bluuebunny/crossref_metadata_2025_split huggingface dataset:
Arbovirus-vector protein interactomics identifies Loquacious as a co-factor for dengue virus replication in Aedes mosquitoes
Authors: Besson Benoit , Lezcano Oscar M. , Overheul Gijs J. , Janssen Kirsten , Spruijt Cornelia G. , Vermeulen Michiel , Qu Jieqiong , van Rij Ronald P. 
Published: February 2022

ABSTRACTEfficient virus replication in Aedes vector mosquitoes is essential for the transmission of arboviral diseases such as dengue virus (DENV) in human populations. Like in vertebrates, virus-host protein-protein interactions are essential for viral replication and immune evasion in the mosquito vector. Here, 79 mosquito host proteins interacting with DENV non-structural proteins NS1 and NS5 were identified by label-free mass spectrometry, followed by a functional screening. We confirmed interactions with host factors previously observed in mammals, such as the oligosaccharyltransferase complex, and we identified protein-protein interactions that seem to be specific for mosquitoes. Among the interactors, the double-stranded RNA (dsRNA) binding protein Loquacious (Loqs), an RNA interference (RNAi) cofactor, was found to be essential for efficient replication of DENV and Zika virus (ZIKV) in mosquito cells. Loqs did not affect viral RNA stability or translation of a DENV replicon and its proviral activity was independent of its RNAi regulatory activity. Interestingly, Loqs colocalized with DENV dsRNA in viral replication organelles in infected cells and directly interacted with high affinity with DENV RNA in the 3’ untranslated region in vitro (KD = 100-200 nM). Our study provides an interactome for DENV NS1 and NS5 and identifies Loqs as a key proviral host factor in mosquitoes. We propose that DENV hijacks a factor of the RNAi mechanism for replication of its own RNA.AUTHOR SUMMARYDengue virus is a mosquito-transmitted virus endemic to the tropics and subtropics, affecting an estimated 390 million people yearly. While the mechanisms of infection, pathogenesis and immune evasion have been extensively studied in humans, replication in Aedes mosquitoes has received much less attention, despite being a critical step in the arbovirus transmission cycle. Here, we used a proteomic approach to identify Aedes mosquito proteins recruited by dengue virus non- structural proteins NS1 and NS5. In addition to previously established host proteins that interact with DENV in mammals, we identified Loquacious, a double-stranded RNA binding protein involved in the antiviral RNAi immune response of mosquitoes. Unexpectedly, our data showed Loquacious functions as a proviral factor that is recruited to replication organelles to facilitate viral RNA replication. We propose that DENV exploits host immune components, such as Loquacious, for its own benefit.
Habitat Suitability Modeling and Ecological Forecasting of Northern Goshawk Nesting Habitat
Authors: Wright Marylin. E. , Jackson Jenelle. , Tornberg Risto. , Higa Erica. , Clayton A. , McCartney Sean. , Ranglack Dustin H , Bickford Nate 
Published: February 2022

ABSTRACTNorthern Goshawks (Accipiter gentilis) are dynamic forest raptors often used as a management indicator species in forest management planning. Despite their use as indicators, there is a limited understanding of habitat requirements for goshawks, especially in dry forested landscapes as climate change occurs. We examined goshawk nesting habitat on the Helena-Lewis and Clark National Forest (HLCNF) in central Montana to further understand climate change on goshawk nesting habitat. The HLCNF receives low annual precipitation, making this forest useful to understand climate change in dry forest in structure and ecology. We measured characteristics of nest sites throughout the HLCNF and used principle component analysis to predict important variables for nest trees and nesting habitat for goshawks in this landscape. We also used remote sensing and GIS to create a composite map predicting areas of high, medium and low suitability for nesting habitat for goshawks in the HLCNF. We used the composite map to predict potential impacts of mountain pine beetle (Dendroctonus ponderosae), fire, and climate change to Northern Goshawk habitat in the HLCNF. The best indicators of a chosen nest tree were diameter at breast height, tree height, and tree status, which can be considered indicative of trees preferred for nesting by goshawks. The best indicators for nest forest were canopy closure, slope angle, and slope position, which indicate habitat areas of high suitability for goshawk nesting. Two forecast models where developed based on climate change predictions. After overlapping a projected mountain pine beetle risk map and fire frequency risk map onto the modeled of high suitability goshawk nesting habitat, we calculated that 52 % of modeled high suitability habitat may be at risk for mountain pine beetle blight and 66 % high suitability habitat at risk for frequent wildfires, which will reduce goshawk habitat quality.
Air pollution induces Staphylococcus aureus USA300 respiratory tract colonisation mediated by specific bacterial genetic responses dependent on the global virulence gene regulators Agr and Sae
Authors: Purves Jo , Hussey Shane. J. K. , Corscadden Louise , Purser Lillie , Hall Andie , Misra Raju , Monks Paul S. , Ketley Julian M. , Andrew Peter W. , Morrissey Julie A. 
Published: February 2022

