bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacterial and fungal communities are differentially modified by melatonin in agricultural soils under abiotic stress
Authors: Madigan Andrew P. , Egidi Eleonora , Bedon Frank , Franks Ashley E. , Plummer Kim M. 
Published: May 2019

AbstractAn extensive body of evidence from this last decade indicates that melatonin enhances plant resistance to several biotic and abiotic stressors. This has led to an interest in the use of melatonin in agriculture to reduce negative physiological effects from environmental stresses that affect yield and crop quality. However, there are no reports regarding the effects of melatonin on soil microbial communities under abiotic stress, despite the importance of microbes for plant root health and function. Three agricultural soils associated with different land usage histories (pasture, canola or wheat) were placed under abiotic stress by cadmium (100 or 280 mg/kg) or salt (4 or 7 g/kg) and treated with melatonin (0.2 and 4 mg/kg). Automated Ribosomal Intergenic Spacer Analysis (ARISA) was used to generate Operational Taxonomic Units (OTU) for microbial community analysis in each soil. Significant differences in richness (α diversity) and community structures (β diversity) were observed between bacterial and fungal assemblages across all three soils, demonstrating the effect of melatonin on soil microbial communities under abiotic stress. The analysis also indicated that the microbial response to melatonin is governed by the type of soil and history. The effects of melatonin on soil microbes needs to be regarded in potential future agricultural applications.
The Geometric Sparse Matrix Completion Model for Predicting Drug Side effects
Authors: Galeano Diego , Paccanaro Alberto 
Published: May 2019

AbstractPair-input associations for drug-side effects are obtained through expensive placebo-controlled experiments in human clinical trials. An important challenge in computational pharmacology is to predict missing associations given a few entries in the drug-side effect matrix, as these predictions can be used to direct further clinical trials. Here we introduce the Geometric Sparse Matrix Completion (GSMC) model for predicting drug side effects. Our high-rank matrix completion model learns non-negative sparse matrices of coefficients for drugs and side effects by imposing smoothness priors that exploit a set of pharmacological side information graphs, including information about drug chemical structures, drug interactions, molecular targets, and disease indications. Our learning algorithm is based on the diagonally rescaled gradient descend principle of non-negative matrix factorization. We prove that it converges to a globally optimal solution with a first-order rate of convergence. Experiments on large-scale side effect data from human clinical trials show that our method achieves better prediction performance than six state-of-the-art methods for side effect prediction while offering biological interpretability and favouring explainable predictions.
Phosphoproteomic identification of Xin as a novel requirement for skeletal muscle disuse atrophy
Authors: Li Zhencheng , Jensen Pia , Abrigo Johanna , Henriquez-Olguin Carlos , Gingrich Molly , Rytter Nicolai , Gliemann Lasse , Richter Erik A. , Hawke Thomas , Cabello-Verrugio Claudio , Larsen Martin R. , Jensen Thomas E. 
Published: May 2019

AbstractBackgroundImmobilization of skeletal muscle in a stretched position is associated with marked protection against disuse atrophy. Some intramyocellular changes in known proteins and post-translational modifications were previously linked to this phenomenon but there are likely many presently unknown proteins and post-translational modifications that contribute to this beneficial effect.MethodsTo identify novel proteins and phosphorylation events involved in stretch-induced reduction of disuse atrophy, we conducted a global unbiased screen of the changes occurring in skeletal muscle in control vs. 1 day and 1 week stretched cast-immobilized mouse tibialis anterior muscle, using quantitative tandem mass spectrometry on HILIC-fractionated muscle peptides with follow-up studies in transgenic mice and humans.ResultsOur mass spectrometry analyses detected 11714 phosphopeptides and 2081 proteins, of which 53 phosphopeptides and 5 proteins, 125 phosphopeptides and 43 proteins were deregulated after 1D and 7D of stretched immobilization, respectively. The sarcomere and muscle tendinous junction-associated putative multi-adaptor protein Xin was among the most highly upregulated proteins both in terms of phosphorylation and protein expression and was confirmed to increase with stretch but not disuse atrophy in mice and to increase and decrease with exercise and cast immobilization, respectively, in humans. Xin-/-mice were partially protected against disuse but not denervation atrophy in both stretched and flexed immobilized muscles compared to WT.ConclusionThis study identified Xin as a novel protein involved in disuse atrophy and also provides a resource to guide future hypothesis-driven investigations into uncovering critical factors in the protection against disuse atrophy.
Ubiquitination of the yeast receptor Atg32 modulates mitophagy
Authors: Vigié Pierre , Gonzalez Cécile , Manon Stephen , Bhatia-Kissova Ingrid , Camougrand Nadine 
Published: May 2019

