bluuebunny/crossref_metadata_2025 huggingface dataset:
Performance evaluation of a non-invasive one-step multiplex RT-qPCR assay for detection of SARS-CoV-2 direct from human saliva
Authors: Jenkins Harry H. , Tellechea Lopez Ana A. , Tarantini Francesco Saverio , Tomlin Hannah , Scales Danielle , Lee I-Ning , Wu Siyu , Hyde Ralph , Lis-Slimak Katarzyna , Byaruhanga Timothy , Thompson Jamie L. , Pijuan-Galito Sara , Doolan Lara , Kaneko Kazuyo , Gwynne Penny , Reffin Caroline , Park Emily , Dey Jayasree , Hill Jack , Arendt-Tranholm Asta , Stroud Amy , Petrie Moira , Denning Chris , Benest Andrew V. , Seedhouse Claire
Published: March 2022

Polymerase chain reaction (PCR) has proven to be the gold-standard for SARS-CoV-2 detection in clinical settings. The most common approaches rely on nasopharyngeal specimens obtained from swabs, followed by RNA extraction, reverse transcription and quantitative PCR. Although swab-based PCR is sensitive, swabbing is invasive and unpleasant to administer, reducing patient compliance for regular testing and resulting in an increased risk of improper sample collection. To overcome these obstacles, we developed a non-invasive one-step RT-qPCR assay performed directly on saliva specimens. The University of Nottingham Asymptomatic Testing Service (UoNATS) protocol simplifies sample collection and bypasses the need for RNA extraction, additives, or extraneous processing steps, thus helping to encourage more regular testing and reducing processing time and costs. We have evaluated the assay against the performance criteria specified by the UK regulatory bodies and attained accreditation (BS EN ISO/IEC 17025:2017) for SARS-CoV-2 diagnostic testing by the United Kingdom Accreditation Service (UKAS). We observed a sensitivity of 1 viral copy per microlitre of saliva and demonstrated a concordance of >99.4% between our results and those of other accredited testing facilities. We concluded that saliva is a stable medium with surprising longevity, and allows for a highly precise, repeatable, and robust testing method.
Efficacy and safety of a patch containing adipose-derived stem cells for skin wound healing – results form a comprehensive pre-clinical evaluation program
Authors: Brembilla Nicolo C. , Modarressi Ali , André-Lévigne Dominik , Brioudes Estelle , Lanza Florian , Vuagnat Hubert , Durual Stéphane , Marger Laurine , Boehncke Wolf-Henning , Krause Karl-Heinz , Preynat-Seauve Olivier
Published: March 2022

Mesenchymal stem cell-based therapies are emerging as innovative approaches to treat chronic wounds. A common administration route used in clinical trials consists of local injections leading to uncontrolled/sub-optimal delivery. This study reports a comprehensive pre-clinical evaluation program on the mechanism of action, efficacy and safety of an easy-to-use patch that concentrates Adipose-derived Stem Cells (ASCs) in a clinical-grade sponge of porcine crosslinked-gelatin. ASCs were prepared from the fat of ischemic patients. Transcriptome and proteome of ASC-patches and ASC monolayers were assessed by microarrays, bio-arrays and mass spectrometry. Tumorigenesis was investigated in immunosuppressed mice according to the European Pharmacopeia. Angiogenesis was assessed in vivo in the chick chorioallantoic membrane model. Efficacy of the ASC-patch was tested in a rat model of ischemic full-thickness skin defect. Cell stability was assessed by luminescence using ASC-patches generated from ASCs stably transduced with firefly luciferase. ASCs from ischemic patients upregulated the transcription of multiple genes involved in skin wound healing when cultured within the ASC-patch formulation. The patch was not only a concentrator, but also a reservoir of both ASC-derived regenerative factors and sponge-derived soluble fragments having healing capacity. The secretome of the ASC-patch promoted dermal fibroblast survival and epidermal epithelialization. No tumor formation was observed in immunodeficient Nude mice subcutaneously transplanted with the ASC-patch. Transplanted patches were early invaded by new vessels in vivo, and a marked angiogenesis was confirmed in two independent animal models. Finally, ASC-patches prepared from syngeneic rats promoted faster healing and re-vascularization of full-thickness skin defects in a rat animal model. Of note, ASCs were viable and locally stable for at least two weeks in vivo. We provide here compelling pre-clinical evidence that patches concentrating ASCs within crosslinked gelatin may represent a convenient and effective tool for the management of chronic wounds.
Temporin B forms hetero-oligomers with Temporin L, modifies its membrane activity and increases the cooperativity of its antibacterial pharmacodynamic profile
Authors: Ferguson Philip M. , Clarke Maria , Manzo Giorgia , Hind Charlotte K. , Clifford Melanie , Sutton J. Mark , Lorenz Christian D. , Phoenix David A. , Mason A. James
Published: March 2022