SummaryExposure to particulate matter (PM), a major component of air pollution, is associated with exacerbation of chronic respiratory disease, and infectious diseases such as community acquired pneumonia. Although PM can cause adverse health effects through direct damage to host cells, our previous study showed that PM can also impact bacterial behaviour by promoting in vivo colonisation. In this study we describe the genetic mechanisms involved in the bacterial response to exposure to black carbon (BC), a constituent of PM found in most sources of air pollution. We show that Staphylococcus aureus strain USA300 LAC grown in BC prior to inoculation showed increased murine respiratory tract colonisation and pulmonary invasion in vivo, as well as adhesion and invasion of human epithelial cells in vitro. Global transcriptional analysis showed that BC has a widespread effect on S. aureus transcriptional responses, altering the regulation of the major virulence gene regulators Sae and Agr and causing increased expression of genes encoding toxins, proteases, and immune evasion factors. Together these data describe a previously unrecognised causative mechanism of air pollution-associated infection, in that exposure to BC can increase bacterial colonisation and virulence factor expression by acting directly on the bacterium rather than via the host.Originality-Significance StatementThis study shows that exposure to air pollution results in a global change in gene expression in bacteria. Specifically, our data show that in the important human pathogen Staphylococcus aureus, exposure to a major constituent of air pollution, black carbon (BC) results in widespread changes in global gene expression, altering the expression of key virulence determinants. Furthermore, S. aureus that are exposed to BC prior to inoculation show increased colonisation of the murine nasopharynx and lungs in vivo, and increased adhesion and invasion in lung epithelial cells in vitro. These findings indicate that air pollution has a significant and direct impact on bacteria, altering their behaviour and their potential to colonise and invade during infection. While many studies have taken a host-focussed approach to studying the impact of air pollution on human health, this study takes a pathogen-focussed approach to further the understanding of these fundamental interactions to identify new causative mechanisms of the detrimental effects of air pollution. This is critical for understanding the adverse health effects caused by exposure to air pollution, the single largest environmental risk to human health in the world.
Model-free prediction of microbiome compositions
Authors: Asher Eitan E. , Bashan Amir 
Published: February 2022

AbstractThe recent recognition of the importance of the microbiome to the host’s health and well-being, has yielded efforts to develop therapies that aim to shift the microbiome from a disease-associated steady-state to a healthier one. Direct manipulation techniques of the species’ assemblage are currently available, e.g., using probiotics or narrow-spectrum antibiotics to introduce or eliminate specific taxa. However, predicting the species’ abundances at the new steady-state remains a challenge, mainly due to the difficulties of deciphering the delicate underlying network of ecological interactions or constructing a predictive model for such complex ecosystems. Here, we propose a model-free method to predict the species’ abundances at the new steady state based on their presence/absence configuration by utilizing a multi-dimensional k-nearest-neighbors (kNN) regression algorithm. By analyzing data from numeric simulations of ecological dynamics, we show that our predictions, which consider the presence/absence of all species holistically, outperform both the null model that uses the statistics of each species independently and a predictive neural network model. We analyze real metagenomic data of human-associated microbial communities and found that by relying on a small number of ‘neighboring’ samples, i.e., samples with similar species assemblage, the kNN predicts the species abundance better than the whole-cohort average. By studying both real metagenomic and simulated data, we show that the predictability of our method is tightly related to the dissimilarity-overlap relationship of the training data. Our results demonstrate how model-free methods can prove useful in predicting microbial communities and may facilitate the development of microbial-based therapies.
Deep sequencing of yeast and mouse tRNAs and tRNA fragments using OTTR
Authors: Gustafsson H. Tobias , Galan Carolina , Yu Tianxiong , Upton Heather E. , Ferguson Lucas , Kaymak Ebru , Weng Zhiping , Collins Kathleen , Rando Oliver J. 
Published: February 2022

