bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Ferrous Iron Transporter FeoB1 is Essential for Clostridioides difficile Toxin Production and Pathogenesis in Mice
Authors: Deshpande Aditi , Olaitan Abiola O. , Mckelvey Ann M. , Rutherford Jacob T. , Hurdle Julian G. 
Published: March 2022

ABSTRACTFerrous iron is the dominant form of iron in the oxygen-limited large intestine, the site for Clostridioides difficile infection (CDI). We investigated the extent to which C. difficile requires the ferrous iron transporter 1 (FeoB1), a main permease for iron acquisition, using in vitro and in vivo approaches. Construction of feoB1 deletion mutant in C. difficile R20291 (i.e., R20291ΔfeoB1) decreased intracellular iron content by ~25%. This was accompanied by reduced synthesis of TcdA and TcdB toxins and downregulation of tcdA and tcdB genes, which was reflected by a ~1000-fold reduction in cytopathy against Vero cells. Complementation with WT feoB1 restored toxin production. R20291ΔfeoB1 was avirulent in mice with underlying colitis. In this model, mice are prone to develop severe CDI, but mice infected with the mutant lacked diarrheal symptoms, had lesser inflammatory responses, bacterial bioburdens and cecal toxin titers. Transcriptional and biochemical analyses revealed ΔfeoB1 altered metabolic pathways that negatively impact toxin production, including downregulation of the oxidative branch of the Kreb cycle and an associated cellular accumulation of pyruvate. Hence FeoB1 influences multiple bioenergetic and redox pathways, which in turn inhibits toxin biosynthesis. Targeting FeoB1 could be a potential therapeutic strategy to impede the colonization and pathogenesis of C. difficile, even in the setting of colitis where CDI is more severe and intestinal bleeding may occur.AUTHOR SUMMARYClostridioides difficile is a major cause of antibiotic associated diarrhea that result in significant morbidity and mortality in hospitals. The ability of C. difficile to cause disease and damage the gut is directly related to the production of toxin A and toxin B. Without these toxins, C. difficile is not virulent. There is need to identify drug targets and therapeutic strategies that prevent C. difficile from producing toxins A and B. For C. difficile to colonize the large bowel, it must acquire ferrous iron, which is thought to be the main form of iron within the oxygen-limited large bowel environment. We show that genetic deletion of the ferrous iron transporter FeoB1 stops C. difficile from producing significant amounts of toxins under in vitro conditions. Importantly, the mutant R20291ΔfeoB1 was avirulent when tested in a mouse model that favors the development of severe infections. Avirulence of R20291ΔfeoB1 was related to the strain having significant metabolic changes that negatively impact toxin production. For example, cells could not properly metabolize pyruvate, which became accumulated in cells; pyruvate is known to reduce the production of toxins A and B. Our study provides new insights into how FeoB1 affects C. difficile colonization and disease development, indicating FeoB1 could be a drug target to stop toxin production in this bacterium.
Information Decay and Enzymatic Information Recovery for DNA Data Storage
Authors: Meiser Linda C. , Gimpel Andreas L. , Deshpande Tejas , Libort Gabriela , Chen Weida D. , Heckel Reinhard , Nguyen Bichlien H. , Strauss Karin , Stark Wendelin J. , Grass Robert N. 
Published: March 2022

ABSTRACTSynthetic DNA has been proposed as a storage medium for digital information due to its high theoretical storage density and anticipated long storage horizons. However, under all ambient storage conditions, DNA undergoes a slow chemical decay process resulting in nicked (broken) DNA strands, and the information stored in these strands is no longer readable. In this work we design an enzymatic repair procedure, which is applicable to the DNA pool prior to readout and can partially reverse the damage. Through a chemical understanding of the decay process, an overhang at the 3’ end of the damaged site is identified as obstructive to repair via the base excision-repair (BER) mechanism. The obstruction can be removed via the enzyme apurinic/apyrimidinic endonuclease I (APE1), thereby enabling repair of hydrolytically damaged DNA via Bst polymerase and Taq ligase. Simulations of damage and repair reveal the benefit of the enzymatic repair step for DNA data storage, especially when data is stored in DNA at high storage densities (= low physical redundancy) and for long time durations.
ReLo is a simple and quick colocalization assay to identify and characterize direct protein-protein interactions
Authors: Salgania Harpreet Kaur , Metz Jutta , Jeske Mandy 
Published: March 2022

