. Ric-8B mutant mouse embryos are smaller than their wild type littermates and show neural tube defects at the cranial region. This approach also allowed us to identify the biological pathways that are involved in the observed phenotypes, the G protein and mTORC2 signaling pathways. mTORC2 plays particular important roles also in the adult brain, and has been implicated in neurological disorders. Ric-8B is highly conserved in mammals, including humans. Our mutant mice provide a model to study the complex molecular and cellular processes underlying the interplay between Ric-8B and mTORC2 in neuronal function.
Trickle infection and immunity toTrichuris muris
Authors: Glover Maya , Colombo Stefano A.P. , Thornton David J. , Grencis Richard K. 
Published: June 2019

AbstractThe majority of experiments investigating the immune response to gastrointestinal helminth infection use a single bolus infection. However,in situindividuals are repeatedly infected with low doses. Therefore, to model natural infection, mice were repeatedly infected (trickle infection) with low doses ofTrichuris muris. Trickle infection resulted in the slow acquisition of immunity reflected by a gradual increase in worm burden followed by a partial expulsion. Flow cytometry revealed that the CD4+ T cell response shifted from Th1 dominated to Th2 dominated, which coincided with an increase in Type 2 cytokines. The development of resistance following trickle infection was associated with increased worm expulsion effector mechanisms including goblet cell hyperplasia, Muc5ac production and increased epithelial cell turn over. Depletion of CD4+ T cells reversed resistance confirming their importance in protective immunity following trickle infection. In contrast, depletion of group 2 innate lymphoid cells did not alter protective immunity.T. muristrickle infection resulted in a dysbiotic mircrobiota which began to recover alpha diversity following the development of resistance.These data support trickle infection as a robust and informative model for analysis of immunity to chronic intestinal helminth infection more akin to that observed under natural infection conditions and confirms the importance of CD4+ T cell adaptive immunity in host protection.Author SummaryInfection with parasitic worms (helminths) is a considerable cause of morbidity in humans. Understanding how we respond to infection is crucial to developing novel therapies. Laboratory models of helminth infection have been a valuable tool in understanding fundamental immune responses to infection. However, typically an individual mouse will be infected with a large, single-dose of the parasite. This is in contrast to the natural scenario in which individuals will receive frequent low level exposures. What is unknown is how repeated infection alters the development of immunity to infection. We have developed a laboratory model to tackle this question. We infected mice with the model helminthTrichuris murison a weekly basis and assessed a range of responses in comparison with a more traditional infection system. We found striking differences in the dynamics of the infection, the host immune response, and in changes to host gut microbial populations. Our study shows how resistance to helminth infection can develop over time in response to repeat infection, and provides a model system that better reflects human immunity to this parasite.
Defining the Subcellular Distribution and Metabolic Channeling of Phosphatidylinositol
Authors: Pemberton Joshua G. , Kim Yeun Ju , Sengupta Nivedita , Eisenreichova Andrea , Toth Daniel J. , Boura Evzen , Balla Tamas 
Published: June 2019

AbstractPhosphatidylinositol (PtdIns) is an essential structural component of eukaryotic membranes that also serves as the common precursor for polyphosphoinositide (PPIn) lipids. Despite the recognized importance of PPIn species for signal transduction and membrane homeostasis, there is still a limited understanding of how the dynamic regulation of PtdIns synthesis and transport contributes to the turnover of PPIn pools. To address these shortcomings, we capitalized on the substrate selectivity of a bacterial enzyme, PtdIns-specific PLC, to establish a molecular toolbox for investigations of PtdIns distribution and availability within intact cells. In addition to its presence within the ER, our results reveal low steady-state levels of PtdIns within the plasma membrane (PM) and endosomes as well as a relative enrichment of PtdIns within the cytosolic leaflets of the Golgi complex, peroxisomes, and outer mitochondrial membranes. Kinetic studies also demonstrate the requirement for sustained PtdIns supply from the ER for the maintenance of monophosphorylated PPIn species within the PM, Golgi complex, and endosomal compartments.SummaryPemberton et al. characterize a molecular toolbox for the visualization and manipulation of phosphatidylinositol (PtdIns) within intact cells. Results using these approaches define the steady-state distribution of PtdIns across subcellular membrane compartments as well as provide new insights into the relationship between PtdIns availability and polyphosphoinositide turnover.
Abbreviated assessment of psychopathology in patients with suspected seizure disorders
Authors: Malpas Charles B , Wang Albert D , Leong Michelle , Johnstone Benjamin , Rayner Genevieve , Kalincik Tomas , Kwan Patrick , O’Brien Terence J , Velakoulis Dennis 
Published: June 2019

