bluuebunny/crossref_metadata_2025_split huggingface dataset:
High transcriptional error rates vary as a function of gene expression level
Authors: Meer K.M. , Nelson P.G. , Xiong K. , Masel J. 
Published: February 2019

AbstractErrors in gene transcription can be costly, and organisms have evolved to prevent their occurrence or mitigate their costs. The simplest interpretation of the drift barrier hypothesis suggests that species with larger population sizes would have lower transcriptional error rates. However, Escherichia coli seems to have a higher transcriptional error rate than species with lower effective population sizes, e.g. Saccharomyces cerevisiae. This could be explained if selection in E. coli were strong enough to maintain adaptations that mitigate the consequences of transcriptional errors through robustness, on a gene by gene basis, obviating the need for low transcriptional error rates and associated costs of global proofreading. Here we note that if selection is powerful enough to evolve local robustness, selection should also be powerful enough to locally reduce error rates. We therefore predict that transcriptional error rates will be lower in highly abundant proteins on which selection is strongest. However, we only expect this result when error rates are high enough to significantly impact fitness. As expected, we find such a relationship between expression and transcriptional error rate for non C➔U errors in E. coli (especially G➔A), but not in S. cerevisiae. We do not find this pattern for C➔U changes in E. coli, presumably because most deamination events occurred during sample preparation, but do for C➔U changes in S. cerevisiae, supporting the interpretation that C➔U error rates estimated with an improved protocol, and which occur at rates comparable to E. coli non C➔U errors, are biological.
B cell tetherin: a flow-cytometric cell-specific assay for response to Type-I interferon predicts clinical features and flares in SLE
Authors: El-Sherbiny Yasser M. , Yusof Md. Yuzaiful Md. , Psarras Antonios , Hensor Elizabeth M. A. , Kabba Kumba Z. , Dutton Katherine , Mohamed Alaa A.A. , Elewaut Dirk , McGonagle Dennis , Tooze Reuben , Doody Gina , Wittmann Miriam , Emery Paul , Vital Edward M. 
Published: February 2019

ABSTRACTObjectiveType I interferon (IFN-I) responses are broadly associated with autoimmune disease including SLE. Given the cardinal role of autoantibodies in SLE, we investigated whether a B lineage cell-specific IFN assay might correlate with SLE activity.MethodsB cells and PBMCs were stimulated with IFN-I and IFN-II. Gene expression was scrutinised for pathway-related membrane protein expression. A flow-cytometric assay for tetherin (CD317), an IFN-induced protein ubiquitously expressed on leucocytes, was validatedin vitrothen clinically against SLE diagnosis, plasmablast expansion, and BILAG-2004 score in a discovery cohort (156 SLE; 30 RA; 22 healthy controls). A second longitudinal validation cohort of 80 patients was also evaluated for SLE flare prediction.ResultsIn vitro, a close cell-specific and dose-responsive relationship between IFN-I responsive genes and cell surface tetherin in all immune subsets existed. Tetherin expression was selectively responsive to the IFN-I compared to IFN-II and -III. In the discovery cohort memory B-cell tetherin was best associated with diagnosis (SLE/HC: effect size=0.11, p=0.003;SLE/RA: effect size=0.17, p<0.001); plasmablast numbers in rituximab-treated patients (Rho=0.38, p=0.047) and BILAG-2004. Association were equivalent or stronger than interferon score or monocyte tetherin. The validation cohort confirmed this relationship with memory B-cell tetherin predictive of future clinical flares (Hazard Ratio=2.29 (1.01–4.64), p=0.022).ConclusionMemory B cell surface tetherin, a reflection of cell-specific IFN response in a convenient flow cytometric assay, was associated with SLE diagnosis, disease activity and predicted flares better than other cell subsets or whole blood assays in independent validation cohorts.
Non-catalytic binding sites induce weaker long-range evolutionary rate gradients than catalytic sites in enzymes
Authors: Sharir-Ivry Avital , Xia Yu 
Published: February 2019

