bluuebunny/crossref_metadata_2025 huggingface dataset:
Improved peptide backbone fragmentation is the primary advantage of MS-cleavable crosslinkers
Authors: Kolbowski Lars , Lenz Swantje , Fischer Lutz , Sinn Ludwig R , O’Reilly Francis J , Rappsilber Juri
Published: November 2021

Proteome-wide crosslinking mass spectrometry studies have coincided with the advent of MS-cleavable crosslinkers that can reveal the individual masses of the two crosslinked peptides. However, recently such studies have also been published with non-cleavable crosslinkers suggesting that MS-cleavability is not essential. We therefore examined in detail the advantages and disadvantages of using the most popular MS-cleavable crosslinker, DSSO. Indeed, DSSO gave rise to signature peptide fragments with a distinct mass difference (doublet) for nearly all identified crosslinked peptides. Surprisingly, we could show that it was not these peptide masses that proved the main advantage of MS-cleavability of the crosslinker, but improved peptide backbone fragmentation that allowed for more confident peptide identification. We also show that the more intricate MS3-based data acquisition approaches lack sensitivity and specificity, causing them to be outperformed by the simpler and faster stepped HCD method. This understanding will guide future developments and applications of proteome-wide crosslinking mass spectrometry.
Circular RNA signatures of human healing and non-healing wounds
Authors: Toma Maria A. , Liu Zhuang , Wang Qizhang , Zhang Letian , Li Dongqing , Sommar Pehr , Landén Ning Xu
Published: November 2021

Background

Although the widespread expression of circular RNAs (circRNAs) has only been recognized recently, increasing evidence has suggested their important roles in health and disease. To identify clinically relevant circRNAs with potential for wound diagnosis and therapy, an in-depth characterization of circRNA expression in human healing and non-healing wounds is a prerequisite that has not been attained yet.

Methods

We collected wound-edge biopsies through the healing process of healthy donors and in chronic non-healing venous ulcers (VU). Paired total RNA- and small RNA-sequencing were performed to profile circRNAs, protein-coding mRNAs, and microRNA expression. We analyzed the co-expression relationship between circRNAs and mRNAs with weighted correlation network analysis (WGCNA) and constructed circRNA-microRNA-mRNA networks. For the circRNAs surfaced in the in-silico analysis, after validating their expression with RT-PCR and sequencing, we silenced hsa-CHST15_0003 and hsa-TNFRSF21_0001 expression in keratinocytes with siRNAs and studied their function with transcriptomic profiling and live-cell monitoring.

Results

Our study unravels the dynamically changed expression patterns of circRNAs during human skin wound healing and their abnormal expression signature in VU, which are presented as a searchable web resource (http://130.229.28.87/shiny/circRNA_wholebiopsy-shinyApp/).In silicoanalysis deciphers the circRNA-miRNAs-mRNA networks specific to the inflammatory and proliferative phases of wound repair and VU, the biological processes that circRNAs are involved, and the circRNAs that could act as miRNAs sponge in human wounds. Importantly, we found that hsa-CHST15_0003 and hsa-TNFRSF21_0001, two circRNAs upregulated in VU, hampered keratinocyte migration while promoting proliferation through modulating gene networks underpinning these cellular processes.

Conclusion

By integrating circRNA, mRNA, and miRNA expression profiles in a unique collection of clinical samples, we identify the circRNAs that are relevant to human wound healing physiology and pathology. This study paves the way to decipher the functional significance of circRNAs in tissue repair.
Pre- and post-oviposition behavioural strategies to protect eggs against extreme winter cold in an insect with maternal care
Authors: Tourneur Jean-Claude , Cole Claire , Vickruck Jess , Dupont Simon , Meunier Joel
Published: November 2021

Depositing eggs in an area with adequate temperature is often crucial for mothers and their offspring, as the eggs are immobile and therefore cannot avoid exposure to sub-optimal temperatures. However, the importance of temperature on oviposition site selection is less clear when mothers can avoid these potential adverse effects by both moving their eggs after oviposition and providing other forms of egg care. In this study, we addressed this question in the European earwig, an insect in which mothers care for the eggs during several months in winter, frequently moving them during this period. We set up 60 females from two random natural populations (as this species often exhibits population-specific life-history traits and behaviours) under controlled thermal gradients, and recorded the temperature at which they built their nests, tested whether they moved their eggs after an experimental temperature change, and measured the effects on egg development and hatching rate. Our results demonstrate that females indeed select oviposition sites according to temperature, and can move their eggs to reach warmer temperatures. We also show that these warmer temperatures are necessary to ensure egg hatching. Although this set of behavioural thermoregulations is present in the two tested populations, we found a population-specific modality of expression. These included the range of temperatures explored before oviposition, temperature selected at oviposition and dynamics of egg transport following a temperature change. Overall, our study sheds light on a new post-oviposition strategy in female insects that overwinter with their eggs for coping with temperature changes. More generally, it also reveals that egg care and/or egg transport do not prevent behavioural thermoregulation via oviposition site selection and highlights the diversity of behaviours that insects can adopt to enhance their tolerance to global climate change.
RNA-binding protein Orb2 causes microcephaly and supports centrosome asymmetry inDrosophilaneural stem cells
Authors: Robinson Beverly V. , Buehler Joseph , Hailstock Taylor , Adebambo Temitope H. , Fang Junnan , Mehta Dipen S. , Lerit Dorothy A.
Published: November 2021

