bluuebunny/crossref_metadata_2025 huggingface dataset:
A novel widespread MITE element in the repeat-rich genome of theCardiniumendosymbiont of the spiderOedothorax gibbosus
Authors: Halter Tamara , Hendrickx Frederik , Horn Matthias , Manzano-Marín Alejandro
Published: June 2022

Free-living bacteria have evolved multiple times to become host-restricted endosymbionts. The transition from a free-living to a host-restricted lifestyle comes with a number of different genomic changes, including a massive loss of genes. In host-restricted endosymbionts, gene inactivation and genome reduction is facilitated by mobile genetic elements, mainly insertion sequences (ISs). ISs are small autonomous mobile elements, and one of, if not the most, abundant transposable elements in bacteria. Proliferation of ISs is common in some facultative endosymbionts, and is likely driven by the transmission bottlenecks, which increase the level of genetic drift. In the current study we present a manually curated genome annotation for aCardiniumendosymbiont of the dwarf spiderOedothorax gibbosus. Cardiniumspecies are host-restricted endosymbionts that, similarly toWolbachiaspp., include strains capable of manipulating host reproduction. Through the focus on mobile elements, the annotation revealed a rampant spread of ISs, extending earlier observations in otherCardiniumgenomes. We found that a large proportion of IS elements are actually pseudogenised, with many displaying evidence of recent inactivation. Most notably, we describe the lineage-specific emergence and spread of a novel IS-derivedMiniatureInverted repeatTransposableElement (MITE), likely being actively maintained by intact copies of its parental IS982-family element. This work highlights the relevance of manual curation of these repeat-rich endosymbiont genomes for the discovery of novel MITEs, as well as the possible role these understudied elements might play in genome streamlining.
Dynamic interplay of protrusive microtubule and contractile actomyosin forces drives tissue extension
Authors: Singh Amrita , Thale Sameedha , Leibner Tobias , Ricker Andrea , Nüsse Harald , Klingauf Jürgen , Ohlberger Mario , Matis Maja
Published: June 2022

In order to shape a tissue, cell-based mechanical forces have to be integrated into global force patterns. Over the last decades, the importance of actomyosin contractile arrays, which are the key constituents of various morphogenetic processes, has been established for many tissues. Intriguingly, recent studies demonstrate that the microtubule cytoskeleton mediates folding and elongation of the epithelial sheet during Drosophila morphogenesis, placing microtubule mechanics en par with actin-based processes. While these studies establish the importance of both cytoskeletal systems during cell and tissue rearrangements, a mechanistic explanation of their functional hierarchy is currently missing. Here, we dissect the individual roles of these two key generators of mechanical forces during epithelium elongation. We demonstrate that microtubules dictate cell shape changes and actomyosin refines them. Combining experimental and numerical approaches, we find that altering the microtubule and actomyosin functions results in predictable changes in tissue shape. We further show that planar polarized microtubule patterning is independent of cell geometry and actomyosin-based mechanics. These results support a hierarchical mechanism, whereby microtubule-based forces in some epithelial systems prime actomyosin-generated forces.
Antagonistic action of Siah2 and Pard3/JamC to promote germinal zone exit of differentiated cerebellar granule neurons by modulating Ntn1 signaling via Dcc
Authors: Laumonnerie Christophe , Shamambo Maleelo , Stabley Daniel R. , Lewis Tommy L. , Trivedi Niraj , Howell Danielle , Solecki David J
Published: June 2022

Germinal zone (GZ) exit is at the top of a cascade of events promoting the maturation of neurons and their assembly into neuronal circuits. Developing neurons and their progenitors must interpret varied niche signals like morphogens, guidance molecules, extracellular matrix, or adhesive cues to navigate GZ occupancy. How newborn neurons integrate multiple cell-extrinsic niche cues with their cell-intrinsic machinery in exiting a GZ is unknown. We establish cooperation between cell polarity-regulated adhesion and Netrin-1 signaling comprises a coincidence detection circuit repelling maturing neurons from their GZ. In this circuit, the Partitioning defective 3 (Pard3) polarity protein and Junctional adhesion molecule-C (JAM-C) adhesion protein promote, while the Seven in absentia 2 (Siah2) ubiquitin ligase inhibits, Deleted in colorectal cancer (DCC) receptor surface recruitment to gate differentiation linked repulsion to GZ Netrin-1. These results demonstrate cell polarity as a central integrator of adhesive- and guidance cues cooperating to spur GZ exit.

Highlights

-Netrin1 expressed in the cerebellar GZ ranges from an attractive to repulsive cue depending on differentiation status or extracellular matrix context.

-Modulation of DCC expression levels impacts the nature of the Netrin1 response and GZ occupancy status.

-Siah2, Pard3, and JamC function to modulate responsiveness to purified Netrin1 and cooperate with Dcc to regulate GZ exit.

