bluuebunny/crossref_metadata_2025_split huggingface dataset:
AlphaFold predicted structure of the Hsp90-like domains of the neurodegeneration linked protein sacsin reveals key residues for ATPase activity
Authors: Perna Laura , Romano Lisa E. L. , Prodromou Chrisostomos , Chapple J. Paul 
Published: October 2022

AbstractThe ataxia-linked protein sacsin has three regions of partial homology to Hsp90’s N-terminal ATP binding domain. Although a crystal structure for the Hsp90-like domain of sacsin has been reported the precise molecular interactions required for ATP-binding and hydrolysis are unclear. To better understand how sacsin may function as an ATPase we utilized an AlphaFold predicted structure of its Hsp90-like domain. Superimposition onto Hsp90, and other modelling approaches, have resulted in novel insights into sacsin’s structure. These encompass identification of residues within the sacsin Hsp90-like domains that are required for ATP binding and hydrolysis, including the catalytic arginine residues equivalent to that of the Hsp90 middle domain. Importantly, our analysis allows comparison of the Hsp90 middle domain with corresponding sacsin regions and has identified that sacsin has a shorter lid segment than the N-terminal domain of Hsp90. We also speculate, from a structural viewpoint, why ATP competitive inhibitors of Hsp90 do not appear to affect sacsin. Together our analysis supports the hypothesis that sacsin’s function is ATP-driven and would be consistent with it having a role as a molecular chaperone. We propose that the SR1 regions of sacsin be renamed as HSP-NRD (Hsp90 N-Terminal Repeat Domain; residues 84-324) and the fragment immediately after as HSP-MRD (Hsp90 Middle Repeat Domain; residues 325-518).
Absence ofStaphylococcus aureusin wild populations of fish supports a spillover hypothesis
Authors: Matuszewska Marta , Dabrowska Alicja , Murray Gemma G. R. , Kett Steve M. , Vick Andy J. A. , Banister Sofie C. , Pantoja Munoz Leonardo , Cunningham Peter , Welch John J. , Holmes Mark A. , Weinert Lucy A. 
Published: October 2022

AbstractStaphylococcus aureusis a human commensal and opportunistic pathogen that can also colonise and cause disease in other animal species. In humans and livestock, whereS. aureusis most studied, there is evidence that strains have different host specialisms. Recent studies have foundS. aureusin many wild animals, including fish, whose physiologies and ecologies are very different to humans. However, it remains unclear whetherS. aureusis adapted to and persisting within these species, or if its presence is due to repeated spillover from a source population. Distinguishing between these two scenarios is important for both public health and conservation. In this study we looked for evidence to support the hypothesis that the presence ofS. aureusin fish is the result of spillover, through testing for the presence ofS. aureusin fish that are isolated from likely source populations. We sampled 123 brown trout and their environment from 16 sites in the Scottish Highlands. All these sites are remote and have very low populations density of wild animal species known to carryS. aureus, but were selected to represent variable levels of exposure to humans, avian and livestock species. While our sampling methods readily detectedS. aureusfrom the external and internal organs of a farmed fish, we did not detectS. aureusin any wild trout or their environment from any of the 16 sites. We sequenced 12S. aureusisolates from the farmed fish. While they were all from clonal-complex 45, the genomic diversity was high enough to indicate repeated acquisition from a source population. In addition, the presence of a φSa3 prophage containing a human immune evasion cluster indicates a recent history of these isolates within human populations. Taken together, our results support the presence ofS. aureusin fish being due to spillover from other host populations, rather than the adaptation ofS. aureusto aquaculture or fish populations. Given predictions that fish consumption will increase, more whole genome sequencing ofS. aureusin aquaculture is needed to understand the presence ofS. aureusin these environments and to mitigate the risk to fish and human health.
How a methanogen assimilates sulfate: Structural and functional elucidation of the complete sulfate-reduction pathway
Authors: Jespersen Marion , Wagner Tristan 
Published: October 2022