AbstractMitophagy, the process that degrades mitochondria selectively through autophagy, is involved in the quality control of these organelles. In yeast, the presence of the Atg32 protein on the outer mitochondrial membrane allows for the recognition and targeting of superfluous or damaged mitochondria for degradation. Some posttranslational modifications, such as phosphorylation, are crucial for the execution of the mitophagy process. In our study, we showed that in the stationary phase of growth, and to a lesser extent during starvation, the Atg32 protein level decreases. The fact that a decline in Atg32 level can be prevented by inhibition of the proteolytic activity of proteasome may indicate that Atg32 is also ubiquitylated. In fact, mass spectrometry analysis of purified Atg32 protein showed ubiquitination of lysine residue in position 282. These different patterns of posttranslational modifications of Atg32 could allow cells to control the mitophagy process carefully.
Aggregated and hyperstable damage-associated molecular patterns are released during ER stress to modulate immune function
Authors: Andersohn Alexander , Garcia M. Iveth , Fan Ying , Thompson Max C. , Akimzhanov Askar M. , Abdullahi Abdikarim , Jeschke Marc G. , Boehning Darren 
Published: May 2019

AbstractChronic ER stress occurs when protein misfolding in the ER lumen remains unresolved despite activation of the unfolded protein response. We have shown that traumatic injury such as a severe burn leads to chronic ER stressin vivoleading to systemic inflammation which can last for more than a year. The mechanisms linking chronic ER stress to systemic inflammatory responses is not clear. Here we show that induction of chronic ER stress leads to the release of known and novel damage-associated molecular patterns (DAMPs). The secreted DAMPs are aggregated and markedly protease resistant. ER stress-derived DAMPs activate dendritic cells which are then capable of polarizing naïve T cells. Our findings indicate that induction of chronic ER stress may lead to the release of hyperstable DAMPs into the circulation resulting in persistent systemic inflammation and adverse outcomes.
Cotranslational folding cooperativity of contiguous domains of α-spectrin
Authors: Kemp Grant , Nilsson Ola B. , Tian Pengfei , Best Robert B. , von Heijne Gunnar 
Published: May 2019

AbstractProteins synthesized in the cell can begin to fold during translation before the entire polypeptide has been produced, which may be particularly relevant to the folding of multidomain proteins. Here, we study the cotranslational folding of adjacent domains from the cytoskeletal protein α-spectrin using Force Profile Analysis (FPA). Specifically, we investigate how the cotranslational folding behavior of the R15 and R16 domains are affected by their neighboring R14 and R16, and R15 and R17 domains, respectively. Our results show that the domains impact each other’s folding in distinct ways that may be important for the efficient assembly of α-spectrin, and may reduce its dependence on chaperones. Furthermore, we directly relate the experimentally observed yield of full-length protein in the FPA assay to the force exerted by the folding protein in pN. By combining pulse-chase experiments to measure the rate at which the arrested protein is converted into full-length protein with a Bell model of force-induced rupture, we estimate that the R16 domain exerts a maximal force on the nascent chain of ∼15 pN during cotranslational folding.SignificanceIn living cells, proteins are produced in a sequential way by ribosomes. This vectoral process allows the growing protein chain to start to fold before translation has been completed. Thereby, cotranslational protein folding can be significantly different than the folding of a full-length protein in isolation. Here we show how structurally similar repeat domains, normally produced as parts of a single long polypeptide, affect the cotranslational folding of their neighbors. This provides insight into how the cell may efficiently produce multidomain proteins, paving the way for future studiesin vivoor with chaperones. We also provide an estimated magnitude of the mechanical force on the nascent chain generated by cotranslational folding, calculated from biochemical measurements and molecular dynamics simulations.
The evolution of parasite host range in genetically diverse host populations
Authors: Gibson Amanda K , Baffoe-Bonnie Helena S , Penley McKenna J , Lin Julie , Owens Raythe , Khalid Arooj , Morran Levi T. 
Published: May 2019

