bluuebunny/crossref_metadata_2025 huggingface dataset:
Early-childhood inflammation blunts the transcriptional maturation of cerebellar neurons
Authors: Ament Seth A. , Cortes-Gutierrez Marcia , Herb Brian R. , Mocci Evelina , Colantuoni Carlo , McCarthy Margaret M.
Published: July 2022

Inflammation early in life is a clinically established risk factor for autism spectrum disorders and schizophrenia, yet the impact of inflammation on human brain development is poorly understood. The cerebellum undergoes protracted postnatal maturation, making it especially susceptible to perturbations contributing to risk of neurodevelopmental disorders. Here, using single-cell genomics, we characterize the postnatal development of cerebellar neurons and glia in 1-5-year-old children, comparing those who died while experiencing inflammation vs. non-inflamed controls. Our analyses reveal that inflammation and postnatal maturation are associated with extensive, overlapping transcriptional changes primarily in two subtypes of inhibitory neurons: Purkinje neurons and Golgi neurons. Immunohistochemical analysis of a subset of these brains revealed no change to Purkinje neuron soma size but evidence for increased activation of microglia in those subjects experiencing inflammation. Maturation- and inflammation-associated genes were strongly enriched for those implicated in neurodevelopmental disorders. A gene regulatory network model integrating cell type-specific gene expression and chromatin accessibility identified seven temporally specific gene networks in Purkinje neurons and suggested that the effects of inflammation correspond to blunted cellular maturation.

One Sentence Summary

Post-mortem cerebelli from children who perished under conditions that included inflammation exhibit transcriptomic changes consistent with blunted maturation of Purkinje neurons compared to those who succumbed to sudden accidental death.
Contributions of Ccr4 and Gcn2 to the translational response of C. neoformans to host-relevant stressors and Integrated Stress Response induction
Authors: Knowles Corey M. , Goich David , Bloom Amanda L. M. , Kalem Murat C. , Panepinto John C.
Published: July 2022

In response to the host environment, Cryptococcus neoformans must rapidly reprogram its translatome from one which promotes growth to one which is responsive to host temperature and oxidative stress. This reprogramming is primarily driven through the Gcn2-mediated repression of translation initiation and Ccr4-mediated removal of abundant pro-growth mRNAs from the translating pool. Here we investigate the contributions of these two pathways to the translational response to stress, and show that the response to oxidative stress is primarily driven by Gcn2 whereas temperature and oxidative stress both require Ccr4. Temperature stress, but not oxidative stress, result in an increase in RNase I resistant disome. Further, eIF2α phosphorylation varies in response to the type and magnitude of stress, yet all tested conditions induce translation of integrated stress response (ISR) transcription factor Gcn4, but not necessarily the Gcn4-dependent transcription. Finally, we define the ISR regulon in response to oxidative stress in C. neoformans. Together this study identifies the differential response to host-relevant stressors in an environmental fungus which can adapt to the environment inside the human host.
CGAN-Cmap: protein contact map prediction using deep generative adversarial neural networks
Authors: Madani Mohammad , Behzadi Mohammad Mahdi , Song Dongjin , Ilies Horea , Tarakanova Anna
Published: July 2022

Protein contact maps represent spatial pairwise inter-residue interactions, providing a protein’s translationally and rotationally invariant topological representation. Accurate contact map prediction has been a critical driving force for improving protein structure prediction, one of computational biology’s most challenging problems in the last half-century. While many computational tools have been developed to this end, most fail to predict accurate contact maps for proteins with insufficient homologous protein sequences, and exhibit low accuracy for long-range contacts. To address these limitations, we develop a novel hybrid model, CGAN-Cmap, that uses a generative adversarial neural network embedded with a series of modified squeeze and excitation residual networks. To exploit features of different dimensions, we build the generator of CGAN-Cmap via two parallel modules: sequential and pairwise modules to capture and interpret distance profiles from 1D sequential and 2D pairwise feature maps, respectively, and combine them during the training process to generate the contact map. This novel architecture helps to improve the contact map prediction by surpassing redundant features and encouraging more meaningful ones from 1D and 2D inputs simultaneously. We also introduce a new custom dynamic binary cross-entropy (BCE) as the loss function to extract essential details from feature maps, and thereby address the input imbalance problem for highly sparse long-range contacts in proteins with insufficient numbers of homologous sequences. We evaluate the performance of CGAN-Cmap on the 11th, 12th, 13th, and 14th Critical Assessment of protein Structure Prediction (CASP 11, 12, 13, and 14) and CAMEO test sets. CGAN-Cmap significantly outperforms state-of-the-art models, and in particular, it improves the precision of medium and long-range contact by at least 3.5%. Furthermore, our model has a low dependency on the number of homologous sequences obtained via multiple sequence alignment, suggesting that it can predict protein contact maps with good accuracy for those proteins that lack homologous templates. These results demonstrate an efficient approach for fast and highly accurate contact map prediction toward construction of protein 3D structure from protein sequence.