To maintain a balance of self-renewal versus neurogenesis, neural stem cells (NSCs) undergo asymmetric cell division along an invariant polarity axis instructed by centrosomes. In the NSCs of the third instarDrosophilalarval brain, the interphase centrosomes are defined by marked asymmetries in protein composition and functional activity as microtubule-organizing centers. Here we show that a conserved RNA-binding protein, Orb2, supports NSC centrosome asymmetry by localizing to the cytoplasm, where it promotes robust apical centrosome maturation and transient basal centrosome inactivation, required for centrosome segregation and spindle morphogenesis. Orb2 is required cell autonomously within NSCs to support centrosome asymmetry and maintenance of the stem cell pool. We suggest Orb2 plays opposing roles in centrosome activation and inactivation at the apical versus basal centrosomes respectively, possibly through the translational regulation of multiple mRNAs. Conversely, loss oforb2manifests in microcephaly independent of Orb2 function in NSCs. Bioinformatics uncovers a significant overlap among RNA targets betweenDrosophilaOrb2 and human CPEB4, consistent with a conserved role for CPEB proteins in centrosome regulation and neurodevelopment.
A drug discovery-oriented non-invasive protocol for protein crystal cryoprotection by dehydration, with application for crystallization screening
Authors: Bellini Dom
Published: November 2021

In X-ray macromolecular crystallography, cryoprotection of crystals mounted on harvesting loops is achieved when the water in the sample solvent transitions to vitreous ice before crystalline ice forms. This is achieved by rapid cooling in liquid nitrogen or propane. Protocols for protein crystal cryoprotection are based on either increasing environmental pressure or reducing the water fraction in the solvent. This study presents a new protocol for cryoprotecting crystals. It is based on vapour diffusion dehydration of the crystal drop to reduce the water fraction in the solvent by adding a highly concentrated salt solution, 13 M potassium formate (KF13), directly to the reservoir. Cryoprotection by the KF13 protocol is non-invasive to the crystal, high throughput, not labour intensive, can benefit diffraction resolution and ligand binding, and is very useful in cases with high redundancy such as drug discovery projects which utilize very large compound or fragment libraries. Moreover, an application of KF13 to discover new crystal hits from clear drops of equilibrated crystallization screening plates is also shown.
Plants species’ influence on rhizosphere microbial communities depends on N availability
Authors: Potter Teal S. , Anacker Brian L. , Churchill Amber C. , Bowman William D.
Published: November 2021

Purpose

Plants and soil microbes both influence how ecosystems respond to environmental change. Yet, we lack the ability to generalize how plants and soil microbes influence each other in the same or varying soil conditions. This limitation thwarts ecologists’ ability to understand and predict effects of environmental changes such and elevated anthropogenic nitrogen (N) deposition. Accordingly, we examined the specificity of plant species’ influence on soil microbial community composition.

Methods

We tested (1) whether congeneric grass species have unique effects on soil microbial communities, (2) how relative abundances of microbial taxa can be explained by Poa phylogeny, plant traits, and range-wide traits (annual temperature and soil pH), and (3) whether N addition alters associations between Poa species and soil microbes, and (4) whether the magnitude of microbial community change in response to elevated N can be explained by plant growth responses to N. We conducted a greenhouse experiment with seven Poa species and native soils.

Results

We found that individual Poa species were associated with different soil fungi but similar soil bacteria. Differences in microbial composition were not attributable to Poa phylogeny, plant traits, or range-wide traits. Nitrogen addition enhanced the unique effects of Poa species on fungal and bacterial community compositions.

Conclusion

These results demonstrate how ecological interactions of related plant species vary depending on resource supply, revealing important context dependency for accurately predicting microbially-mediated nutrient cycling and ecosystem responses to changes in nutrient availability.
Molecular Basis of Antibiotic Self-Resistance in a Bee Larvae Pathogen
Authors: Dang Tam , Loll Bernhard , Müller Sebastian , Skobalj Ranko , Ebeling Julia , Bulatov Timur , Gensel Sebastian , Göbel Josefine , Wahl Markus C. , Genersch Elke , Mainz Andi , Süssmuth Roderich D.
Published: November 2021

Paenibacillus larvae, the causative agent of the devastating honey-bee disease American Foulbrood, produces the cationic polyketide-peptide hybrid paenilamicin that displays high antibacterial and antifungal activity. Its biosynthetic gene cluster contains a gene coding for theN-acetyltransferase PamZ. We show that PamZ acts as self-resistance factor inP. larvaeby deactivation of paenilamicin. Using tandem MS, NMR spectroscopy and synthetic diastereomers, we identified the N-terminal amino group of the agmatinamic acid as theN-acetylation site. These findings highlight the pharmacophore region of paenilamicin, which we very recently identified as a new ribosome inhibitor. Here, we further elucidated the crystal structure of PamZ:acetyl-CoA complex at 1.34 Å resolution. An unusual tandem-domain architecture provides a well-defined substrate-binding groove decorated with negatively-charged residues to specifically attract the cationic paenilamicin. Our results will help to understand the mode of action of paenilamicin and its role in pathogenicity ofP. larvaeto fight American Foulbrood.
Protonation-Dependent Sequencing of 5-Formylcytidine in RNA
Authors: Link Courtney N. , Gamage Supuni Thalalla , Gallimore Diamond A. , Kopajtich Robert , Evans Christine N. , Nance Samantha R. , Fox Stephen D. , Andresson Thorkell , Chari Raj , Ivanic Joseph , Prokisch Holger , Meier Jordan L.
Published: November 2021

