bluuebunny/crossref_metadata_2025 huggingface dataset:
Building Bridges: Mycelium Mediated Plant-Plant Electrophysiological Communication
Authors: Thomas Matthew Adam , Cooper Robin Lewis
Published: July 2022

Whether through root secretions or by emitting volatile organic compounds, plant communication has been well-documented. While electrical activity has been documented in plants and mycorrhizal bodies on the individual and ramet, electrical propagation as a means of communication between plants has been hypothesized but understudied. This study aimed to test the hypothesis that plants can communicate with one another electrically via conductively isolated mycelial pathways. We created a bio-electric circuit linking two plants using a mycelial network with a blend of endomycorrhizal fungi grown on potato dextrose agar forming the isolated conductive pathway between plants. Using this plant-fungal biocircuit we assessed electrical propagation between Pisum sativum and Cucumis sativus We found that electrical signals were reliably conducted across the mycelial bridges from one plant to another upon the induction of a wound response. Our findings provide evidence that mechanical input can be communicated between plant species and opens the door to testing how this information can affect plant and fungal physiology.

Simple Summary

Most plants form underground relationships with fungi. These relationships are mutually beneficial. The plants and fungi share, trade, and distribute resources between themselves, their neighbors, and their offspring. Plants employ diverse methods to detect and respond to their environment and the production of electric signals is one of these methods. It would be favorable to a plant’s survival and the survival of their neighbors, if this plant could transmit and share the information these electrical signals contain. Possible avenues of transmission exist in the roots, and the fungi these roots are in contact with. If a fungal mass is in contact with the roots of multiple plants, it could propagate electrical signals throughout the plant network. We found that electric signals were reliably transmitted from one plant to another via fungal pathways upon the induction of a wound response. Our findings provide evidence that mechanical input can be communicated between plant species and opens the door to testing how this information can affect plant physiology.
Drosophila immune priming to Enterococcus faecalis relies on immune tolerance rather than resistance
Authors: Cabrera Kevin , Hoard Duncan S. , Martinez Daniel I. , Wunderlich Zeba
Published: July 2022

Most multicellular organisms, including fruit flies, possess an innate immune response, but lack an adaptive immune response. Even without adaptive immunity, “immune priming” allows organisms to survive a second infection more effectively after an initial, non-lethal infection. We used Drosophila melanogaster to study the transcriptional program that underlies priming. Using an insect-derived strain of Gram-positive Enterococcus faecalis, we found a low dose infection enhances survival of a subsequent high dose infection. The enhanced survival in primed animals does not correlate with a decreased bacterial load, implying that the organisms tolerate, rather than resist the infection. We measured the transcriptome associated with immune priming in the fly immune organs: the fat body and hemocytes. We found many genes that were only upregulated in re-infected flies. In contrast, there are very few genes that either remained transcriptionally active throughout the experiment or more efficiently re-activated upon reinfection. Measurements of priming in immune deficient mutants revealed IMD signaling is largely dispensable for responding to a single infection, but needed to fully prime; while Toll signaling is required to respond to a single infection, but dispensable for priming. Overall, we found a primed immune response to E. faecalis relies on immune tolerance rather than bacterial resistance and drives a unique transcriptional response.
DNA-binding mechanism and evolution of Replication Protein A
Authors: Madru Clément , Martinez-Carranza Markel , Laurent Sébastien , Alberti Alessandra C. , Chevreuil Maelenn , Raynal Bertrand , Haouz Ahmed , Le Meur Rémy A. , Delarue Marc , Flament Didier , Krupovic Mart , Legrand Pierre , Sauguet Ludovic
Published: July 2022

Replication Protein A (RPA) is a heterotrimeric single stranded DNA-binding protein with essential roles in DNA replication, recombination and repair, in both eukaryotic and archaeal cells. By using an integrative approach that combines three crystal structures, four cryo-EM structures in complex with single-stranded DNA (ssDNA) of different lengths, we extensively characterized RPA from Pyrococcus abyssi in different states. These structures show two essential features conserved in eukaryotes: a trimeric core and a module that promotes cooperative binding to ssDNA, as well as a newly identified archaeal-specific domain. These structures reveal for the first time how ssDNA is handed over from one RPA complex to the other, and uncover an unanticipated mechanism of self-association on ssDNA tracts. This work constitutes a significant step forward in the molecular understanding of the structure and DNA-binding mechanism of RPA, with far-reaching implications for the evolution of this primordial replication factor in Archaea and Eukarya.
Age-dependent NMDA receptor function is regulated by the Amyloid Precursor Protein
Authors: Rajao-Saraiva Joana , Temido-Ferreira Mariana , Coelho Joana E , Ribera Aurore , Moreno Sebastien , Willem Michael , Marie Helene , Lopes Luisa V. , Pousinha Paula A
Published: July 2022