Data availability

All datasets and source codes are provided in: https://github.com/mahan-fcb/CGAN-Cmap-A-protein-contact-map-predictor
Reorganization of bird communities along a rainforest elevation gradient during a strong El Niño event in Papua New Guinea
Authors: Sam Katerina , Jorge Leonardo Ré , Koane Bonny , Hazell Richard , Shearman Phil , Novotny Vojtech
Published: July 2022

The El Niño 2015 event, most extreme since 1997, led to severe droughts in tropical wet Papua New Guinea (PNG), reducing May to October dry season rainfall by - 75% in the lowlands and 25% in the highlands. Such droughts are likely to have significant effects on terrestrial ecosystems, but they have been poorly explored in Papua New Guinea. Here we report changes in bird community composition prior, during and after 2015 El Niño event along the elevational gradient ranging from 200 m to 2,700 m a.s.l. at the Mt. Wilhelm rainforest in PNG. The abundance of birds in lowlands dropped by 60% but increased by 40% at elevations above 1700m during El Niño year. In the following year, the individual bird species reached mean population sizes similar to pre-El Niño years but did not fully recover. Species richness roughly followed the pattern of observed abundance and quickly and fully re-established after the event to the pre-El Niño values. Thus, at least some terrestrial birds seem to react quickly to the extreme droughts in lowlands and shifted to less affected mountain habitats. We recorded upper elevational range limits to shifts by more than 500m asl in 22 bird species (out of 237 recorded in total) during El Niño year, in contrast to their typical ranges. Our study suggests that a strong El Niño event can have strong but reversible effects on bird communities as long as they have an opportunity to move to more favourable sites through undisturbed habitats.
Hypoxia potentiates the inflammatory fibroblast phenotype promoted by pancreatic cancer cell-derived cytokines
Authors: Schwörer Simon , Ros Manon , Tsanov Kaloyan M. , Cimino Francesco V. , Lowe Scott W. , Carmona-Fontaine Carlos , Thompson Craig B.
Published: July 2022

Cancer-associated fibroblasts (CAFs) are a major cell type in the stroma of solid tumors and can exert both tumor-promoting and tumor-restraining functions. This functional heterogeneity is correlated with the existence of transcriptionally distinct subpopulations of CAFs. CAF heterogeneity is observed in pancreatic ductal adenocarcinoma (PDAC), a tumor characterized by a remarkably dense and hypoxic stroma that features tumor-restraining myofibroblastic CAFs (myCAFs) and tumor-supporting inflammatory CAFs (iCAFs). While CAF heterogeneity can be driven in part by tumor cell-produced cytokines, other determinants shaping CAF identity and function are largely unknown.In vivo, we found that iCAFs display a hypoxic gene expression and biochemical profile and are enriched in hypoxic regions of PDAC tumors. Hypoxia leads fibroblasts to acquire an inflammatory gene expression signature and synergizes with cancer cell-derived cytokines to promote an iCAF phenotype in a HIF-1α dependent fashion. Furthermore, we show that HIF-1α stabilization is sufficient to induce an iCAF phenotype in stromal cells introduced into PDAC organoid co-cultures and to promote PDAC tumor growth. These findings indicate hypoxia-induced HIF-1α as a regulator of CAF heterogeneity and promoter of tumor progression in PDAC.
Spatial structure formation by RsmE-regulated extracellular secretions in Pseudomonas fluorescens Pf0-1
Authors: Evans Anton , Wells Meghan , Denk Jordan , Mazza William , Santos Raziel , Delprince Amber , Kim Wook
Published: July 2022

Cells in microbial communities on surfaces live and divide in close proximity, which greatly enhances the potential for social interactions. Spatiogenetic structures manifest through competitive and cooperative interactions among the same and different genotypes within a shared space, and extracellular secretions appear to function dynamically at the forefront. A previous experimental evolution study utilizing Pseudomonas fluorescens Pf0-1 colonies demonstrated that diverse mutations in the rsmE gene are repeatedly and exclusively selected through the formation of a dominant spatial structure. RsmE’s primary molecular function is translation repression, and its homologs regulate various social and virulence phenotypes. Pseudomonas spp. possess multiple paralogs of Rsm proteins, and RsmA, RsmE, and RsmI are the most prevalent. Here, we demonstrate that the production of a mucoid polymer and a biosurfactant are exclusively regulated through RsmE, contradicting the generalized notion of functional redundancy among the Rsm paralogs. Furthermore, we identify the biosurfactant as the cyclic lipopeptide gacamide A. Competition and microscopy analyses show that the mucoid polymer is solely responsible for creating a space of low cellular density, which is shared exclusively by the same genotype. Gacamide A and other RsmE-regulated products appear to establish a physical boundary that prevents the encroachment of the competing genotype into the newly created space. Although cyclic lipopeptides and other biosurfactants are best known for their antimicrobial properties and reducing surface tension to promote the spreading of cells on various surfaces, they also appear to help define spatial structure formation within a dense community.

IMPORTANCE

In densely populated colonies of the bacterium Pseudomonas fluorescens Pf0-1, diverse mutations in the rsmE gene are naturally selected by solving the problem of overcrowding. Here, we show that RsmE-regulated secretions function together to create and protect space of low cell density. A biosurfactant generally promotes the spreading of bacterial cells on abiotic surfaces, however, it appears to function atypically within a crowded population by physically defining genotypic boundaries. Another significant finding is that these secretions are not regulated by RsmE’s paralogs that share high sequence similarity. The experimental pipeline described in this study is highly tractable and should facilitate future studies to explore additional RsmE-regulated products and address why RsmE is functionally unique from its paralogs.
High Frequencies of Phenotypically and Functionally Senescent and Exhausted CD56+CD57+PD-1+ Natural Killer Cells, SARS-CoV-2-Specific Memory CD4+ and CD8+ T cells Associated with Severe Disease in Unvaccinated COVID-19 Patients
Authors: Srivastava Ruchi , Dhanushkodi Nisha , Prakash Swayam , Coulon Pierre Gregoire , Vahed Hawa , Zayou Latifa , Quadiri Afshana , BenMohamed Lbachir
Published: July 2022