Chemical modification of cytidine in non-coding RNAs plays a key role in regulating translation and disease. However, the distribution and dynamics of many of these modifications remains unknown due to a lack of sensitive site-specific sequencing technologies. Here we report a protonation-dependent sequencing reaction for detection of 5-formylcytidine (5fC) and 5-carboxycytidine (5caC) in RNA. First, we evaluate how protonation combined with electron-withdrawing substituents alters the molecular orbital energies and reduction of modified cytidine nucleosides, highlighting 5fC and 5caC as reactive species. Next, we apply this reaction to detect these modifications in synthetic oligonucleotides as well as endogenous human tRNA. Finally, we demonstrate the utility of our method to characterize a patient-derived model of 5fC-deficiency, where it enables facile monitoring of both pathogenic loss and exogenous rescue of NSUN3-dependent 5fC within the wobble base of human mitochondrial tRNAMet. These studies showcase the ability of protonation to enhance the reactivity and sensitive detection of 5fC in RNA, and provide a molecular foundation for applying optimized sequencing reactions to better understand the role of oxidized RNA cytidine nucleobases in disease.
Treatment of infection-induced vascular pathologies is protective against persistent rough morphotype Mycobacterium abscessus infection in zebrafish
Authors: Kam Julia Y , Wright Kathryn , Britton Warwick J , Oehlers Stefan H
Published: November 2021

Mycobacterium abscessus infections are of increasing global prevalence and are often difficult to treat due to complex antibiotic resistance profiles. While there are similarities between the pathogenesis of M. abscessus and tuberculous mycobacteria, including granuloma formation and stromal remodeling, there are distinct molecular differences at the host-pathogen interface. Here we have used a zebrafish-M. abscessus model and host-directed therapies that were previously identified in the zebrafish-M. marinum model to identify potential host-directed therapies against M. abscessus infection. We find efficacy of anti-angiogenic and vascular normalizing therapies against rough M. abscessus infection, but no effect of anti-platelet drugs.
TFAP2 paralogs facilitate chromatin access for MITF at pigmentation genes but inhibit expression of cell-cell adhesion genes independently of MITF
Authors: Kenny Colin , Dilshat Ramile , Seberg Hannah , Otterloo Eric Van , Bonde Gregory , Helverson Annika , Franke Christopher M. , Steingrímsson Eiríkur , Cornell Robert A.
Published: November 2021

In developing melanocytes and in melanoma cells, multiple paralogs of the Activating-enhancer-binding Protein 2 family of transcription factors (TFAP2) contribute to expression of genes encoding pigmentation regulators, but their interaction with Microphthalmia transcription factor (MITF), a master regulator of these cells, is unclear. Supporting the model that Tfap2 facilitates MITF’s ability to activate expression of pigmentation genes, single-cell seq analysis of zebrafish embryos revealed that pigmentation genes are only expressed in the subset of mitfa- expressing cells that also express Tfap2 paralogs. To test this model in SK-MEL-28 melanoma cells we deleted the two TFAP2 paralogs with highest expression, TFAP2A and TFAP2C, creating TFAP2 knockout (TFAP2-KO) cells. We then assessed gene expression, chromatin accessibility, binding of TFAP2A and of MITF, and the chromatin marks H3K27Ac and H3K27Me3 which are characteristic of active enhancers and silenced chromatin, respectively. Integrated analyses of these datasets indicate TFAP2 paralogs directly activate enhancers near genes enriched for roles in pigmentation and proliferation, and directly repress enhancers near genes enriched for roles in cell adhesion. Consistently, compared to WT cells, TFAP2-KO cells proliferate less and adhere to one another more. TFAP2 paralogs and MITF co-operatively activate a subset of enhancers, with the latter necessary for MITF binding and chromatin accessibility. By contrast, TFAP2 paralogs and MITF do not appear to co-operatively inhibit enhancers. These studies reveal a mechanism by which TFAP2 profoundly influences the set of genes activated by MITF, and thereby the phenotype of pigment cells and melanoma cells.
Cell-Projection Pumping of Fibroblast Contents into Osteosarcoma SAOS-2 Cells Correlates with Increased SAOS-2 Proliferation and Migration, and also with Altered Morphology
Authors: Mahadevan Swarna , Cornwell James A , Chami Belal , Kelly Elizabeth , Zoellner Hans
Published: November 2021