AbstractBy growing on sulfate as the sole source of sulfur,Methanothermococcus thermolithotrophicusbreaks a dogma: the ancient metabolic pathways methanogenesis and sulfate-reduction should not co-occur in one organism due to toxic intermediates and energetic barriers. Using a complementary approach of physiological, biochemical, and structural studies, we provide a snapshot of the complete sulfate-reduction pathway of the methanogenic archaeon. While the first two reactions proceed via an ATP-sulfurylase and APS-kinase, common to other organisms, the further steps are catalysed by non-canonical enzymes. 3’-phosphoadenosine-5’-phosphosulfate (PAPS) released by the APS-kinase is converted into sulfite and 3’-phosphoadenosine-5’-phosphate (PAP) by a new class of PAPS-reductase that shares high similarity with the APS-reductases involved in dissimilatory sulfate-reduction. The generated PAP is efficiently hydrolysed by a PAP-phosphatase that was likely derived from an RNA exonuclease. Finally, the F420-dependent sulfite-reductase converts sulfite to sulfide for cellular assimilation. While metagenomic and metatranscriptomic studies suggest that genes of the sulfate-reduction pathway are present in various methanogens,M. thermolithotrophicususes a distinct way to assimilate sulfate. We propose that its entire sulfate-assimilation pathway was derived from a “mix-and-match” strategy in which the methanogen acquired assimilatory and dissimilatory enzymes from other microorganisms and shaped them to fit its physiological needs.
Generalized strategy for engineering mammalian cell-compatible RNA-based biosensors from random sequence libraries
Authors: Allchin Everett R. , Rosch Jonah C. , Kim Hyosung , Lippmann Ethan S. 
Published: October 2022

AbstractFluorescent RNA-based biosensors are useful tools for real-time detection of molecules in living cells. These biosensors typically consist of a chromophore-binding aptamer and a target-binding aptamer, whereby the chromophore-binding aptamer is destabilized until a target is captured, which causes a conformational change to permit chromophore binding and an increase in fluorescence. The target-binding region is typically fabricated using known riboswitch motifs, which are already known to have target specificity and undergo structural changes upon binding. However, known riboswitches only exist for a limited number of molecules, significantly constraining biosensor design. To overcome this challenge, we designed a framework for producing mammalian cell-compatible biosensors using aptamers selected from a large random library by capture-SELEX. As a proof-of-concept, we generated and characterized a fluorescent RNA biosensor against L-dopa, the precursor of several neurotransmitters. Overall, we suggest that this approach will have utility for generating RNA biosensors that can reliably detect custom targets in mammalian cells.
Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis
Authors: Kehrer Thomas , Cupic Anastasija , Ye Chengjin , Yildiz Soner , Bouhhadou Mehdi , Crossland Nicholas A , Barrall Erika , Cohen Phillip , Tseng Anna , Çağatay Tolga , Rathnasinghe Raveen , Flores Daniel , Jangra Sonia , Alam Fahmida , Mena Nacho , Aslam Sadaf , Saqi Anjali , Marin Arturo , Rutkowska Magdalena , Ummadi Manisha R. , Pisanelli Giuseppe , Richardson R. Blake , Veit Ethan C. , Fabius Jacqueline M. , Soucheray Margaret , Polacco Benjamin J. , Evans Matthew J. , Swaney Danielle L. , Gonzalez-Reiche Ana S. , Sordillo Emilia M. , van Bakel Harm , Simon Viviana , Zuliani-Alvarez Lorena , Fontoura Beatriz M. A. , Rosenberg Brad R. , Krogan Nevan J. , Martinez-Sobrido Luis , García-Sastre Adolfo , Miorin Lisa 
Published: October 2022