AbstractParasites vary enormously in their host range. Why are some parasites specialists and others generalists? We tested the hypothesis that genetically diverse host populations select for parasites with broader host ranges than genetically homogeneous host populations. To do so, we selected for increased killing ability of the bacterial parasiteSerratia marcescensin populations of the hostCaenorhabditis elegansthat were either diverse (50% mix of genotypes N2 and LTM1) or homogenous (100% N2 or LTM1). We found mixed support for the hypothesis. After 20 generations of selection, parasites selected in diverse host populations maintained a broad host range, as shown by the retention of high killing ability of a novel host genotype. Parasites selected in diverse populations killed N2 hosts equally well as parasites selected in homogenous populations of N2. However, N2-selected parasites lost killing ability against the novel host, consistent with the evolution of narrow host ranges in homogenous environments. In contrast, parasites selected in homogenous LTM1 populations did not specialize: they did not increase in their killing ability on LTM1 and did not lose killing ability against the novel host. Our results argue that the evolution of host range depends upon both the identity and diversity of hosts that a parasite encounters.
Genetic editing of SEC61, SEC62, and SEC63 abrogates human cytomegalovirus US2 expression in a signal peptide-dependent manner
Authors: Schuren Anouk B.C. , Boer Ingrid G.J. , Bouma Ellen , Lebbink Robert Jan , Wiertz Emmanuel J.H.J. 
Published: May 2019

AbstractNewly translated proteins enter the ER through the SEC61 complex, via either co- or post-translational translocation. In mammalian cells, few substrates of post-translational SEC62- and SEC63-dependent translocation have been described. Here, we targeted all components of the SEC61/62/63 complex by CRISPR/Cas9, creating knock-outs or mutants of the individual subunits of the complex. We show that functionality of the human cytomegalovirus protein US2, which is an unusual translocation substrate with a low-hydrophobicity signal peptide, is dependent on expression of not only SEC61α, -β, and -γ, but also SEC62 and SEC63, suggesting that US2 may be a substrate for post-translational translocation. This phenotype is specific to the US2 signal peptide.
Metabolic overlap in environmentally diverse microbial communities
Authors: Hester Eric R. , Jetten Mike S.M. , Welte Cornelia U. , Lücker Sebastian 
Published: May 2019

AbstractThe majority of microbial communities consist of hundreds to thousands of species, creating a massive network of organisms competing for available resources within an ecosystem. In natural microbial communities it appears that many microbial species have highly redundant metabolisms and seemingly are capable of utilizing the same substrates. This is paradoxical, as theory indicates that species requiring a common resource should outcompete one another. To better understand why microbial species can co-exist, we developed Metabolic Overlap (MO) as a new metric to survey the functional redundancy of microbial communities at the genome scale across a wide variety of ecosystems. Using metagenome-assembled genomes, we surveyed over 1200 studies across ten ecosystem types. We found the highest MO in extreme (i.e., low pH/high temperature) and aquatic environments, while the lowest MO was observed in communities associated with animal hosts, or the built/engineered environment. In addition, different metabolism subcategories were explored for their degree of metabolic overlap. For instance, overlap in nitrogen metabolism was among the lowest in Animal and Engineered ecosystems, while the most was in species from the Built environment. Together, we present a metric that utilizes whole genome information to explore overlapping niches of microbes. This provides a detailed picture of potential metabolic competition and cooperation between species present in an ecosystem, indicates the main substrate types sustaining the community and serves as a valuable tool to generate hypotheses for future research.
Sub-lethal insecticide exposure affects host biting efficiency of Kdr-resistant Anopheles gambiae
Authors: Diop Malal M , Chandre Fabrice , Rossignol Marie , Porciani Angélique , Chateau Mathieu , Moiroux Nicolas , Pennetier Cédric 
Published: May 2019