Unvaccinated COVID-19 patients display a large spectrum of symptoms, ranging from asymptomatic to severe symptoms, the latter even causing death. Distinct Natural killer (NK) and CD4+ and CD8+ T cells immune responses are generated in COVID-19 patients. However, the phenotype and functional characteristics of NK cells and T-cells associated with COVID-19 pathogenesis versus protection remain to be elucidated. In this study, we compared the phenotype and function of NK cells SARS-CoV-2-specific CD4+ and CD8+ T cells in unvaccinated symptomatic (SYMP) and unvaccinated asymptomatic (ASYMP) COVID-19 patients. The expression of senescent CD57 marker, CD45RA/CCR7differentiation status, exhaustion PD-1 marker, activation of HLA-DR, and CD38 markers were assessed on NK and T cells from SARS-CoV-2 positive SYMP patients, ASYMP patients, and Healthy Donors (HD) using multicolor flow cytometry. We detected significant increases in the expression levels of both exhaustion and senescence markers on NK and T cells from SYMP patients compared to ASYMP patients and HD controls. In SYMP COVID-19 patients, the T cell compartment displays several alterations involving naive, central memory, effector memory, and terminally differentiated T cells. The senescence CD57 marker was highly expressed on CD8+ TEM cells and CD8+ TEMRA cells. Moreover, we detected significant increases in the levels of proinflammatory TNF-α, IFN-γ, IL-6, IL-8, and IL-17 cytokines from SYMP COVID-19 patients, compared to ASYMP COVID-19 patients and HD controls. The findings suggest exhaustion and senescence in both NK and T cell compartment is associated with severe disease in critically ill COVID-19 patients.

IMPORTANCE

Unvaccinated COVID-19 patients display a large spectrum of symptoms, ranging from asymptomatic to severe symptoms, the latter even causing death. Distinct Natural killer (NK) and CD4+ and CD8+ T cells immune responses are generated in COVID-19 patients. In this study, we detected significant increases in the expression levels of both exhaustion and senescence markers on NK and T cells from unvaccinated symptomatic (SYMP) compared to unvaccinated asymptomatic (ASYMP) COVID-19 patients. Moreover, we detected significant increases in the levels of proinflammatory TNF-α, IFN-γ, IL-6, IL-8, and IL-17 cytokines from SYMP COVID-19 patients, compared to ASYMP COVID-19 patients. The findings suggest exhaustion and senescence in both NK and T cell compartment is associated with severe disease in critically ill COVID-19 patients.

TWEET

Significant exhaustion and senescence in both NK and T cells were detected in unvaccinated symptomatic COVID-19 patients, suggesting a weakness in both innate and adaptive immune systems leads to severe disease in critically ill COVID-19 patients.
Site-specific analysis reveals candidate cross-kingdom small RNAs, tRNA and rRNA fragments, and signs of fungal RNA phasing in the barley-powdery mildew interaction
Authors: Kusch Stefan , Singh Mansi , Thieron Hannah , Spanu Pietro D. , Panstruga Ralph
Published: July 2022

The establishment of host-microbe interactions requires molecular communication between both partners, which involves the mutual transfer of noncoding small RNAs. Previous evidence suggests that this is also true for the barley powdery mildew disease, which is caused by the fungal pathogen Blumeria hordei. However, previous studies lacked spatial resolution regarding the accumulation of small RNAs upon host infection by B. hordei. Here, we analysed site-specific small RNA repertoires in the context of the barley-B. hordei interaction. To this end, we dissected infected leaves into separate fractions representing different sites that are key to the pathogenic process: epiphytic fungal mycelium, infected plant epidermis, isolated haustoria, a vesicle-enriched fraction from infected epidermis, and extracellular vesicles. Unexpectedly, we discovered enrichment of specific 31- to 33-base long 5’-terminal fragments of barley 5.8S ribosomal RNA (rRNA) in extracellular vesicles and infected epidermis, as well as particular B. hordei tRNA fragments in haustoria. We describe canonical small RNAs from both the plant host and the fungal pathogen that may confer cross-kingdom RNA interference activity. Interestingly, we found first evidence of phased small RNAs (phasiRNAs) in B. hordei, a feature usually attributed to plants, which may be associated with the post-transcriptional control of fungal coding genes, pseudogenes, and transposable elements. Our data suggests a key and possibly site-specific role for cross-kingdom RNA interference and noncoding RNA fragments in the host-pathogen communication between B. hordei and its host barley.
Aptamer Proteomics for Biomarker Discovery in Heart Failure with Reduced Ejection Fraction
Authors: Zhang Luqing , Cunningham Jonathan W. , Claggett Brian L. , Jacob Jaison , Mendelson Mike , Serrano-Fernandez Pablo , Kaiser Sergio , Yates Denise , Healey Margaret , Chen Chien-Wei , Turner Gordon , Patel-Murray Natasha , Zhao Faye , Beste Michael T. , Laramie Jason M. , Abraham William T. , Jhund Pardeep S. , Kober Lars , Packer Milton , Rouleau Jean , Zile Michael R. , Prescott Margaret F. , Lefkowitz Martin , McMurray John J.V. , Solomon Scott D. , Chutkow William
Published: July 2022

Background

Systematically characterizing associations between circulating proteins and risk for subsequent clinical events may improve clinical risk prediction and shed light on unrecognized biological pathways in heart failure (HF). Large-scale assays measuring thousands of proteins now enable broad proteomic investigation in clinical trials.