-Pard3 and JamC promote both basal and Netrin1 stimulated DCC surface recruitment to control GZ exit and Netrin1 repulsion
Deep haplotype analyses of target-site resistance locusACCasein blackgrass enabled by pool-based amplicon sequencing
Authors: Kersten Sonja , Rabanal Fernando A. , Herrmann Johannes , Hess Martin , Kronenberg Zev N. , Schmid Karl , Weigel Detlef
Published: June 2022

Rapid adaptation of weeds to herbicide applications in agriculture through resistance development is a widespread phenomenon. In particular, the grassAlopecurus myosuroidesis an extremely problematic weed in cereal crops with the potential to manifest resistance in the course of only a few generations. Target-site resistances (TSRs), with their strong phenotypic response, play an important role in this rapid adaptive response. Recently, using PacBio’s long-read amplicon sequencing technology in hundreds of individuals, we were able to decipher the genomic context in which TSR mutations occur. However, sequencing individual amplicons is both costly and time consuming, thus impractical to implement for other resistance loci or applications. Alternatively, pool-based approaches overcome these limitations and provide reliable allele frequencies, albeit at the expense of not preserving haplotype information. In this proof-of-concept study, we sequenced with PacBio High Fidelity (HiFi) reads long-range amplicons (13.2 kb) encompassing the entireACCasegene in pools of over hundred individuals, and resolved them into haplotypes using the clustering algorithm PacBio amplicon analysis (pbaa), a new application for pools and for plants. From these amplicon pools, we were able to recover most haplotypes from previously sequenced individuals of the same population. In addition, we analyzed new pools from a Germany-wide collection ofA. myosuroidespopulations and found that TSR mutations originating from soft sweeps of independent origin were common. Forward-in-time simulations indicate that TSR haplotypes will persist for decades even at relatively low frequencies and without selection, pointing to the importance of accurate measurement of TSR haplotype prevalence for weed management.
Auxin-dependent acceleration of cell division rates regulates root growth at elevated temperature
Authors: Ai Haiyue , Bellstaedt Julia , Bartusch Kai Steffen , Eschen-Lippold Lennart , Babben Steve , Balcke Gerd Ulrich , Tissier Alain , Hause Bettina , Andersen Tonni Grube , Delker Carolin , Quint Marcel
Published: June 2022

Roots are highly plastic organs enabling plants to acclimate to a changing below-ground environment. In addition to abiotic factors like nutrients or mechanical resistance, plant roots also respond to temperature variation. Below the heat stress threshold,Arabidopsis thalianaseedlings react to elevated temperature by promoting primary root growth, possibly to reach deeper soil regions with potentially better water saturation. While above-ground thermomorphogenesis is enabled by thermo-sensitive cell elongation, it was unknown how temperature modulates root growth. We here show that roots are able to sense and respond to elevated temperature independent of shoot-derived signals. A yet unknown root thermosensor seems to employ auxin as a messenger to promote primary root growth. Growth is primarily achieved by accelerating cell division rates in the root apical meristem, likely maintained via temperature-sensitive organization of the polar auxin transport system. Hence, the primary cellular target of elevated ambient temperature differs fundamentally between root and shoot tissues, while the messenger auxin that relays temperature information to elongating or dividing cells, respectively, remains the same.
Rab7/Retromer-based endolysosomal trafficking facilitates effector secretion and host invasion in rice blast
Authors: Chen Xin , Selvaraj Poonguzhali , Lin Lili , Fang Wenqin , Wu Congxian , Yang Piao , Zhang Jing , Abubakar Yakubu Saddeeq , Yang Fan , Lu Guodong , Liu Wende , Wang Zonghua , Naqvi Naweed I. , Zheng Wenhui
Published: June 2022

Secretion is a fundamental process in all living organisms. Using conventional secretion pathways, many plant pathogens release effectors into the host plants to downregulate immunity and promote infection. However, this does not always constitute the only way that effectors are sorted and tracked to their final destination such as the biotrophic interfacial complex-associated effectors produced by the blast fungus Magnaporthe oryzae. Here, we uncover a novel unconventional route originating from fungal vacuolar membrane to the host interface and plasma membrane. We found that a GFP-MoRab7 labeled vacuole is closely associated with the interface structure throughout M. oryzae invasive growth. Conditional inactivation of MoRab7 impaired the establishment of the biotrophy interface and secretion of Pwl2 effector. To perform the vacuolar trafficking pathway, MoRab7 first recruits the retromer complex to the vacuole membrane, enabling it recognizes a batch of SNARE proteins, including the v-SNARE MoSnc1. Live-cell imaging supports both retromer complex component and MoSnc1 protein labeled vesicles showing the trafficking dynamics toward the interface or plasma membrane, and then fusion with target membranes. Lastly, disruption of the MoRab7/Retromer/MoSnc1-based endolysosomal cascade affects effector secretion and fungal pathogenicity. Taken together, we discovered an unconventional protein and membrane trafficking route starting from the fungal endolysosomes to the M. oryzae-rice interaction interface, and dissect the role of MoRab7/Retromer/MoSnc1 constituent sorting machinery in effector secretion during invasive growth in M. oryzae.
Impact of daily octenidine skin washing on antiseptic tolerance of coagulase-negative staphylococci in two neonatal intensive care units with different bathing practices
Authors: Felgate Heather , Quinn Charlotte , Richardson Ben , Hudson Carol , Sethi Dheeraj , Oddie Sam , Clarke Paul , Webber Mark
Published: June 2022

Background

Coagulase Negative Staphylococci (CoNS) are responsible for 80-90 % of catheter related sepsis in neonates which can cause life threatening and damaging effects. NICUs within the UK use various practices to decolonise neonates to prevent infection ranging from regular full body bathing to localised skin decontamination before insertion of indwelling devices. There is a disparity in bathing practices for infants admitted onto neonatal units, with some choosing to regularly bathe infants and others not, and some routinely washing with skin antiseptics, and others not.