ABSTRACTThe characterization of protein-protein interactions (PPIs) is fundamental for understanding biochemical processes. Many methods have been established to identify and study direct PPIs; however, the screening and investigation of PPIs involving large or poorly soluble proteins remain challenging. As a result, we developed ReLo, a simple, rapid, and versatile cell culture-based method for detecting and investigating interactions in a cellular context. Importantly, our data strongly suggest that with ReLo specifically direct binary PPIs are detected. By applying additional bridging experiments ReLo can also be used to determine the binding topology of subunits within multiprotein complexes. Moreover, ReLo has the potential to identify protein domains that mediate complex formation, screen for interfering point mutations, study interactions that depend on conformation or protein arginine methylation, and it is sensitive to drugs that mediate or interfere with an interaction. Taken together, ReLo is a simple and quick alternative for the study of PPIs particularly when established methods fail.
A family of unusual immunoglobulin superfamily genes in an invertebrate histocompatibility complex
Authors: Huene Aidan L. , Sanders Steven M. , Ma Zhiwei , Nguyen Anh-Dao , Koren Sergey , Michaca Manuel H. , Mullikin James C. , Phillippy Adam M. , Schnitzler Christine E. , Baxevanis Andreas D. , Nicotra Matthew L. 
Published: March 2022

ABSTRACTMost colonial marine invertebrates are capable of allorecognition, the ability to distinguish between themselves and conspecifics. One long-standing question is whether invertebrate allorecognition genes are homologous to vertebrate histocompatibility genes. In the cnidarian Hydractinia symbiolongicarpus, allorecognition is controlled by at least two genes, Allorecognition 1 (Alr1) and Allorecognition 2 (Alr2), which encode highly polymorphic cell surface proteins that serve as markers of self. Here, we show that Alr1 and Alr2 are part of a family of 41 Alr genes, all of which reside a single genomic interval called the Allorecognition Complex (ARC). Using sensitive homology searches and highly accurate structural predictions, we demonstrate that the Alr proteins are members of the immunoglobulin superfamily (IgSF) with V-set and I-set Ig domains unlike any previously identified in animals. Specifically, their primary amino acid sequences lack many of the motifs considered diagnostic for V-set and I-set domains, yet they adopt secondary and tertiary structures nearly identical to canonical Ig domains. Thus, the V-set domain, which played a central role in the evolution of vertebrate adaptive immunity, was present in the last common ancestor of cnidarians and bilaterians. Unexpectedly, several Alr proteins also have immunoreceptor tyrosine-based activation motifs (ITAMs) and immunoreceptor tyrosine-based inhibitory motifs (ITIMs) in their cytoplasmic tails, suggesting they could participate in pathways homologous to those that regulate immunity in humans and flies. This work expands our definition of the IgSF with the addition of a family of unusual members, several of which play a role in invertebrate histocompatibility.Significance StatementThe immunoglobulin superfamily (IgSF) is one of the largest and most functionally versatile domain families in animal genomes. Although their amino acid sequences can vary considerably, IgSF domains have been traditionally defined by conserved residues at several key positions in their fold. Here, we sequenced an invertebrate histocompatibility complex and discovered a family of IgSF genes with amino acid sequences that lack most of these residues yet are predicted to adopt folds virtually identical to canonical V-set and I-set IgSF domains. This work broadens the definition of the IgSF and shows that the V-set domain was present earlier in animal evolution than previously appreciated.
FAM172A controls the nuclear import and alternative splicing function of AGO2
Authors: Sallis Sephora , Bérubé-Simard Félix-Antoine , Grondin Benoit , Leduc Elizabeth , Azouz Fatiha , Bélanger Catherine , Pilon Nicolas 
Published: March 2022