AbstractEnzymes exhibit a strong long-range evolutionary constraint that extends from their catalytic site and affects even distant sites, where site-specific evolutionary rate increases monotonically with distance. While protein-protein sites in enzymes was previously shown to induce only a weak conservation gradient, a comprehensive relationship between different types of functional sites in proteins and the magnitude of evolutionary rate gradients they induce has yet to be established. Here, we systematically calculate the evolutionary rate (dN/dS) of sites as a function of distance from different types of binding sites on enzymes and other proteins: catalytic sites, non-catalytic ligand binding sites, allosteric binding sites, and protein-protein interaction sites. We show that catalytic binding sites indeed induce significantly stronger evolutionary rate gradient than all other types of non-catalytic binding sites. In addition, catalytic sites in enzymes with no known allosteric function still induce strong long-range conservation gradients. Notably, the weak long-range conservation gradients induced by non-catalytic binding sites on enzymes is nearly identical in magnitude to those induced by ligand binding sites on non-enzymes. Finally, we show that structural determinants such as local solvent exposure of sites cannot explain the observed difference between catalytic and non-catalytic functional sites. Our results suggest that enzymes and non-enzymes share similar evolutionary constraints only when examined from the perspective of non-catalytic functional sites. Hence, the unique evolutionary rate gradient from catalytic sites in enzymes is likely driven by the optimization of catalysis rather than ligand binding and allosteric functions.
Limits to environmental masking of genetic quality in sexual signals
Authors: Howie James Malcolm , Dawson Harry Alexander Cordeaux , Pomiankowski Andrew , Fowler Kevin 
Published: February 2019

AbstractThere is considerable debate over the value of male sexual ornaments as signals of genetic quality. Studies alternately report that environmental variation enhances or diminishes the genetic signal, or leads to crossover where genotypes perform well in one environment but poorly in another. A unified understanding is lacking. We conduct the first experimental test examining the dual effects of distinct low and high genetic quality (inbred versus crossed parental lines) and low, through high, to extreme environmental stress (larval diets) on a condition-dependent male ornament. We find that differences in genetic quality signalled by the ornament (male eyespan inDiasemopsis meigeniistalk-eyed flies) become visible and are amplified under high stress but are overwhelmed in extreme stress environments. Variance among distinct genetic lines increases with environmental stress in both genetic quality classes, but at a slower rate in high quality outcrossed flies. Individual genetic lines generally maintain their ranks across environments, except among high quality lines under low stress conditions, where low genetic variance precludes differentiation between ranks. Our results provide a conceptual advance, demonstrating a unified pattern for how genetic and environmental quality interact. They show when environmental conditions lead to the amplification of differences in signals of genetic quality and thereby enhance the potential indirect genetic benefits gained by female mate choice.
The impact of distillery effluent irrigation on plant-growth-promoting traits and taxonomic composition of bacterial communities in agricultural soil
Authors: Kumari Priyanka , Tripathi Binu M. , Singh Ram N. , Saxena Anil K. , Kaushik Rajeev 
Published: February 2019

AbstractLong-term irrigation of agricultural fields with distillery effluent (DE) may alter the physical, chemical and biological properties of the soil. Microorganisms are critical to the maintenance of soil health and productivity. However, the impact of DE irrigation on activity and taxonomy of soil microorganisms is poorly understood. Here we studied plant-growth-promoting (PGP) traits and taxonomic composition of bacterial communities in agricultural soil irrigated with DE in conjugation with irrigation water, using cultivation-dependent and - independent methods. Most of the bacterial isolates obtained from DE irrigated soil were found to display PGP traits (phosphate solubilization, siderophore, indolic compounds and ammonia production). Diverse bacterial taxa were found in both culturable bacterial community and 16S rRNA gene clone library, which belonged to bacterial phylaProteobacteria(Alpha-, Beta- and Gamma- subdivisions),Firmicutes, Actinobacteria, Acidobacteria, BacteroidetesandGemmatimonadates. Overall, these results indicate that PGP traits and taxonomic diversity of soil bacterial communities were not severely impacted by DE irrigation.
Virtual Microbes evolve multiple mechanisms to the same end: anticipating a serial transfer protocol
Authors: van Dijk Bram , Meijer Jeroen , Cuypers Thomas D , Hogeweg Paulien 
Published: February 2019