Aim

To compare the abundance of CoNS within two UK NICUs with different approaches to skin bathing and to test their tolerances to antiseptics.

Methods

A collection of CoNS from two UK based NICUs with differing bathing routines for neonates were collated and tested for susceptibility to the antiseptics in use, octenidine and chlorhexidine.

Findings

Regular bathing of neonates in octenidine did not decrease the abundance of organisms on neonatal skin. Isolates from the unit where octenidine was in frequent use did not show any increased antiseptic tolerance. Isolates from the unit where regular bathing was not routine practice were less susceptible to both antiseptics.

Conclusion

Frequent whole-body skin washing with octenidine does not appear to result in a lasting reduction in numbers of organisms found on the skin but also does not appear to select for antiseptic tolerant CoNS.
Clinical Application of Coronary Computed Tomography Angiography in Patients with Suspected Coronary Artery Disease
Authors: Blad Jared N. , Smith Hayden L. , Hurdelbrink Jonathan R. , Craig Steven R. , Wolford Brent , Wendl Elizabeth , Telles-Garcia Nelson A.
Published: June 2022

Background

Coronary computed tomography angiography (CCTA) has emerged as a helpful tool in the evaluation of patients with chest pain and suspected coronary artery disease (CAD). The study objective was to evaluate the clinical application of CCTA for assessment of patients presenting with chest pain at a large single urban tertiary health care center located in the US.

Methods

A retrospective review of observational data from center was conducted. The study sample included outpatients aged 18 years or older who underwent CCTA during January 2018 through February 2020.

Results

There were 158 patients in the study, with sixty-two percent having stress testing within 6-months prior to CCTA. Fifty-five percent of these patients had abnormal stress test findings but demonstrated no CAD on CCTA. Among the patients with normal stress tests, 24.4% demonstrated CAD on CCTA. Twenty-five patients underwent invasive coronary angiography (ICA) within the 6-months following CCTA. For these patients, the positive predictive value of CCTA was 91.3% (95% CI: 72.0%, 99.0%) and negative predictive value was 100.0% (95% CI: 15.8%, 100.0%) when compared to ICA results. In addition, CCTA demonstrated myocardial bridging in 10.0% and an anomalous coronary vessel in 8.8% of patients.

Conclusions

This study revealed that CCTA is being used as a diagnostic test in patients presenting with chest pain at the study center. Among patients with prior stress testing, these results were at times potentially inconsistent with the findings from the CCTA. In addition, the CCTA was able to identify variants in anatomical structures.
Inhibition of DNA-PKcs impairs the activation and cytotoxicity of CD4+ helper and CD8+ effector T cells
Authors: Azevedo-Pouly Ana C. , Appell Lauren E. , Burdine Lyle , Rogers Lora J. , Morehead Lauren C. , Barker Melanie , Waldrip Zachary J. , Koss Brian , Burdine Marie Schluterman
Published: June 2022

Modulation of T cell activity is an effective strategy for the treatment of autoimmune diseases, immune-related disorders and cancer. This highlights a critical need for continued investigation of proteins that regulate T cell function. The kinase DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is emerging as a potent regulator of the immune system spurring interest in its use as a therapeutic target for immune-related diseases. In murine models of autoimmune disease including asthma and rheumatoid arthritis, treatment with small molecule DNA-PKcs inhibitors, which are in clinical trials for cancer therapy, decreased disease severity. Additionally, DNA-PKcs inhibitors reduced T cell-mediated graft rejection and extended graft survival in a murine allogenic skin graft rejection model. These in vivo studies suggest the therapeutic use of DNA-PKcs inhibitors for autoimmune and T cell-mediated disorders. In this study, we sought to further characterize the effects of DNA-PKcs inhibitors on T cells to better understand their clinical potential. We determined that pharmacological inhibition of DNA-PKcs abrogated activation of murine and human CD4+ and CD8+ T cells as evident by reduced expression of the activation markers CD69 and CD25. Furthermore, inhibition of DNA-PKcs impeded metabolic pathways and proliferation of anti-CD3/CD28 activated CD4+ and CD8+ T cells as well as peptide-stimulated OTI-CD8+ T cells. This reduced the ability of OTI-CD8+ T cells to kill cancer cells and the expression of IFNγ and the cytotoxic genes eomes, perforin and granzyme B. These results suggest a novel role for DNA-PKcs in early T cell activation. Furthermore, our data support the therapeutic potential of DNA-PKcs inhibitors on diseases of immune dysregulation.
Quantification of Aquatic Unicellular Diazotrophs by Immunolabeled Flow Cytometry
Authors: Geisler Eyal , Siebner Hagar , Rahav Eyal , Bar-Zeev Edo
Published: June 2022