ABSTRACTWe and others have previously shown that the SARS-CoV-2 accessory protein ORF6 is a powerful antagonist of the interferon (IFN) signaling pathway by directly interacting with Nup98-Rae1 at the nuclear pore complex (NPC) and disrupting bidirectional nucleo-cytoplasmic trafficking. In this study, we further assessed the role of ORF6 during infection using recombinant SARS-CoV-2 viruses carrying either a deletion or a well characterized M58R loss-of-function mutation in ORF6. We show that ORF6 plays a key role in the antagonism of IFN signaling and in viral pathogenesis by interfering with karyopherin(importin)-mediated nuclear import during SARS-CoV-2 infection bothin vitro, and in the Syrian golden hamster modelin vivo. In addition, we found that ORF6-Nup98 interaction also contributes to inhibition of cellular mRNA export during SARS-CoV-2 infection. As a result, ORF6 expression significantly remodels the host cell proteome upon infection. Importantly, we also unravel a previously unrecognized function of ORF6 in the modulation of viral protein expression, which is independent of its function at the nuclear pore. Lastly, we characterized the ORF6 D61L mutation that recently emerged in Omicron BA.2 and BA.4 and demonstrated that it is able to disrupt ORF6 protein functions at the NPC and to impair SARS-CoV-2 innate immune evasion strategies. Importantly, the now more abundant Omicron BA.5 lacks this loss-of-function polymorphism in ORF6. Altogether, our findings not only further highlight the key role of ORF6 in the antagonism of the antiviral innate immune response, but also emphasize the importance of studying the role of non-spike mutations to better understand the mechanisms governing differential pathogenicity and immune evasion strategies of SARS-CoV-2 and its evolving variants.ONE SENTENCE SUMMARYSARS-CoV-2 ORF6 subverts bidirectional nucleo-cytoplasmic trafficking to inhibit host gene expression and contribute to viral pathogenesis.
Morphological and phylogenetic resolution ofConoideocrella luteorostrata(Hypocreales: Clavicipitaceae), a potential biocontrol fungus forFiorinia externain United States Christmas tree production areas
Authors: Lovett Brian , Barrett Hana , Macias Angie M. , Stajich Jason E. , Kasson Lindsay R. , Kasson Matt T. 
Published: October 2022

AbstractThe entomopathogenic fungusConoideocrella luteorostrata(Hypocreales: Clavicipitaceae) has recently been implicated in natural epizootics among exotic elongate hemlock scale (EHS) insects in Fraser fir Christmas tree farms in the eastern U.S. Since 1913, asexual populations ofC. luteorostratahave been reported from various plant-feeding Hemiptera in the southeastern U.S., but a thorough morphological and phylogenetic examination of the species, particularly detailed characterization of populations involved in recent epizootics in EHS, are lacking. The recovery of multiple strains ofC. luteorostratafrom mycosed EHS cadavers collected in Ashe County North Carolina provided an opportunity to conduct pathogenicity assays and morphological and phylogenetic studies to investigate genus- and species-level boundaries among members of the Clavicipitaceae. Pathogenicity assays confirmedC. luteorostratacauses mortality of EHS first instar crawlers, an essential first step in developingC. luteorostrataas a biocontrol. The results of the morphological study failed to recover a sexual stage from EHS cadavers or pure cultures, but revealed conidia aligned with previous measurements of the paecilomyces-like asexual state ofC. luteorostrata(6.9 µm x 2.6 µm average), with colony and conidiophore morphology consistent with previously reported observations. Additionally, a hirsutella-like synanamorph ofC. luteorostratawas observed for the first time under specific lab conditions. In both a four-locus, 54-taxa Clavicipitaceae-wide phylogenetic analysis including the D1–D2 domains of the nuclear 28S rRNA gene (28S), elongation factor 1 alpha (EF1-α), DNA-directed RNA polymerase II subunit 1 (RPB1) and DNA-directed RNA polymerase II subunit 2 (RPB2) and a two-locus, 38-taxa (28S & EF1-α) phylogenetic analysis,C. luteorostrata,C. tenuisandC. krungchingensiswere resolved as strongly supported monophyletic lineages across all loci and both methods (maximum likelihood & Bayesian inference) of phylogenetic inference with the exception of 28S forC. tenuis. Despite the strong support for individualConoideocrellaspecies, none of the analyses supported the monophyly of the genus, with the inclusion ofDussiella. Due to the paucity of publicly available RPB1 and RPB2 sequence data forConoideocrella, EF1-α provided superior delimitation of intraspecies groupings forC. luteorostrataandC. tenuisand should be used in future studies. Further development ofC. luteorostrataas a biocontrol agent against EHS both in Christmas tree farms and surrounding hemlock forests will require additional surveys across diverse Hemiptera and expanded pathogenicity testing to better understand host range and efficacy of this fungus.
Evidence of a novel viral membrane fusion mechanism shared by the Hepaci, Pegi and Pestiviruses
Authors: Oliver Michael R. , Toon Kamilla , Lewis Charlotte B. , Devlin Stephen , Gifford Robert J. , Grove Joe 
Published: October 2022