AbstractBackgroundExperimental evolution of microbes often involves a serial transfer protocol, where microbes are repeatedly diluted by transfer to a fresh medium, starting a new growth cycle. This protocol has revealed that evolution can be remarkably reproducible, where microbes show parallel adaptations both on the level of the phenotype as well as the genotype. However, these studies also reveal a strong potential for divergent evolution, leading to diversity both between and within replicate populations. We here study howin silicoevolved Virtual Microbe “wild types” (WTs) adapt to a serial transfer protocol to investigate both the generic evolutionary adaptation to such an environment which are independent of prior evolution, and the variety of ways in which the adaptation is implemented at the individual and ecosystem level.ResultsWe show that all pre-evolved WTs evolve to anticipate the regularity of the serial transfer protocol by adopting a fine-tuned balance of growth and survival. We find that this anticipation can be done in a variety of ways, either by a single lineage or by several lineages in consort. Interestingly, replicate populations of the same WT initially show similar trajectories, but may subsequently diverge along a growth rate versus yield trade-off.ConclusionsWe find that all ourin silicoWTs show the same anticipation effects — fitting the periodicity of a serial transfer protocol — but do so by a variety of mechanisms. Our results reveal new insights into the dynamics and relevant selection pressures in experimental evolution, but also highlight how, in an eco-evolutionary context, numerous mechanisms can evolve to the same end.
LRRK2-mediated phosphorylation of HDAC6 regulates HDAC6-cytoplasmic dynein interaction and aggresome formation
Authors: Lucas Richard M. , Bauer Claudia S. , Chinnaiya Kavitha , Schwartzentruber Aurélie , MacDonald Ruby , Collins Mark O. , Aasly Jan O. , Brønstad Gunnar , Ferraiuolo Laura , Mortiboys Heather , Vos Kurt J. De 
Published: February 2019

AbstractMutations in LRRK2 are the most common cause of dominantly inherited Parkinson’s disease (PD). A proportion of LRRK2 PD exhibits Lewy pathology with accumulations of α-synuclein and ubiquitin in intracellular aggregates that are indistinguishable from idiopathic PD. LRRK2 is a multi-domain protein with both GTPase and kinase activities that has been shown to affect various cellular processes including protein homeostasis, however how PD mutations in LRRK2 may lead to accumulation of ubiquitinated protein aggregates remains unclear.A main cellular pathway to remove aggregated ubiquitinated proteins is aggrephagy: the histone deacetylase HDAC6 recognizes ubiquitinated misfolded proteins and recruits them to the molecular motor cytoplasmic dynein which transports them to the perinuclear region where they are trapped in aggresomes that are subsequently removed by macroautophagy.Here we identified HDAC6 as a novel LRRK2 substrate and show that LRRK2 regulates HDAC6-dependent aggresome formation. LRRK2 directly interacted with the HDAC6 deacetylase domains via its Roc domain and phosphorylated HDAC6 on serine-22. Serine-22 phosphorylation of HDAC6 enhanced its interaction with cytoplasmic dynein and stimulated recruitment of ubiquitinated proteins to aggresomes. Knockdown or knockout of LRRK2 impaired HDAC6-mediated aggresome formation. PD mutant LRRK2 G2019S showed reduced interaction with HDAC6 and did not support aggresome formation to the same extend as wild type LRRK2. This was recapitulated in LRRK2 G2019S patient-derived iAstrocytes that showed an aggresome formation defect.In conclusion our data reveal HDAC6 as a target of LRRK2 and suggest that deregulation of HDAC6-mediated aggresome formation and aggrephagy could contribute to the pathology of PD.
Distinct subdivisions of human medial parietal cortex are recruited differentially for memory recall of places and people
Authors: Silson Edward H , Steel Adam , Kidder Alexis , Gilmore Adrian W , Baker Chris I 
Published: February 2019

