bluuebunny/crossref_metadata_2025 huggingface dataset:
Random effects modelling vs logistic regression for the inclusion of cluster level covariates in propensity scores for medical device and surgical epidemiology
Authors: Du Mike , Prats-Uribe Albert , Khalid Sara , Prieto-Alhambra Daniel , Strauss Victoria Y , Khalid Sara
Published: February 2022

Purpose

Surgeon and hospital related features such as surgeries volume can be associated with treatment choices and treatment outcomes. Accounting for these covariates with propensity score (PS) analysis can be challenging due to clustered nature of the data. Previous studies have not focused solely on the PS estimation strategy when treatment effects are estimated using random effects model(REM). We studied PS estimation for clustered data using REM compared with logistic regression.

Methods

Six different PS estimation strategies were tested using simulations with variable cluster-level confounding intensity (odds ratio(OR)=1.01 to OR=2.5): i) logistic regression PS excluding cluster- level confounders; ii) logistic regression PS including cluster-level confounders; iii) same as ii) but including cross-level interactions; iv), v) and vi), similar to i), ii) and iii) respectively but using REM instead of logistic regression PS. Same analysis were tested in a randomised controlled trial emulation of partial vs total knee replacement surgery. Simulation metrics included bias and mean square error (MSE). For trial emulation, we compared observational vs trial-based treatment effect estimates.

Results

In most simulated scenarios, logistic regression including cluster-level confounders gave more accurate estimates with the lowest bias and MSE. E.g. with 50 clusters x 200 individuals and confounding intensity OR=1.5, the relative bias= 10% and MSE= 0.003 for (i), compared to 21% and, 0.010 for (iv). In the Trial emulation, all 6 PS strategies gave similar treatment effect estimates.

Conclusions

Logistic regression including patient and surgeon/hospital-level confounders appears to be the preferred strategy for PS estimation. Further investigation with more complex clustered structure is suggested.

Competing interests

Prof. Prieto-Alhambra’s research group has received grant support from Amgen, Chesi-Taylor, Novartis, and UCB Biopharma. His department has received advisory or consultancy fees from Amgen, Astellas, AstraZeneca, Johnson, and Johnson, and UCB Biopharma and fees for speaker services from Amgen and UCB Biopharma. Janssen, on behalf of IMI-funded EHDEN and EMIF consortiums, and Synapse Management Partners have supported training programs organised by DPA’s department and open for external participants organized by his department outside submitted work.

Ethics Approval and Informed Consent

This study was approved by the secretary of state, having considered the recommendation from the Confidentiality Advisory Group (CAG reference: 17/CAG/0174). Informed ethical approval was given on the use of pseudonymised patients data included in the study.
Intracellular flow cytometry complements RT-qPCR detection of circulating SARS-CoV-2 variants of concern
Authors: Vanhulle Emiel , Provinciael Becky , Stroobants Joren , Camps Anita , Maes Piet , Vermeire Kurt
Published: February 2022

Despite the efficacy of current vaccines against SARS-CoV-2, the spread of the virus is still not under control, as evidenced by the ongoing circulation of the highly contagious SARS-CoV-2 Omicron variant. Basic and antiviral research on SARS-CoV-2 relies on cellular assays of virus replication in vitro. In addition, accurate detection of virus-infected cells and released virus particles is needed to study virus replication and to profile new candidate antiviral drugs. Here, by flow cytometry, we detect SARS-CoV-2 infection at single cell level and distinguish infected Vero E6 cells from uninfected bystander cells. Furthermore, based on the viral nucleocapsid expression, subpopulations of infected cells that are in an early or late phase of viral replication can be differentiated. Importantly, this flow cytometric technique complements RT-qPCR detection and can be applied to all current SARS-CoV-2 variants of concern, including the highly mutated Omicron variant.

Method summary

This study describes the characterization of SARS-CoV-2 infected cells using intracellular flow cytometric viral nucleocapsid staining that complements RT-qPCR quantification of viral RNA. The technique makes it possible to distinguish between infected cells in the early (low N) or late phase (high N) of viral replication. It can also be applied to the different variants of concern of SARS-CoV-2, including the Omicron variant.
Bile Salts and N-Acetyl-D-Glucosamine induce transcription of the vieSAB Operon in Vibrio cholerae El Tor
Authors: Shull Lauren M. , Camilli Andrew
Published: February 2022

The vieSAB operon regulates motility, biofilm formation and cholera toxin production in the classical biotype of V. cholerae. Classical biotype mutants lacking the cyclic-di-GMP phosphodiesterase and response regulator vieA or its cognate sensor kinase vieS fail to effectively colonize the infant mouse small intestine, are less motile than the wild-type strain, and are hyper-biofilm formers. However, deletion of vieA or vieS in the currently-circulating El Tor biotype does not have a demonstrable effect on these phenotypes. To begin to understand the role of vieSAB in the El Tor biotype, we studied its regulation and the effect of vieA expression on bacterial physiology, separating the functional roles of VieA’s enzymatic and DNA-binding activities. We identify bile salts and N-acetylglucosamine, which can be found at high concentration in the small intestine, as stimulating expression of vieSAB during in vitro growth. We show that, in contrast to many response regulators, VieA does not regulate its own expression. Together, these data indicate that V. cholerae upregulates vieSAB in response to small-intestinal signals, allowing VieA to alter the physiology of the cell through its transcriptional regulation and cyclic-di-GMP signaling activities in order to adapt to the human host.
Exploring different virulent proteins of human respiratory syncytial virus for designing a novel epitope-based polyvalent vaccine: Immunoinformatics and molecular dynamics approaches
Authors: Moin Abu Tayab , Ullah Md. Asad , Patil Rajesh B. , Faruqui Nairita Ahsan , Sarkar Bishajit , Araf Yusha , Das Sowmen , Kapil Uddin Khaza Md. , Hossain Md Shakhawat , Miah Md. Faruque , Moni Mohammad Ali , Chowdhury Dil Umme Salma , Islam Saiful
Published: February 2022