AbstractThe massive use of insecticide-treated nets (ITNs) has drastically changed the environment for malaria vector mosquitoes, challenging their host-seeking behaviour and biting success. Here, we investigated the effect of a brief exposure to an ITN on the biting behaviour of Anopheles mambiae mosquitoes and the interaction between such behaviour and the kdr mutation that confers resistance to pyrethroids. To this aim, we developed a video assay to study the biting behaviour of mosquitoes with similar genetic background, but different kdr locus genotypes (SS i.e. homozygous susceptible, RS i.e. heterozygous and RR i.e. homozygous resistant), after a brief exposure to either control untreated nets or one of two types of pyrethroid-treated nets (deltamethrin or permethrin). In presence of untreated nets, the kdr mutation did not influence mosquito blood feeding success but caused differences in feeding and prediuresis durations and blood meal size. Exposure to deltamethrin ITN decreased the blood feeding success rate of RR and RS mosquitoes, whereas in presence of permethrin ITN, the kdr mutation increased the blood-feeding success of mosquitoes. Exposure to the two types of pyrethroid-treated nets reduced feeding duration, prediuresis duration and blood meal size of all three genotypes. Our study demonstrates a complex interaction between insecticide exposure and the kdr mutation on the biting behavior of mosquitoes, which may substantially impact malaria vector fitness and disease transmission.
Obesity-induced gut microbiota dysbiosis can be ameliorated by fecal microbiota transplantation: a multiomics approach
Authors: Guirro Maria , Costa Andrea , Gual-Grau Andreu , Herrero Pol , Torrell Helena , Canela Núria , Arola Lluís 
Published: May 2019

AbstractObesity and its comorbidities are currently considered an epidemic, and the involved pathophysiology is well studied. Recently, the gut microbiota has emerged as a new potential therapeutic target for the treatment of obesity. Diet and antibiotics are known to play crucial roles in changes in the microbiota ecosystem and the disruption of its balance; therefore, the manipulation of gut microbiota may represent a strategy for obesity treatment. Fecal microbiota transplantation, during which fecal microbiota from a healthy donor is transplanted to an obese subject, has aroused interest as an effective approach for the treatment of obesity. To determine its success, a multiomics approach was used that combined metagenomics and metaproteomics to study microbiota composition and function.To do this, a study was performed in rats that evaluated the effect of a hypercaloric diet on the gut microbiota, and this was combined with antibiotic treatment to deplete the microbiota before fecal microbiota transplantation to verify its effects on gut microbiota-host homeostasis. Our results showed that a high-fat diet induces changes in microbiota biodiversity and alters its function in the host. Moreover, we found that antibiotics depleted the microbiota enough to reduce its bacterial content. Finally, we assessed the use of fecal microbiota transplantation as an obesity therapy, and we found that it reversed the effects of antibiotics and reestablished the microbiota balance, which restored normal functioning and alleviated microbiota disruption.
Assembly tolerance analysis based on the Jacobian model and skin model shapes
Authors: Liu Ting , Cao Yan-Long , Zhao Qijian , Yang Jiangxin , Cui Lujun 
Published: May 2019

Purpose
The purpose of this paper is to carry out an assembly tolerance analysis by means of a combined Jacobian model and skin model shape. The former is based on small displacements modeling of points using 6 × 6 transformation matrices of open kinematic chains in robotics. The latter easily models toleranced features with all kinds of geometric deviations.