Quantifying the number of aquatic diazotrophs is highly challenging and relies mainly on microscopical approaches and/or molecular tools that are based on nif genes. However, it is still challenging to count diazotrophs, especially the unicellular fraction, despite their significant contribution to the aquatic nitrogen cycle. In this study a new method was developed to quantify unicellular diazotrophs by immunolabeling the nitrogenase enzyme followed by identification and quantification via flow cytometry. The new quantification method was initially developed using a diazotrophic monoculture (Vibrio natriegens) and verified by various auxiliary approaches. It was found that only 15-20% of the total number of V. natriegens cells have synthesized the nitrogenase enzyme, even though the media was anaerobic, and N limited. This approach was further tested in samples from marine and freshwater environments. It was found that the ratio of diazotrophs to total bacteria was 0.1% in the Mediterranean Sea, while 4.7% along the Jordan River. In contrast, the specific N2 fixation per unicellular diazotrophs was highest in the Mediterranean Sea (88 attomole N cell-1 d-1) while the total N2 fixation rates were lowest in the lake and the river (0.2 nmole N L-1 d-1). Overall, we expect that this direct quantification approach will provide new insights on the number and contribution of unicellular diazotrophs to total N2 fixation in marine and freshwater environments under various conditions.
Unique Pakistani gut microbiota highlights population-specific microbiota signatures of type 2 diabetes mellitus
Authors: Saleem Afshan , Ikram Aamer , Dikareva Evgenia , Lahtinen Emilia , Matharu Dollwin , Pajari Anne-Maria , de Vos Willem M. , Hasan Fariha , Salonen Anne , Jian Ching
Published: June 2022

Biogeographic variations in the gut microbiota reflect host and environmental factors delineating human populations, and are pivotal to understand global patterns of host-microbiota interactions in health and prevalent lifestyle-related diseases, such as type 2 diabetes mellitus (T2D). Pakistani adults, having an exceptionally high prevalence of T2D, are one of the most understudied populations in microbiota research to date. The aim of the present study is to examine the gut microbiota across individuals from Pakistan and other populations of non-industrialized and industrialized lifestyles with a focus on T2D. The fecal samples from 94 urban-dwelling Pakistani adults with and without T2D were profiled by 16S ribosomal RNA gene amplicon sequencing and qPCR, and plasma samples quantified for circulating levels of lipopolysaccharide binding protein (LBP) and the activation ability of Toll-like receptor (TLR)-signaling. Publicly available datasets generated with comparable molecular methods were retrieved for comparative analysis. Overall, urbanized Pakistanis’ gut microbiota was similar to that of transitional or non-industrialized populations, depleted in Akkermansiaceae and enriched in Prevotellaceae (dominated by the non-Westernized clades of Prevotella copri). The relatively high proportion of Atopobiaceae appeared to be a unique characteristic of the Pakistani gut microbiota. The Pakistanis with T2D had elevated levels of LBP and TLR-signaling in circulation as well as gut microbial signatures atypical of other populations e.g., increased relative abundance of Libanicoccus/Parolsenella, limiting the inter-population extrapolation of gut microbiota-based classifiers for T2D. Taken together, our findings call for more global representation of understudied populations to extend the applicability of microbiota-based diagnostics and therapeutics.
Wild-type allele of TaHRC suppresses calcium-mediated plant immune response by hijacking TaCAXIP4 to trigger FHB susceptibility in wheat
Authors: Chen Hui , Su Zhenqi , Tian Bin , Hao Guixia , Trick Harold N. , Bai Guihua
Published: June 2022

Fusarium head blight (FHB) is one of the most destructive diseases of wheat worldwide. Epidemics of FHB cause a serious reduction in grain yield and quality of wheat and result in significant economic losses to wheat producers. Recently, we have cloned a histidine-rich calcium-binding protein gene (TaHRC) as the causal gene for Fhb1 and demonstrated that the wild-type allele of TaHRC conditions FHB susceptibility and a large deletion including the start codon resulted in FHB resistance. However, the molecular mechanisms on how TaHRC regulating FHB susceptibility remains unknown. In this study, we conducted yeast two-hybrid screening (Y2H) against the wheat cDNA expression libraries using TaHRC as bait and identified a cation exchanger (CAX)-interacting protein 4 (TaCAXIP4) as the candidate protein that interacts with TaHRC to affect calcium transport activity. The strong interaction was further confirmed by Bimolecular fluorescence complementation (BiFC) assays. Using gene editing, we edited three different sites (one before and one within and one after the NLS domain) of TaHRC in a susceptible wheat cultivar ‘Bobwhite’ using the CRISPR/Cas9 gene editing technology and demonstrated the N-terminus carrying NLS domain of TaHRC plays a critical role for the interaction and conditions TaHRC function on FHB susceptibility. We determined that the interaction between TaCAXIP4 and TaHRC occurs in the nuclei of cells by subcellular colocalization assay. Intriguingly, we found TaHRC can sequester TaCAXIP4 to suppress the Ca2+ transporting activity of TaCAX1 (a H+/Ca2+ antiporter) through yeast calcium suppression assay and suggested wild-type TaHRC may hijack TaCAXIP4 to suppresses calcium-mediated plant immune response during Fusarium infection in wheat. Furthermore, we performed the reactive oxygen species (ROS) assays and further showed that TaHRC might suppress the chitin-triggered plant immune responses during Fusarium infection by sequestering TaCAXIP4 to trigger FHB susceptibility, which facilitates the pathogen spread within a wheat spike. This work provides first line of evidence to support wild type Fhb1 is a susceptible gene and how Fhb1 wild type allele regulate FHB susceptibility.
A Bivalent Omicron-containing Booster Vaccine Against Covid-19
Authors: Chalkias Spyros , Harper Charles , Vrbicky Keith , Walsh Stephen R. , Essink Brandon , Brosz Adam , McGhee Nichole , Tomassini Joanne E. , Chen Xing , Chang Ying , Sutherland Andrea , Montefiori David C. , Girard Bethany , Edwards Darin K. , Feng Jing , Zhou Honghong , Baden Lindsey R. , Miller Jacqueline M. , Das Rituparna
Published: June 2022