Human Respiratory Syncytial Virus (RSV) is one of the most prominent causes of lower respiratory tract infections (LRTI), contributory to infecting people from all age groups - a majority of which comprises infants and children. The implicated severe RSV infections lead to numerous deaths of multitudes of the overall population, predominantly the children, every year. Consequently, despite several distinctive efforts to develop a vaccine against the RSV as a potential countermeasure, there is no approved or licensed vaccine available yet, to control the RSV infection effectively. Therefore, through the utilization of immunoinformatics tools, a computational approach was taken in this study, to design and construct a multi-epitope polyvalent vaccine against the RSV-A and RSV-B strains of the virus. Potential predictions of the T-cell and B-cell epitopes were followed by extensive tests of antigenicity, allergenicity, toxicity, conservancy, homology to human proteome, transmembrane topology, and cytokine-inducing ability. The most promising epitopes (i.e. 13 CTL epitopes, 9 HTL epitopes, and 10 LBL epitopes) exhibiting full conservancy were then selected for designing the peptide fusion with appropriate linkers, having hBD-3 as the adjuvant. The peptide vaccine was modeled, refined, and validated to further improve the structural attributes. Following this, molecular docking analysis with specific TLRs was carried out which revealed excellent interactions and global binding energies. Additionally, molecular dynamics (MD) simulation was conducted which ensured the stability of the interactions between vaccine and TLR. Furthermore, mechanistic approaches to imitate and predict the potential immune response generated by the administration of vaccines were determined through immune simulations. Owing to an overall evaluation, in silico cloning was carried out in efforts to generate recombinant pETite plasmid vectors for subsequent mass production of the vaccine peptide, incorporated within E.coli. However, more in vitro and in vivo experiments can further validate its efficacy against RSV infections.
Imaging minimal bacteria at the nanoscale: a reliable and versatile process to perform Single Molecule Localization Microscopy in mycoplasmas
Authors: Rideau Fabien , Villa Audrey , Belzanne Pauline , Verdier Emeline , Hosy Eric , Arfi Yonathan
Published: February 2022

Mycoplasmas are the smallest free-living organisms. These bacteria are important models for both fundamental and Synthetic Biology, owing to their highly reduced genomes. They are also relevant in the medical and veterinary fields, as they are pathogenic of both humans and most livestock species. Mycoplasma cells have minute sizes, often in the 300-800 nanometers range. As these dimensions are close to the diffraction limit of visible light, fluorescence imaging in mycoplasmas is often poorly informative. Recently developed “Super-Resolution Imaging” techniques can break this diffraction limit, improving the imaging resolution by an order of magnitude and offering a new nanoscale vision of the organization of these bacteria. These techniques have however not been applied to mycoplasmas before. Here, we describe an efficient and reliable protocol to perform Single-Molecule Localization Microscopy (SMLM) imaging in mycoplasmas. We provide a polyvalent transposon-based system to express the photo-convertible fluorescent protein mEos3.2, enabling Photo-Activated Localization Microscopy (PALM) in most Mycoplasma species. We also describe the application of direct STochastic Optical Reconstruction Microscopy (dSTORM). We showcase the potential of these techniques by studying the subcellular localization of two proteins of interest. Our work highlights the benefits of state-of-the-art microscopy techniques for mycoplasmology and provides an incentive to further the development SMLM strategies to study these organisms in the future.

Importance

Mycoplasmas are important models in biology, as well as highly problematic pathogens in the medical and veterinary fields. The very small size of these bacteria, well below the micron, limits the usefulness of traditional fluorescence imaging methods as their resolution limit is similar to the dimensions of the cells. Here, to bypass this issue, we established a set of state-of-the-art “Super-Resolution Microscopy” techniques in a wide range of Mycoplasma species. We describe two strategies: PALM, based on the expression of a specific photo-convertible fluorescent protein; and dSTORM, based on fluorophore-coupled antibody labeling. With these methods, we successfully performed single-molecule imaging of proteins of interest at the surface of the cells and in the cytoplasm, at lateral resolutions well below 50 nanometers. Our work paves the way toward a better understanding of mycoplasma’s biology through imaging of subcellular structures at the nanometer scale.
CACNB4 overexpression decreases dendritic spine density in sex-specific manner
Authors: Parker Emily M. , Kindja Nathan L. , DeGiosio Rebecca A. , Salisbury Ryan B. , Krivinko Josh M. , Cheetham Claire E. J. , MacDonald Matthew L. , Sweet Robert A.
Published: February 2022