Design/methodology/approach
This paper presents the procedure of performing tolerance analysis by means of the Jacobian model and skin model shape for assemblies. The point cloud-based discrete representative is able to model the actual toleranced surfaces instead of the ideal or associated ones in an assembly, which brings the simulation tools closer to reality.

Findings
The proposed method has the advantage of skin model shape which is suitable for geometric tolerances management along the product life cycle and contact analysis of kinematic small variations, as well as, with the Jacobian, enabling transformation of locally expressed parts deviations to globally expressed functional requirements. The result of the case study shows the accuracy of the method.

Research limitations/implications
The proposed approach has not been developed fully; other functional features such as the pyramid are still ongoing challenges.

Practical implications
It is an effective method for supporting design, manufacturing and inspection by providing a quantitative analysis of the effects of multi-tolerances on the final functional key characteristics and for predicting the quality level.

Originality/value
The paper is original in taking advantages of both Jacobian model and skin model shape to consider all geometric tolerances in assembly.
Beyond gaming
Authors: Hooker Robert , Wasko Molly , Paradice David , Teigland Robin , Hofacker Charles 
Published: May 2019

PurposeThe purpose of this paper is to test flow as a construct distinctly separate from its antecedents, and the resulting impact on brand attitudes and purchase intent within realistic online shopping three-dimensional virtual environments (3-DVEs).Design/methodology/approachThis research utilizes a field study, combined with a survey research design of 348 3-DVE participants.FindingsThe findings reveal that flow is not a unidimensional construct but rather, a mental state that should be measured separately from its antecedents, with the possibility that certain antecedents may be more relevant than others in different activities. Furthermore, the authors received strong support for the overarching hypothesized model separating the nine dimensions associated with engagement in an activity as antecedents of flow, which, in turn, influences brand attitude and thereafter purchase intention.Research limitations/implicationsThis study was limited to one type of activity within one 3-DVE but is balanced by the difficulty in gaining access to organizations and computer-mediated environments of this type for examining such phenomena.Practical implicationsBusinesses using 3-DVEs to market brands should focus their efforts on creating highly enjoyable experiences that result in the feeling of a loss of sense of time for the participants in order to ultimately positively influence purchase intentions.Originality/valuePrior research focused on fantasy-based, game-oriented environments, while also neglecting to test all elements of flow, examining “similar to flow” constructs or measuring flow as a unidimensional construct.
Examining the legitimacy of Sukuk structure via Shariah pronouncements
Authors: Ahmed Essia Ries , Islam Aminul , Amran Azlan Bin 
Published: May 2019

Purpose
The purpose of this paper is to investigate and detect disclosure on the legitimacy identity of Sukuk structure in Shariah pronouncements. The study also examines the role of Shariah supervisory board on disclosure of legitimacy in Shariah pronouncements.

Design/methodology/approach
A total of 54 Islamic Sukuk in Malaysia representing the whole population were selected. Secondary data were used and sourced from Shariah pronouncements on Sukuk. Using descriptive statistics, the existence and the extent of existence of legitimacy disclosure on Sukuk in Islamic financial institutions in Malaysia were ascertained.

Findings
Using descriptive statistics, the existence and the extent of existence of legitimacy disclosure on Sukuk in Islamic financial institutions in Malaysia was ascertained. The research found that there is empirical evidence showing the effect of Shariah supervisory board on disclosure of legitimacy identity in Shariah pronouncements.

Originality/value
This study offers significant contribution to existing legitimacy of Sukuk structure literature. The study added a new discussion, i.e. legitimacy disclosure on the Sukuk. The study is intended to increase public awareness for legitimacy identity of Sukuk in the importance of Shariah compliancy not only in the form but also in substance. In addition, this study will give more benefits for Islamic financial institutions in the sense that they should amend some of their regulatory frameworks to push the Sukuk market investors to move toward asset-backed structure.