Background

Updated vaccination strategies against acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern are needed. Interim results of the safety and immunogenicity of the bivalent omicron-containing mRNA-1273.214 booster candidate are presented.

Methods

In this ongoing, phase 2/3 trial, the 50-μg bivalent vaccine mRNA-1273.214 (25-μg each ancestral Wuhan-Hu-1 and omicron B.1.1.529 spike SARS-CoV-2 mRNAs) was compared to the authorized 50-μg mRNA-1273 booster in adults who previously received 2-dose primary series of 100-μg mRNA-1273 and a first booster dose of 50-μg mRNA-1273 at least 3 months prior. Primary objectives were safety and reactogenicity, and immunogenicity of 50-μg mRNA-1273.214 compared with 50-μg mRNA-1273. Immunogenicity data 28 days after the booster dose are presented.

Results

Four hundred thirty-seven and 377 participants received 50-μg of mRNA-1273.214, or mRNA-1273, respectively. Median time between first and second booster doses of mRNA-1273.214 and mRNA-1273 were similar (136 and 134 days, respectively). In participants with no prior SARS-CoV-2 infection, observed omicron neutralizing antibody geometric mean titers (GMTs [95% confidence interval]) after the mRNA-1273.214 and mRNA-1273 booster doses, were 2372.4 (2070.6−2718.2) and 1473.5 (1270.8−1708.4) respectively and the model-based GMT ratio (97.5% confidence interval) was 1.75 (1.49−2.04). All pre-specified non-inferiority (ancestral SARS-CoV-2 with D614G mutation [D614G] GMT ratio; ancestral SARS-CoV-2 [D614G] and omicron seroresponse rates difference) and superiority primary objectives (omicron GMT ratio) for mRNA-1273.214 compared to mRNA-1273 were met. Additionally, mRNA-1273.214 50-μg induced a potent neutralizing antibody response against omicron subvariants BA.4/BA.5 and higher binding antibody responses against alpha, beta, gamma, delta and omicron variants. Safety and reactogenicity profiles were similar and well-tolerated for both vaccines groups.

Conclusion

The bivalent vaccine mRNA-1273.214 50-μg was well-tolerated and elicited a superior neutralizing antibody response against omicron, compared to mRNA-1273 50-μg, and a non-inferior neutralizing antibody response against the ancestral SARS-CoV-2 (D614G), 28 days after immunization, creating a new tool as we respond to emerging SARS-CoV-2 variants.
A novel time-lapse imaging method for studying developing bacterial biofilms
Authors: Futo Momir , Široki Tin , Koska Sara , Čorak Nina , Tušar Anja , Domazet-Lošo Mirjana , Domazet-Lošo Tomislav
Published: June 2022

In nature, bacteria prevailingly reside in the form of biofilms. These elaborately organized surface-bound assemblages of bacterial cells show numerous features of multicellular organization. We recently showed that biofilm growth is a true developmental process, which resembles developmental processes in multicellular eukaryotes. To study the biofilm growth, in a fashion of eukaryotic ontogeny, it is essential to define dynamics and critical transitional phases of this process. The first step in this endeavor is to record the gross morphological changes of biofilm ontogeny under standardized conditions. This visual information is instrumental in guiding the sampling strategy for the later omics analyses of biofilm ontogeny. However, none of the currently available visualizations methods is specifically tailored for recording gross morphology across the whole biofilm development. To address this void, here we present an affordable Arduino-based approach for time-lapse visualization of complete biofilm ontogeny. The major challenge in recording biofilm development on the air-solid interphase is water condensation, which compromises filming directly through the lid of a Petri dish. To overcome these trade-offs, we developed an Arduino microcontroller setup which synchronizes a robotic arm, responsible for opening and closing the Petri dish lid, with the activity of a stereomicroscope-mounted camera and lighting conditions. We placed this setup into microbiological incubator that maintains temperature and humidity during the biofilm growth. As a proof-of-principle, we recorded biofilm development of five Bacillus subtilis strains that show different morphological and developmental dynamics.
MYB and ELF3 differentially modulate labor-inducing gene expression in myometrial cells
Authors: Shchuka Virlana M. , Khader Nawrah , Dorogin Anna , Shynlova Oksana , Mitchell Jennifer A.
Published: June 2022