AbstractHuman medial parietal cortex (MPC) is implicated in multiple cognitive processes including memory recall, visual scene processing and navigation. It is also considered a core component of the default mode network. Here, we combine fMRI data across three independent experiments to demonstrate distinct subdivisions of MPC that are selectively recruited during memory recall of either specific places or specific people. First, distinct regions of MPC were identified on the basis of differential functional connectivity with medial and lateral regions of anterior ventral temporal cortex (VTC). Second, these same medial regions exhibited differential responses to the visual presentation of different stimulus categories, with clear preferences for scenes and faces, respectively. Third, and most critically, these regions were selectively recruited during either place or people memory recall. These subdivisions also showed a striking relationship with ventral and dorsal divisions of the default mode network. Taken together, these data reveal distinct subdivisions within MPC for the recall of places and people and moreover, suggest that the organizing principle defining the medial-lateral axis of VTC is reflected in MPC, but in the context of memory recall.
Faizal & Shabana Foundation: a venture philanthropic approach to education
Authors: Sahasranamam Sreevas , Mitra Sumit 
Published: February 2019

Learning outcomes
Learning outcomes are as follows: understand venture philanthropy in India; discuss in what ways venture philanthropy is different from charity; identify the aims of venture philanthropy and the strategy adopted to achieve those objectives; analyze the role of the unique structuring of a venture philanthropy working in tandem with the government to achieve its objectives; identify the nature and source of dilemmas of disengagement from a project by the venture philanthropist; and understand the role of antecedents and outcomes on how a firm views its social impact initiative (in the Indian context).

Case overview/synopsis
The Faizal and Shabana Foundation (F&SF) made one of the largest philanthropic investments in Kerala, India for the redevelopment of Government Vocational Higher Secondary School for Girls, Nadakkavu. The foundation applied a strategic approach to their philanthropic investment making it a unique case of venture philanthropy. The uniqueness of this case lies in the fact that, this is one among those rare cases where venture philanthropy has been successfully implemented within a government educational context. This case highlights how a private philanthropic organization went about executing a project and faced several challenges of scaling up the redevelopment model to other government schools. The other salient aspect is that this case delves into the dilemma faced by a philanthropist of either using the existing model for scaling up or adopting a totally different model.

Complexity academic level
Undergraduate and postgraduate business management courses.

Supplementary materials
Teaching Notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.

Subject code
CSS: 11: Strategy.
Spatial analysis of the factors influencing housing quality for renters in a traditional Nigerian city
Authors: Olowu Falilat Yetunde , Jaiyeoba Emmanuel Babatunde , Agbabiaka Hafeez Idowu , Daramola Olawunmi Johnson 
Published: February 2019

PurposeRental housing is an important form of accommodation; evaluating its quality will improve the quality of designs, standard living of renters, new dimension to policy guiding rental housing and enhance the values of rental houses. This study aims to examine the factors influencing rental housing quality in Ile-Ife, Nigeria.Design/methodology/approachMulti-stage sampling procedure was used to select tenants for the study. Residential areas were stratified into three densities: high, medium and low. Out of the 18 residential areas identified, six, eight and four were in the high, medium and low densities, respectively. Five residential areas were selected based on high concentrations of rental housing. The selected areas are Mokuro and Iloro (high density), Ife City and Eleyele (medium density) and Aladanla (low density). Systematic sampling technique was used to select 550 buildings where an adult tenant was selected per building for questionnaire administration.FindingsThe results of the principal component analysis established that four factors were generated for the high-density, nine factors for the medium-density and five factors for low-density areas as the major factors influencing rental housing quality. The variation in the number of factors generated and the percentage variance explained by the factors could be associated to the peculiarities across the densities in terms of the socioeconomic characteristics and housing characteristics of the renters.Originality/valueThis study examined the factors influencing housing quality for renters in Ile-Ife, Nigeria. It provides information on the three residential densities in terms of the variation in their housing morphology. The study went further to establish the relationship among the three musketeers such as socioeconomic characteristic of renters, housing characteristics and housing quality, under three dimensions environmental, internal building and external Building. Therefore, the contribution of this study strengthens the position that a minimum standard and schedule of upgrade and maintenance should be meted out for landlords to carry out repairs at interval, so as to make the housing unit and environment habitable for tenants.
Fineman and vulnerability
Authors: Cummins Ian 
Published: February 2019