The canonical voltage-gated calcium channel (VGCC) subunit complex is comprised of the α1 subunit, the ion permeable channel, plus three auxiliary subunits: β, α2δ and γ. β is the most extensively studied auxiliary subunit and is necessary for proper forward trafficking of the α1 subunit to the plasma membrane. α1 subunits mediate voltagedependent movement of calcium ions into the cytoplasm of neurons, including at dendritic sites, where increased intracellular calcium initiates signaling cascades that shape structural and functional plasticity of dendritic spines. Genetic studies strongly implicate calcium signaling dysfunction in the etiology of neurodevelopmental disorders including schizophrenia. Dendritic spine density (DSD) is significantly decreased in schizophrenia in primary auditory cortex where DSD is driven by loss of small spines, and small spine loss is associated with increased peptide levels of ALFDFLK found in the VGCC β subunit β4. OverexpessingCACNB4to increase β4 levels selectively reduced small spine density in cortical neuron cultures. The studies described herein set out to validate thisin vitroobservation in an intact mammalian system within a neurodevelopmental context. We overexpressedCACNB4in neurodevelopment and assessed DSD and morphology in cerebral cortex of male and female mice at an adult timpoint. We then characterized β protein levels and β4 protein-protein interactions in male and female mouse cortex. Overexpression selectively reduced small dendritic spine density but this effect was present only in female mice and did not appear to result from estrous stage. Instead, the sex-dependent effect on DSD corresponded to sex differences in the β4 interactome of male versus female mice: the VGCC β subunit β1b was significantly enriched in the β4 interactome of brain tissue of male mice, and thus may have served to mitigate VGCC overexpression-mediated spine loss in male mice.
Sex and age differences in cognitive bias and neural activation in response to cognitive bias
Authors: Hodges Travis E. , Lee Grace Y. , Noh Sophia H. , Galea Liisa A.M.
Published: February 2022

Cognitive symptoms of depression, including negative cognitive bias, are more severe in women than in men. Current treatments to reduce negative cognitive bias are not effective and sex differences in the neural activity underlying cognitive bias may play a role. Here we examined sex and age differences in cognitive bias and functional connectivity in a novel paradigm. Male and female rats underwent an 18-day cognitive bias procedure, in which they learned to discriminate between two contexts (shock paired context A, no-shock paired context B), during either adolescence (postnatal day (PD 40)), young adulthood (PD 100), or middle-age (PD 210). Cognitive bias was measured as freezing behaviour in response to an ambiguous context (context C), with freezing levels akin to the shock paired context coded as negative bias. All animals learned to discriminate between the two contexts, regardless of sex or age. However, adults (young adults, middle-aged) displayed a greater negative cognitive bias compared to adolescents, and middle-aged males had a greater negative cognitive bias than middle-aged females. Females had greater neural activation of the nucleus accumbens, amygdala, and hippocampal regions to the ambiguous context compared to males, and young rats (adolescent, young adults) had greater neural activation in these regions compared to middle-aged rats. Functional connectivity between regions involved in cognitive bias differed by age and sex, and only adult males had negative correlations between the frontal regions and hippocampal regions. These findings highlight the importance of examining age and sex when investigating the underpinnings of negative cognitive bias and lay the groundwork for determining what age- and sex-specific regions to target in future cognitive bias studies.

Highlights

Middle-aged males had a greater negative cognitive bias than middle-aged females

Adult rats displayed a greater negative cognitive bias compared to adolescents

Greater neural activity in females than males in limbic and reward regions

Greater role of the frontal cortex activation in the cognitive bias of adults

Functional connectivity in response to cognitive bias differed by age and sex
The new archaeal order Lutiacidiplasmatales reveals convergent evolution in Thermoplasmatota
Authors: Sheridan Paul O. , Meng Yiyu , Williams Tom A. , Gubry-Rangin Cécile
Published: February 2022

The archaeal Terrestrial Miscellaneous Euryarchaeota Group (TMEG) has been identified in various environments, and the single genome investigated thus far suggests that these organisms are anaerobic sulfite reducers. We assembled 35 new TMEG genomes that, based on genome analysis, appear to possess aerobic and facultative anaerobic lifestyles and may oxidise rather than reduce sulfite. We propose naming this order (representing 16 genera) “Lutiacidiplasmatales” due to their occurrence in various acidic environments and placement within the phylum Thermoplasmatota. A phylum-level analysis revealed that Thermoplasmatota evolution had been punctuated by several periods of high levels of novel gene family acquisition. Several essential metabolisms, such as aerobic respiration and acid tolerance, were likely acquired independently by divergent lineages through convergent evolution rather than inherited from a common ancestor. Ultimately, this study describes the terrestrially prevalent Lutiacidiciplasmatales and indicates convergent evolution as an important evolutionary driving force in archaeal lineages with complex histories.
Breasi-CRISPR: an efficient genome editing method to interrogate protein localization and protein-protein interactions in the embryonic mouse cortex
Authors: Meyerink Brandon L. , Pratiksha KC , Tiwari Neeraj K. , Kittock Claire M. , Klein Abigail , Evans Claire , Pilaz Louis-Jan
Published: February 2022