Spontaneous uterine contractions are initiated when smooth muscle cells (SMCs) within the uterine muscle, or myometrium, transition from a functionally dormant to an actively contractile phenotype at the end of the pregnancy period. We know that this process is accompanied by gestational time point-specific differences in the SMC transcriptome, which can be modulated by the Activator protein 1 (AP-1), Nuclear factor kappa beta (Nf-κβ), Estrogen receptor (ER), and Progesterone receptor (PR) transcription factors. Less is known, however, about the additional proteins that might assist these factors in conferring the transcriptional changes observed at labor onset. Here, we present functional evidence for the roles of two proteins previously understudied in the SMC context – MYB and ELF3 – which can contribute to the regulation of labor-driving gene transcription. We show that the MYB and ELF3 genes exhibit elevated transcript expression levels in mouse and human myometrial tissues during spontaneous term labor. The expression of both genes was also significantly increased in mouse myometrium during preterm labor induced by the progesterone antagonist, mifepristone (RU486), but not during infection-simulating preterm labor induced by intrauterine infusion of Lipopolysaccharide (LPS). Furthermore, both MYB and ELF3 proteins affect labor-driving gene promoter activity, although in surprisingly opposing ways: Gja1 and Fos promoter activation increases in the presence of MYB and decreases in the presence of ELF3. Collectively, our study adds to the current understanding of the transcription factor network that defines the transcriptomes of SMCs during late gestation and implicates two new players in the control of labor timing.
Three-dimensional chromatin organisation shapes origin activation and replication fork directionality
Authors: Giles Katherine A. , Lamm Noa , Taberlay Phillippa C. , Cesare Anthony J.
Published: June 2022

Faithful DNA replication requires the orderly firing of replication origins across the genome. At present, we lack details around how origins are selected for activation and the subsequent impact of this on replication dynamics. Here, we have investigated how chromatin organisation contributes to replication initiation and dynamics by intersecting ChIP-seq, Hi-C, Repli-seq, and OK-seq data from primary and tumour cells lines. We found replication initiation is significantly enriched at TAD boundaries, co-localizing with CTCF and cohesin in early and mid S-phase. Strong replication fork directionality (RFD) from initiation zones in TAD boundaries could occur in a bi- or uni-directional manner, which highly correlated with replication timing. While TAD boundaries were largely invariant, a minority of initiation zones were shared across cell lines, indicative of cell type specific regulation. These data are consistent with chromatin structure organizing replication initiation and dynamics, ensuring orderly completion of replication from TAD boundaries into TAD internal regions.
Phytochromes mediate germination inhibition under red, far-red, and white light in Aethionema arabicum
Authors: Mérai Zsuzsanna , Xu Fei , Musilek Andreas , Ackerl Florian , Khalil Sarhan , Soto-Jiménez Luz Mayela , Lalatović Katarina , Klose Cornelia , Tarkowská Danuše , Turečková Veronika , Strnad Miroslav , Scheid Ortrun Mittelsten
Published: June 2022

The view on the role of light during seed germination stems mainly from studies with Arabidopsis, where light is required to initiate this process. In contrast, white light is a strong inhibitor of germination in other plants, exemplified by accessions of Aethionema arabicum, another Brassicaceae. Their seeds respond to light with gene expression changes of key regulators converse to Arabidopsis, resulting in antipodal hormone regulation and prevention of germination. The photoreceptors involved in this process in A. arabicum were unknown. Screening the first mutant collection of A. arabicum, we identified koy-1, a mutant that lost light inhibition of germination, due to a deletion in the promoter of HEME OXYGENASE 1, the gene for a key enzyme in the biosynthesis of the phytochrome chromophore. koy-1 seeds are unresponsive to red- and far-red light and hyposensitive under white light. Comparison of hormone and gene expression between wild type and koy- 1 revealed that very low light fluence stimulates germination, while high irradiance of red and far-red light is inhibitory, indicating a dual role of phytochromes in light-regulated seed germination. The mutation also affects the ratio between the two fruit morphs of A. arabicum, suggesting that light reception via phytochromes can fine-tune several parameters of propagation in adaptation to conditions in the habitat.

One sentence summary

Characterization of a phytochrome chromophore biosynthesis mutant demonstrates an active role of phytochromes in the light-inhibited seed germination in Aethionema arabicum.
Artificial intelligence based decision-making in accounting and auditing: ethical challenges and normative thinking
Authors: Lehner Othmar Manfred , Ittonen Kim , Silvola Hanna , Ström Eva , Wührleitner Alena
Published: June 2022

Purpose

This paper aims to identify ethical challenges of using artificial intelligence (AI)-based accounting systems for decision-making and discusses its findings based on Rest's four-component model of antecedents for ethical decision-making. This study derives implications for accounting and auditing scholars and practitioners.

Design/methodology/approach

This research is rooted in the hermeneutics tradition of interpretative accounting research, in which the reader and the texts engage in a form of dialogue. To substantiate this dialogue, the authors conduct a theoretically informed, narrative (semi-systematic) literature review spanning the years 2015–2020. This review's narrative is driven by the depicted contexts and the accounting/auditing practices found in selected articles are used as sample instead of the research or methods.