ABSTRACTAmong the major classes of RNAs in the cell, tRNAs remain the most difficult to characterize via deep sequencing approaches, as tRNA secondary structure and nucleotide modifications can both interfere with cDNA synthesis by commonly-used reverse transcriptases (RTs). Here, we benchmark a recently-developed RNA cloning protocol, termed Ordered Two-Template Relay (OTTR), to characterize intact tRNAs and tRNA fragments in budding yeast and in mouse tissues. We find that OTTR robustly captures full-length tRNAs in budding yeast and in mouse testis, with relatively low levels of premature termination at known barriers – 1-methylguanine, N2,N2-dimethylguanine, and 1-methyladenine – to typical reverse transcriptases. Moreover, these and several other nucleotide modifications leave misincorporation signatures in OTTR datasets which enables their detection without any additional protocol steps. Turning to analysis of small RNAs such as tRNA cleavage products, we compare OTTR with several standard small RNA-Seq protocols, finding that OTTR provides the most accurate picture of tRNA fragment levels by comparison to “ground truth” Northern blots. Applying this protocol to mature mouse spermatozoa, our data dramatically alter our understanding of the small RNA cargo of mature mammalian sperm, revealing a far more complex population of tRFs – including both 5’ and 3’ tRNA halves derived from the majority of tRNAs – than previously appreciated. Taken together, our data confirm the superior performance of OTTR to commercial protocols in analysis of tRNA fragments, and force a reappraisal of potential epigenetic functions of the sperm small RNA payload.
Human XIST RNA acts early to condense architecture which facilitates A-repeat density-dependent initiation of gene silencing
Authors: Valledor Melvys , Byron Meg , Dumas Brett , Carone Dawn M. , Hall Lisa L. , Lawrence Jeanne B. 
Published: February 2022

SUMMARYXIST RNA triggers gene silencing chromosome-wide and transforms a euchromatic chromosome into a condensed Barr body. XIST is heavily studied in mouse ES cells, but here an inducible iPSC system allows analysis of initial steps in human chromosome silencing, revealing key points not known in either system. XIST RNA distribution was examined relative to biochemical and transcriptional changes directly within architecture of individual chromosome territories. Within a few hours of induction, XIST transcripts distribute as a large “sparse zone” and a smaller “dense zone”, which, importantly, exhibit different effects on chromatin. Very sparse transcripts immediately trigger bright staining for H2AK119ub and CIZ1, a structural matrix protein. In contrast, H3K27me3 enrichment comes hours later and is much more restricted to the smaller dense RNA zone, which enlarges as the chromosome condenses. Importantly, silencing of several genes examined occurred well after architectural condensation, suggesting a possibly separable step. Surprisingly, we show the small A-repeat fragment of XIST can alone silence endogenous genes; however, results indicate this requires high local RNA density for effective histone deacetylation. Results support a concept whereby XIST RNA acts directly to condense the chromosome territory, comprised largely of non-coding DNA, which facilitates a required step to initiate gene silencing by the A-repeat. Hence, compacted architecture is not a consequence of collective gene silencing, but an early step required for chromosome-wide gene silencing.
Understanding the Separation of Timescales in Rhodococcus erythropolis Proteasome Core Particle Assembly
Authors: Itagi Pushpa , Kante Anupama , Lagunes Leonila , Deeds Eric J. 
Published: February 2022