AbstractThe poorly characterized protein FAM172A is mutated in some individuals affected by a disorder of neural crest development called CHARGE syndrome. We also know that FAM172A can interact with the main CHARGE syndrome-associated protein CHD7 and the small RNA-binding protein AGO2 at the chromatin-spliceosome interface. Focusing on this intriguing FAM172A-AGO2 interaction, we now report that FAM172A is one of the long sought-after regulator of AGO2 nuclear import. This FAM172A function relies on its nuclear localization signal, being enhanced by CK2-mediated phosphorylation and abrogated by a CHARGE syndrome-associated missense mutation. Accordingly, Fam172a and Ago2 genetically interact in mice, and neural crest-specific depletion of Ago2 is sufficient to phenocopy CHARGE syndrome without impacting post-transcriptional gene silencing. Rapamycin-mediated rescue suggests that observed morphological anomalies are instead due to alternative splicing defects. This work thus demonstrates that non-canonical nuclear functions of AGO2 and associated regulatory mechanisms may be clinically relevant.
Morph-dependent nematode infection and its association with host movement in the land snail Cepaea nemoralis (Mollusca, Gastropoda)
Authors: Dahirel Maxime , Proux Marine , Gérard Claudia , Ansart Armelle 
Published: March 2022

AbstractHost behaviour can be influenced by parasitic risk and infection through a variety of direct and indirect mechanisms. We can expect individuals expressing different phenotypes to also differ in the ways their behaviour is altered by parasites. We used the land snail Cepaea nemoralis, a species with various shell colour morphs differing in behaviour and physiology, as a model to study the link between parasite response and individual behaviour variation. We analysed metazoan parasite abundance and its relation to behaviour (movement and food intake) in snails from three shell morphs (from light unbanded to darker five-banded) and from two neighbouring populations from contrasted environments. Snails were parasitized by mites, trematodes and nematodes, from rarest to most frequent. We confirm that terrestrial gastropods can defend against infection by trapping parasitic nematodes in their shell. We show that nematode encapsulated in shells can uncover past infections even when a snail population is currently nematode-free, possibly due to parasite seasonality. We present new observations suggesting that not only nematodes but also mites might be encapsulated in shells. Infection levels varied between morphs, with darker snails harbouring fewer nematodes. Behaviour (movement and food intake) was linked to nematode, but not trematode infection. Individuals with higher nematode load ate less, irrespective of morph and population. The most-infected morph (unbanded snails) showed reduced activity in the nematode-infected population compared to the one that was nematode-free at sampling time. As a result, parasites may cancel previously described behavioural differences between morphs. We discuss the possible mechanisms explaining morph-dependent responses to parasites, and how parasite risk may be an unseen force shaping C. nemoralis morph variation in space and time. We conclude on the possible ecological consequences of the link, mediated by shell colour, between thermal and immune responses.
Extrafollicular responses are sufficient to drive initiation of autoimmunity and early disease hallmarks of lupus
Authors: Voss Lasse F. , Howarth Amanda J. , Wittenborn Thomas R. , Hummelgaard Sandra , Juul-Madsen Kristian , Kastberg Kristian S. , Pedersen Mathias K. , Jensen Lisbeth , Papanastasiou Anastasios D. , Vorup-Jensen Thomas , Weyer Kathrin , Degn Søren E. 
Published: March 2022