We earlier reported that cell-projection pumping transfers fibroblast contents to cancer cells, and this alters cancer cell phenotype. We now report on single-cell tracking of time lapse recordings from co-cultured fluorescent fibroblasts and SAOS-2 osteosarcoma cells, tracking 5,201 cells across 7 experiments. The fluorescent lipophilic marker DiD was used to label fibroblast organelles, and to trace transfer of fibroblast cytoplasm into SAOS-2. We related SAOS-2 phenotypic change to levels of fluorescence transfer from fibroblasts to SAOS-2, and also to what we term ‘compensated fluorescence’, that numerically projects mother cell fluorescence post-mitosis, into daughter cells. Comparison of absolute with compensated fluorescence, allowed deduction if phenotypic effects in mother SAOS-2, were inherited by their daughters. SAOS-2 receipt of fibroblast fluorescence correlated by Kendall’s tau: with cell-profile area, and without evidence for persistence in daughter cells (median tau = 0.51, p < 0. 016); negatively and weakly with cell circularity, and with evidence for persistence (median tau = −0.19, p < 0.05); and very weakly with cell migration velocity, and without evidence for persistence (median tau = 0.01, p < 0.016). Also, mitotic SAOS-2 had higher rates of prior fluorescence uptake (median = 64.9 units/day), compared with non dividing cells (median = 35.6 units/day, p < 0.016), and there was no evidence for persistence post-mitosis. We conclude there is appreciable impact of cell-projection pumping on cancer cell phenotype, relevant to cancer histopathological diagnosis, clinical spread, and growth, with most effects ‘reset’ by cancer cell mitosis.
CEP162 deficiency causes human retinal degeneration and reveals a dual role in ciliogenesis and neurogenesis
Authors: Nuzhat Nafisa , Van Schil Kristof , Liakopoulos Sandra , Bauwens Miriam , Rey Alfredo Duenas , Käseberg Stephan , Jäger Melanie , Willer Jason R. , Winter Jennifer , Truong Hanh , Gruartmoner Nuria , Van Heetvelde Mattias , Wolf Joachim , Merget Robert , Grasshoff-Derr Sabine , Van Dorpe Jo , Hoorens Anne , Stöhr Heidi , Mansard Luke , Roux Anne-Françoise , Langmann Thomas , Dannhausen Katharina , Rosenkranz David , Wissing Karl Martin , Van Lint Michel , Rossmann Heidi , Häuser Friederike , Nürnberg Peter , Thiele Holger , Zechner Ulrich , Pearring Jillian N. , De Baere Elfride , Bolz Hanno J.
Published: November 2021

Defects in primary or motile cilia result in a variety of human pathologies, and retinal degeneration is frequently associated with these so-called ciliopathies. We show that homozygosity for a truncating variant in CEP162, a centrosome and microtubule-associated protein required for transition zone (TZ) assembly during ciliogenesis and neuronal differentiation in the retina, causes late-onset retinitis pigmentosa in 2 unrelated families. The mutant CEP162-E646R*5 protein is expressed and properly localized to the mitotic spindle but missing from the basal body in primary and photoreceptor cilia. This impairs recruitment of TZ components to the basal body and corresponds to complete loss of CEP162 function at the ciliary compartment, reflected by delayed formation of dysmorphic cilia. In contrast, rescue of increased cell death in the developing mouse retina after shRNA knockdown of Cep162 by expression of CEP162-E646R*5 indicates that the mutant retains its role for retinal neurogenesis. Human retinal degeneration thus results from specific loss of ciliary CEP162 function.

Graphical abstract
Inhibition of infection-induced vascular permeability modulates host leukocyte recruitment to Mycobacterium marinum granulomas in zebrafish
Authors: Kam Julia Y , Cheng Tina , Garland Danielle C , Britton Warwick J , Tobin David M , Oehlers Stefan H
Published: November 2021

Mycobacterial granuloma formation involves significant stromal remodeling and the growth of leaky, granuloma-associated vasculature. These permeable blood vessels aid mycobacterial growth, as anti-angiogenic or vascular normalizing therapies are beneficial host-directed therapies in pre-clinical models of tuberculosis. Here we demonstrate that vascular normalization through vascular endothelial-protein tyrosine phosphatase inhibition decreases granuloma hypoxia, the opposite effect of hypoxia-inducing anti-angiogenic therapy. Vascular normalization leads to increased T cell and decreased neutrophil recruitment to granulomas, correlates of a protective immune response against mycobacterial infection.
Ser68 phosphoregulation is essential for CENP-A deposition, centromere function and viability in mice
Authors: Liu Yuting , Wang Kehui , Huang Li , Zhao Jicheng , Chen Xinpeng , Wu Qiang , Yu Zhouliang , Li Guohong
Published: November 2021

Centromere identity is defined by nucleosomes containing CENP-A, a histone H3 variant. The deposition of CENP-A at centromeres is tightly regulated in a cell-cycle-dependent manner. We previously reported that the spatiotemporal control of centromeric CENP-A incorporation is mediated by the phosphorylation of CENP-A Ser68. However, a recent report argued that Ser68 phosphoregulation is dispensable for accurate CENP-A loading. Here, we report that the substitution of Ser68 of endogenous CENP-A with either Gln68 or Glu68 severely impairs CENP-A deposition and cell viability. We also find that mice harboring the corresponding mutations are lethal. Together, these results indicate that the dynamic phosphorylation of Ser68 ensures cell-cycle-dependent CENP-A deposition and cell viability.
Microbial consortiums of putative degraders of low-density polyethylene-associated compounds in the ocean
Authors: Pinto Maria , Zhao Zihao , Klun Katja , Libowitzky Eugen , Herndl Gerhard J
Published: November 2021