AbstractThe 20S proteasome Core Particle (CP) is a molecular machine that is a key component of cellular protein degradation pathways. Like other molecular machines, it is not synthesized in an active form, but rather as a set of subunits that assemble into a functional complex. The CP is conserved across all domains of life and is composed of 28 subunits, 14 α and 14 β, arranged in four stacked 7-member rings (α7β7β7α7). While details of CP assembly vary across species, the final step in the assembly process is universally conserved: two half proteasomes (HP: α7β7) dimerize to form the CP. In the bacterium Rhodococcus erythropolis, experiments have shown that the formation of the HP is completed within minutes, while the dimerization process takes hours. The N-terminal propeptide of the β subunit, which is autocatalytically cleaved off after CP formation, plays a key role in regulating this separation of time scales. However, the detailed molecular mechanism of how the propeptide achieves this regulation is unclear. In this work, we used Molecular Dynamics (MD) simulations to characterize HP conformations and found that the HP exists in two states: one where the propeptide interacts with key residues in the HP dimerization interface and likely blocks dimerization, and one where this interface is free. We found that a propeptide mutant that dimerizes extremely slowly is essentially always in the non-dimerizable state, while the WT rapidly transitions between the two. Based on these simulations, we designed a propeptide mutant that favored the dimerizable state in MD simulations. In vitro assembly experiments confirmed that this mutant dimerizes significantly faster than WT. Our work thus provides unprecedented insight into how this critical step in CP assembly is regulated, with implications both for efforts to inhibit proteasome assembly and for the evolution of hierarchical assembly pathways.
A centromeric RNA-associated protein complex affects germ line development in Drosophila melanogaster
Authors: Höcker Saskia L. , Akan Izlem Su , Simon Alexander M. , Yildirim Kerem , Kenéz Lili A. , Lohmann Ingrid , Erhardt Sylvia 
Published: February 2022

AbstractIn many metazoans, centromeres are embedded in large blocks of highly repetitive (peri-) centromeric heterochromatin from which non-coding RNAs emanate that have been assigned diverse functions in different species. However, little is known about their functional details or regulation. The pericentromere of the X chromosome in Drosophila melanogaster contains a multi mega-base array of the 359 bp satellite repeats from the 1.688 family, which is transcribed into a lncRNA (SAT III RNA). We performed a SAT III RNA pulldown assay and identified a SAT III RNA-associated complex of four previously uncharacterized proteins and show that they affect germline development. These factors not only interact with each other and with SAT III RNA but also co-regulate each other. RNAi depletion of any of the factors leads to severe defects in the developing germline and sterility. Moreover, we show that the complex plays a crucial role in SAT III RNA repression, as RNAi depletion of the factors leads to a drastic increase of SAT III RNA levels. Importantly, genetic reduction of SAT III RNA level in the RNAi-depleted flies partially rescued the germ line defects and infertility phenotype. Based on our results we hypothesize that the identified complex functions in the germline to regulate SAT III RNA levels, possibly to offset effects of chromatin remodelling taking place in the developing germline.
Fashion entrepreneurial self-efficacy: development and validation of a domain-specific scale
Authors: Lang Chunmin , Liu Chuanlan 
Published: February 2022

PurposeThe purpose of this research is to develop a multidimensional measurement of fashion domain entrepreneurial self-efficacy (FDESE) based on which fashion entrepreneurs will be able to better develop strategies to gain and sustain success in their business development. The research is crucial to advocate fashion entrepreneurship and will provide direction for fashion business incubation services.Design/methodology/approachThis research included three stages with mixed qualitative and quantitative approaches: conceptualizing construct definition and specifying domain(s) to generate initial items, scale purification and scale validation. This study started with reviewing the literature and individual interviews among 19 fashion entrepreneurs, which generated 72 initial items. An online survey was then conducted with individuals who are running or have the intention to run fashion businesses, yielding 249 useable samples for scale purification, which generated 21 items for the validation phase. Lastly, another online survey was administered to individuals who are currently running fashion businesses which resulted in 258 valid responses included for scale validation.FindingsA measure of FDESE that is both reliable and valid was developed, including 21 items across four distinct dimensions: passion for fashion business (five items), marketing and branding (seven items), financial management (five items) and creativity (four items).Originality/valueThis study is the first attempt to develop practical scales measuring self-efficacy that focus on fashion domain entrepreneurship. The newly developed FDESE scale indicates that entrepreneurship not only involves marketing skills, financial knowledge, creativity, leadership, and proactivity but also requires passion and persistence.
Enterprise agility – its meaning, managerial expectations and barriers to implementation – a survey of three countries
Authors: Zakrzewska Małgorzata , Jarosz Szymon , Piwowar-Sulej Katarzyna , Sołtysik Mariusz 
Published: February 2022