AbstractMany autoimmune diseases are characterized by germinal center (GC) derived affinity-matured, class-switched autoantibodies. Strategies to block GC formation and progression are currently being explored clinically, however, extrafollicular responses may also contribute to early events in autoimmunity. To investigate the relative contribution of these two pathways in autoimmune disease development, we leveraged a transgenic strategy to genetically block the GC pathway. Surprisingly, this accelerated extrafollicular responses and failed to curb autoimmune progression in two lupus models.In vitro, loss of the GC transcription factor Bcl-6 prevented cellular expansion and accelerated plasma cell differentiation, suggesting thein vivophenotype was caused by rewiring of B cell intrinsic transcriptional programming. In a competitive scenarioin vivo, B cells harboring the genetic GC block contributed disproportionately to the plasma cell output. Taken together, this emphasizes the extrafollicular pathway as a key contributor to autoimmune progression, and suggests that strategies aimed at blocking GCs should simultaneously target this pathway to avoid rerouting the pathogenic response.Highlights-A genetic GC block fails to prevent autoimmune progression in two lupus models-An intrinsic GC block drives B cell differentiation into terminally differentiated plasma cellsin vitro-B cells harboring a GC block competitively contribute to the plasma cell compartment in an autoreactive settingin vivo-Lupus mice with a GC block display immune complex deposition in kidney glomeruli that is indistinguishable from their wild-type counterpartsSummaryAffinity-matured autoantibodies generated in germinal centers are a hallmark of autoimmune diseases. Voss et al. block germinal centers in two autoimmune models, but surprisingly find that disease progresses unimpeded. They identify the extrafollicular pathway as a ‘backdoor to autoimmunity’.
The importance of m6A topology in chicken embryo mRNA; a precise mapping of m6A at the conserved chicken β-actin zipcode
Authors: Baron Francis , Zhang Mi , Archer Nathan , Bellows Eleanor , Knight Helen M. , Welham Simon , Rutland Catrin S , Mongan Nigel P. , Hayes Christopher J. , Fray Rupert G. , Bodi Zsuzsa 
Published: March 2022

AbstractN6-Methyladenosine (m6A) in mRNA regulates almost every stage in the mRNA life cycle, and the development of methodologies for the high throughput detection of methylated sites in mRNA using m6A-specific methylated RNA immunoprecipitation with next-generation sequencing (MeRIPSeq) or m6A individual-nucleotide-resolution cross-linking and immunoprecipitation (miCLIP) have revolutionized the m6A research field. Both of these methods are based on immunoprecipitation of fragmented mRNA. However, it is well documented that antibodies often have nonspecific activities, thus verification of identified m6A sites using an antibody-independent method would be highly desirable. We mapped and quantified the m6A site in the chicken β-actin zipcode based on the data from chicken embryo MeRIPSeq results and our RNA-Epimodification Detection and Base-Recognition (RedBaron) antibody independent assay. We also demonstrated that methylation of this site in the β-actin zipcode enhances ZBP1 binding in vitro, whilst methylation of a nearby adenosine abolishes binding. This suggests that m6A may play a role in regulating localised translation of β-actin mRNA, and the ability of m6A to enhance or inhibit a reader protein’s RNA binding highlights the importance of m6A detection at nucleotide resolution.
Applying an interactive learning approach provided by an academic coach in a graduate-level accounting course
Authors: Wen Lei , Wang Yingqi 
Published: March 2022

PurposeThe paper makes a significant contribution to the accounting education literature by examining the impact of using online meetings with an academic coach on student-perceived learning outcomes, course and instructor evaluations in an online graduate-level accounting course.Design/methodology/approachA quasi-experimental design is adopted by the author to compare the students' evaluations in fall 2018 and in spring 2019 in an online graduate-level accounting course taught by the same instructor and assisted by the same academic coach.FindingsThe study finds that the use of online meetings with an academic coach helps students have a much positive view about the course and a better perception about the instructor's teaching effectiveness for the course. The offering of online meetings by an academic coach also improves students' evaluation about the academic coach in an online graduate-level accounting course.Originality/valueThe paper provides a new perspective to investigate students' perception with the use of online meetings with an academic coach.
Building a bridge between civic agriculture and civic engagement: farmers’ markets as communication infrastructure
Authors: Witzling Laura , Shaw Bret R. 
Published: March 2022