Findings

In the thematic coding of the selected papers the authors identify five major ethical challenges of AI-based decision-making in accounting: objectivity, privacy, transparency, accountability and trustworthiness. Using Rest's component model of antecedents for ethical decision-making as a stable framework for our structure, the authors critically discuss the challenges and their relevance for a future human–machine collaboration within varying agency between humans and AI.

Originality/value

This paper contributes to the literature on accounting as a subjectivising as well as mediating practice in a socio-material context. It does so by providing a solid base of arguments that AI alone, despite its enabling and mediating role in accounting, cannot make ethical accounting decisions because it lacks the necessary preconditions in terms of Rest's model of antecedents. What is more, as AI is bound to pre-set goals and subjected to human made conditions despite its autonomous learning and adaptive practices, it lacks true agency. As a consequence, accountability needs to be shared between humans and AI. The authors suggest that related governance as well as internal and external auditing processes need to be adapted in terms of skills and awareness to ensure an ethical AI-based decision-making.
Understanding the determinants of ePharmacy services: the moderating effect of technology discomfort
Authors: Gani Mohammad Osman , Rahman Muhammad Sabbir , Faroque Anisur R. , Sabit Ahmad Anas , Fattah Fadi Abdel
Published: June 2022

Purpose

The purpose of this study is to understand the determinants affecting behavioral intention (BI) to use ePharmacy services. The moderating role of technology discomfort in the relationship between BI and the actual use of ePharmacies in the context of Bangladesh is also examined.

Design/methodology/approach

A descriptive, quantitative approach was used to consider the UTAUT-2 model. Using the convenience sampling method, 255 responses were collected. The data were analyzed using Smart-PLS 3.2 software to investigate the hypothesized relationships.

Findings

The findings reveal that website information, doctors’ services, performance expectancy, return policy, social influence, perceived reliability and facilitating conditions are significantly related to the BI to use ePharmacy services. Interestingly, the structural equation modeling results also confirmed that technology discomfort has no moderating effect on the relationship between BI and actual usage behavior.

Research limitations/implications

This research provides theoretical contribution by extending the practical knowledge focusing on the relationship of ePharmacy, BI and actual usage behavior by using UTAUT-2 model – a relevant and unexplored issue in the easting literature, offering several research opportunities as the future avenue.

Practical implications

The result highlights the economic and social relevance from the perspective of a developing country. As people are showing their intention toward ePharmacy, managers and decision-makers need to take strategic decision to overcome any difficulties. Policymakers need to improve their services for the expansion of ePharmacy through different development projects.

Originality/value

This study advances past studies on the use of ecommerce in the pharmaceutical industry and provides a general understanding of customers in developing countries.
Video-conferencing applications for educational continuity: an inquiry towards building institutional resilience
Authors: Lexman Rahul R. , Baral Rupashree
Published: June 2022

Purpose

The purpose of this paper is to explore the role of Video conferencing (VC) applications towards building institutional resilience and facilitate educational continuity in Higher Educational Institutions (HEIs). Through our study, we aimed to uncover mental reflections of faculty based on their experiences in using VC platforms for handling online classes.

Design/methodology/approach

Data were collected primarily through semi structured interviews with 25 Business school faculty from India, supplemented with data from observation and secondary sources. Following the Gioia approach, a conceptual framework was developed using the identified themes and dimensions.

Findings

The study revealed that low self-regulation, learner disengagement, need for top management support and instructor challenges were the aggregate dimensions that required focused attention while using tools such as VC applications towards designing effective institutional resilience interventions for educational continuity.

Practical implications

Findings of this study may help the policy-makers of HEIs in developing an effective plan to increase the effectiveness of educational resilience interventions in the digital learning environments. The implications are much wider than the scope of higher education landscape and may be extended to the corporate learning and development lexicon.

Originality/value

This study is an early attempt that employed a systematic qualitative approach to explore and capture mental reflections of faculty on the use of VC applications towards building institutional resilience for educational continuity during crisis situations.
Project control system (PCS) implementation in engineering and construction projects: an empirical study in Saudi’s petroleum and chemical industry
Authors: Jawad Sahar , Ledwith Ann , Khan Rashid
Published: June 2022

Purpose

There is growing recognition that effective project control systems (PCS) are critical to the success of projects. The relationship between the individual elements of PCS and successfully achieving project objectives has yet to be explored. This research investigates the enablers and barriers that influence the elements of PCS success and drive project objectives.

Design/methodology/approach

This study adopts a mixed approach of descriptive analysis and regression models to explore the impact of six PCS elements on project outcomes. Petroleum and chemical projects in Saudi Arabia were selected as a case study to validate the research model.

Findings

Data from a survey of 400 project managers in Saudi’s petroleum and chemical industry reveal that successful PCS are the key to achieving all project outcomes, but they are particularly critical for meeting project cost objectives. Project Governance was identified as the most important of the six PCS elements for meeting project objectives. A lack of standard processes emerged as the most significant barrier to achieving effective project governance, while having skilled and experienced project team members was the most significant enabler for implementing earned value.

Practical implications

The study offers a direction for implementing and developing PCS as a strategic tool and focuses on the PCS elements that can improve project outcomes.