AbstractEnveloped viruses encode specialised glycoproteins that mediate fusion of viral and host membranes. Discovery and understanding of the molecular mechanisms of fusion has been achieved through structural analyses of glycoproteins from many different viruses, and yet the fusion mechanisms of some viral genera remain unknown. We have employed systematic genome annotation and AlphaFold modelling to predict the structures of the E1E2 glycoproteins from sixty viral species in the Hepaci, Pegi and Pestivirus genera. Whilst the predicted structure of E2 varied widely, E1 exhibited a very consistent fold across genera, despite little or no homology at the sequence level. Critically, the structure of E1 is unlike any other known viral glycoprotein. This is the first evidence that the Hepaci, Pegi and Pestiviruses possess a common and novel membrane fusion mechanism. Comparison of E1E2 models from various species reveals recurrent features that are likely to be mechanistically important and sheds light on the evolution of membrane fusion in these viral genera. These findings provide new fundamental understanding of viral membrane fusion and are relevant to structure-guided vaccinology.
Molecular programs of regional specification and neural stem cell fate progression in developing macaque telencephalon
Authors: Micali Nicola , Ma Shaojie , Li Mingfeng , Kim Suel-Kee , Mato-Blanco Xoel , Sindhu Suvimal , Arellano Jon I. , Gao Tianliuyun , Duque Alvaro , Santpere Gabriel , Sestan Nenad , Rakic Pasko 
Published: October 2022

AbstractEarly telencephalic development involves patterning of the distinct regions and fate specification of the neural stem cells (NSCs). These processes, mainly characterized in rodents, remain elusive in primates and thus our understanding of conserved and species-specific features. Here, we profiled 761,529 single-cell transcriptomes from multiple regions of the prenatal macaque telencephalon. We defined the molecular programs of the early organizing centers and their cross-talk with NSCs, finding primate-biased signaling active in the antero-ventral telencephalon. Regional transcriptomic divergences were evident at early states of neocortical NSC progression and in differentiated neurons and astrocytes, more than in intermediate transitions. Finally, we show that neuropsychiatric disease- and brain cancer-risk genes have putative early roles in the telencephalic organizers’ activity and across cortical NSC progression.One-Sentence SummarySingle-cell transcriptomics reveals molecular logics of arealization and neural stem cell fate specification in developing macaque brain
An empirical study on individual performance and turnover intention among university employees: a multiple mediation model
Authors: Aftab Muhammad , Bokhari Syed Asad Abbas , Ali Murad 
Published: October 2022

PurposeThe purpose of this study is to investigate the behavior of individual employee's performance concerning their organizational citizenship and turnover intention in the higher education sector. This study attempts to examine the effects of two potential sequential mediators – job satisfaction and employee engagement – on employees' job embeddedness, organizational citizenship behavior, and turnover intention.Design/methodology/approachThis study is based on a survey conducted among the employees of major universities in the Republic of Korea. A total of 213 valid responses are used to analyze the hypotheses.FindingsThe results suggest that the relationship between job embeddedness and organizational citizenship behavior is significantly mediated by job satisfaction. However, the mediating role of job satisfaction on the link between job embeddedness and employees' intention to leave is not significant. Relatedly, employee engagement has a significant mediating effect on job embeddedness and organizational citizenship behavior but no demonstrable mediating effect between job embeddedness and employees' turnover intentions.Practical implicationsThe results provide guidance that can assist organizations in increasing their employees' organizational citizenship behavior and lowering their intentions to leave, particularly in the education sector.Originality/valueThis study contributes to existing knowledge regarding the roles that job satisfaction and employee engagement play as two potential sequential mediators in the relation between job embeddedness and organizational citizenship behavior.
The role and place of mentorship for young people with blindness and low vision in educational contexts
Authors: Cain Melissa , Blackstock Danika Rhiannon , Fanshawe Melissa , Sukhai Mahadeo , Latour Ainsley 
Published: October 2022