In developing tissues, knowing the localization and interactors of proteins of interest is key to understanding their function. This can be challenging when the researched protein lacks reliable antibodies. Here, we combine Easi-CRISPR with in utero electroporation to tag endogenous proteins within embryonic mouse brains. This method is called Breasi-CRISPR (Brain Easi-CRISPR), and enables knock-in of both short and long epitope tag sequences in genes of interest with high efficiency. Using Breasi-CRISPR, we were able to visualize epitope tagged proteins known to have either high or low expression levels, such as ACTB, LMNB1, EMD, FMRP, NOTCH1, and RPL22. Detection was possible by immunohistochemistry as soon as one day after electroporation at embryonic day 13 (E13). Two and five days after electroporation, we observed efficient gene editing in up to 50% of electroporated cells. Moreover, tagged proteins could be detected by immunoblotting in lysates from individual cortices two days after electroporation. Next, we demonstrated that Breasi-CRISPR enables the tagging of proteins with fluorophores in an efficient manner, allowing the visualization of endogenous proteins via live-imaging in organotypic brain slices two days after electroporation. Finally, we used Breasi-CRISPR to perform co-IP mass-spectrometry analyses of tagged autism-related protein FMRP to discover its interactome in the embryonic cortex. Together, these data show Breasi-CRISPR is a powerful tool with diverse applications that will propel the understanding of protein function in neurodevelopment.
A dendritic mechanism for balancing synaptic flexibility and stability
Authors: Yaeger Courtney E. , Vardalaki Dimitra , Zhang Qinrong , Pham Trang L.D. , Brown Norma J. , Ji Na , Harnett Mark T.
Published: February 2022

Biological and artificial neural networks learn by modifying synaptic weights, but it is unclear how these systems can retain previous knowledge and also acquire new information. Here we show that cortical pyramidal neurons can solve this plasticity-versus-stability dilemma by differentially regulating synaptic plasticity at distinct dendritic compartments. Oblique dendrites of adult mouse layer 5b cortical pyramidal neurons selectively received monosynaptic thalamic input, integrated linearly, and— surprisingly—lacked synaptic potentiation. In contrast, basal dendrites, which do not receive thalamic input, exhibited conventional NMDA receptor-mediated supralinear integration and synaptic potentiation. Congruently, spiny synapses on oblique branches showed low structural plasticity in vivo. A selective decline in NMDAR activity and expression at synapses on oblique dendrites was controlled by an experience-dependent critical period. Our results demonstrate a new biological mechanism for how single neurons can safeguard a set of inputs from ongoing plasticity by altering synaptic properties at distinct dendritic domains.
Behavioural analysis of loss of function zebrafish supports baz1b as master regulator of domestication
Authors: Torres-Perez Jose Vicente , Anagianni Sofia , Mech Aleksandra Maria , Havelange William , Garcia-Gonzalez Judit , Fraser Scott E , Vallortigara Giorgio , Brennan Caroline Helen
Published: February 2022

Domestication is associated with both morphological and behavioural phenotypic changes that differentiate domesticated species from their wild counterparts. Some of the traits are those purposely targeted by the selection process, whilst others co-occur as a result of selection. The combination of traits is referred to as the domestication syndrome and their shared characteristics has given rise to the neural crest domestication syndrome (NCDS) hypothesis. According to this hypothesis, the phenotypic changes are a consequence of a selection towards animals with mild underdevelopment of the neural crest. A similar mechanism is suggested to affect some species of self-domesticated animals, including humans. Recent research supports a role for BAZ1B, one of the haplo-insufficient genes in Williams syndrome (WS), in the evolution of craniofacial features of modern humans. Interestingly, WS recapitulates some of the traits observed in the domestication syndrome, including hypersociability and reduced facial bones. However, the evidence linking BAZ1B to behavioural phenotypes associated with domestication is presumptive. Here, we use zebrafish as a model to test the hypothesis that baz1b loss-of-function leads to both morphological and behavioural phenotypes associated with the domestication syndrome by influencing the development of the neural crest. Our research provides further evidence supporting the NCDS hypothesis and baz1b's role in this process.
Microbiomes of the bloom-forming alga,Phaeocystis globosa, are stable, consistently recruited communities with symbiotic and opportunistic modes
Authors: Mars Brisbin Margaret , Mitarai Satoshi , Saito Mak A. , Alexander Harriet
Published: February 2022

Phaeocystisis a cosmopolitan, bloom-forming phytoplankton genus that contributes significantly to global carbon and sulfur cycles. During blooms,Phaeocystisspecies produce large carbon-rich colonies, thus creating a unique interface for bacterial interactions. While bacteria are known to interact with phytoplankton—e.g., they promote growth by producing phytohormones and vitamins—such interactions have not been shown forPhaeocystis. Therefore, we investigated the composition and function ofP. globosamicrobiomes. Specifically, we tested whether microbiome compositions are consistent across individual colonies from fourP. globosastrains, whether similar microbiomes are re-recruited after antibiotic treatment, and how microbiomes affectP. globosagrowth under limiting conditions. Results illuminated a core colonialP. globosamicrobiome—including bacteria from the orders Alteromonadales, Burkholderiales, and Rhizobiales—that was re-recruited after microbiome disruption. Consistent microbiome composition and recruitment is indicative thatP. globosamicrobiomes are stable-state systems undergoing deterministic community assembly and suggests there are specific, beneficial interactions betweenPhaeocystisand bacteria. Growth experiments with axenic and nonaxenic cultures demonstrated that microbiomes allowed continued growth when B-vitamins were withheld, but that microbiomes accelerated culture collapse when nitrogen was withheld. In sum, this study reveals interactions betweenPhaeocystiscolonies and microbiome bacteria that could influence large-scale phytoplankton bloom dynamics and biogeochemical cycles.
Identifying inputs to visual projection neurons in Drosophila lobula by analyzing connectomic data
Authors: Tanaka Ryosuke , Clark Damon A.
Published: February 2022