The pharmacodynamic profile of antimicrobial peptides (AMPs) and their in vivo synergy are two factors that are thought to restrict resistance evolution and ensure their conservation. The frog Rana temporaria secretes a family of closely related AMPs, temporins A-L, as an effective chemical dermal defence. The antibacterial potency of temporin L has been shown to increase synergistically in combination with both temporins B and A but this is modest. Here we show that the less potent temporin B enhances the cooperativity of the in vitro antibacterial activity of the more potent temporin L against EMRSA-15 and that this may be associated with an altered interaction with the bacterial plasma membrane, a feature critical for the antibacterial activity of most AMPs. Addition of buforin II, a histone H2A fragment, can further increase the cooperativity. Molecular dynamics simulations indicate temporins B and L readily form hetero-oligomers in models of Gram-positive bacterial plasma membranes. Patch-clamp studies show transmembrane ion conductance is triggered with lower amounts of both peptides and more quickly, when used in combination, but conductance is of a lower amplitude and pores are smaller. Temporin B may therefore act by forming temporin L/B hetero-oligomers that are more effective than temporin L homo-oligomers at bacterial killing and/or by reducing the probability of the latter forming until a threshold concentration is reached. Exploration of the mechanism of synergy between AMPs isolated from the same organism may therefore yield antibiotic combinations with advantageous pharmacodynamic properties.
Unblocking genome editing of major animal mycoplasmas using CRISPR/Cas9 base editor systems
Authors: Ipoutcha Thomas , Rideau Fabien , Gourgues Geraldine , Arfi Yonathan , Lartigue Carole , Blanchard Alain , Sirand-Pugnet Pascal
Published: March 2022

Mycoplasmas are minimal bacteria that infect humans, wildlife, and most economically important livestock species. Mycoplasma infections cause a large range of chronic inflammatory diseases, eventually leading to death in some animals. Due to the lack of efficient recombination and genome engineering tools, the production of mutant strains for the identification of virulence factors and the development of improved vaccine strains is still a bottleneck for many mycoplasma species. Here, we demonstrate the efficacy of a CRISPR-derived genetic tool to introduce targeted mutations in three major pathogenic species that span the phylogenetic diversity of these bacteria: the avian pathogen Mycoplasma gallisepticum and the two most important bovine mycoplasmas, Mycoplasma bovis and Mycoplasma mycoides subsp. mycoides. As a proof of concept, we successfully used an inducible dCas9-cytidine deaminase system to disrupt several major virulence factors in these pathogens. Various induction times and inducer concentrations were evaluated to optimize editing efficiency. The optimized system was sufficiently powerful to disrupt 54 of 55 insertion sequence transposases in a single step. Whole genome sequencing showed that off-target mutations were limited and suggest that most variations detected in the edited genomes are Cas9-independent. This effective, rapid, and easy-to-use genetic tool opens a new avenue for the study of these important animal pathogens and, most likely, the entire class Mollicutes.

Significance

Mycoplasmas are minimal wall-less pathogenic bacteria that infect a wide range of hosts, including humans, livestock, and wild animals. Major pathogenic species cause acute to chronic infections involving still poorly characterized virulence factors. The lack of precise genome editing tools has hampered functional studies for many species, leaving multiple questions about the molecular basis of their pathogenicity unanswered. We developed a CRISPR-derived base editor for three major pathogenic species, Mycoplasma gallisepticum, Mycoplasma bovis, and Mycoplasma mycoides subsp. mycoides. Several virulence factors were successfully targeted and we were able to edit up to 54 target sites in a single step. The availability of this efficient and easy-to-use genetic tool will greatly facilitate functional studies in these economically important bacteria.
Comparative thermophysiology of marine Synechococcus CRD1 strains isolated from different thermal niches in iron-depleted areas
Authors: Ferrieux Mathilde , Dufour Louison , Doré Hugo , Ratin Morgane , Guéneuguès Audrey , Chasselin Léo , Marie Dominique , Rigaut-Jalabert Fabienne , Le Gall Florence , Sciandra Théo , Monier Garance , Hoebeke Mark , Corre Erwan , Xia Xiaomin , Liu Hongbin , Scanlan David J. , Partensky Frédéric , Garczarek Laurence
Published: March 2022

Marine Synechococcus cyanobacteria are ubiquitous in the ocean, a feature likely related to their extensive genetic diversity. Amongst the major lineages, clades I and IV preferentially thrive in temperate and cold, nutrient-rich waters, whilst clades II and III prefer warm, nitrogen or phosphorus-depleted waters. The existence of such cold (I/IV) and warm (II/III) thermotypes is corroborated by physiological characterization of representative strains. A fifth clade, CRD1, was recently shown to dominate the Synechococcus community in iron-depleted areas of the world ocean and to encompass three distinct ecologically significant taxonomic units (ESTUs CRD1A-C) occupying different thermal niches, suggesting that distinct thermotypes could also occur within this clade.

Here, using comparative thermophysiology of strains representative of these three CRD1 ESTUs we show that the CRD1A strain MITS9220 is a warm thermotype, the CRD1B strain BIOS-U3-1 a cold temperate thermotype, and the CRD1C strain BIOS-E4-1 a warm temperate stenotherm. Curiously, the CRD1B thermotype lacks traits and/or genomic features typical of cold thermotypes. In contrast, we found specific physiological traits of the CRD1 strains compared to their clade I, II, III and IV counterparts, including a lower growth rate and photosystem II maximal quantum yield at most temperatures and a higher turnover rate of the D1 protein. Together, our data suggests that the CRD1 clade prioritizes adaptation to low-iron conditions over temperature adaptation, even though the occurrence of several CRD1 thermotypes likely explains why the CRD1 clade as a whole occupies most iron-limited waters.
Constitutive 5-HT2C receptor knock-out facilitates fear extinction through altered activity of a dorsal raphe-bed nucleus of the stria terminalis pathway
Authors: Süß Sandra T. , Kremer Daniel , Olbricht Linda M. , Herlitze Stefan , Spoida Katharina
Published: March 2022