AbstractPurposePsychopathology is common in patients undergoing investigation for seizure-related disorders. Psychometric examination using self-report instruments, such as the SCL-90-R, can assist diagnosis. The SCL-90-R, however, is a lengthy instrument and might not be tolerated by all patients. We assessed several abbreviated forms of the SCL-90-R in patients undergoing video encephalographic monitoring (VEM).Method687 patients completed the SCL-90-R and scores were computed for the full SCL-90-R and five abbreviated forms. Correlations and mean differences were computed between different forms. Classification accuracy was assessed via receiver operating characteristic (ROC) curves, and measurements models were examined using confirmatory factor analysis (CFA).ResultsAll abbreviated forms were strongly correlated with the SCL-90-R for general psychopathology (r= .93 – .99), depression (r= .89 – .95), anxiety (r= .97 – .98), psychosis (r= .95 – .99), and obsessive-compulsive symptoms (r= .97). Classification performance was similar across forms for depression and anxiety, with high negative predictive values (.90 – .94) and lower positive predictive values (.34 – .38). Classification performance for psychotic and obsessive-compulsive disorders was poor. Differences were observed between the full SCL-90-R and its abbreviated forms across most domains (d= 0.00 – 0.65). The published measurement model was most strongly validated for the SCL-27, SCL-14, and the SCL-K-9.ConclusionsThese five SCL-90-R abbreviated forms show high convergent validity with the full version. In patients undergoing investigation for seizure-related disorders, the BSI or BSI-18 are most appropriate where screening for both depression and anxiety is required. The SCL-K-9 is appropriate when only a single measure of global psychological distress is required. None of the instruments were able to detect psychotic or obsessive-compulsive symptoms with great accuracy. Caution should be exercised when making direct comparisons across the different forms.
Binding of single-mutant epidermal growth factor (EGF) ligands alter the stability of the EGF receptor dimer and promote growth signaling
Authors: Pascarelli Stefano , Merzhakupova Dalmira , Uechi Gen-Ichiro , Laurino Paola 
Published: June 2019

AbstractThe Epidermal Growth Factor Receptor (EGFR) is a membrane-anchored tyrosine kinase that is able to selectively respond to multiple extra-cellular stimuli. Previous studies have indicated that the modularity of this system is affected by ligand-induced differences in the stability of the dimerized receptor in a process known as “Biased signaling”. However, this hypothesis has not been explored using single-mutant ligands thus far. Herein, we developed a new approach to identify residues responsible for functional divergence combining the conservation and co-evolution information of ortholog and paralog genes encoding the epidermal growth factor (EGF) ligand. Then, we mutated these residues and assessed the mutants’ effects on the receptor by employing a combination of molecular dynamics (MD) and biochemical techniques. Although the EGF mutants had comparable binding affinities to the wild type ligand for EGFR, the EGF mutants induced a different phosphorylation and cell growth pattern in multiple cell lines. The MD simulations of the EGF mutants show a long-range effect on the receptor dimer interface. For the first time in this study, a single mutation in EGF is shown to be enough to alter the activation of the pathway at the cellular level. These results also support the theory of biased signaling in the tyrosine kinase receptor system and demonstrate a promising new way to study ligand-receptor interactions.
Mutations of the YidC Insertase alleviate stress from σM-dependent membrane protein overproduction in Bacillus subtilis
Authors: Zhao Heng , Sachla Ankita J. , Helmann John D. 
Published: June 2019

AbstractIn Bacillus subtilis, the extracytoplasmic function σ factor σM regulates cell wall synthesis and is critical for intrinsic resistance to cell wall targeting antibiotics. The anti-σ factors YhdL and YhdK form a complex that restricts the basal activity of σM, and the absence of YhdL leads to runaway expression of the σM regulon and cell death. Here, we report that this lethality can be suppressed by gain-of-function mutations in spoIIIJ, which encodes the major YidC membrane protein insertase in B. subtilis. B. subtilis PY79 SpoIIIJ contains a single amino acid substitution in the substrate-binding channel (Q140K), and this allele suppresses the lethality of high SigM. Analysis of a library of YidC variants reveals that increased charge (+2 or +3) in the substrate-binding channel can compensate for high expression of the σM regulon. Derepression of the σM regulon induces secretion stress, oxidative stress and DNA damage responses, all of which can be alleviated by the YidCQ140K substitution. We further show that the fitness defect caused by high σM activity is exacerbated in the absence of SecDF protein translocase or σM-dependent induction of the Spx oxidative stress regulon. Conversely, cell growth is improved by mutation of specific σM-dependent promoters controlling operons encoding integral membrane proteins. Collectively, these results reveal how the σM regulon has evolved to up-regulate membrane-localized complexes involved in cell wall synthesis, and to simultaneously counter the resulting stresses imposed by regulon induction.Author SummaryBacteria frequently produce antibiotics that inhibit the growth of competitors, and many naturally occurring antibiotics target cell wall synthesis. In Bacillus subtilis, the alternative σ factor σM is induced by cell wall antibiotics, and upregulates genes for peptidoglycan and cell envelope synthesis. However, dysregulation of the σM regulon, resulting from loss of the YhdL anti-σM protein, is lethal. We here identify charge variants of the SpoIIIJ(YidC) membrane protein insertase that suppress the lethal effects of high σM activity. Further analyses reveal that induction of the σM regulon leads to high level expression of membrane proteins that trigger envelope stress, and this stress is countered by specific genes in the σM regulon.
Flow separation control of NACA-2412 airfoil with bio-inspired nose
Authors: Raj Mohamed Mohamed Arif , Guven Ugur , Yadav Rajesh 
Published: June 2019