Polyethylene (PE) is one of the most abundant plastics in the ocean. The development of a biofilm on PE in the ocean has been reported, yet whether some of the biofilm-forming organisms can biodegrade this plastic in the environment remains unknown. Via metagenomics analysis, we taxonomically and functionally analysed three biofilm communities using low-density polyethylene (LDPE) as their sole carbon source for two years. Several of the taxa that increased in relative abundance over time were closely related to known degraders of alkane and other hydrocarbons. Alkane degradation has been proposed to be involved in PE degradation, and most of the organisms increasing in relative abundance over time harboured genes encoding proteins essential in alkane degradation, such as the genes alkB and CYP153, encoding an alkane monooxygenase and a cytochrome P450 alkane hydroxylase. Weight loss of PE sheets when incubated with these communities and chemical and electron microscopic analyses provided evidence for alteration of the PE surface over time. Taken together, these results provide evidence for the utilization of LDPE-associated compounds by the prokaryotic communities. This study identifies a group of genes potentially involved in the degradation of the LDPE polymeric structure and/or associated plastic additives in the ocean and describes a phylogenetically diverse community of plastic biofilm-dwelling microbes with the potential of utilizing LDPE-associated compounds as carbon and energy source.

Importance

Low-density polyethylene (LDPE) is one of the most used plastics worldwide and a large portion of it ends up in the ocean. Very little is known about its fate in the ocean and whether it can be biodegraded by microorganisms. By combining 2-year incubations with metagenomics, respiration measurements and LDPE surface analysis, we identified bacteria and associated genes and metabolic pathways potentially involved in LDPE biodegradation. After two years of incubation, two of the microbial communities exhibited a very similar taxonomic composition mediating changes to the LDPE pieces they were incubated with. We provide evidence that there are plastic-biofilm dwelling bacteria in the ocean, that might have the potential to degrade LDPE-associated compounds, and that alkane degradation pathways might be involved.
Interplay of adherens junctions and matrix proteolysis determines the invasive pattern and growth of squamous cell carcinoma
Authors: Kato Takuya , Jenkins Robert P. , Derzsi Stefanie , Tozluoglu Melda , Rullan Antonio , Hooper Steven , Chaleil Raphael A. G. , Fu Xiao , Joyce Holly , Thavaraj Selvam , Bates Paul A. , Sahai Erik
Published: November 2021

Cancers, such as squamous cell carcinoma, frequently invade as multicellular units. However, these invading units can be organized in a variety of ways, ranging from thin discontinuous strands to thick ‘pushing’ collectives. Here we employ an integrated experimental and computational approach to identify the factors that determine the mode of collective cancer cell invasion. We find that matrix proteolysis is linked to the formation of wide strands, but has little effect on the maximum extent of invasion. Cell-cell junctions also favour wide strands, but our analysis also reveals a requirement for cell-cell junctions for efficient invasion in response to uniform directional cues. Unexpectedly, the ability to generate wide invasive strands is coupled to the ability to grow effectively when surrounded by ECM in 3D assays. Combinatorial perturbation of both matrix proteolysis and cell-cell adhesion demonstrates that the most aggressive cancer behaviour, both in terms of invasion and growth, is achieved at high levels of cell-cell adhesion and high levels of proteolysis. Contrary to expectation, cells with canonical mesenchymal traits – no cell-cell junctions and high proteolysis – exhibit reduced growth and lymph node metastasis. Thus, we conclude that the ability of squamous cell carcinoma cells to invade effectively is also linked to their ability to generate space for proliferation in confined contexts. These data provide an explanation for the apparent advantage of retaining cell-cell junctions in SCC.
Single-cell Transcriptomic Analysis Reveals the Cellular Heterogeneity of Mesenchymal Stem Cells
Authors: Zhang Chen , Han Xueshuai , Liu Jingkun , Chen Lei , Lei Ying , Chen Kunying , Si Jia , Wang Tian-yi , Zhou Hui , Zhao Xiaoyun , Zhang Xiaohui , An Yihua , Li Yueying , Wang Qian-fei
Published: November 2021

Ex vivo-expanded mesenchymal stem cells (MSCs) have been demonstrated to be a heterogeneous mixture of cells exhibiting varying proliferative, multipotential, and immunomodulatory capacities. However, the exact characteristics of MSCs remain largely unknown. By single-cell RNA sequencing of 61,296 MSCs derived from bone marrow and Wharton’s jelly, we revealed five distinct subpopulations. The developmental trajectory of these five MSC subpopulations were mapped, revealing a differentiation path from stem-like active proliferative cells (APCs) to multipotent progenitor cells, followed by the branching into two paths – adipogenesis or osteochondrogenesis – and subsequent differentiation into unipotent prechondrocytes. The stem-like APCs, expressing the perivascular mesodermal progenitor markers CSPG4/MCAM/NES, uniquely exhibited strong proliferation and stemness signatures. Remarkably, the prechondrocyte subpopulation specifically expressed immunomodulatory genes and was able to suppress activated CD3+ T cell proliferation in vitro, supporting the role of this population in immunoregulation. In summary, our analysis mapped the heterogeneous subpopulations of MSCs and identified two subpopulations with potential functions in self-renewal and immunoregulation. Our findings advance the definition of MSCs by identifying the specific functions of its heterogeneous cellular composition, allowing for more specific and effective MSC application through the purification of its functional subpopulations.
A Community-Developed Extension to Darwin Core for Reporting the Chronometric Age of Specimens
Authors: Brenskelle Laura , Wieczorek John , Davis Edward , Wallis Neill J. , Emery Kitty , LeFebvre Michelle J. , Guralnick Rob
Published: November 2021