Serotonin 2C receptors (5-HT2CRs) are widely distributed throughout the brain and are strongly implicated in the pathophysiology of anxiety disorders such as post-traumatic stress disorder (PTSD). Although in recent years, a considerable amount of evidence supports 5-HT2CRs facilitating effect on anxiety behavior, the involvement in learned fear responses and fear extinction is rather unexplored. Here we used a 5-HT2CR knock-out mouse line (2CKO) to gain new insights into the involvement of 5-HT2CRs in the neuronal fear circuitry. Using a cued fear conditioning paradigm, our results revealed that global loss of 5-HT2CRs exclusively accelerates fear extinction, without affecting fear acquisition and fear expression. To investigate the neuronal substrates underlying the extinction enhancing effect, we mapped the immediate-early gene product cFos, a marker for neuronal activity, in the dorsal raphe nucleus (DRN), amygdala and bed nucleus of the stria terminalis (BNST). Surprisingly, besides extinction-associated changes, our results revealed alterations in neuronal activity even under basal home cage conditions in specific subregions of the DRN and the BNST in 2CKO mice. Neuronal activity in the dorsal BNST was shifted in an extinction-supporting direction due to 5-HT2CR knock-out. Finally, the assessment of DRN-BNST connectivity using antero- and retrograde tracing techniques uncovered a discrete serotonergic DRC-BNSTad pathway showing increased activity in 2CKO mice. Thus, our results provide new insights for the fear extinction network by revealing a specific serotonergic DRC-BNSTad pathway underlying a 5-HT2CR-sensitive mechanism with high significance in the treatment of PTSD.
DiSCERN - Deep Single Cell Expression ReconstructioN for improved cell clustering and cell subtype and state detection
Authors: Hausmann Fabian , Ergen-Behr Can , Khatri Robin , Marouf Mohamed , Hänzelmann Sonja , Gagliani Nicola , Huber Samuel , Machart Pierre , Bonn Stefan
Published: March 2022

Single cell sequencing provides detailed insights into biological processes including cell differentiation and identity. While providing deep cell-specific information, the method suffers from technical constraints, most notably a limited number of expressed genes per cell, which leads to suboptimal clustering and cell type identification. Here we present DISCERN, a novel deep generative network that reconstructs missing single cell gene expression using a reference dataset. DISCERN outperforms competing algorithms in expression inference resulting in greatly improved cell clustering, cell type and activity detection, and insights into the cellular regulation of disease. We used DISCERN to detect two unseen COVID-19-associated T cell types, cytotoxic CD4+and CD8+Tc2 T helper cells, with a potential role in adverse disease outcome. We utilized T cell fraction information of patient blood to classify mild or severe COVID-19 with an AUROC of 81% that can serve as a biomarker of disease stage. DISCERN can be easily integrated into existing single cell sequencing workflows and readily adapted to enhance various other biomedical data types.
Diet suppresses tumour initiation by maintaining quiescence of mutation-bearing neural stem cells
Authors: Amodeo Valeria , Davies Timothy , Martinez-Segura Amalia , Clements Melanie , Ragdale Holly Simpson , Bailey Andrew , Silva Dos Santos Mariana , MacRae James I. , Mokochinski Joao , Kramer Holger , Garcia-Diaz Claudia , Gould Alex P. , Marguerat Samuel , Parrinello Simona
Published: March 2022

Glioblastoma is thought to originate from neural stem cells (NSCs) of the subventricular zone that acquire genetic alterations. In the adult brain, NSCs are largely quiescent, suggesting that deregulation of quiescence maintenance may be a pre-requisite for tumour initiation. Although inactivation of the tumour suppressor p53 is a frequent event in gliomagenesis, whether, or how, it affects quiescent NSCs (qNSCs) remains unclear. Here we show that p53 maintains quiescence by inducing fatty acid oxidation (FAO) and that acute p53 deletion in qNSCs results in their premature activation to a proliferative state. Mechanistically, this occurs through direct transcriptional induction of PPARGC1a, which in turn activates PPARα to upregulate FAO genes. Strikingly, dietary supplementation with fish oil containing omega-3 fatty acids, natural PPARα ligands, fully restores quiescence of p53-deficient NSCs and delays tumour initiation in a glioblastoma mouse model. Thus, diet can silence glioblastoma driver mutations, with important implications for cancer prevention.
NAK associated protein 1/NAP1 is required for mitosis and cytokinesis by activating TBK1
Authors: Paul Swagatika , Sarraf Shireen A. , Nam Ki Hong , Zavar Leila , Biswas Sahitya Ranjan , Fritsch Lauren E. , DeFoor Nicole , Yaron Tomer M. , Johnson Jared L. , Huntsman Emily M. , Cantley Lewis C. , Ordureau Alban , Pickrell Alicia M.
Published: March 2022