Electron microscopy-based connectomes provide important insights into how visual circuitry of fruit fly Drosophila computes various visual features, guiding and complementing behavioral and physiological studies. However, connectomic analyses of lobula, a putative center of object-like feature detection, remains underdeveloped, largely because of incomplete data on the inputs to the brain region. Here, we attempted to map the columnar inputs into the Drosophila lobula neuropil by performing connectivity- and morphology-based clustering on a densely reconstructed connectome dataset. While the dataset mostly lacked visual neuropils other than lobula, which would normally help identify inputs to lobula, our clustering analysis successfully extracted clusters of cells with homogeneous connectivity and morphology, likely representing genuine cell types. We were able to draw a correspondence between the resulting clusters and previously identified cell types, revealing previously undocumented connectivity between lobula input and output neurons. While future, more complete connectomic reconstructions are necessary to verify the results presented here, they can serve as a useful basis for formulating hypotheses on mechanisms of visual feature detection in lobula.
Structure-based electron-confurcation mechanism of the Ldh-EtfAB complex
Authors: Kayastha Kanwal , Katsyv Alexander , Himmrichs Christina , Welsch Sonja , Schuller Jan M. , Ermler Ulrich , Müller Volker
Published: February 2022

Lactate oxidation with NAD+ as electron acceptor is a highly endergonic reaction and some anaerobic bacteria overcome the energetic hurdle by flavin-based electron bifurcation/confurcation (FBEB/FBEC) using a lactate dehydrogenase (Ldh) in concert with the electron transferring proteins EtfA and EtfB. The electron cryo-microscopically (cryo-EM) characterized (Ldh-EtfAB)2 complex of Acetobacterium woodii at 2.43 Å resolution consists of a mobile EtfAB shuttle located between the rigid central Ldh and the peripheral EtfAB base units. The FADs of Ldh and the EtfAB shuttle contact each other thereby forming the D (dehydrogenase conducting) state. The intermediary Asp37 and Asp139 may harmonize the redox potentials between the FADs and the pyruvate/lactate pair crucial for FBEC. A plausible novel B (bifurcation conducting) state with the EtfAB base and shuttle FADs in a productive electron transfer distance was derived by integrating Alphafold2 calculations. Kinetic analysis of enzyme variants shed light on the connection between NAD binding/release and D-to-B state transition. The FBEC inactivity when truncating the ferredoxin domain of EtfA substantiates its role as redox relay. Lactate oxidation in Ldh is based on the catalytic base His423 and a metal center. On this basis, a comprehensive catalytic mechanism of the FBEC process was outlined.
Cooperativity and folding kinetics in a multi-domain protein with interwoven chain topology
Authors: Liu Zhenxing , Thirumalai D.
Published: February 2022

Although a large percentage of eukaryotic proteomes consist of proteins with multiple domains, not much is known about their assembly mechanism, especially those with complicated native state architectures. Some have complex topology in which the structural elements along the sequence are interwoven in such a manner that the domains cannot be separated by cutting at any location along the sequence. We refer to such proteins as Multiply connected Multidomain Proteins (MMPs). The phoshotransferase enzyme Adenylate Kinase (ADK) with three domains (NMP, LID, and CORE), the subject of this study, is an example of MMP. We devised a coarse-grained model to simulate ADK folding initiated by changing either the temperature or guanidinium chloride (GdmCl) concentration. The simulations reproduce the experimentally measured melting temperatures that are associated with two equilibrium transitions, FRET efficiency as a function of GdmCl concentration, and the global folding times nearly quantitatively. Although the NMP domain orders independently, cooperative interactions between the LID and the CORE domains are required for complete assembly of the enzyme. The kinetic simulations show that on the collapse time scale, but less than the global folding time, multiple interconnected metastable states are populated, attesting to the folding heterogeneity. The network connectivity between distinct states shows that the CORE domain folds only after the NMP and LID domains are formed, reflecting the interwoven nature of the chain topology. We propose that the rules for MMP folding must also hold for the folding of RNA enzymes.
Class II UvrA protein Ecm16 requires ATPase activity to render resistance against echinomycin
Authors: Erlandson Amanda , Gade Priyanka , Kim Chu-Young , Mera Paola
Published: February 2022

II.