PurposeThe aim of the article is to define the way of understanding of agile in enterprises, to verify the factors limiting agility implementation, as well as to understand what the expectations of enterprise management towards agile implementation are.Design/methodology/approachThe article uses both literature studies and empirical research. The research was conducted in 2019 in 152 companies located in Luxemburg, Croatia and Poland, which have implemented an agile approach to management.FindingsIn most of the surveyed organisations, agile is understood as a methodology for creating projects or applications. The most common barriers to implementing agile in the surveyed enterprises are culture too deeply rooted in traditional methodologies and the lack of funds to introduce transformations. Growth in productivity and competitiveness and reducing delivery time stand out among the most common expectations of the management of the surveyed enterprises.Originality/valueThe article is in line with the idea of analysing the key factors of a successful agile implementation, which can be a guideline for an enterprise to manage the adoption of agility. The article utilises original research tools, provides comparisons between countries and presents implications for practitioners and researchers.
Resource type and SME alliance formation: the contingent role of perceived environmental uncertainty
Authors: Prabhudesai Rohit , Pangarkar Nitin , Prasad Ch.V.V.S.N.V. 
Published: February 2022

PurposeThe aim of the study was to determine how the different types of resources possessed by a small- and medium-sized enterprise (SME), in conjunction with the environmental uncertainty perceived by the SME's managers, affect SME's alliance formation.Design/methodology/approachPersonal interview method was used to collect responses to a survey instrument from Indian SMEs. Logistic regression technique was used to analyze the responses obtained from 127 manufacturing enterprises.FindingsThe study finds that while both tangible and intangible resources possessed by an enterprise positively influence the enterprise's alliance formation, the influence of intangible resources is significantly stronger. The authors also observed the interactive effect between each resource type and environmental uncertainty to be a significant predictor of alliance formation.Research limitations/implicationsThe study does not account for temporal effects such as changes in resources and perceived environmental uncertainty, which may affect alliance formation. Similarly, because the data were obtained from a geographically restricted sample, replication of the study in other geographies may be necessary for generalizing the results.Originality/valueThe paper responds to the call for research to link firm resources and perceived environmental uncertainty toward explaining alliance formation by SMEs. The study went beyond making a distinction between the two types of resources by explicating how the interaction of resource type and environmental uncertainty will affect alliance formation.
Timed reading activity for developing EFL students' reading skills in mixed-ability classes
Authors: Hazaea Abduljalil Nasr , Almekhlafy Sultan Saleh Ahmed 
Published: February 2022

PurposeStudents of mixed-ability learning together in one class is a challenge for all educators, especially in English as foreign language (EFL) contexts. Timed reading activity (TRA) is an activity that can help educators address the learning needs of students in such a context. The present study investigated the effectiveness of the TRA in enhancing EFL students' reading rate and reading comprehension as well as in making them aware of potentially wrong reading strategies that they may be using.Design/methodology/approachA classroom intervention was designed for a group of preparatory year (PY) students at a Saudi university. The study sample consisted of one intact class of 29 students. Data were collected from pre- and post-tests of students' reading rate and reading comprehension as well as progress charts. In addition, a questionnaire was used to identify the reading strategies used by the students.FindingsThe results showed that the TRA generally enhanced the reading comprehension and the reading rate of EFL mixed-ability students as well as raised their awareness of their use of wrong fast reading strategies.Originality/valueThe results of the study support the use of TRA as a remedial reading activity in EFL mixed-ability classes.