Darwin Core, the data standard used for sharing modern biodiversity and paleodiversity occurrence records, has previously lacked proper mechanisms for reporting what is known about the estimated age range of specimens from deep time. This has led to data providers putting these data in fields where they cannot easily be found by users, which impedes the reuse and improvement of these data by other researchers. Here we describe the development of the Chronometric Age Extension to Darwin Core, a ratified, community-developed extension that enables the reporting of ages of specimens from deeper time and the evidence supporting these estimates. The extension standardizes reporting about the methods or assays used to determine an age and other critical information like uncertainty. It gives data providers flexibility about the level of detail reported, focusing on the minimum information needed for reuse while still allowing for significant detail if providers have it. Providing a standardized format for reporting these data will make them easier to find and search and enable researchers to pinpoint specimens of interest for data improvement or accumulate more data for broad temporal studies. The Chronometric Age Extension was also the first community-managed vocabulary to undergo the new Biodiversity Informatics Standards (TDWG) review and ratification process, thus providing a blueprint for future Darwin Core extension development.
Transcriptional expression changes during compensatory plasticity in the prothoracic ganglion of the adult cricket Gryllus bimaculatus
Authors: Wang Felicia , Fisher Harrison , Morse Maeve , Ledwidge Lisa L. , O’Brien Jack , Kingston Sarah E. , Beckman Justin , Johnson Jasmine J. , Miranda Portillo Lyn S. , Al Musawi Tabarak N. , Rubenstein Alexandra W. , Michaelson David A. , Horch Hadley Wilson
Published: November 2021

Most adult organisms are limited in their capacity to recover from neurological damage. The auditory system of the Mediterranean field cricket, Gryllus bimaculatus, presents a compelling model for investigating neuroplasticity due to its unusual capabilities for structural reorganization into adulthood. Specifically, the dendrites of the central auditory neurons of the prothoracic ganglion sprout in response to the loss of auditory afferents. Deafferented auditory dendrites grow across the midline, a boundary they normally respect, and form functional synapses with the contralateral auditory afferents, restoring tuning-curve specificity. The molecular pathways underlying these changes are entirely unknown. Here, we used a multiple k-mer approach to re-assemble a previously reported prothoracic ganglion transcriptome that included ganglia collected one, three, and seven days after unilateral deafferentation in adult, male animals. We used EdgeR and DESeq2 to perform differential expression analysis and we examined Gene Ontologies to further understand the potential molecular basis of this compensatory anatomical plasticity. Enriched GO terms included those related to protein translation and degradation, enzymatic activity, and Toll signaling. Extracellular space GO terms were also enriched and included the upregulation of several protein yellow family members one day after deafferentation. Investigation of these regulated GO terms help to provide a broader understanding of the types of pathways that might be involved in this compensatory growth and can be used to design hypotheses around identified molecular mechanisms that may be involved in this unique example of adult structural plasticity.
Host Species is Linked to Pathogen Genotype for the Amphibian Chytrid Fungus (Batrachochytrium dendrobatidis)
Authors: Byrne Allison Q. , Waddle Anthony W. , Saenz Veronica , Ohmer Michel , Jaeger Jef R. , Richards-Zawacki Corinne L. , Voyles Jamie , Rosenblum Erica Bree
Published: November 2021

Host-pathogen specificity can arise from certain selective environments mediated by both the host and pathogen. Therefore, understanding the degree to which host species identity is correlated with pathogen genotype can help reveal historical host-pathogen dynamics. One animal disease of particular concern is chytridiomycosis, typically caused by the global panzootic lineage of the amphibian chytrid fungus (Batrachochytrium dendrobatidis, Bd), termed the Bd-GPL. This pathogen lineage has caused devastating declines in amphibian communities around the world. However, the origin of Bd-GPL and the fine-scale transmission dynamics of this lineage have remained a mystery. This is especially the case in North America where Bd-GPL is widespread, but disease outbreaks occur sporadically. Herein, we use Bd genetic data collected throughout the United States from amphibian skin swab and cultured isolate samples to investigate Bd genetic patterns. We highlight two case studies in Pennsylvania and Nevada where Bd-GPL genotypes are strongly correlated with host species identity. Specifically, in some localities bullfrogs (Rana catesbeiana) are infected with Bd-GPL lineages that are distinct from those infecting other sympatric amphibian species. Overall, we reveal a previously unknown association of Bd genotype with host species and identify the eastern United States as a Bd diversity hotspot and potential ancestral population for Bd-GPL.
Clinicopathologic and molecular analysis of aBCOR–CCNB3undifferentiated sarcoma of the kidney reveals significant epigenetic alterations
Authors: Hagoel Tamara J. , Cortes Gomez Eduardo , Gupta Ajay , Twist Clare J. , Kozielski Rafal , Martin Jeffrey C. , Gao Lingui , Kuechle Joseph , Singh Prashant K. , Lynch Miranda , Wei Lei , Liu Song , Wang Jianmin , Ohm Joyce E.
Published: November 2021