Subcellular location and activation of Tank Binding Kinase 1 (TBK1) govern precise progression through mitosis. Either loss of activated TBK1 or its sequestration from the centrosomes causes error in mitosis and growth defects. Yet, what regulates its recruitment and activation on the centrosomes is unknown. We identified that NAK Associated Protein 1 (NAP1) is essential for mitosis which binds to TBK1 on the centrosomes to activate it. Loss of NAP1 causes several mitotic and cytokinetic defects due to inactivation of TBK1. Our quantitative phosphoproteomics identified numerous TBK1 substrates that are not only confined to the centrosomes but also are associated with microtubules. Substrate motifs analysis indicates that TBK1 acts upstream of other essential cell cycle kinases like Aurora and PAK kinases. We also identified NAP1 as a TBK1 substrate at S318 promoting its degradation by ubiquitin proteasomal system acting as a negative regulatory step. These data uncover an important distinct function for the NAP1-TBK1 complex during cell division.
Three functionally distinct classes of cGAS proteins in nature revealed by self-DNA-induced interferon responses
Authors: Mosallanejad Kenta , Zhou Wen , Govande Apurva A. , Hancks Dustin C. , Kranzusch Philip J. , Kagan Jonathan C.
Published: March 2022

Innate immune pattern recognition receptors (PRRs) emerged early in evolution. It is generally assumed that structurally homologous proteins in distinct species will operate via similar mechanisms. We tested this prediction through the study of interferon responses to self-DNA by the enzymatic PRR cyclic GMP-AMP synthase (cGAS). Contrary to expectations, we identified three functional classes of this PRR in mammals. Class 1 proteins (including human) contained a catalytic domain that was intrinsically self-DNA reactive and stimulated interferon responses in diverse cell types. This reactivity was prevented by an upstream N-terminal domain. Class 2 and 3 proteins were either not self-DNA reactive (including chimpanzee) or included proteins whose N-terminal domain promoted self-DNA reactivity (mouse). While self-DNA reactivity of Class 1 cGAS was linked to an ability to access intra-mitochondrial DNA, mitochondrial localization was not associated with other classes. These studies reveal unexpected diversity in the mechanisms of self-DNA reactivity of a PRR.

One Sentence Summary

The regulation of self-DNA reactivity of cGAS is evolutionarily diverse in mammals.
Development of a Novel Bruton’s Tyrosine Kinase Inhibitor that exerts Anti-Cancer Activities Potentiates Response of Chemotherapeutic Agents In Multiple Myeloma Stem Cell-Like Cells
Authors: Elbezanti Weam Othman , Al-Odat Omar S. , Chitren Robert , Singh Jaikee Kumar , Srivastava Sandeep Kumar , Gowda Krishne , Amin Shantu , Robertson Gavin P. , Jonnalagadda Subash C. , Budak-Alpdogan Tulin , Pandey Manoj K.
Published: March 2022

Despite recent improvements in multiple myeloma (MM) treatment, MM remains an incurable disease and most patients experience a relapse. The major reason for myeloma recurrence is the persistent stem cell-like population. It has been demonstrated that overexpression of Bruton’s tyrosine kinase (BTK) in MM stem cell-like cells is correlated with drug resistance and poor prognosis. We have developed a novel small BTK inhibitor, KS151, which is unique compared to other BTK inhibitors. Unlike ibrutinib, and the other BTK inhibitors such as acalabrutinib, orelabrutinib, and zanubrutinib that covalently bind to the C481 residue in the BTK kinase domain, KS151 can inhibit BTK activities without binding to C481. This feature of KS151 is important because C481 becomes mutated in many patients and causes drug resistance. We demonstrated that KS151 inhibits in vitro BTK kinase activities and is more potent than ibrutinib. Furthermore, by performing a semi-quantitative, sandwich-based array for 71-tyrosine kinase phosphorylation, we found that KS151 specifically inhibits BTK. Our western blotting data showed that KS151 inhibits BTK signaling pathways and is effective against bortezomib-resistant cells as well as MM stem cell-like cells. Moreover, KS151 potentiates the apoptotic response of bortezomib, lenalidomide, and panobinostat in both MM and stem cell-like cells. Interestingly, KS151 inhibits stemness markers and is efficient in inhibiting Nanog and Gli1 stemness markers even when MM cells were co-cultured with bone marrow stromal cells (BMSCs). Overall, our results show that we have developed a novel BTK inhibitor effective against the stem cell-like population, and potentiates the response of chemotherapeutic agents.
Voltage-Sensing Phosphatase (VSP) Regulates Endocytosis-Dependent Nutrient Absorption in Chordate Enterocytes
Authors: Ratanayotha Adisorn , Matsuda Makoto , Kimura Yukiko , Takenaga Fumiko , Mizuno Tomoaki , Hossain Md. Israil , Higashijima Shin-ichi , Kawai Takafumi , Ogasawara Michio , Okamura Yasushi
Published: March 2022

Voltage-sensing phosphatase (VSP) is a unique membrane protein that translates membrane electrical activities into the changes of phosphoinositide profiles. VSP orthologs from various species have been intensively investigated toward their biophysical properties, primarily using a heterologous expression system. In contrast, the physiological role of VSP in native tissues remains largely unknown. Here we report that zebrafish VSP (Dr-VSP) is functionally expressed on the endomembranes of lysosome-rich enterocytes (LREs) that mediate dietary protein absorption via endocytosis in the zebrafish mid-intestine. Dr-VSP-deficient LREs were remarkably defective in forming endosomal vacuoles after initial uptake of dextran and mCherry. Dr-VSP-deficient zebrafish exhibited growth restriction and higher mortality during the critical period when zebrafish larvae rely primarily on exogenous feeding via intestinal absorption. Furthermore, our comparative study on marine invertebrate Ciona intestinalis VSP (Ci-VSP) revealed co-expression with endocytosis-associated genes in absorptive epithelial cells of the Ciona digestive tract, corresponding to zebrafish LREs. These findings signify a crucial role of VSP in regulating endocytosis-dependent nutrient absorption in specialized enterocytes across animal species.