N-methyl-D-aspartate receptors (NMDARs) are critical for the maturation and plasticity of glutamatergic synapses. In the hippocampus, NMDARs mainly contain GluN2A and/or GluN2B regulatory subunits. The amyloid precursor protein (APP) has emerged as a putative regulator of NMDARs, but the impact of this interaction to their function is largely unknown. By combining patch-clamp electrophysiology and molecular approaches, we unravel a dual mechanism by which APP controls GluN2B-NMDARs, depending on the life stage. We show that APP is highly abundant specifically at the postnatal postsynapse. It interacts with GluN2B-NMDARs, controlling its synaptic content and mediated currents, both in infant mice and primary neuronal cultures. Upon aging, the APP amyloidogenic derived C-terminal fragments, rather than APP full length, contribute to aberrant GluN2B-NMDAR currents. Accordingly, we found that the APP processing is increased upon aging, both in mice and human brain, and interfering with this mechanism normalized the aberrant currents. While the first mechanism might be essential for synaptic maturation during development, the latter could contribute to age-related synaptic impairments.
Testis-specific H2BFWT disrupts nucleosome integrity through reductions of DNA-histone interactions
Authors: Ding Dongbo , Pang Matthew Y.H. , Deng Mingxi , Nguyen Thi Thuy , Sun Xulun , Xu Zhichun , Zhang Yingyi , Zhai Yuanliang , Yan Yan , Ishibashi Toyotaka
Published: July 2022

During spermatogenesis, multiple testis-specific histone variants are involved in the dynamic chromatin transitions. H2BFWT is a primate testis-specific H2B variant with hitherto unclear functions, and SNPs of H2BFWT are closely associated with male non-obstructive infertility. Here, we found that H2BFWT is preferentially localized in the sub-telomeric regions and the promoters of genes highly expressed in testis from differentiated spermatogonia to early spermatocytes. Cryo-EM structural analysis shows that H2BFWT nucleosomes are defined by weakened interactions between H2A-H2BFWT dimer and H4, and between histone octamer and DNA. Furthermore, one of its SNPs, H2BFWTH100R further destabilizes nucleosomes and increases the nucleosome unwrapping rate by interfering with the interaction with H4K91. Our results suggest that H2BFWT may be necessary for the regulation of spermatogenesis-related gene expression by decreasing transcriptional barriers, and that H2BFWTH100R overdrives its nucleosome-destabilizing effects which causes infertility.
mTORC1 hyperactivation causes sensory integration deficits due to habenula impairment
Authors: Doszyn Olga , Kedra Magdalena , Zmorzynska Justyna
Published: July 2022

Mechanistic target of rapamycin complex 1 (mTORC1) is an integration hub for extracellular and intracellular signals necessary for proper brain development. Hyperactivation of mTORC1 is found in many developmental diseases, including autism spectrum disorder (ASD). Atypical reactivity to sensory stimuli is often found in patients with ASD. The most frequent hereditary cause of ASD is Tuberous Sclerosis Complex (TSC), in which inactivating mutations in the TSC1 or TSC2 genes result in hyperactivation of the mTORC1 pathway. We have discovered that the zebrafish model of TSC, tsc2vu242/vu242 mutants lack light preference, a behavior requiring integration of multiple sensory inputs. Here, we show that the lack of light preference in tsc2vu242/vu242 zebrafish is caused by aberrant sensory integration of light stimuli in the left dorsal habenula. Single-cell calcium imaging analysis revealed that tsc2vu242/vu242 fish showed impaired function of the left dorsal habenula, in which neurons exhibited higher activity and lacked habituation to the light stimuli resulting in atypical response to light. Lack of light-preference behavior and abnormal neuronal activity in the left dorsal habenula were rescued by rapamycin, indicating that hyperactive mTorC1 causes aberrant habenula function and impaired sensory integration resulting in lack of light preference. Our results link sensory integration deficits seen in TSC patients suffering from ASD with hyperactive mTORC1 and suggest that mTORC1 hyperactivity contributes to atypical reactivity to sensory stimuli in ASD.
Pore-forming protein βγ-CAT drives extracellular nutrient scavenging under cell starvation
Authors: Liu Ling-Zhen , Liu Long , Shi Zhi-Hong , Bian Xian-Ling , Wang Qi-Quan , Xiang Yang , Zhang Yun
Published: July 2022

Nutrient acquisition is essential for cells. βγ-CAT is a pore-forming protein (PFP) and trefoil factor complex assembled under tight regulation identified in toad Bombina maxima. Here, we reported that B. maxima cells secreted βγ-CAT under glucose and glutamine deficiency to scavenge extracellular proteins for their nutrient supply and survival. AMP-activated kinase signaling positively regulated the expression and secretion of βγ-CAT. The PFP complex promoted albumin and ovalbumin uptake through endolysosomal pathways. Elevated intracellular amino acids, enhanced ATP production, and eventually prolonged cell survival were observed in the presence of βγ-CAT and extracellular albumin or ovalbumin. Liposome assays indicated that high concentration of ATP (around 1–5 mM) negatively regulated the opening of βγ-CAT channels. Collectively, these results uncovered that βγ-CAT is an essential element in cell nutrient scavenging under cell starvation by driving vesicular uptake of extracellular proteins, providing a new paradigm for PFPs in cell nutrient acquisition and metabolic flexibility.
stAPAminer: Mining Spatial Patterns of Alternative Polyadenylation for Spatially Resolved Transcriptomic Studies
Authors: Ji Guoli , Tang Qi , Zhu Sheng , Zhu Junyi , Ye Pengchao , Xia Shuting , Wu Xiaohui
Published: July 2022