Methods

Serum levels of 4076 proteins were measured at baseline in the ATMOSPHERE (n=1258, 487 events over 6 years) and PARADIGM-HF (n=1257, 287 events over 4 years) trials of chronic HF with reduced ejection fraction using a modified aptamer-based proteomics assay. Proteins associated with the primary endpoint of HF hospitalization or cardiovascular death were identified in the ATMOSPHERE discovery cohort by Cox regression adjusted for age, sex, treatment arm, and anticoagulant use (false discovery rate<0.05), and were replicated in PARADIGM-HF (Bonferroni-corrected p<0.05). A proteomic risk score was derived in ATMOSPHERE using Cox LASSO penalized regression and evaluated in PARADIGM-HF compared to the MAGGIC clinical risk score and N-terminal pro-B-type natriuretic peptide (NT-proBNP) immunoassay. For proteins that were associated with the primary endpoint, two-sample Mendelian randomization was performed using genetic and outcome data from both trials and protein quantitative trait loci from deCODE to infer causal associations.

Results

We identified 377 serum proteins that were associated with the primary endpoint in ATMOSPHERE and replicated 167 in PARADIGM-HF. Prognostic proteins included known HF biomarkers such as Growth Differentiation Factor 15, NT-BNP, and Angiopoietin-2, and also a previously unrecognized HF biomarker: Sushi, Von Willebrand Factor Type A, EGF and Pentraxin Domain Containing 1 (SVEP1, HR 1.60 [95% CI 1.44-1.79] per standard deviation [SD], p=2×10−17). A 64-protein risk score derived in ATMOSPHERE predicted the primary endpoint in PARADIGM-HF with greater discrimination (C-statistic 0.70) than the MAGGIC clinical score (C-statistic 0.61), NT-proBNP (C-statistic 0.65), or both (C-statistic 0.66). Genetically controlled levels of BNP, WISP2, FSTL1, and CTSS were associated with the primary endpoint by Mendelian randomization.

Conclusions

We identified SVEP1, an extracellular matrix protein known to cause inflammation in vascular smooth muscle cells, as a new HF biomarker associated with risk of hospitalization or death. A 64-protein score improved risk discrimination compared with NT-proBNP and may assist in identifying high-risk patients.
Pioneer activity distinguishes activating from non-activating pluripotency transcription factor binding sites
Authors: Maresca Michela , van den Brand Teun , Li Hangpeng , Teunissen Hans , Davies James , de Wit Elzo
Published: July 2022

Genome-wide transcriptional activity involves the binding of many transcription factors to thousands of sites in the genome. Determining which sites are directly driving transcription remains a challenge. Here we use acute protein depletion of the pioneer transcription factors OCT4 and SOX2 to establish their functionality in maintaining chromatin accessibility. We show that thousands of accessible sites are lost within an hour of protein depletion, indicating rapid turnover of these sites in the absence of pioneer factors. To understand the relationship with transcription we performed nascent transcription analysis and found that open chromatin sites that are maintained by SOX2 are highly predictive of gene expression, in contrast to SOX2 binding sites that do not maintain accessibility. We use CRISPR-Cas9 genome editing in the Klf2 locus to functionally validate a predicted regulatory element. We conclude that the regulatory activity of SOX2 is exerted largely at sites where it maintains accessibility and that other binding sites are largely dispensable for gene regulation.
The hidden secrets of the dental calculus: Calibration of a mass spectrometry protocol for dental calculus protein analysis
Authors: Bender Omer , Tzabag Dana , Gavish Talia , Meyrom Noa , Zamir Neta , May Hila , Sarig Rachel , Bar Daniel Z.
Published: July 2022

Dental calculus is a solid deposit that forms and accumulates on the tooth surface, entrapping oral microorganisms, biomolecules, and other micro-debris found in the oral cavity. Mass spectrometry analysis of its protein content opens a vista into the subject’s diet, oral flora, and even some aspects of health, thus providing new insight and expanding our knowledge of archaic cultures. Multiple experimental protocols have been proposed for the optimal extraction of proteins from dental calculus. Herein, we compared various experimental conditions in order to calibrate and validate a protocol for protein extraction. Our results show that a high concentration of acetic acid followed by mechanical crushing and sonication provided the highest protein yield, while acetone precipitation enabled the identification of more distinct proteins. We validated this protocol using archeological samples, identifying human and microbial proteins in specimens from the 8th and 17th centuries (approximately 250–1300 years ago). These findings demonstrate that the developed protocol is useful for studying excavated archaeological samples and that it might be utilized to explore the biohistory, dietary habits, and microbiome of archaic populations.
Single-cell transcriptome analysis reveals heterogeneity and a dynamic regenerative response of quiescent radial glia in adult zebrafish brain
Authors: Kutsia Manana , Takeuchi Yuki , Ranawat Nishtha , Masai Ichiro
Published: July 2022