Originality/value

This research contributes to project management knowledge and differs from previous attempts in two ways. Firstly, it investigates the elements of PCS that are critical to achieving project scope, schedule and cost objectives; secondly, enablers and barriers of PCS success are examined to see how they influence each element independently.
Multi-criteria analysis of barriers to building information modeling (BIM) adoption for SMEs in New Zealand construction industry
Authors: Hall Andrew Thomas , Durdyev Serdar , Koc Kerim , Ekmekcioglu Omer , Tupenaite Laura
Published: June 2022

Purpose

Building information modeling (BIM) is a prominent concept to digitalize data collection and analysis processes. Small and medium-sized enterprises (SMEs) account for a considerable percentage of the works performed in the construction industry. The adoption rate of BIM by SMEs is still, however, not at the desired level in the New Zealand construction industry. This study aims to evaluate barriers to BIM implementation for SMEs in the New Zealand construction industry.

Design/methodology/approach

This study adopted four-step methodology to evaluate barriers to BIM adoption for SMEs. First, a comprehensive literature review, followed by a focus group discussion was performed to identify barriers to BIM adoption. Then, analytical hierarchy process (AHP) was used to assess identified barriers. Finally, experts’ agreements (both internal and external) were ensured by consistency analysis and Kendall’s coefficient of concordance (Kendall’s W) tests.

Findings

The findings indicate that (1) interoperability between software platforms, (2) lack of government mandate on BIM usage at project level, (3) high cost of acquiring the software and licensing required to use BIM and (4) lack of client demand for adopting BIM were the most significant barriers in terms of technological, governmental, resource and cultural categories, respectively. Further investigation of the expert evaluation showed strong consistencies (each expert separately) and agreements (among experts) in each AHP matrix.

Practical implications

Primary focus should be training of local market (particularly SMEs) professionals as the shortage in qualified professionals makes the country-wide adoption challenging. The publicity in the local market can help SMEs understand how BIM is leveraged for further improvements in project performance.

Originality/value

Overall, this research not only provides a roadmap for the widespread adoption of BIM within SMEs in New Zealand through analysis of the barriers encountered but also highlights the power that policymakers hold over the mass adoption of BIM within SMEs.
Developing non-exercise activity thermogenesis (NEAT) through building design
Authors: Marsh Alastair Thomas Matthew , Jahja Naufan Ashraf , Gleed Fiona , Peacock Oliver , Coley David , Codinhoto Ricardo
Published: June 2022

Purpose

Physical inactivity has a considerable negative impact on health. Physical activity has reduced partly due to workplace and lifestyle changes, causing people to spend more time in buildings and increasing sedentary behaviour. The purpose of this paper is to address a largely untapped opportunity for designers and managers to improve building users’ health by designing buildings that raise users’ Non-Exercise Activity Thermogenesis (NEAT) levels. In this research a conceptual model was developed to assess buildings’ performance in providing NEAT-promoting opportunities through building design features and management, in relation to building users’ propensity for NEAT behaviours.

Design/methodology/approach

The conceptual model was developed by a multi-disciplinary team of researchers and data to populate the model was obtained through a survey of 75 buildings in Jakarta (Indonesia).

Findings

The presented proof-of-concept shows that the model’s “meso-scale” approach to study physical activity and building design can lead to potential improvements of NEAT levels and physical activity in buildings.

Originality/value

The review of precedent models shows that this subject has been researched at micro-scale (i.e. detailed monitoring of individuals’ movement) and macro-scale (i.e. epidemiological studies of populations’ health). The presented model is original, as it explores a “meso-scale”(i.e. building scale) that is unique.
Fossil fuel price policy and sustainability: energy, environment, health and economy
Authors: Mohamad Taghvaee Vahid , Nodehi Mehrab , Assari Arani Abbas , Rishehri Mehrnoosh , Nodehi Shahab Edin , Khodaparast Shirazi Jalil
Published: June 2022

Purpose

This study aims to develop a price policy for fossil fuel consumption, as it is an effective instrument to manage the demand-side of energy economics.

Design/methodology/approach

This research estimates the demand elasticities of diesel, gasoline, fuel oil and kerosene by using static, dynamic and error-correction models in log-linear form.

Findings

The findings show that fossil fuel demand responds to price changes less than income changes, as fuel price is inelastic, but income is elastic. In that respect, the impact of price change decreases constantly with increasing energy price, followed by subsidy reform. Subsidy removal and price policy reformation is the UN recommendation for subsidizing countries, including Iran, to reduce fossil fuel consumption, whose intensity depends on the price elasticities.

Practical implications

As a result of this price policy, diesel, gasoline and liquefied petroleum gas prices should increase at least 1.8%–7.3%, 4.4%–6.4% and 7%–8.6%, respectively, and gradually within 2018–2030. The price policy improves all the pillars of sustainable development, including economy, environment and social (health). Overall, such a target can potentially save 3%–29% of diesel, 34%–56% of gasoline and 15%–20% of liquefied petroleum gas, as well as reduce 15%–40% of CO2 emissions annually, and can save potentially more than 510,000 lives annually. Thus, the energy price policy can fundamentally improve sustainability.

Originality/value

The estimated elasticities outline the required prices to decrease the fossil fuels, according to the UN mitigation targets, as price policy recommendation.

Graphical abstract