Alternative polyadenylation (APA) contributes to transcriptome complexity and gene expression regulation, which has been implicated in various cellular processes and diseases. Single-cell RNA-seq (scRNA-seq) has led to the profile of APA at the single-cell level, however, the spatial information of cells is not preserved in scRNA-seq. Alternatively, spatial transcriptomics (ST) technologies provide opportunities to decipher the spatial context of the transcriptomic landscape within single cells and/or across tissue sections. Pioneering studies on ST have unveiled potential spatially variable genes and/or splice isoforms, however, the pattern of APA usages in spatial contexts remains unappreciated. Here, we developed a toolkit called stAPAminer for mining spatial patterns of APA from spatial barcoded ST data. APA sites were identified and quantified from the ST data. Particularly, an imputation model based on K-nearest neighbors algorithm was designed for recovering APA signals. Then APA genes with spatial patterns of APA usage variation were identified. By analyzing the well-established ST data of mouse olfactory bulb (MOB), we present a detailed view of spatial APA usage across morphological layers of MOB with stAPAminer. We complied a comprehensive list of genes with spatial APA dynamics and obtained several major spatial expression patterns representing spatial APA dynamics in different morphological layers. Extending this analysis to two additional replicates of the MOB ST data, we found that spatial APA patterns of many genes are reproducible among replicates. stAPAminer employs the power of ST for exploring transcriptional atlas of spatial APA patterns with spatial resolution, which is available at https://github.com/BMILAB/stAPAminer.
Agency and Expectations in Pain Treatment: An Investigation of the Active Inference Model
Authors: Strube Andreas , Horing Björn , Rose Michael , Büchel Christian
Published: July 2022

The fact that we cannot tickle ourselves is traditionally explained by the attenuation of somatosensation by predictions from a forward model of self-generated movements. Alternatively, it has been suggested within the framework of active inference that Bayes-optimal reduction of sensory precision can explain this phenomenon. Combining a pain paradigm with stimulus-related expectations allows to compare both models through predictions from the Bayesian account of expectation-based hypoalgesia, where pain is influenced by the precisions of somatosensation and expectation. In two experiments, heat pain was sham-treated either externally or by the subject, while a cue created higher or lower treatment expectations. Both experiments revealed greater pain relief under self-treatment and high treatment expectations. Electroencephalography revealed a modulation of theta-to-beta frequencies linked to agency and top-down modulations of pain perception. Computational modeling showed that this is better explained by an attenuation of somatosensation than a downregulation of somatosensation precision, favoring the forward model.
Establishment of Transgenic Fluorescent Mice for Screening Synaptogenic Adhesion Molecules
Authors: Yang Lei , Zhang Jingtao , Zhang Yanning , Wang Li , Wang Xiaotong , Wang Shanshan , Li Ke , Wei Mengping , Zhang Chen
Published: July 2022

Synapse is the fundamental structure for neurons to transmit information between cells. The proper synapse formation is crucial for developing neural circuits and cognitive functions of the brain. The aberrant synapse formation has been proved to cause many neurological disorders, including autism spectrum disorders and intellectual disability. Synaptic cell adhesion molecules (CAMs) are thought to play a major role in achieving mechanistic cell-cell recognition and initiating synapse formation via trans-synaptic interactions. Although several synaptic CAMs, such as neurexins, neuroligins, SynCAMs, and LRRTMs, have been identified as synaptogenic molecules, these molecules so far as we know cannot fully explain the mechanism of synapse formation. There should be other synaptogenic adhesion molecules that remain undiscovered. Artificial synapse formation (ASF) assays, the commonly used method for screening synaptogenesis molecules, is time-consuming and labor-intensive due to the long-lasting immunostaining step. To skip this step, we generated synaptotagmin 1-tdTomato (Syt1-TDT) transgenic mice by inserting the tdTomato-fused synaptotagmin 1 coding sequence into the genome of C57BL/6J mice. In the brain of Syt1-TDT transgenic mice, the Syt1-TDT signals were widely observed in different areas. In the cultured hippocampal neurons, the Syt1-TDT signals merged with several synaptic markers, suggesting the well synaptic localization of Syt1-TDT. Compared to the wild-type (WT) mouse neurons, cultured hippocampal neurons from Syt1-TDT transgenic mice presented normal synaptic neurotransmission. In ASF assays, neurons from Syt1-TDT transgenic mice could form synaptic connections with HEK293T cells expressing neuroligin2, LRRTM2, and Slitrk2 without immunostaining. Therefore, our work suggested that the Syt1-TDT transgenic mice with the ability to label synapses by tdTomato will be a convenient tool for screening synaptogenic molecules.
Elucidating the patterns of pleiotropy and its biological relevance in maize
Authors: Khaipho-Burch Merritt , Ferebee Taylor , Giri Anju , Ramstein Guillaume , Monier Brandon , Yi Emily , Romay M. Cinta , Buckler Edward S.
Published: July 2022