In zebrafish telencephalon, radial glial cells (RGs) show a remarkable ability to regenerate damaged neural tissue by re-initiating cell proliferation to produce neural precursors to rebuild the lost neural circuit. However, it is not fully understood how RGs respond to brain damage to initiate this regenerative response. Here we applied single-cell transcriptomics to RGs in adult zebrafish telencephalon and identified five RG subtypes, which are classified into four quiescent RGs (qRGs) and one proliferating RG (pRG). The four qRGs differentially express distinct subsets of qRG markers, suggesting heterogeneity of qRG in zebrafish adult brain. Interestingly, one qRG subtype shows high expression of ribosomal proteins, and its fraction increases in response to brain damage. Consistently, the mTOR pathway is activated in RGs near the injury site. It was reported that inflammatory responses of brain-resident immune cells, microglia, are required for inducing regenerative responses of RGs in zebrafish. Genetical elimination of microglia not only suppressed the damage-induced regenerative response of RGs, but also decreased the fraction of the ribosomal expression-enriched qRGs. Our pseudo-time analysis suggests that putative dormant RGs produce ribosomal expression-enriched qRGs through activation of ribosomal genesis, as well as suppression of cholesterol biogenesis, and pRGs through activation of the JAK/STAT pathway. Our findings reveal heterogeneity of qRGs in adult zebrafish brain and their dynamic regenerative response to brain damage.
Ubiquitination of the GluA1 subunit of AMPA receptors is required for synaptic plasticity, memory and cognitive flexibility
Authors: Guntupalli Sumasri , Park Pojeong , Han Dae Hee , Ringuet Mitchell , Blackmore Daniel G. , Jhaveri Dhanisha J. , Koentgen Frank , Widagdo Jocelyn , Kaang Bong-Kiun , Anggono Victor
Published: July 2022

Activity-dependent changes in the number of AMPA-type glutamate receptors (AMPARs) at the synapse underpin the expression of long-term potentiation (LTP) and long-term depression (LTD), cellular correlates of learning and memory. Post-translational ubiquitination has emerged as a key regulator of the trafficking and surface expression of AMPARs, with ubiquitination of the GluA1 subunit at Lys-868 controlling the post-endocytic sorting of the receptors into the late endosome for degradation, and thereby regulating their stability at synapses. However, the physiological significance of GluA1 ubiquitination remains unknown. In this study, we generated mice with a knock-in mutation in the major GluA1 ubiquitination site (K868R) to investigate the role of GluA1 ubiquitination in synaptic plasticity, learning and memory. Our results reveal that these mice have normal basal synaptic transmission but exhibit enhanced LTP and deficits in LTD. They also display deficits in short-term spatial memory and cognitive flexibility. These findings underscore the critical roles of GluA1 ubiquitination for bidirectional synaptic plasticity and cognition.
Identification and full genome analysis of the first putative virus of sea buckthorn (Hippophae rhamnoidesL.)
Authors: Balke Ina , Zeltina Vilija , Zrelovs Nikita , Kalnciema Ieva , Resevica Gunta , Ludviga Rebeka , Jansons Juris , Moročko-Bičevska Inga , Segliņa Dalija , Zeltins Andris
Published: July 2022

The agricultural importance of sea buckthorn (Hippophae rhamnoidesL.) is rapidly increasing. Several bacterial and fungal pathogens infecting sea buckthorn have been identified and characterized; however, the viral pathogens are not yet known. In this study, we identified, isolated, and sequenced a virus from a wild plantation of sea buckthorn for the first time. Sequence analysis of the obtained viral genome revealed high similarity with sequences of several viruses belonging to the genusMarafivirus, especially olive latent virus 3 (OLV-3). The genome of the new virus is 6,989 nucleotides (nt) in length according to 5′ and 3′ rapid amplification of cDNA ends (RACE) (without polyA-tail), with 5′ and 3′ untranslated regions being 133 and 109 nt long, respectively. The viral genome encoded two open reading frames (ORFs). ORF1 encoded a polyprotein of 1,954 amino acids (aa) with the characteristic marafivirus non-structural protein domains—methyltransferase, Salyut domain, papain-like cysteine protease, helicase, and RNA-dependent RNA polymerase. ORF1 was separated from ORF2 by a six nt and encoded the coat protein (CP). CP had typical signatures of minor (30.96 kDa) and major (21.18 kDa) forms. Both CP forms were cloned and expressed in a bacterial expression system, and only the major CP was able to self-assemble into 30 nm virus-like particles that resembled the native virus, thus demonstrating that minor CP is not essential for virion assembly. We suggest the newly discovered virus to be named as “Sea buckthorn marafivirus”, abbreviated as “SBuMV”.