Purpose
The purpose of this paper is to achieve an optimum flow separation control over the airfoil using passive flow control method by introducing bio-inspired nose near the leading edge of the NACA 2412 airfoil.

Design/methodology/approach
Two distinguished methods have been implemented on the leading edge of the airfoil: forward facing step, which induces multiple accelerations at low angle of attack, and cavity/backward facing step, which creates recirculating region (axial vortices) at high angle of attack.

Findings
The porpoise airfoil (optimum bio-inspired nose airfoil) delays the flow separation and improves the aerodynamic efficiency by increasing the lift and decreasing the parasitic drag. The maximum increase in aerodynamic efficiency is 22.4 per cent, with an average increase of 8.6 per cent at all angles of attack.

Research limitations/implications
The computational analysis has been done for NACA 2412 airfoil at low subsonic speed.

Practical implications
This design improves the aerodynamic performance and increases structural strength of the aircraft wing compared to other conventional high-lift devices and flow-control devices.

Originality/value
Different bio-inspired nose designs which are inspired by the cetacean species have been analysed for NACA 2412 airfoil, and optimum nose design (porpoise airfoil) has been found.
When in Rome, do as the Romans do
Authors: Memon Mumtaz Ali , Mirza Muhammad Zeeshan , Lim Bibiana , Umrani Waheed Ali , Hassan Mohamed Ayyub , Cham Tat Huei , Shahzad Khurram 
Published: June 2019

PurposeInternational students are considered as a huge and potentially lucrative segment for various products of the tourism industry in Malaysia. One of the tourism products is the local food they consume. The purpose of this paper is to investigate key factors that contribute to international students’ intention to consume Malay food. Drawing on the theory of planned behavior (TPB), the present study examines the impact of attitude, subject norm and perceived behavioral control (PBC) on international students’ intention to consume Malay food.Design/methodology/approachA quantitative approach using self-administered questionnaire was adopted. A total of 163 samples were collected from international students studying in five different Malaysian higher education institutions. A partial least squares structural equation modeling technique was used to test the hypothesized model.FindingsThe findings highlight that attitude, subject norms and PBC significantly motivate international students to consume local food. The subject norm toward consuming local food was revealed as the strongest predictor of international students’ intention to consume Malay food.Originality/valueAlthough this is one of the early studies that uses the TPB in assessing the factors that influence international students’ intention to consume local food, this paper is driven by and aimed for practical consideration and thus making a significant contribution to practice. Specifically, the findings of the present study provide important implications for tourism industry practitioners to plan and implement initiatives that may promote local food among international students studying in Malaysian institutions.
Benchmarking the Lean Six Sigma performance measures: a balanced score card approach
Authors: Raval Shruti J. , Kant Ravi , Shankar Ravi 
Published: June 2019

Purpose
The purpose of this paper is to develop the balance score card (BSC) approach based Lean Six Sigma (LSS) performance measurement system and investigate the critical measures currently practiced by Indian manufacturing organizations.

Design/methodology/approach
This study offers insights of LSS performance measurement from manufacturing industry. Initially, the BSC-based framework is developed to recognize the adoption of LSS performance measures. Then, the framework is applied to nine Indian manufacturing organizations to assess the LSS performance measure practice.

Findings
The BSC-based framework of LSS performance evaluation for manufacturing industry is formulated. Then, adoption of these LSS performance measures is investigated with nine Indian manufacturing organizations. The result indicates significant variability in terms of practicing level of LSS measures. However, the majority of organizations are more sensitive to the customer perspectives.

Practical implications
This study reveals a background as to why the performance measurement is required for the success of LSS and for providing practical guidelines for designing performance metrics. The framework interrelates and captures various LSS perspectives and indicator measures, and furnishes a comprehensive outlook of the organization for strategic analysis. This study provides BSC-based template for performing the benchmarking study. This analysis may serve as a reference point for manufacturing organization to determine their system weaknesses, and assist them to concentrate on their most vital and suitable criteria and objectives. However, the analysis contributes to the knowledge on LSS performance measurement system and catches differences in theory and practice, paving the approach to newer research.

Originality/value
This study renders an industry-oriented LSS performance measurement practical approach and suggests the easily adopted vital performance measures for different manufacturing organizations.