Pleiotropy - when a single gene controls two or more seemingly unrelated traits - has been shown to impact genes with effects on flowering time, leaf architecture, and inflorescence morphology in maize. However, the genome-wide impact of true biological pleiotropy across all maize phenotypes is largely unknown. Here we investigate the extent to which biological pleiotropy impacts phenotypes within maize through GWAS summary statistics reanalyzed from previously published metabolite, field, and expression phenotypes across the Nested Association Mapping population and Goodman Association Panel. Through phenotypic saturation of 120,597 traits, we obtain over 480 million significant quantitative trait nucleotides. We estimate that only 1.56-32.3% of intervals show some degree of pleiotropy. We then assessed the relationship between pleiotropy and various biological features such as gene expression, chromatin accessibility, sequence conservation, and enrichment for gene ontology terms. We find very little relationship between pleiotropy and these variables when compared to permuted pleiotropy. We hypothesize that biological pleiotropy of common alleles is not widespread in maize and is highly impacted by nuisance terms such as population structure and linkage disequilibrium. Natural selection on large standing natural variation in maize populations may target wide- and large-effect variants, leaving the prevalence of detectable pleiotropy relatively low.

Author Summary

The genetic basis of complex traits has been thought to exhibit pleiotropy, which is the notion that a single locus can control two or more unrelated traits. Widespread reports in the human disease literature show genomic signatures of pleiotropic loci across many traits. However, little is known about the prevalence and behavior of pleiotropy in maize across a large number of phenotypes. Using association mapping of common alleles in over one hundred thousand traits, we determine how pleiotropic each region was and use these quantitative scores to functionally characterize each region of the genome. Our results show little evidence that pleiotropy is a common phenomenon in maize. We observed that maize does not exhibit the same pleiotropic characteristics as human diseases in terms of prevalence, gene expression, chromatin accessibility, or sequence conservation. Rather than pervasive pleiotropy, we hypothesize that strong selection on large and wide effect loci and the need for trait independence at the gene level keep the prevalence of pleiotropy low, thus, allowing for the adaptation of maize varieties to novel environments and conditions.
Male Guinea baboons are oblivious to their females’ whereabouts
Authors: Treschnak Dominique , Zinner Dietmar , Fischer Julia
Published: July 2022

In group-living species, evolution puts a premium on the ability of individuals to track the state, whereabouts, and interactions of others. The value of social information might vary with the degree of competition within and between groups, however. We investigated male monitoring of female location in wild Guinea baboons (Papio papio). Guinea baboons live in socially tolerant multi-level societies with one-male-units comprising 1-6 females and young at the core. Using field playback experiments, we first tested whether male Guinea baboons (N=14) responded more strongly to playbacks of associated vs. non-associated females, which was the case. In the second and core experiment, we tested whether males (N=22 males, N=62 trials) keep track of the whereabouts of associated females by playing back unit females’ calls from locations that were either consistent or inconsistent with the actual position of the female. Contrary to predictions, males responded equally strongly in both conditions. While males seem to recognize their females by voice, they might lack the attention or motivation to track their females’ movement patterns. These results reinforce the view that the value of social information may vary substantially with the distribution of power in a society. While highly competitive regimes necessitate high attention to deviations from expected patterns, egalitarian societies allow for a certain degree of obliviousness.
Isoform- and ligand-specific modulation of the adhesion GPCR ADGRL3/Latrophilin3 by a synthetic binder
Authors: Kordon Szymon P. , Dutka Przemysław , Adamska Justyna M. , Bandekar Sumit J. , Leon Katherine , Adams Brock , Li Jingxian , Kossiakoff Anthony A. , Araç Demet
Published: July 2022

Adhesion G protein-coupled receptors (aGPCRs) are cell-surface proteins with large extracellular regions that bind to multiple ligands to regulate key biological functions including neurodevelopment and organogenesis. Modulating a single function of a specific aGPCR isoform while affecting no other function and no other receptor is not trivial. Here, we engineered an antibody, termed LK30, that binds to the extracellular region of the aGPCR ADGRL3, and specifically acts as an agonist for ADGRL3 but not for its isoform, ADGRL1. The LK30/ADGRL3 complex structure revealed that the LK30 binding site on ADGRL3 overlaps with the binding site for an ADGRL3 ligand – teneurin. In cellular-adhesion assays, LK30 specifically broke the trans-cellular interaction of ADGRL3 with teneurin, but not with another ADGRL3 ligand – FLRT3. Our work provides proof of concept for the modulation of isoform- and ligand-specific aGPCR functions using unique tools, and thus establishes a foundation for the development of fine-tuned aGPCR-targeted therapeutics.
Molecular characterization of extended-spectrum beta-lactamase-producing extra-intestinal pathogenic Escherichia coli isolated in a university teaching hospital Dakar-Senegal
Authors: Dossouvi Komla Mawunyo , Ba Bissoume Sambe , Lo Gora , Cissé Abdoulaye , Ba-Diallo Awa , Ndiaye Issa , Dieng Assane , Ndiaye Serigne Mbaye Lo , Fall Cheikh , Tine Alioune , Karam Farba , Diagne-Samb Habsa , Ngom-Cisse Safietou , Diop-Ndiaye Halimatou , Toure-Kane Coumba , Gaye-Diallo Aïssatou , Mboup Souleymane , Boye Cheikh Saad Bouh , Dièye Yakhya , Seck Abdoulaye , Camara Makhtar
Published: July 2022