Author summary

Sea buckthorn is an exceptionally valuable plant that is currently widely cultivated as multipurpose horticultural species for food, pharmacology, cosmetics, and landscape conservation. Diseases and pests directly affect the cultivation of SBT. To date, several pests and diseases, mainly fungal and bacterial, but no viral, sea buckthorn have been reported. Identification of new pathogens would assist in the development of control strategies, and quarantine purposes and ensure sustainable sea buckthorn cultivation. Here, for the first time, we present a virus putatively infecting sea buckthorn. We had characterized its full genome, cloned and expressed minor and major forms of coat protein either individually or co-expressed. We also showed that major coat protein-derived virus-like particles self- assembled directly in the bacterial cells, and the majority of the expressed CPs were soluble. Our study suggests that the minor CP is not essential for the assembly of seemingly structurally intact viral particles, meaning that it can have other functions.
Mice generated with induced pluripotent stem cells derived from mucosal-associated invariant T cells
Authors: Sugimoto Chie , Fujita Hiroyoshi , Wakao Hiroshi
Published: July 2022

The function of mucosal-associated invariant T (MAIT) cells, a burgeoning member of innate-like T cells abundant in humans and implicated in many diseases, remains obscure. To explore this, mice with a rearranged T cell receptor (TCR) α or β locus, specific for MAIT cells, were generated via induced pluripotent stem cells derived from MAIT cells and designated Vα19 and Vβ8 mice, respectively. Both mice expressed large amounts of MAIT cells. The MAIT cells from these mice were activated by cytokines and an agonist to produce IFN-γ and IL-17. While Vβ8 mice showed resistance in a cancer metastasis model, Vα19 mice did not. Adoptive transfer of MAIT cells from the latter into the control mice, however, recapitulated the resistance. This has implications for understanding the role of MAIT cells in health and disease and in developing treatments for the plethora of diseases in which MAIT cells are implicated.
Root organogenesis induction in Epipremnum aureum stem cuttings with plant biostimulants and synthetic rooting hormone
Authors: Villafuerte D.E. , Angeles E. , Bayog A. , Duka R. , Meñoza N.L. , Sanchez M.A. , De Jesus R.
Published: July 2022

Plant organogenesis induction is a vital method to regenerate explants and produce complete organisms. In this study, we analyzed the applicability of three different root biostimulants and a commercially available synthetic rooting hormone (RH) for root organogenesis induction in Epipremnum aureum stem cuttings. The biostimulants used were Aloe vera gel (AV1), and garlic (GR2) and turmeric extracts (TM3), and the synthetic RH (TakeRoot®) used contained an active ingredient, indole butyric acid (0.01%). The E. aureum stem cuttings were placed in hydroponic pots and root development rates were monitored for up to 30 days. Recorded data from five parameters were analyzed: (1) number of rooted cuttings, (2) number of roots per stem cutting, (3) length of the longest and (4) shortest roots of the cuttings, and (5) rooting time. Stem cuttings were quantified using ImageJ software. The results showed that compared to the application of TakeRoot®, treatment with the biostimulant AV1 produced the longest roots, whereas stem cuttings treated with GR2 and TM3 did not produce significant results. Moreover, AV1 induced root organogenesis 16.67% faster than did TakeRoot® but no significant difference (p<0.05) was observed in the case of number of roots promoted per cutting. This study provides scientific evidence for the application of naturally derived RHs in the propagation of stem cuttings. Furthermore, Aloe vera gel, known for plant growth benefits, is the best choice for plant root propagation.
Pathogenicity of novel Monosporascus species in accessions of four melon botanical groups
Authors: Costa Francisco Cleilson Lopes , Paiva Negreiros Andréia Mitsa , Sales Rui , de Sousa Nunes Glauber Henrique
Published: July 2022

The Monosporascus root rot and vine decline (MRRVD) can be caused by the fungal species Monosporascus cannonballus and M. eutypoides. The Monosporascus species recently described in Brazil (M. brasiliensis, M. caatinguensis, M. mossoroensis, M. nordestinus and M. semiaridus) are potentially causal agents of the MRRVD. This work was made to evaluate them comparing to M. cannonballus pathogenicity, and to evaluate melon accessions reaction in four botanical groups of melon. MRRVD was evaluated by the severity of the damages in the roots and by the root dry matter reduction index (RIDM). On average, the studied species caused damage to melon accessions. After all, only M. brasiliensis, M. caatinguensis and M. nordestinus were virulent according to the accessions evaluated (A-16, C-32 syn. Pat 81, ‘Goldex’ and ‘HBJ’), i.e., accession-species interaction occurred, and among them, M. caatinguensis was the most virulent. The accession A-16 (acidulus group) showed higher resistance (<10 % of root dry mass loss) to M. cannonballus, M. caatinguensis and M. nordestinus. The accession C-32 was susceptible to M. caatinguensis and moderately resistant to the others. The accession A-16 was the most promising one and can be used as a donor of resistance alleles or as a rootstock.
Crystal structures of glutamyl-tRNA synthetase from Elizabethkingia anopheles and E. meningosepticum
Authors: Brooks Lauryn , Subramanian Sandhya , Dranow David M. , Mayclin Stephen J. , Myler Peter J. , Asojo Oluwatoyin A.
Published: July 2022

Elizabethkingia bacteria are globally emerging pathogens that cause opportunistic and nosocomial infections, with up to 40% mortality among the immunocompromised. Elizabethkingia species are in the pipeline of organisms for high-throughput structural analysis at the Seattle Structural Genomics Center for Infectious Disease (SSGCID). These efforts include the structure–function analysis of potential therapeutic targets. Glutamyl-tRNA synthetase (GluRS) is essential for tRNA aminoacylation and is under investigation as a bacterial drug target. The SSGCID produced, crystallized and determined high-resolution structures of GluRS from E. meningosepticum (EmGluRS) and E. anopheles (EaGluRS). EmGluRS was co-crystallized with glutamate, while EaGluRS is an apo structure. EmGluRS shares ∼97% sequence identity with EaGluRS but less than 39% sequence identity with any other structure in the Protein Data Bank. EmGluRS and EaGluRS have the prototypical bacterial GluRS topology. EmGluRS and EaGluRS have similar binding sites and tertiary structures to other bacterial GluRSs that are promising drug targets. These structural similarities can be exploited for drug discovery.
Measuring diversity, equity and inclusion: a holistic approach
Authors: Chaudhry Smita
Published: July 2022

Purpose

This paper aims to explore how organizations can measure diversity, equity and inclusion, and what are the potential areas where they can take initiatives to meet the diversity, equity and inclusion goals.