Bacteria use various strategies to become antibiotic resistant. The molecular details of these strategies are not fully understood. We can increase our understanding by investigating the same strategies found in antibiotic-producing bacteria. In this work, we characterize the self-resistance protein Ecm16 encoded by echinomycin-producing bacteria. Ecm16 is a structural homolog of the Nucleotide Excision Repair (NER) protein UvrA. Expression ofecm16in the heterologous systemEscherichia coliwas sufficient to render resistance against echinomycin. Ecm16 preferentially binds double-stranded DNA over single-stranded DNA and is likely to primarily interact with the backbone of DNA using a nucleotide-independent binding mode. Ecm16’s binding affinity for DNA increased significantly when the DNA is intercalated with echinomycin. Ecm16 can repair echinomycin-induced DNA damage independently of NER. Like UvrA, Ecm16 has ATPase activity and this activity is essential for Ecm16’s ability to render echinomycin resistance. Notably, UvrA and Ecm16 were unable to complement each other’s function. Increasing the cellular levels of UvrA inE. coliwas insufficient to render echinomycin resistance. Similarly, Ecm16 was unable to repair DNA damage that is specific to UvrA. Together, our findings identify new mechanistic details of how a refurbished DNA repair protein Ecm16 can specifically render resistance to the DNA intercalator echinomycin. Our results, together with past observations, suggest a model where Ecm16 recognizes double helix distortions caused by echinomycin and repairs the problem independently of NER.
Synthetic genetic circuits enable reprogramming of plant roots
Authors: Brophy Jennifer A. N. , Magallon Katie J. , Kniazev Kiril , Dinneny José R.
Published: February 2022

The shape of a plant’s root system influences its ability to reach essential nutrients in the soil and to acquire water during drought. Progress in engineering plant roots to optimize water and nutrient acquisition has been limited by our capacity to design and build genetic programs that alter root growth in a predictable manner. Here, we construct synthetic genetic circuits to control gene expression with high spatial precision across root tissues. These circuits produce specific patterns of gene expression by combining the activity of multiple native promoters using logical operations. We then use the circuits to predictably alter root structure. This work demonstrates the ability of synthetic genetic circuits to control gene expression across tissues and offers an exciting means to reprogram plant growth.
Requirement of cholesterol for calcium-dependent vesicle fusion by stabilizing synaptotagmin-1-induced membrane bending
Authors: Ali Moussa Houda Yasmine , Shin Kyung Chul , Ponraj Janarthanan , Kim Soo Jin , Ryu Je-Kyung , Mansour Said , Park Yongsoo
Published: February 2022

Cholesterol is essential for neuronal activity and function. Cholesterol depletion in the plasma membrane impairs synaptic transmission. However, the molecular mechanisms by which cholesterol deficiency leads to defects in vesicle fusion remain poorly understood. Here we show that cholesterol is required for Ca2+-dependent native vesicle fusion using the in-vitro reconstitution of fusion and amperometry to monitor exocytosis in chromaffin cells. Purified native vesicles were crucial for the reconstitution of physiological Ca2+-dependent fusion, whereas vesicle-mimicking liposomes failed to reproduce the cholesterol effect. Intriguingly, cholesterol had no effect on membrane binding of synaptotagmin-1, a Ca2+ sensor for ultrafast fusion. Cholesterol stabilizes local membrane bending induced by synaptotagmin-1, thereby lowering the energy barrier for Ca2+-dependent fusion to occur. Our data provide evidence that cholesterol depletion abolishes Ca2+-dependent vesicle fusion by disrupting synaptotagmin-1-induced membrane bending, and suggests that cholesterol is an important lipid regulator for Ca2+-dependent fusion.
Changes in chromatin accessibility are not concordant with transcriptional changes for single-factor perturbations
Authors: Kiani Karun , Sanford Eric M. , Goyal Yogesh , Raj Arjun
Published: February 2022

A major goal in the field of transcriptional regulation is the mapping of changes in the binding of transcription factors to the resultant changes in gene expression. Recently, methods for measuring chromatin accessibility have enabled us to measure changes in accessibility across the genome, which are thought to correspond to transcription factor binding events. In concert with RNA-sequencing, these data in principle enable such mappings; however, few studies have looked at their concordance over short duration treatments with specific perturbations. Here, we used tandem, bulk ATAC-seq and RNA-seq measurements from MCF-7 breast carcinoma cells to systematically evaluate the concordance between changes in accessibility and changes in expression in response to retinoic acid and TGF-β. We found two classes of genes whose expression showed a significant change: those that showed some change in accessibility of nearby chromatin, and those that showed virtually no change despite strong changes in expression. The peaks associated with genes in the former group had a lower baseline accessibility prior to exposure to signal. Focusing the analysis specifically on peaks with motifs for transcription factors associated with retinoic acid and TGF-β signaling did not reduce the lack of correspondence. Analysis of paired chromatin accessibility and gene expression data from distinct paths along the hematopoietic differentiation trajectory showed a much stronger correspondence, suggesting that the multifactorial biological processes associated with differentiation may lead to changes in chromatin accessibility that reflect rather than drive altered transcriptional status. Together, these results show many gene expression changes can happen independent of changes in accessibility of local chromatin in the context of a single-factor perturbation and suggest that some changes to accessibility changes may occur after changes to expression, rather than before.
Control of Craniofacial Development by the Collagen Receptor, Discoidin Domain Receptor 2
Authors: Mohamed Fatma F. , Ge Chunxi , Cowling Randy T. , Ono Noriaki , Binrayes Abdul-Aziz , Greenberg Barry , Kaartinen Vesa M. , Franceschi Renny T.
Published: February 2022