Extra-intestinal pathogenic Escherichia coli (ExPEC), a predominant Gram-negative bacterial pathogen, express a wide range of virulence factors and is responsible of several diseases including urinary tract infections (UTI), nosocomial pneumonia, bacteremia, and neonatal meningitis. ExPEC isolates are often multidrug resistant (MDR) and clones producing extended-spectrum beta-lactamases (ESBL) are increasingly reported all over the world.

Seventy-eight clinical ExPEC strains were selected for this study. The majority was from UTIs (n=51), while the rest (n=27) was from pus, sputum, bronchial fluid and vaginal samples (non-uropathogenic ExPEC). Interestingly, 49 out of the 78 ExPEC isolates where considered as community-acquired (CA) and 29 hospital-acquired (HA) bacteria. Antibiotic susceptibility testing was performed using the Kirby-Bauer disc diffusion method. Standard polymerase chain reaction (PCR) was used to screen major ESBL genes (blaCTX-M, blaOXA-1, blaTEM, blaSHV) and blaCTX-M variants (blaCTX-M-1, blaCTX-M-9, blaCTX-M-15, blaCTX-M-25).

All the ExPEC strains were resistant to ampicillin, ticarcillin, amoxicillin/clavulanic acid combination, cefalotin, cefotaxime, ceftazidime, cefepime and aztreonam, but showed a high susceptibity to fosfomycin (98.7%, n = 77), ertapenem (96.2%, n = 75), and imipenem (100%). Moreover, isolates harbored at least one ESBL gene, including blaCTX-M (98.7%), blaOXA-1 (78.2%), blaTEM (44.9%) and blaSHV (3.8%). The CTX-M variants were also found with the predominance of blaCTX-M-1 (90.9%) and blaCTX-M-15 (90.9%) followed by blaCTX-M-9 (11.7%), while blaCTX-M-25 was not detected.

Despite the resistance to most of the tested antibiotics, ExPEC isolates showed fortunately a good susceptibility to fosfomycin and carbapenems. blaCTX-M (blaCTX-M1, blaCTX-M15) and blaOXA-1 seem to be E. coli major ESBL genes circulating in Senegal. No significant difference was noted when comparing prevalence of ESBL genes detected from CA and HA strains, and from UPEC and non-uropathogenic ExPEC. The high level of resistance to antimicrobials observed stresses the need of establishing an epidemiological surveillance of antimicrobial resistance in both community and hospital settings.
Circulating androgen regulation by androgen-catabolizing gut bacteria in male mouse gut
Authors: Hsiao Tsun-Hsien , Chou Chia-Hong , Chen Yi-Lung , Wang Po-Hsiang , Brandon-Mong Guo-Jie , Lee Tzong-Huei , Wu Tien-Yu , Li Po-Ting , Li Chen-Wei , Lai Yi-Li , Tseng Yu-Lin , Shih Chao-Jen , Chen Mei-Jou , Chiang Yin-Ru
Published: July 2022

Abnormally high circulating androgen levels have been considered a causative factor for benign prostatic hypertrophy and prostate cancer. Recent studies suggested that gut bacteria can alter sex steroid profile of host; however, the underlying mechanisms and bacterial taxa remain elusive.Thauerasp. strain GDN1 is an unusual betaproteobacterium capable of aerobic and anaerobic androgen catabolism in environmental conditions (37°C) resembling the mammalian gut. The strain GDN1 administration to C57BL/6J mice through oral gavage profoundly affected gut bacterial community, along with an approximately 50% reduction in serum androgen level in male mice. Our RT–qPCR results revealed the differential expression of aerobic and anaerobic androgen catabolic genes in the mouse ileum (microaerobic) and caecum (anaerobic), respectively. Furthermore, androgenic ring-cleaved metabolites were detected in the mouse fecal extract. This study discovered that androgen serves as a carbon source of gut microbes and that androgen-catabolizing gut bacteria can modulate host circulating androgen levels.

Highlights

Thauerasp. strain GDN1 administration through oral gavage regulated mouse serum androgen levels.

The biochemical, genetic, and metabolite profile analyses revealed the occurrence of bacterial androgen catabolism in the mouse gut.

Androgen catabolism proceeds through the O2-dependent and O2-independent catabolic pathways in mouse ileum and caecum, respectively.

A possibility to harnessThauerasp. strain GDN1 as a functional probiotic to treat hyperandrogenism.