Summary statement

Voltage-sensing phosphatase (VSP) is identified in absorptive enterocytes, revealing its crucial role in promoting endocytosis and nutrient absorption during early development.
Structural and Functional Insights into the Action Mode of A Mitochondrial AAA+ Disaggregase CLPB
Authors: Wu Damu , Liu Yan , Dai Yuhao , Wang Guopeng , Lu Guoliang , Chen Yan , Li Ningning , Lin Jinzhong , Gao Ning
Published: March 2022

The human AAA+ ATPase CLPB (SKD3) is a protein disaggregase in the mitochondrial intermembrane space and functions to promote the solubilization of various mitochondrial proteins. CLPB deficiency by mutations is associated with a few human diseases with neutropenia and neurological disorders. Unlike canonical AAA+ proteins, CLPB contains a unique ankyrin repeat domain (ANK) at its N-terminus. The mechanism of CLPB functions as a disaggregase and the role of its ANK domain are currently unclear. Herein, we report a comprehensive structural characterization of human CLPB in both the apo- and substrate-bound states. CLPB assembles into homo- tetradecamers in apo-state and is remodeled into homo-dodecamers upon binding to substrates. Conserved pore- loops on the ATPase domains form a spiral staircase to grip and translocate the substrate in a step-size of two amino acid residues. The ANK domain is not only responsible for maintaining the higher-order assembly but also essential for the disaggregase activity. Interactome analysis suggests that the ANK domain may directly interact with a variety of mitochondrial substrates. These results reveal unique properties of CLPB as a general disaggregase in mitochondria and highlight its potential as a target for the treatment of various mitochondria-related diseases.
NudF-boosted strategy to improve the yield of DXS pathway
Authors: Prasanna Devi , Shantier Shaza Wagiealla , Runthala Ashish
Published: March 2022

Background

Terpenoids form a large pool of highly diverse organic compounds possessing several economically important properties, including nutritional, aromatic, and pharmacological properties. The DXP pathway’s end enzyme, nuclear distribution protein (NudF), interacting with isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP), is critical for the synthesis of isoprenol/prenol/downstream compounds. The enzyme is yet to be thoroughly investigated to increase the overall yield of terpenoids in the Bacillus subtilis, which is widely used in industry and is generally regarded as safe (GRAS) bacterium. The study aims to analyze the evolutionary conservation across the active site, and map the key residues for mutagenesis studies. The study would allow us customize the metabolic load towards the synthesis of prenol or isoprenol or any of the downstream molecules.

Results

The 37-sequence dataset, extracted from 103 Bacillus subtilis entries, show a high phylogenetic divergence, and only six one-motif sequences ASB92783.1, ASB69297.1, ASB56714.1, AOR97677.1, AOL97023.1, and OAZ71765.1 show monophyly relationship, unlike a complete polyphyly relationship between the other 31 three-motif sequences. Further, only 47 of 179 residues of the representative sequence CUB50584.1 are observed to be significantly conserved. Docking analysis shows a preferential bias of ADP-ribose pyrophosphatase towards IPP, and a nearly 3-fold energetic difference is observed between IPP and DMAPP. Computational saturation mutagenesis of the seven hotspot residues identifies two key positions LYS78 and PHE116, encoded within loop1 and loop7, majorly interact with the ligands DMAPP and IPP, and their mutants K78I/K78L and PHE116D/PHE116E are found to stabilize the overall conformation. The loops are hereby shown to play a regulatory role in guiding the promiscuity of NudF towards a specific ligand.

Conclusion

The study map the phylogenetic relationship between the 37 representative B.subtiis NudF sequences, and through sequence conservation, structural contact map, topological flexibility, and saturation mutagenesis of the active site residues, the essential residues regulating the interaction of NudF with IPP/DMAPP are deciphered. The study robustly screens its mutational landscape and localizes the two crucial residues LYS78 and PHE116 for directing the mutagenesis studies. The preliminary docking and simulation results also suggest a preferential bias of ADP-ribose pyrophosphatase towards IPP over DMAPP. The findings would pave the way for the development of novel enzyme variants with highly improved catalytic ability for the large-scale bioproduction of specific terpenoids with significant neutraceutical or commercial value.
Π-Π Interactions Stabilize PeptoMicelle-Based Formulations of Pretomanid Derivatives Leading to Promising Therapy Against Tuberculosis in Zebrafish and Mouse Models
Authors: Dal Nils-Jørgen K. , Schäfer Gabriela , Thompson Andrew M. , Schmitt Sascha , Redinger Natalja , Alonso-Rodriguez Noelia , Johann Kerstin , Ojong Jessica , Wohlmann Jens , Best Andreas , Koynov Kaloian , Zentel Rudolf , Schaible Ulrich E. , Griffiths Gareth , Barz Matthias , Fenaroli Federico
Published: March 2022