PurposeThe purpose of this article is to understand the role and value of mentorship for young people with blindness and low vision (BLV) through their education and work journey and to provide a conceptual framework for developing mentoring opportunities for young people with BLV.Design/methodology/approachExperiences of formal and informal mentorship were gathered within two distinct groups: adolescents with BLV in Australia and young adults with BLV in Canada. Qualitative data were collected from semi-structured individualized interviews regarding the experiences, understanding, and valuing of mentorship within these groups.FindingsResults indicate the importance of informal role models and formal mentors within the lives of participants and how these become more refined and specific over time. Australian students valued role models as examples of success and inspiration for their own goals. Canadian mentees desired mentors as examples of personal lived experiences and providers of career-specific advice.Originality/valueThe study is original in its focus on the role of mentors for young people with blindness or low vision.
International marketing strategy of emerging market firms: the case of Bangladesh
Authors: Fregidou-Malama Maria , Chowdhury Ehsanul Huda , Hyder Akmal S. 
Published: October 2022

Purpose
This study aims to increase understanding of factors influencing the international marketing (IM) strategy of products from emerging markets (EMs) to international markets.

Design/methodology/approach
This study conducted case studies by collecting qualitative data through semistructured interviews with respondents from four food product companies in Bangladesh.

Findings
This study finds that the firms employ local Bangladeshi people who are knowledgeable in the company culture. They strategically focus on countries where the Bangladeshi diaspora lives and initially target them, approaching natives later. They adapt and customize products to the importers’ requirements to make them visible and increase understanding between product providers and local customers. The findings show that EM firms encounter a mentality that poor countries produce poor quality products; this mindset makes the internationalization of their business difficult.

Research limitations/implications
This research contributes to international product marketing of EM firms by constructing a model of a modern people-oriented marketing strategy for food products. This study contributes to literature on culture by illustrating that the cultural dimensions of collectivism and uncertainty avoidance enhance the development of networks and trust and impact marketing strategy.

Originality/value
This study theorizes the importance of context and an innovation-driven modern people-oriented IM strategy that adapts to customers’ preferences for food products and emphasizes the contribution of diaspora. This research reveals that Bangladeshi firms face challenges both because customers link the country and the companies to low-quality products and because governmental regulations prevent them from establishing a local presence in other countries. This study analyzes challenges EM firms face in the process of IM and the factors affecting Bangladesh in particular.
Large‐scale investigation of zoonotic viruses in the era of high‐throughput sequencing
Authors: Kawasaki Junna , Tomonaga Keizo , Horie Masayuki 
Published: October 2022

AbstractZoonotic diseases considerably impact public health and socioeconomics. RNA viruses reportedly caused approximately 94% of zoonotic diseases documented from 1990 to 2010, emphasizing the importance of investigating RNA viruses in animals. Furthermore, it has been estimated that hundreds of thousands of animal viruses capable of infecting humans are yet to be discovered, warning against the inadequacy of our understanding of viral diversity. High‐throughput sequencing (HTS) has enabled the identification of viral infections with relatively little bias. Viral searches using both symptomatic and asymptomatic animal samples by HTS have revealed hidden viral infections. This review introduces the history of viral searches using HTS, current analytical limitations, and future potentials. We primarily summarize recent research on large‐scale investigations on viral infections reusing HTS data from public databases. Furthermore, considering the accumulation of uncultivated viruses, we discuss current studies and challenges for connecting viral sequences to their phenotypes using various approaches: performing data analysis, developing predictive modeling, or implementing high‐throughput platforms of virological experiments. We believe that this article provides a future direction in large‐scale investigations of potential zoonotic viruses using the HTS technology.