Graphical Abstract

In brief

Hsiao et al. found that oral administration of androgen-catabolizingThaueraspecies regulated mouse serum androgen level. They characterized the gut microbe–mediated androgen catabolism through genetic and biochemical analyses. Their discovery portends a possibility of harnessing androgen-catabolic gut bacteria as functional probiotics to treat hyperandrogenism.
Knowledge-based prediction of DNA hydration using hydrated dinucleotides as building blocks
Authors: Biedermannová Lada , Černý Jiří , Malý Michal , Nekardová Michaela , Schneider Bohdan
Published: July 2022

Water plays an important role in stabilizing the structure of DNA and mediating its interactions. Here, the hydration of DNA was analyzed in terms of dinucleotide fragments from an ensemble of 2727 nonredundant DNA chains containing 41 853 dinucleotides and 316 265 associated first-shell water molecules. The dinucleotides were classified into categories based on their 16 sequences and the previously determined structural classes known as nucleotide conformers (NtCs). The construction of hydrated dinucleotide building blocks allowed dinucleotide hydration to be calculated as the probability of water density distributions. Peaks in the water densities, known as hydration sites (HSs), uncovered the interplay between base and sugar-phosphate hydration in the context of sequence and structure. To demonstrate the predictive power of hydrated DNA building blocks, they were then used to predict hydration in an independent set of crystal and NMR structures. In ten tested crystal structures, the positions of predicted HSs and experimental waters were in good agreement (more than 40% were within 0.5 Å) and correctly reproduced the known features of DNA hydration, for example the `spine of hydration' in B-DNA. Therefore, it is proposed that hydrated building blocks can be used to predict DNA hydration in structures solved by NMR and cryo-EM, thus providing a guide to the interpretation of experimental data and computer models. The data for the hydrated building blocks and the predictions are available for browsing and visualization at the website https://watlas.datmos.org/watna/.
Study on the symbiotic development path of traditional villages in the county based on the grey relation analysis: the case of Xunxian County in Henan, China
Authors: Gao Changzheng , Hou Juepin , Gong Jian
Published: July 2022

Purpose

Abundance of cultural resources is a typical feature of traditional villages. It is particularly important to explore the development path of traditional villages from the perspective of cultural resources.

Design/methodology/approach

Based on symbiosis theory, establish a symbiotic development mechanism of traditional village characteristic cultural elements and use grey relation analysis (GRA) to evaluate the resource advantages of different cultural attributes. This paper proposes the traditional village development model of different symbiotic units in the county. An empirical study is conducted in conjunction with the national historical and cultural city of Xunxian County, Henan, China.

Findings

The results show that (1) according to the different attributes of humanistic cultural resources, artificial cultural resources and natural cultural resources in traditional villages, different symbiotic units can be divided, and advantageous resources can be shared through the symbiotic interface; (2) using GRA to calculate the grey relational degree between cultural resources sequence of different attributes and the sum of cultural resources sequence in the county and define as the active degree of humanistic culture, the inheritance degree of artificial culture and the integrity of natural cultural resources are shown to reflect the status of the inheritance of humanistic cultural resources, the existence of artificial cultural resources, and the protection of natural cultural resources; and (3) a comparative analysis of the active degree, inheritance, and integrity of each symbiotic unit leads to the proposal of three symbiotic models of folklore vitality, characteristic space, and natural ecology, all of which are beneficial to promote the formation of a symbiotic environment.

Originality/value

The main innovation of this paper is to put forward the research scale of symbiosis theory in the field of urban and rural planning at the county level, delimit the symbiosis units of traditional villages at the county level, complete the quantitatively evaluate cultural resources in different symbiotic units with GRA, revealing the symbiotic development mechanism of cultural resources characteristic elements in traditional villages.
Influencing supply chain practice: the action principles approach applied to pandemic risk management
Authors: van Hoek Remko , Lacity Mary , Willcocks Leslie
Published: July 2022

Purpose

This paper offers a novel approach for conducting impactful research on emerging topics or practices. This method is particularly relevant in the face of emerging phenomena and new dynamics, such as the impact of the COVID-19 pandemic on supply chain risks. Because these new phenomena and dynamics are relatively unexplored, little prior knowledge exists in literature and industry, and they represent a large opportunity and/or challenge to practitioners.

Design/methodology/approach

The action principles research (APR) approach, as a newer version of critically engaged research (CER), offers comparison against more traditional empirical or intervention-based research. The authors illustrate the approach with a pandemic risk-management study.

Findings

The APR approach originated in the information technology field. It is highly applicable for researchers who are seeking to more expeditiously support decision making and actioning on new dynamics and emerging topics and practice in supply chain management than is allowed by traditional methods and longitudinal CER.

Originality/value

In the context of ongoing calls for relevance, impact and actionable findings on pandemic risk management, this paper describes an approach to developing timely findings that are actionable for practitioners and that advance science around dynamic and emerging topics or practices. We hope this will grow societal value of research, particularly in the face of the COVID-19 pandemic and the new dynamics and uncertainties that managers face in modern supply chains.
Exploring job resources as predictors of employees' effective coping with job stress
Authors: Zampetakis Leonidas A. , Gkorezis Panagiotis
Published: July 2022

Purpose

The purpose of this paper is to shed more light on the relative impact of the various workplace resources on employees' effective coping with job stress symptoms, taking into account synergistic and antagonistic effects. The authors used job demands-resources (JD-R) theory as an overarching theoretical framework to test the hypotheses.