Development of the craniofacial skeleton requires interactions between progenitor cells and the collagen-rich extracellular matrix (ECM). The mediators of these interactions are not well-defined. Mutations in discoidin domain receptor 2 (DDR2), a non-integrin collagen receptor, are associated with craniofacial abnormalities, such as midface hypoplasia and open fontanels. However, the exact role of DDR2 in craniofacial morphogenesis is not known. As will be shown,Ddr2-deficient mice exhibit defects in craniofacial bones including impaired calvarial growth and frontal suture formation, cranial base hypoplasia due to aberrant chondrogenesis and delayed ossification at growth plate synchondroses. As established by localization and lineage tracing studies,Ddr2is expressed in progenitor cell-enriched craniofacial regions including sutures and synchondrosis resting zone cartilage, overlapping with Gli1+ cells, and contributing to chondrogenic and osteogenic lineages during skull growth. Tissue-specific knockouts further established the requirement forDdr2in Gli1+ skeletal progenitors and chondrocytes and suggest important functions in chondrocyte proliferation and orientation as well as ECM organization. These studies establish a cellular basis for regulation of craniofacial morphogenesis by this understudied collagen receptor.
Synthesis, crystal structure, Hirshfeld surface and void analysis of bis(μ2-4-aminobenzoato-κ2
O:O′)bis[bis(4-aminobenzoato-κ2
O,O′)diaquathulium(III)] dihydrate
Authors: Ali Kasumova Samira , Ashfaq Muhammad , Tahir Muhammad Nawaz , Movsumov Elman Muhammad , Munawar Khurram Shahzad
Published: February 2022

The asymmetric unit of the title compound, [Tm2(C7H6NO2)6(H2O)4]·2H2O, contains three 4-aminobenzoate (4ABA) ligands, two coordinated water molecules, a thulium metal ion, and a water molecule of crystallization. The overall structure of the complex (4ABA-Tm) is in the form of a dimer. In the dinuclear thulium complex, symmetry-relevant TmO8 coordination polyhedra are formed by the O atoms of two chelating 4-aminobenzoate ligands, the O atoms of two non-chelating 4-aminobenzoate ligands, and two water molecules. The Tm—O bond lengths range from 2.216 (3) to 2.471 (3) Å with the Tm...Tm separation in the dinuclear complex being 4.7863 (5) Å. The crystal structure features O—H...N, N—H...O, and O—H...O hydrogen-bonding interactions. Further stabilization of the crystal packing is due to C—H...π and off-set π–π stacking interactions. Hirshfeld surface analysis indicates that H...H contacts are the most significant contributors to the crystal packing (45.9%). In addition, a void analysis was performed to check the strength of the crystal packing.
Methodological Insights Accounting talk: developing conversation analysis in accounting research
Authors: Baker Max , Andrew Jane , Roberts John
Published: February 2022

Purpose

This paper proposes a research method for analysing talk about accounting concepts, systems and numbers. The authors argue that studying accounting talk in situ is a fruitful way to understand both the role accounting plays in the framing of relationships between individuals and the associated emotional content of these exchanges. As such, the authors argue that conversation analysis (CA) is a useful complement to interviews in qualitative research.

Design/methodology/approach

The authors introduce a specific approach to CA called positioning theory, which captures the linguistic and emotional subtleties embedded within interpersonal interactions, and the way accounting impacts and mediates these relations through measuring, assessment and control. The authors draw on one particularly animated conversation about accounting in a manufacturing company. The conversation was a largely emotional and animated exchange between individuals where talk about accounting was imbued with metaphors, violence, sex and humour.

Findings

While participants in conversations may appear to draw on similar forms of language and expression, CA allows researchers to see that the meaning of these shared expressions change based on who is saying them, whom they are saying them to and how they are saying them. Dissecting conversations as they unfold, offers a more nuanced and multifaceted understanding of accounting as central to the social fabric of organisational life.

Originality/value

As opposed to interviews, which often suffer from the rationality of hindsight (referred to as retrospective rationality), CA captures the unfolding nature of accounting talk in real-time–not upon reflection.
Energy-aware multipath routing in WSN using improved invasive weed elephant herd optimization
Authors: Vishal Sharad Hingmire , Desai Santosh R. , Krishnrao Kanse Yuvraj
Published: February 2022

Purpose

In a wireless sensor network (WSN), the sensor nodes are distributed in the network, and in general, they are linked through wireless intermediate to assemble physical data. The nodes drop their energy after a specific duration because they are battery-powered, which also reduces network lifetime. In addition, the routing process and cluster head (CH) selection process is the most significant one in WSN. Enhancing network lifetime through balancing path reliability is more challenging in WSN. This paper aims to devise a multihop routing technique with developed IIWEHO technique.

Design/methodology/approach

In this method, WSN nodes are simulated originally, and it is fed to the clustering process. Meanwhile, the CH is selected with low energy-based adaptive clustering model with hierarchy (LEACH) model. After CH selection, multipath routing is performed by developed improved invasive weed-based elephant herd optimization (IIWEHO) algorithm. In addition, the multipath routing is selected based on certain fitness functions like delay, energy, link quality and distance. However, the developed IIWEHO technique is the combination of IIWO method and EHO algorithm.