PurposeThis work aimed to show how farmers’ markets can act as communication infrastructure, and by doing so, facilitate civic engagement. We used communication infrastructure theory (CIT) as a guide.Design/methodology/approachWe integrated findings from two surveys that took place in the US state of Wisconsin. In a survey of Wisconsin farmers’ market leaders, we considered what features farmers’ markets have that may help them act as communication infrastructure. Using data from a survey of Wisconsin residents, we ran a regression model to demonstrate the relationship between farmers’ market attendance and micro-level storytelling about local food.FindingsWe found that farmers’ markets can act as meso-level storytellers and provide a communication action context supportive of civic engagement. Through the farmers’ market leader survey, we found that over half of the markets noted existing partnerships with media outlets. Furthermore, farmers’ markets may connect residents to important organizations in the community. Many farmers’ markets had features to make them more physically and financially accessible, such as accepting food assistance benefits. With the Wisconsin resident survey, we found that farmers’ market attendance predicted storytelling about local food better than overall local food purchasing, further suggesting that markets can facilitate social interactions.Originality/valueWe document an important benefit that farmers’ markets can offer communities: they have the potential to act as communication infrastructure. As stronger communication infrastructure can facilitate civic engagement, this work provides a mechanism by which to connect civic agriculture activities and increased levels of civic engagement.
Research on the identification of medical service quality factors: based on a data-driven method
Authors: Gao Huiying , Lu Shan , Kou Xiaojin 
Published: March 2022

PurposeThe purpose of this study is to identify medical service quality factors that patients care about and establish a medical service quality evaluation index system by analyzing online reviews of medical and healthcare service platforms in combination with a questionnaire survey.Design/methodology/approachThis study adopts a combination of review mining and questionnaire surveys. The latent Dirichlet allocation (LDA) model was used to mine hospital reviews on the medical and healthcare service platform to obtain the medical service quality factors that patients pay attention to, and then the questionnaire was administered to obtain the relative importance of these factors to patients' perception of service quality. Finally, the index system was established.FindingsThe medical service quality factors patients care about include medical skills and ethics, registration service, operation effect, consulting communication, drug therapy, diagnosis process and medical equipment.Research limitations/implicationsThe identification of medical service quality factors provides a reference for medical institutions to improve their medical service quality.Originality/valueThis study uses online review mining to obtain medical service quality factors from the perspective of patients, which is different from previous methods of obtaining factors from relevant literature or expert judgments; then, based on the mining results, a medical service quality evaluation index system is established by using questionnaire data.
The digital transformation of Swiss small and medium-sized enterprises: insights from digital tool adoption
Authors: Kraft Corin , Lindeque Johan P. , Peter Marc K. 
Published: March 2022

PurposeThe study explores the alignment of Swiss small and medium-sized enterprise (SME) managers' understanding of digital transformation, with evidence of digital tool adoption in managerial and operative work. This reveals opportunities for more fully realizing the potential of digital transformation for SMEs.Design/methodology/approachThis multiple-case study, with four theoretically sampled cases, analyzes data from the qualitative answers of 1,593 respondents to a survey of Swiss SMEs about digital transformation. The study draws on a convenience sample of Swiss SME managers.FindingsThe analysis shows little understanding of digital transformation as related to managerial work. However, there are two clear digital tool adoption patterns for managerial work: (1) workflow and workforce management and (2) work-flow and team management. Understandings of digital transformation and operative work focus on the (1) organization of operational work or (2) a combination of organization and changing the way people work. The digital tool adoption in operational work additionally focuses on the digital skills of operational employees.Research limitations/implicationsThe study is only able to identify patters of understanding of digital transformation and digital tool adoption in managerial and operative work. More research is needed to understand why these patterns are observed.Practical implicationsSME managers need to think far more carefully about aligning their vision for digital transformation and the digital tools they adopt in both managerial and operational work, but especially in managerial work.Originality/valueThis is the first empirical study of the digital transformation of Swiss SMEs and their digital tool adoption. Significant potential for alignment is revealed, suggesting potential performance gains are possible.