Undifferentiated soft tissue sarcomas (UDSTSs) are a group of mesenchymal tumors that remain a diagnostic challenge because of their morphologic heterogeneity and unclear histologic origin (Peters et al.,Mod Pathol28:575 [2015]). In this case report, we present the first multiomics molecular signature for aBCOR–CCNB3sarcoma (BCS) that includes mutation analysis, gene expression, DNA methylation, and micro RNA (miRNA) expression. We identify a paucity of additional mutations in this tumor and detail that there is significant dysregulation of gene expression of epigenetic remodeling agents including key members of the PRC, Sin3A/3b, NuRD, and NcoR/SMRT complexes and the DNA methyltransferases DNMT1, DNMT3a, and DNMT3b. This is accompanied by significant DNA methylation changes and dysregulation of multiple miRNAs with known links to tumorigenesis. This study significantly increases our understanding of the BCOR effects on fusion-positive undifferentiated sarcomas at both the genomic and epigenomic level and suggests that as better-tailored and more refined treatment algorithms continue to evolve, epigenetic modifying agents should be further evaluated for their efficacy against these tumors.
Lessons learned from quality management system ISO 9001:2015 certification: practices and barrier identification from Brazilian industrial companies
Authors: Barbosa Luís César Ferreira Motta , de Oliveira Otávio José , Machado Marcio Cardoso , Morais Ana Clara Tomaz , Bozola Patrícia Maria , Santos Manuel Gilberto Freitas
Published: November 2021

Purpose

This study used a qualitative approach on five case studies in Brazilian industrial companies. The research used interviews, document analysis and on-site visits to collect and analyze data. The companies were selected based on the following criteria: operating in the industrial sector, updating their quality management system (QMS) process to ISO 9001: 2015 and agreeing to participate in this study.

Design/methodology/approach

This article aims to investigate the strategies of industrial companies adopted for ISO-9001:2015 certification in light of the six major advances concerning the previous version. Thus, QMS of other organizations can incorporate identified lessons learned, whether certified or not.

Findings

The main finding of the research is the systematization of a set of lessons learned in the experiences of implementing the six significant advances of ISO 9001 concerning the previous version by industrial companies in the State of São Paulo in Brazil. These lessons can and should be used by other organizations to improve their QMSs.

Practical implications

The practices identified in this empirical research can serve as benchmarking to assist quality managers from other companies in QMS certification based on ISO 9001: 2015 or even those not certified but interested in updating their QMSs. Therefore, lessons learned can significantly minimize efforts to improve your projects, processes, products and services. These findings can also help industrial companies improve their production efficiency and effectiveness through quality improvement.

Originality/value

The main novelty of the research is the consolidation of theoretical and practical analysis of the main changes in the latest version of the ISO 9001 standards. The efforts to fulfill those changes result in lessons learned. The “lessons learned” will form a new block of knowledge that will subsidize theoretical (new research) and practical (formulation of a new ISO 9001 standard and helps quality managers improve their systems).
Effects of uniform injection and suction through perforated pentagonal cylinders on the flow and heat transfer
Authors: Vakhshouri Mir Elyad , Çuhadaroğlu Burhan
Published: November 2021

Purpose

The purpose of this paper is to study the effects of uniform injection and suction through a perforated pentagonal cylinder on the flow field and heat transfer.

Design/methodology/approach

The finite-volume method has been used to solve the ensemble-averaged Navier-Stokes equations for incompressible flow at moderate Reynolds number (Re = 22,000) with the k-ɛ turbulence model equations.

Findings

A computational fluid dynamics analysis of turbulent flow past a non-regular pentagonal cylinder with three different aspect ratios aspect ratios has been carried out to investigate the effects of uniform injection/suction through the front and all surfaces of the cylinder. It is found that flow field parameters such as drag coefficient, pressure coefficient and Nusselt number are affected considerably in some cases depend on injection/suction rate (Γ) and perforated wall position.

Research limitations/implications

To optimize the efficiency of the injection and suction through a perforated surface, both wide-ranging and intensive further studies are required. Using various perforation ratios and injection/suction intensities are some possibilities.

Practical implications

Control of the vortex shedding and wake region behind bluff bodies is of vital interest in fluid dynamics. Therefore, applying uniform injection and suction from a perforated bluff body into the main flow can be used as a drag reduction mechanism, thermal protection and heat transfer enhancement.

Originality/value

This study provides unique insights into the active flow control method around pentagonal cylinders that can be useful for researchers in the field of fluid dynamics and aeronautics.
Software reliability prediction and release time management with coverage
Authors: Panwar Saurabh , Kumar Vivek , Kapur P.K. , Singh Ompal
Published: November 2021

Purpose

Software testing is needed to produce extremely reliable software products. A crucial decision problem that the software developer encounters is to ascertain when to terminate the testing process and when to release the software system in the market. With the growing need to deliver quality software, the critical assessment of reliability, cost of testing and release time strategy is requisite for project managers. This study seeks to examine the reliability of the software system by proposing a generalized testing coverage-based software reliability growth model (SRGM) that incorporates the effect of testing efforts and change point. Moreover, the strategic software time-to-market policy based on costreliability criteria is suggested.