Design/methodology/approach

The authors used a factorial survey experiment and a within-person design. Data were obtained from a random sample of 97 Greek employees working in public and private organizations. Multilevel modeling regression techniques were used for data analyses. The authors examined the relative effect of various job resources at different levels on employees' ratings of effective coping with job stress symptoms. In parallel, the authors investigated the possible synergistic and antagonistic interactions between the specific job resources.

Findings

The authors found that managers' leadership and humor style, their relationship with subordinates and coworkers’ support had positive effects on employees' coping with job stress. In addition, the authors found that the manager's leadership style interacts with manager–subordinate relationship quality and coworkers’ support as well as the latter interacts with the manager's humor style and manager–subordinate relationship quality. The study model explained 50% of the variance in effective coping with stress ratings.

Originality/value

The study highlights the importance of workplace resources as contextual variables, for the effective coping with stress symptoms at work. It highlights that a combination of workplace resources produces a net effect that was better than would have been expected based solely on the individual performance of these job resources. As such, the research answer calls to attend to the effects of synergistic effects of workplace resources on effective coping with stress symptoms at work.
Organizational ambidexterity and the learning organization: the strategic role of a corporate university
Authors: Lissillour Raphael , Rodriguez-Escobar Javier Alfonso
Published: July 2022

Purpose

Balancing exploration and exploitation is a strategic challenge for technology-based companies striving to successfully implement ambidexterity in rapidly changing markets. This study aims to look at the extent in which corporate universities can be instrumental in the cross-functional deployment of the resources, capabilities and experience needed to achieve organizational ambidexterity.

Design/methodology/approach

This study is the result of a single case study of ZTE University in China. Data from archives, direct observations, and semi-open interviews have been triangulated and analyzed with pattern matching technique.

Findings

This study analyzed the development of capabilities allowing the strategic combinations of exploration and exploitation, and to clearly witness how the corporate university was dynamically linked with those development.

Originality/value

The empirical results offer new insights on the most relevant capabilities for technology-based companies and notably those that are more likely to be exploited through a corporate university.
Willingness to purchase refurbished products sold online: a qualitative inquiry of young consumers from an emerging market
Authors: Gaur Jighyasu , Srivastava Ankur , Gupta Ritu
Published: July 2022

Purpose

The literature provides evidence of consumers’ willingness to purchase (WTP) refurbished products. However, the studies focusing on young consumers’ (18–24 years) purchasing behaviour of refurbished products from online platforms/stores are limited. Therefore, the purpose of this study is to conduct a qualitative study to identify the key attributes/factors that influence young consumers’ WTP refurbished products.

Design/methodology/approach

Two qualitative techniques, focus group discussion (FGD) and depth interviews (DI), are used for data collection. Criterion sampling is used for sample selection. Consequently, 37 participants (20 for FGD and 17 for DI) from India were recruited.

Findings

The study’s findings indicate six broad attributes/factors (purchase attributes, product attributes, credibility, reviews/support, refurbishment process and ecological factors) that influence young consumers’ WTP refurbished products. In each attribute, some characteristics are unique (for example, greater trust in online platforms/stores, preference for video reviews and historical information of the product) to young consumers.

Originality/value

The current study integrates three literature streams: consumer behaviour in the online/offline context, young consumers’ inclination towards an online purchase and WTP refurbished products. To the best of the authors’ knowledge, this is the first study to do it.
Multiple parasitoid species enhance top‐down control, but parasitoid performance is context dependent
Authors: Thierry Mélanie , Pardikes Nicholas A. , Ximénez‐Embún Miguel G. , Proudhom Grégoire , Hrček Jan
Published: July 2022

Ecological communities are composed of many species, forming complex networks of interactions. Current environmental changes are altering the structure and species composition of ecological networks, which could modify interactions, either directly or indirectly. To predict changes in the functioning of communities, we need to understand whether species interactions are primarily driven by network structure (i.e. topology) or the specific identities of species (i.e. nodes). Yet, this partitioning of effects is challenging and thus rarely explored.

Here we disentangled the influence of network structure and the identities of species on the outcome of consumer–resource interactions using a host–parasitoid system.

We used four common community modules in host–parasitoid communities to represent network structure (i.e. host–parasitoid, exploitative competition, alternative host and a combination of exploitative competition and alternative host). We assembled nine different species combinations per community module in a laboratory experiment using a pool of three Drosophila hosts and three larval parasitoid species (Leptopilina sp., Ganaspis sp. and Asobara sp.). We compared host suppression and parasitoid performance across community modules and species assemblages to identify general effects linked to network structure and specific effects due to species community composition.

We found that multiple parasitoid species enhanced host suppression due to sampling effect, weaker interspecific than intraspecific competition between parasitoids, and synergism. However, the effects of network structure on parasitoid performance were species specific and dependent on the identity of co‐occurring species. Consequently, multiple parasitoid species generally strengthen top‐down control, but the performance of the parasitoids depends on the identity of either the co‐occurring parasitoid species, the alternative host species or both.