Tuberculosis is the deadliest bacterial disease globally, threatening the lives of millions every year. New antibiotic therapies that can shorten the duration of treatment, improve cure rates, and impede the development of drug resistance are desperately needed. Here, we used polymeric micelles to encapsulate four second-generation derivatives of the antitubercular drug pretomanid that had previously displayed much better in vivo activity against Mycobacterium tuberculosis than pretomanid itself. Because these compounds were relatively hydrophobic, we expected that such micellar formulations would increase drug bioavailability, reduce toxicities, and improve therapeutic outcomes. The polymeric micelles were based on polypept(o)ides (PeptoMicelles) and were stabilized in their hydrophobic core by π-π interactions, allowing the efficient encapsulation of aromatic pretomanid derivatives. The stability of these π-π-stabilized PeptoMicelles was demonstrated in water, blood plasma, and lung surfactant by fluorescence cross-correlation spectroscopy and was further supported by prolonged circulation times of several days in the vasculature of zebrafish larvae. The pretomanid derivative with the best in vitro potency against Mycobacterium marinum (“drug D”) was also the most efficacious PeptoMicelle formulation tested in the zebrafish larvae infection model, almost completely eradicating the bacteria at non-toxic doses. This lead formulation was further assessed against Mycobacterium tuberculosis in the susceptible C3HeB/FeJ mouse model, which develops human-like necrotic granulomas. Following intravenous administration, the drug D micellar formulation significantly reduced bacterial burden and inflammatory responses in the lungs and spleens of infected mice.
A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality
Authors: Hawkey Jane , Vezina Ben , Monk Jonathan M. , Judd Louise M. , Harshegyi Taylor , López-Fernández Sebastián , Rodrigues Carla , Brisse Sylvain , Holt Kathryn E. , Wyres Kelly L.
Published: March 2022

The Klebsiella pneumoniae species complex (KpSC) is a set of seven Klebsiella taxa that are found in a variety of niches and are an important cause of opportunistic health care–associated infections in humans. Because of increasing rates of multi-drug resistance within the KpSC, there is a growing interest in better understanding the biology and metabolism of these organisms to inform novel control strategies. We collated 37 sequenced KpSC isolates isolated from a variety of niches, representing all seven taxa. We generated strain-specific genome-scale metabolic models (GEMs) for all 37 isolates and simulated growth phenotypes on 511 distinct carbon, nitrogen, sulfur, and phosphorus substrates. Models were curated and their accuracy was assessed using matched phenotypic growth data for 94 substrates (median accuracy of 96%). We explored species-specific growth capabilities and examined the impact of all possible single gene deletions using growth simulations in 145 core carbon substrates. These analyses revealed multiple strain-specific differences, within and between species, and highlight the importance of selecting a diverse range of strains when exploring KpSC metabolism. This diverse set of highly accurate GEMs could be used to inform novel drug design, enhance genomic analyses, and identify novel virulence and resistance determinants. We envisage that these 37 curated strain-specific GEMs, covering all seven taxa of the KpSC, provide a valuable resource to the Klebsiella research community.
Computational diffraction reveals long-range strains, distortions and disorder in molecular dynamics simulations of irradiated single crystals
Authors: Boulle A. , Chartier A. , Debelle A. , Jin X. , Crocombette J.-P.
Published: March 2022

Atomic-scale simulations, and in particular molecular dynamics (MD), are key assets to model the behavior of the structure of materials under the action of external stimuli, say temperature, strain or stress, irradiation, etc. Despite the widespread use of MD in condensed matter science, some basic material characteristics remain difficult to determine. This is, for instance, the case for the long-range strain tensor, and its root-mean-squared fluctuations, in disordered materials. In this work, computational diffraction is introduced as a fast and reliable structural characterization tool of atomic-scale simulation cells in the case of irradiated single crystals. In contrast to direct-space methods, computational diffraction operates in the reciprocal space and is therefore highly sensitive to long-range spatial correlations. With the example of irradiated UO2 single crystals, it is demonstrated that the normal strains, shear strains and rotations, as well as their root-mean-squared fluctuations (microstrain) and the atomic disorder, are straightforwardly and unambiguously determined. The methodology presented here has been developed with efficiency in mind, in order to be able to provide simple and reliable characterizations either operating in real time, in parallel with other analysis tools, or operating on very large data sets.
Crystal structure of the putative cell-wall lipoglycan biosynthesis protein LmcA from Mycobacterium smegmatis
Authors: Patel Onisha , Brammananth Rajini , Dai Weiwen , Panjikar Santosh , Coppel Ross L. , Lucet Isabelle S. , Crellin Paul K.
Published: March 2022

The bacterial genus Mycobacterium includes important pathogens, most notably M. tuberculosis, which infects one-quarter of the entire human population, resulting in around 1.4 million deaths from tuberculosis each year. Mycobacteria, and the closely related corynebacteria, synthesize a class of abundant glycolipids, the phosphatidyl-myo-inositol mannosides (PIMs). PIMs serve as membrane anchors for hyperglycosylated species, lipomannan (LM) and lipoarabinomannan (LAM), which are surface-exposed and modulate the host immune response. Previously, in studies using the model species Corynebacterium glutamicum, NCgl2760 was identified as a novel membrane protein that is required for the synthesis of full-length LM and LAM. Here, the first crystal structure of its ortholog in Mycobacterium smegmatis, MSMEG_0317, is reported at 1.8 Å resolution. The structure revealed an elongated β-barrel fold enclosing two distinct cavities and one α-helix extending away from the β-barrel core, resembling a `cone with a flake' arrangement. Through xenon derivatization and structural comparison with AlphaFold2-derived predictions of the M. tuberculosis homolog Rv0227c, structural elements were identified that may undergo conformational changes to switch from `closed' to `open' conformations, allowing cavity access. An AlphaFold2-derived NCgl2760 model predicted a smaller β-barrel core with an enclosed central cavity, suggesting that all three proteins, which were collectively termed LmcA, may have a common mechanism of ligand binding through these cavities. These findings provide new structural insights into the biosynthetic pathway for a family of surface lipoglycans with important roles in mycobacterial pathogenesis.
A scalable strategy to solve structures of PDZ domains and their complexes
Authors: Cousido-Siah Alexandra , Carneiro Laura , Kostmann Camille , Ecsedi Peter , Nyitray Laszlo , Trave Gilles , Gogl Gergo
Published: March 2022