Design/methodology/approach

This paper explains the distinction among diversity, equity and inclusion. It elaborates on the separate perspectives that organizations need to adopt to define and measure each one of them. It consequently brings attention to their implications for research, practice and society.

Findings

This paper reveals that the goals of diversity, equity and inclusion, although related, need to be approached independently. The three concepts need to be measured individually and separate initiatives need to be designed and implemented to attain those goals.

Originality/value

This paper highlights the conceptual differences among diversity, equity and inclusion, and their evaluation. It underscores that diversity itself is not sufficient in ensuring organizational performance. Most of the discussion around implementing diversity pays little attention to steps that need to be taken to ensure equity and inclusion of the diverse workforce. This paper seeks to address this gap.
Entropy and institutional theory
Authors: Aksom Herman
Published: July 2022

Purpose

Once introduced and conceptualized as a factor that causes erosion and decay of social institutions and subsequent deinstitutionalization, the notion of entropy is at odds with predictions of institutional isomorphism and seems to directly contradict the tendency toward ever-increasing institutionalization. The purpose of this paper is to offer a resolution of this theoretical inconsistency by revisiting the meaning of entropy and reconceptualizing institutionalization from an information-theoretic point of view.

Design/methodology/approach

It is a theoretical paper that offers an information perspective on institutionalization.

Findings

A mistaken understanding of the nature and role of entropy in the institutional theory is caused by conceptualizing it as a force that counteracts institutional tendencies and acts in opposite direction. Once institutionalization and homogeneity are seen as a product of natural tendencies in the organizational field, the role of entropy becomes clear. Entropy manifests itself at the level of information processing and corresponds with increasing uncertainty and the decrease of the value of information. Institutionalization thus can be seen as a special case of an increase in entropy and a decrease of knowledge. Institutionalization is a state of maximum entropy.

Originality/value

It is explained why institutionalization and institutional persistence are what to be expected in the long run and why information entropy contributes to this tendency. Contrary to the tenets of the institutional work perspective, no intentional efforts of individuals and collective actors are needed to maintain institutions. In this respect, the paper contributes to the view of institutional theory as a theory of self-organization.
Parliamentary engagement in fighting corruption: a discourse on the Parliament of Tanzania
Authors: Lukiko Lukiko Vedastus
Published: July 2022

Purpose

This study aims to examine the participation of the Parliament of Tanzania in the fight against corruption in the country.

Design/methodology/approach

A desk-based research approach based on the review of documents and legal instruments was used.

Findings

The results of this study show that the Parliament of Tanzania has a chequered performance in fighting corruption. While it has passed several anti-corruption-related laws and in some respects succeeded to hold a few government officials accountable for the abuse of public office, there is little evidence to demonstrate its contribution at fighting this conundrum. Factors contributing to this deficiency include irresponsiveness to corruption allegations involving Members of Parliament, parliament’s remote oversight of the anti-corruption agency and shrinking democratic space in the parliament.

Practical implications

Tanzania has relatively high corruption levels. The country’s Development Vision 2025 envisages a nation free of corruption. Hence, efforts are needed from public and private sectors to overcome this conundrum. The parliament holds a special place in that fight. Through its representation, legislative and oversight roles and powers, parliament has a wider opportunity to strengthen anti-corruption in the country. This study shows that the Parliament of Tanzania has not been very effective in that regard. It offers suggestions to strengthen the parliament’s position and engagement to fight corruption.

Originality/value

There is scanty literature on the role of the Parliament of Tanzania in fighting corruption. This study is seminal, as it investigates the Tanzanian anti-corruption arsenal from a crucial organ that is vested with constitutional powers to make laws and oversee the executive and its agencies.
Intersection control with connected and automated vehicles: a review
Authors: Wu Jiaming , Qu Xiaobo
Published: July 2022

Purpose

This paper aims to review the studies on intersection control with connected and automated vehicles (CAVs).

Design/methodology/approach

The most seminal and recent research in this area is reviewed. This study specifically focuses on two categories: CAV trajectory planning and joint intersection and CAV control.

Findings

It is found that there is a lack of widely recognized benchmarks in this area, which hinders the validation and demonstration of new studies.

Originality/value

In this review, the authors focus on the methodological approaches taken to empower intersection control with CAVs. The authors hope the present review could shed light on the state-of-the-art methods, research gaps and future research directions.
Unintended consequences of knowledge management during the COVID-19 pandemic in 2021: the case of Netflix
Authors: Oh Ingyu , Fei Li , Rowley Chris
Published: July 2022

Purpose

Unintended consequences of knowledge management (KM) can be harmful if they are calamitous. However, they can occasionally be advantageous during catastrophes. The purpose of this study is to investigate how KM can be accidentally propitious during the COVID-19 pandemic using the case of Netflix.

Design/methodology/approach

Explanatory factor analysis, multilevel and multiple regressions were used with a sample of 45 countries.