Findings

The performance of developed optimization method is estimated with different metrics, like distance, energy, delay and throughput and achieved improved performance for the proposed method.

Originality/value

This paper presents an effectual multihop routing method, named IIWEHO technique in WSN. The developed IIWEHO algorithm is newly devised by incorporating EHO and IIWO approaches. The fitness measures, which include intra- and inter-distance, delay, link quality, delay and consumption of energy, are considered in this model. The proposed model simulates the WSN nodes, and CH selection is done by the LEACH protocol. The suitable CH is chosen for transmitting data through base station from the source to destination. Here, the routing system is devised by a developed optimization technique. The selection of multipath routing is carried out using the developed IIWEHO technique. The developed optimization approach selects the multipath depending on various multi-objective functions.
Implementing social sustainability through market pressures: an inter-organizational network analysis in the Pakistani apparel supply chain
Authors: Fontana Enrico , Atif Muhammad , Heuer Mark
Published: February 2022

Purpose

This article encourages novel approaches in the SSCM literature to create transformative change for workers in developing countries' apparel supply chains. It examines how suppliers' implementation of social sustainability is moderated by buyers' pressures (through dyadic ties) and by similar suppliers' pressures (through extended ties).

Design/methodology/approach

The article adopts a qualitative method design based on fieldwork and 21 face-to-face interviews with suppliers' senior managers. The data were collected between 2017 and 2020 in the factory premises of suppliers in Pakistan.

Findings

This article distinguishes the pressures that moderate suppliers' implementation of social sustainability positively (top-down encouragement, informal exchange and competitive convergence) and negatively (unrewarded commitment) through social ties. Hence, it shows how suppliers experience constrained proactivity as a state of tension.

Originality/value

The article primarily contributes to the SSCM literature by informing how similar suppliers' pressures in the business community constitute important processes of social governance and are key to create transformative change upstream in apparel supply chains. Against this backdrop, it cautions about buyers' opposite pressures and misuse of their negotiation power, which indirectly holds back and dilutes transformative change.
Fear appeal, coping appeal and mobile health technology persuasion: a two-stage scenario-based survey of the elderly
Authors: Sun Yongqiang , Feng Yafei , Shen Xiao-Liang , Guo Xitong
Published: February 2022

Purpose

Prior researches on the adoption of mobile health services (MHS) concentrate on the subjective cognitive appraisals resulting in technology adoption, while ignoring how to shape those cognitive appraisals by the objective message design strategies which are easier to operate in practice. Based on protection motivation theory (PMT), the current research aims to explore the antecedents of cognitive appraisals by focusing on message design strategies of fear appeal and coping appeal.

Design/methodology/approach

A two-stage scenario-based survey of 204 participants was conducted to collect data. The authors chose SPSS and covariance-based structural equation modeling (CB-SEM) approach with the software LISREL 8.8 to test our model.

Findings

The results show that the relationship between fear appeal and fear arousal is inverted U-shaped such that the degree of fear arousal is the greatest when the fear appeal is at a moderate level. Perceived usefulness for the message with negative framing is higher than that with positive framing. Furthermore, fear appeal and coping appeal have a significant interaction on the adoption of MHS at different stages.

Research limitations/implications

The sample data of this study come from a special health service of a special group in China, which limits the universality of our research results for other groups or health care services. Therefore, future researchers can validate the model in other research scenarios and sample populations.

Originality/value

This study shows how fear appeal and coping appeal work together to influence individuals' adoption intention. The authors’ findings expand the theoretical depth of PMT and fear theory, enriching the theoretical connotation of framing effect in mobile health technology adoption context, which add new insights to design more persuasive messages through fear appeal and coping appeal for researchers and MHS providers in mobile health communication or propaganda.
Supply chain sustainability risk decision support model using integrated Preference Selection Index (PSI) method and prospect theory
Authors: Sutrisno Agung , Kumar Vikas
Published: February 2022

Purpose

The purpose of this paper is to introduce the integrated model of the Preference Selection Index (PSI) and the prospect theory as new means to appraise the impact of supply chain sustainability risks based on five pillars of sustainability. Research has shown that sustainability risk assessment has a strong positive impact on improving the performance of enterprises.

Design/methodology/approach

This study adopts a new decision support model for assessing supply chain sustainability risk based on additional failure mode and effect analysis parameters and its integration with PSI methodology and prospect theory. A case example of the supply chain small and medium enterprise (SME) producing fashion have been used in this study.

Findings

The result of this study reveals some critical supply chain sustainability risks affecting the sustainability of enterprises under study.

Research limitations/implications

The use of a limited sample is often associated as a limitation in the research studies and this study is based on findings from SMEs in the fashion retail supply chain. This preliminary study provides academics and practitioners an exemplar of supply chain sustainability risk assessment using integration of the PSI method and prospect theory.

Practical implications

The result of this study is beneficial for practitioners, particularly owner–managers of SMEs who can use this study as guidance on how to consider risk behavior to identify and select the critical sustainability risks and plan mitigating strategies accordingly.

Originality/value

Scientific studies on using the PSI and its integration with prospect theory as means to assess the criticality of supply chain sustainability risks is very rare. To the best of the authors’ knowledge, this is the first paper that presents the integrated model of the PSI and prospect theory to rank supply chain sustainability risks based on five pillars of sustainability.