The human PDZome represents one of the largest globular domain families in the human proteome, with 266 instances. These globular domains typically interact with C-terminal peptide motifs found in thousands of human proteins. Despite previous efforts, not all PDZ domains have experimentally solved structures and most of their complexes remain to be solved. Here, a simple and cost-effective strategy is proposed for the crystallization of PDZ domains and their complexes. A human annexin A2 fusion tag was used as a crystallization chaperone and the structures of nine PDZ domains were solved, including five domains that had not yet been solved. Finally, these novel experimental structures were compared with AlphaFold predictions and it is speculated how predictions and experimental methods could cooperate in order to investigate the structural landscapes of entire domain families and interactomes.
Heuristic optimization applied to ANN training for predicting renewable energy sources production
Authors: Lorenti Gianmarco , Mariuzzo Ivan , Moraglio Francesco , Repetto Maurizio
Published: March 2022

Purpose

This paper aims to compare stochastic gradient method used for neural network training with global optimizer without use of gradient information, in particular differential evolution.

Design/methodology/approach

This contribute shows the application of heuristic optimization algorithms to the training phase of artificial neural network whose aim is to predict renewable power production as function of environmental variables such as solar irradiance and temperature. The training problem is cast as the minimization of a cost function whose degrees of freedom are the parameters of the neural network. A differential evolution algorithm is substituted to the more usual gradient-based minimization procedure, and the comparison of their performances is presented.

Findings

The two procedures based on stochastic gradient and differential evolution reach the same results being the gradient based moderately quicker in convergence but with a lower value of reliability, as a significant number of runs do not reach convergence.

Research limitations/implications

The approach has been applied to two forecasting problems and, even if results are encouraging, the need for extend the approach to other problems is needed.

Practical implications

The new approach could open the training of neural network to more stable and general methods, exploiting the potentialities of parallel computing.

Originality/value

To the best of the authors’ knowledge, the research presented is fully original for the part regarding the neural network training with differential evolution.
State-owned enterprises’ performance in Indonesia: a strategic typology perspective
Authors: Apriyantopo Wahyu , Aprianingsih Atik , Kitri Mandra Lazuardi
Published: March 2022

Purpose

State-owned enterprises’ (SOEs) goals are perceived as two-sided blades, providing goods or services to the public on one side and escalating the government’s wealth on the other side. Treating the SOEs, government encounters the problem of injection strategy or privatize them. At the same time, managers have the option to formulate the SOEs strategy to boost performance. By using Miles and Snow’s typology strategy and the above factors, this paper investigates those impacts on Indonesia’s SOEs’ performance. This study aims to propose strategic typology as the main predictor with other variables such as the size, ownership structure, market competitiveness and capital subsidy on SOEs.

Design/methodology/approach

The study uses archived SOEs’ financial data from 2014 to 2018 to predict the financial performance using ordinal logistic regression analysis. The additional factors, such as firm size, ownership structure, market concentration and capital subsidy, are incorporated.

Findings

The result demonstrates that SOEs strategic typology, market concentration, size, ownership structure and capital subsidy significantly affect Indonesia’s SOEs’ performance.

Originality/value

To the best of the authors’ knowledge, this paper is the first elaborating government policies for SOEs, such as capital subsidy and state ownership, on the perspective of Miles and Snow’s strategy-performance relationship. Correspondingly, the paper contributes to examine the Indonesian characteristic SOE type with the performance. No single study has previously explored this relationship in the context of SOE in Indonesia.
Does the cashless transaction work? An analysis of policy challenges in an emerging economy
Authors: Panda Debadutta Kumar , Reddy Sriharsha , Vaithianathan Sridhar
Published: March 2022

Purpose

This paper aims to study the adoption of a public policy (cashless transaction system by implementing demonetization) from the institutional and technology adoption theories.

Design/methodology/approach

A mixed-method approach was followed and data was collected from 900 samples randomly selected from different cities in India. The content analysis method was applied to analyze responses collected from personal interviews, and descriptive statistics and cluster analysis methods were used to process the data.

Findings

The determinants of the cashless transaction policy adoption were institutional issues and technology-related issues. The non-adopters were falling into either technology antagonist or technology ignorant, whereas the adopters perceived user-friendliness, necessity and usefulness. Institutional bottlenecks and perceived security issues were serious concerns.

Originality/value

This study examined the factors influencing the adoption and non-adoption of mobile payments for two reasons. First, the nature of adoption here is more of a forced adoption rather than organic/natural adoption. Second the context – emerging market, India – also demands that it would be more useful to carry out exploratory study and understand the factors from the stakeholders – merchants and customers – themselves than examining existing technology adoption theories.
Academic supports, motivation to learn, motivation to transfer and transfer of training: a comparative analysis of public and private universities
Authors: Sharif Shahbaz , Braimah Mary , Dogbey Alice Emmanuela
Published: March 2022

Purpose

Public and private universities keep facilitating knowledge transfer and sharing within academic institutions. Multiple factors have been investigated to strengthen the infrastructure of these universities; however, the researchers have always been trying to explore the best one. Therefore, the purpose of this study is to investigate the influence of academic supports on motivation to learn (MTL) and transfer, in turn, influence transfer of training (TOT). Interestingly, the sector (i.e. public or private universities) unveils TOT to see whether the public sector has best practices or private.