Purpose
The purpose of this paper is to argue that the work of the American feminist political and legal philosopher, Martha Fineman can be the basis for a shift away from the proceduralism and managerialism that has come to dominate social work practice.

Design/methodology/approach
This paper’s work is based on the application of Fineman’s work to social welfare settings.

Findings
Fineman’s work calls for a radical rethinking of our notions of autonomy and vulnerability.

Originality/value
This paper applies Fineman’s work to this field.
Reflections on the theme issue outcomes
Authors: Munjal Sandeep , Tiwari Shweta , Teare Richard 
Published: February 2019

Purpose
This paper aims to profile the Worldwide Hospitality and Tourism Themes’ theme issue “How can the skilling India initiative become a solution to the critical need for skilled labour in the Indian hospitality industry?” with reference to the experiences of the theme editors and writing team.

Design/methodology/approach
This paper uses structured questions to enable the theme editors to reflect on the rationale for the theme issue question, the starting point, the selection of the writing team and material and the editorial process.

Findings
This paper reviews progress relating to the implementation of the “Skill India” initiative and its impact on the skilled-labour shortage as it relates to hospitality and tourism. Arising from the analysis are suggestions and recommendations to enhance the initiative’s effectiveness.

Practical implications
This paper observes that the Skill India initiative is an ambitious effort to facilitate skills-based training, but there are numerous concerns about its design and implementation.

Originality/value
This paper provides insights from both practitioner’s and academic’s perspectives as to how to overcome the gap in the availability of skilled and trained labour in the Indian hospitality industry.
Molecular characterization and expression of sensory neuron membrane proteins in the parasitoid Microplitis mediator (Hymenoptera: Braconidae)
Authors: Shan Shuang , Wang Shan‐Ning , Song Xuan , Khashaveh Adel , Lu Zi‐Yun , Dhiloo Khalid Hussain , Li Rui‐Jun , Gao Xi‐Wu , Zhang Yong‐Jun 
Published: February 2019

AbstractSensory neuron membrane proteins (SNMPs), homologs of the human fatty acid transport protein CD36 family, are observed to play a significant role in chemoreception, especially in detecting sex pheromone in Drosophila and some lepidopteran species. In the current study, two full‐length SNMP transcripts, MmedSNMP1 and MmedSNMP2, were identified in the parasitoid Microplitis mediator (Hymenoptera: Braconidae). Quantitative real‐time polymerase chain reaction analysis showed that the expression of MmedSNMP1 was significantly higher in antennae than in other tissues of both sexes. In addition, the MmedSNMP1 transcript was increased dramatically in newly emerged adults and there were no significant differences between adults with or without mating and parasitic experiences. However, compared with MmedSNMP1, the expression of MmedSNMP2 was widely found in various tissues, significantly increased at half‐pigmented pupae stage and remained at a relatively constant level during the following developmental stages. It was found that MmedSNMP1 contained eight exons and seven introns, which was highly conserved compared with other insect species. In situ hybridization assay demonstrated that MmedSNMP1 transcript was distributed widely in antennal flagella. Among selected chemosensory genes (odorant binding protein, odorant receptor, and ionotropic receptor genes), MmedSNMP1 only partially overlapped with MmedORco in olfactory sensory neurons of antennae. Subsequent immunolocalization results further indicated that MmedSNMP1 was mainly expressed in sensilla placodea of antennae and possibly involved in perceiving plant volatiles and sex pheromones. These findings lay a foundation for further investigating the roles of SNMPs in the chemosensation of parasitoids.