Design/methodology/approach

The fault detection process is modeled as a composite function of testing coverage, testing efforts and the continuation time of the testing process. Also, to assimilate factual scenarios, the current research exhibits the influence of software users refer as reporters in the fault detection process. Thus, this study models the reliability growth phenomenon by integrating the number of reporters and the number of instructions executed in the field environment. Besides, it is presumed that the managers release the software early to capture maximum market share and continue the testing process for an added period in the user environment. The multiattribute utility theory (MAUT) is applied to solve the optimization model with release time and testing termination time as two decision variables.

Findings

The practical applicability and performance of the proposed methodology are demonstrated through real-life software failure data. The findings of the empirical analysis have shown the superiority of the present study as compared to conventional approaches.

Originality/value

This study is the first attempt to assimilate testing coverage phenomenon in joint optimization of software time to market and testing duration.
The impact of healthy workplaces on employee satisfaction, productivity and costs
Authors: Voordt Theo van der , Jensen Per Anker
Published: November 2021

Purpose

This paper aims to explore the added value of healthy workplaces for employees and organizations, in particular regarding employee satisfaction, labour productivity and facility cost.

Design/methodology/approach

The paper is based on a narrative review of journal papers and other sources covering the fields of building research, corporate real estate management, facilities management, environmental psychology and ergonomics.

Findings

The review supports the assumption of positive impacts of appropriate building characteristics on health, satisfaction and productivity. Correlations between these impacts are still underexposed. Data on cost and economic benefits of healthy workplace characteristics is limited, and mainly regard reduced sickness absence. The discussed papers indicate that investing in healthy work environments is cost-effective.

Originality/value

The findings contribute to a better understanding of the complex relationships between physical characteristics of the environment and health, satisfaction, productivity and costs. These insights can be used to assess work environments on these topics, and to identify appropriate interventions in value-adding management of buildings and facilities.
Performing intersectional identity work over time: the historic case of Viola Turner
Authors: Portie-Williamson Madison , Marshall David R. , Novicevic Milorad M. , Mills Albert J. , Lugar Caleb W.
Published: November 2021

Purpose

This study aims to analyze the exemplary historic case of Ms Viola Turner – an African-American insurance executive in the early 1900s to gain insights into how individuals negotiate the tension between intersecting identities and moral foundational values over time.

Design/methodology/approach

This study uses a mixed research design and a genealogical-pragmatic approach to analyze this exemplary case. This study uses computer-aided textual analysis software to analyze interviews conducted with Ms Turner, generating quantitative insights. This study qualitatively codes the interviews to aid in establishing the behavioral patterns across Ms Turner’s lifespan.

Findings

This study found that Ms Turner altered her underlying configurations of moral foundations to better align with her intersecting identities. This study also revealed cross-level interactions of intersecting identities, life stages and social contexts. Individuals manage and cope with power imbalances through these identity-value alignments.

Originality/value

The findings shed light on how intersectional history contributes to understanding the ways in which individuals deal with power relationships embedded in intersecting identities over time.
In-store interactive advertising screens: the effect of interactivity on impulse buying explained by self-agency
Authors: Moes Anne , Fransen Marieke , Fennis Bob , Verhagen Tibert , van Vliet Harry
Published: November 2021

Purpose

Physical stores are increasingly dependent on impulse visits and the impulse purchases of passers-by. Interactive advertising screens in store windows could help retailers increase impulse-visit urges and impulse-buying urges. However, the effects of interactive screens in physical surroundings have not been studied before. Therefore, this study aimed to examine the effect of interactive screens on impulse urges and gain insight into the underlying mechanism that explains the possible effect.

Design/methodology/approach

An interactive screen was placed in a store window. Using three field experiments, we studied the effect of interactivity-level (high vs low) on the impulse-visit and impulse-buying urges of passers-by, and the mediating role of self-agency in these effects.

Findings

Highly interactive (compared to less interactive) advertising screens in store windows positively affect impulse-visit and impulse-buying urges through self-agency. Retailers can therefore use interactive advertising screens to increase the number of impulse purchases if feelings of self-agency are activated.

Originality/value

This is the first study to examine the extent to which interactive screens in a store window enhance the impulse-visit and impulse-buying urges of passers-by and the mediating factor of these effects. By conducting three field experiments, we achieved a high external validity and managed to share very reliable results owing to the replication of the findings.
Local governance of critical infrastructure resilience: Types of coordination in German cities
Authors: Knodt Michèle , Fraune Cornelia , Engel Alice
Published: November 2021

The resilience of critical infrastructures in cities is key to being prepared for future crises. The challenge of enhancing critical infrastructure resilience addresses a multitude of actors. However, we lack conceptual, as well as empirical, understanding of how these different actors are coordinated. Therefore, this contribution asks how the different actors involved in critical infrastructure governance are coordinated at the local level. With the help of a typology of network governance coordination (political leadership, mutual exchange, and positive coordination), we look at the critical infrastructure crisis management in major German cities based on survey data with the scenario of a long‐lasting, supraregional power outage. The results show that political leadership coordination, as a unilateral and information‐based way of addressing public and private actors, is the dominant type. Only a quarter of the cities have chosen measures of mutual exchange coordination based on the consultation in an ad hoc manner. Measures of positive coordination where institutionalized joint planning is central are taken up only by a minority of German cities. Assuming that positive coordination is particularly important in dealing with unexpected events, positive coordination emerges as the missing piece of the resilience puzzle for many German cities.