Design/methodology/approach

This study adopts valid measurement instruments from the literature studies. This study pretests the validity and reliability of the instruments. This study administers the designed survey questionnaire among the faculty members of both public and private universities. This study uses a convenient sampling approach using a quantitative research method. By applying Smart partial least square (PLS) 3.3.3, this study uses structural equation modeling.

Findings

This study supports that organization, supervisor and peer support significantly and positively influence TOT. Additionally, MTL and motivation to transfer (MTT) significantly and positively mediate the link between TOT and organizational, supervisor and peer support. MTL also significantly and positively influences MTT. Most interestingly, the sector significantly and positively moderates the link between TOT and organizational, supervisor and peer support, MTL and transfer.

Practical implications

The results support the public and private universities that they should develop the infrastructure containing learning motivation and transfer for easy TOT. This would be more effective if the in higher educational institutions (HEIs) follow research findings.

Originality/value

This study empirically tests the impacts of academic supports on MTL and transfer, which boosts the TOT. The novelty of the research can be implemented in HEIs’ rules and regulations.
Design optimisation of reinforced concrete pile foundation using generalised reduced gradient algorithm
Authors: Dauda Jamiu Adetayo , Rahmon Suraj A. , Tijani Ibrahim A. , Mohammad Fouad , Okegbenro Wakeel O.
Published: March 2022

Purpose

The purpose of this study is to find the optimum design of Reinforced Concrete (RC) pile foundation to enable efficient use of structural concrete with greater consequences for global environment and economy.

Design/methodology/approach

A non-linear optimisation technique based on the Generalised Reduced Gradient (GRG) algorithm was implemented to find the minimum cost of RC pile foundation in frictional soil. This was achieved by obtaining the optimum pile satisfying the serviceability and ultimate limit state requirements of BS 8004 and EC 7. The formulated structural optimisation procedure was applied to a case study project to assess the efficiency of the proposed design formulation.

Findings

The results prove that the GRG method in Excel solver is an active, fast, accurate and efficient computer programme to obtain optimum pile design. The application of the optimisation for the case study project shows up to 26% cost reduction compared to the conventional design.

Research limitations/implications

The design and formulation of design constraints will be limited to provisions of BS 8004 and EC 7.

Practical implications

Since the minimum quantity of concrete was attained through optimisation, then minimum cement will be used and thus result in minimum CO2 emission. Therefore, the optimum design of concrete structures is a vital solution to limit the damage to the Earth's climate and the physical environment resulting from high carbon emissions.

Originality/value

The current study considers the incorporation of different soil ground parameters in the optimisation process rather than assuming any pile capacity value for the optimisation process.
Bibliometric analysis of fake news indexed in Web of Science and Scopus (2001-2020)
Authors: Patra Raj Kishore , Pandey Neha , Sudarsan Desul
Published: March 2022

Purpose

The purpose of this paper is to investigate the scholarly contribution of literature published on the much-hyped term fake news and associated terms such as misinformation, disinformation and post-truth in various disciplines, which contributes heavily to information disorder.

Design/methodology/approach

The study conducted a bibliometric inquiry of literature published in Scopus and Web of Science (WoS) databases (2001-2020) and steered in-depth quantitative content analysis of top-cited publications. The data mining covers 1,776 and 1,056 publications from WoS and Scopus databases, respectively. Bibliometrix R-package, VOSviewer Software tool and Microsoft Excel were used for analysis.

Findings

The study concluded that the past seven years (2014–2020) are the most productive period in studying fake news and its associated terms due to the unprecedented rise of social media and digital media. The prominent themes of the study were conducted in political, health, technology, media and social media space, whereas the output is minor in the pure science field. It is also inferred that both databases are contributing consistently in the domain of fake news literature.

Practical implications

The study helps in expansion of knowledge based on the research topic as well as in understanding the evolution of fake news in support of further research in this area.

Originality/value

Mapping scholarly contributions of scientific research provides a guiding approach and helps counter the information chaos stimulated by fake news phenomena in the digital era.
The effect of earnings management on external loan price: evidence from China
Authors: Huang Rong , Lin Xiaojun , Xi Xunzhuo , Yuen Desmond Chun Yip
Published: March 2022

Purpose

This paper aims to explore how external creditors assess firms’ financial aggressiveness in China.

Design/methodology/approach

Using bank loan-specific data, the authors investigate whether firms exhibit greater costs of bank loans when they engage in earnings manipulation and whether this association changes when restrictions on lenders’ compensation are promulgated.

Findings

The authors find compelling evidence that bank executives charge higher premiums on firms with accrual earnings management to compensate for additional financial risk but do not charge extra loan prices for firms conducting real earnings management (REM). The authors also find that the enactment of Robust Bank Executive Compensation (REBC) enhances the vigilance of bank executives on the overall client firms’ earnings manipulation, with the exception of REM conducted by state-owned firms.

Originality/value

The authors extend the current literature on the cost of external loans by focusing on bank loans and the influence of REBC. This study offers implications for policymakers in China and other emerging economics to control loan default and financial risk.