Our results highlight the importance of preserving parasitoid diversity for ecosystem functioning and show that other effects depend on species community composition, and may therefore be altered by ongoing environmental changes.
The adoption of social determinants of health documentation in clinical settings
Authors: Kepper Maura M. , Walsh‐Bailey Callie , Prusaczyk Beth , Zhao Min , Herrick Cynthia , Foraker Randi
Published: July 2022

Objective

To understand the frequency of social determinants of health (SDOH) diagnosis codes (Z‐codes) within the electronic health record (EHR) for patients with prediabetes and diabetes and examine factors influencing the adoption of SDOH documentation in clinical care.

Data Sources

EHR data and qualitative interviews with health care providers and stakeholders.

Study Design

An explanatory sequential mixed methods design first examined the use of Z‐codes within the EHR and qualitatively examined barriers to documenting SDOH. Data were integrated and interpreted using a joint display. This research was informed by the Framework for Dissemination and Utilization of Research for Health Care Policy and Practice.

Data Collection/Extraction Methods

We queried EHR data for patients with a hemoglobin A1c > 5.7 between October 1, 2015 and September 1, 2020 (n = 118,215) to examine the use of Z‐codes and demographics and outcomes for patients with and without social needs. Semi‐structured interviews were conducted with 23 participants (n = 15 health care providers; n = 7 billing and compliance stakeholders). The interview questions sought to understand how factors at the innovation‐, individual‐, organizational‐, and environmental‐level influence SDOH documentation. We used thematic analysis to analyze interview data.

Principal Findings

Patients with social needs were disproportionately older, female, Black, uninsured, living in low‐income and high unemployment neighborhoods, and had a higher number of hospitalizations, obesity, prediabetes, and type 2 diabetes than those without a Z‐code. Z‐codes were not frequently used in the EHR (<1% of patients), and there was an overall lack of congruence between quantitative and qualitative results related to the prevalence of social needs. Providers faced barriers at multiple levels (e.g., individual‐level: discomfort discussing social needs; organizational‐level: limited time, competing priorities) for documenting SDOH and identified strategies to improve documentation.

Conclusions

Providers recognized the impact of SDOH on patient health and had positive perceptions of screening for and documenting social needs. Implementation strategies are needed to improve systematic documentation.
Impacts of Covid‐19 Confinement on Transport Companies and Perishable Food Manufacturers in Spain
Authors: González‐Moralejo Silvia Andrés , Miquel Juan Francisco López
Published: July 2022

In 2020, the world suffered a sudden economic recession resulting from an unprecedented health crisis due to Covid‐19 that confined millions of people to their homes and shut down all non‐essential activities. Countries have rapidly realised how vulnerable they are without food producers, manufacturers and distributors. Based on a case study from Spain, this article compiles ‘first‐hand’ information with the aim of revealing the changes that confinement has wrought on perishable food carriers and manufacturers in Spain. The results confirm a general decline in business activity with significant ups and downs depending on the subsector. In addition, they are consistent with ‘Schumpeter’s Paradigm of creative destruction’ in the context of the pressures and disruptions caused by the Covid‐19 pandemic. In this context, austerity offers companies various opportunities for renewal and finding new solutions, products and markets. These include more effective communication strategies and more efficient methods of planning and managing improved food transport, implementation of new technologies, and development of innovative, profitable, and forward‐thinking business schemes to deal with the difficulties caused by confinement. Therefore, it is essential that public authorities and stakeholders, particularly senior managers, focus their attention on the promotion and development of these opportunities.
Microbial community associated with the crustose lichen Rhizocarpon geographicum L. (DC.) living on oceanic seashore: A large source of diversity revealed by using multiple isolation methods
Authors: Miral Alice , Jargeat Patricia , Mambu Lengo , Rouaud Isabelle , Tranchimand Sylvain , Tomasi Sophie
Published: July 2022

Recently, the study of the interactions within a microcosm between hosts and their associated microbial communities drew an unprecedented interest arising from the holobiont concept. Lichens, a symbiotic association between a fungus and an alga, are redefined as complex ecosystems considering the tremendous array of associated microorganisms that satisfy this concept. The present study focuses on the diversity of the microbiota associated with the seashore located lichen Rhizocarpon geographicum, recovered by different culture‐dependent methods. Samples harvested from two sites allowed the isolation and the molecular identification of 68 fungal isolates distributed in 43 phylogenetic groups, 15 bacterial isolates distributed in five taxonomic groups and three microalgae belonging to two species. Moreover, for 12 fungal isolates belonging to 10 different taxa, the genus was not described in GenBank. These fungal species have never been sequenced or described and therefore non‐studied. All these findings highlight the novel and high diversity of the microflora associated with R. geographicum. While many species disappear every day, this work suggests that coastal and wild environments still contain an unrevealed variety to offer and that lichens constitute a great reservoir of new microbial taxa which can be recovered by multiplying the culture‐dependent techniques.