Findings

In the authors’ sample, the hypothesized direct relationship between culture (i.e. individualism, power distance and indulgence) and collective pandemic resilience (CPR) was found. In addition, the hypothesized moderating effect of Netflix KM on the relationship between culture and CPR was partially confirmed. The findings suggest that KM during the pandemic can generate an unintended consequence of intensifying the degree of CPR.

Research limitations/implications

Small sample size, data paucity and the constructed variable of CPR might limit the generalizability of this study’s results. Nonetheless, one important research implication is that KM qua unintended consequences can have a significant moderating effect on the relationship between culture and resilience.

Practical implications

This paper highlights how organizations and society can cocreate the value of KM accidentally for the benefit of a larger public during calamities. Also, firms should proactively search for a wider application of their KM beyond their original intention.

Originality/value

This paper initiates a new discussion of positive consequences of unintended KM. Unlike individual-level studies of collective resilience in the past, to the best of the authors’ knowledge, this study generates country-level implications for the first time.
Using product lifecycle management (PLM) to re-think fashion business education: an assessment of pedagogical practices and learning benefits
Authors: Conlon Jo
Published: July 2022

Purpose

Organisations are investing in systems such as product lifecycle management (PLM) to support product development, collaboration across complex supply chains and to provide a framework for digital transformation. Graduates of apparel programmes would benefit from a knowledge of PLM to help realise the opportunities that PLM offers. The purpose of this paper is to report on an educational research project that used PLM as a context for practice-based learning and as a mechanism to update the learning experience and stimulate the development of future practice.

Design/methodology/approach

This paper reports on the experiences, critical reflections and data from an action research study to establish a learning community through an educational partnership for PLM software within an undergraduate fashion business course. The cohort of the first year of the intervention (n = 28) is the main study population.

Findings

The findings indicate that PLM provided a stimulating learning context supportive of a detailed understanding of current industry practice, critical and innovative thinking and the development of a professional identity.

Research limitations/implications

The opportunity for the development of both industry and educational practice is outlined.

Practical implications

A general introduction to PLM provides important information to support and advance Fashion Industry 4.0. Educational partnerships can reduce barriers to the integration of advanced technologies into the higher education curriculum.

Originality/value

Applications of PLM are under researched in textiles and apparel. The paper contributes to the broadening of the knowledge base of PLM and its potential to achieve strategic transformation of the sector.
Floral and pollination biology of the critically endangered insular orchid Calanthe amamiana: Implications for in situ conservation
Authors: Sugiura Naoto
Published: July 2022

Calanthe amamiana is a terrestrial orchid that thrives on the shady forest floors of broad‐leaved forests on Amami Island, central Ryukyus, Japan. Here, I report on the floral and pollination biology of this critically endangered orchid based on a 7‐year study conducted in the species' natural habitats. As the nectarless flowers are probably self‐compatible but are unable to autonomously self‐pollinate, they need to attract pollen vectors by deceit for pollination. To advertise themselves, the flowering inflorescences, which comprise a few to dozens of flowers, use whitish floral colors that are comparatively conspicuous against the shaded background. The exclusive pollinator was the long‐horned bee Eucera okinawae, which nests in soils of the forest floor, although bee abundance varied considerably among study years. Natural fruit‐set ratios were generally low but showed interannual variation. The annual fruit‐set ratios were positively correlated with annual bee abundance, thereby suggesting that under natural conditions, the orchid is pollinator‐limited. Given that C. amamiana is dependent exclusively on E. okinawae for pollination and is also probably pollinator‐limited, conservation plans for this orchid should take into consideration the welfare of long‐horned bees. In particular, as nectariferous flowers were unavailable within broad‐leaved forests, to satisfy the foraging requirements of long‐horned bees, conservation managers should be cognizant of conservation values of flowering plants distributed in sun‐lit sites near orchid habitats, and manage those in an appropriate manner.
Forensic diagnostic approach of peri‐volcanic area fatalities: About two cases at piton de la Fournaise
Authors: Pefferkorn Eulalie , Lossois Maisy , Le Gallo Arnaud , Loire Christophe , Bascou Agathe , Berthezène Jean‐Marie
Published: July 2022

The Piton de la Fournaise, located on the island of Reunion, is a particularly active volcano that gathers many observers during its eruptions. However, this activity, if not supervised, can involve many risks. During the eruption of Piton de la Fournaise in April 2021, two geology students camped in the peri‐eruptive zone. They were found dead 48 h later on the surface and were not in the immediate vicinity of a fumarole. The autopsy revealed superficial traumatic injuries, which did not explain the death. Internal examination of both victims showed a nonspecific asphyxia syndrome and hemorrhagic pulmonary edema, with no cause of death identified. Microscopic analysis confirmed the autopsy findings without providing new diagnostic elements. Toxicological analysis revealed abnormally high levels of sulfurous gases (H2S and SO2) in the blood and lungs of both victims. The interpretation of all the forensic data allows us to conclude that the death was secondary to volcanic sulfur gas poisoning, despite the atypical context of this event. However, the meteorological conditions of the night of the event may have caused a stagnation of toxic volcanic gases on the ground, with concentrations high enough to cause fatal intoxication in these two persons, although they were not in a confined environment as is usually the case in cases of sulfur poisoning. The dramatic outcome of this event required a rigorous forensic diagnostic approach and reminds us of the need to respect safety conditions in peri‐volcanic areas.