bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mucosal vaccination for SARS-CoV-2 elicits superior systemic T central memory function and cross-neutralizing antibodies against variants of concern
Authors: O’Neill Aled , Kala Monica Palanichamy , Wah Tan Chee , Saron Wilfried A.A. , Mantri Chinmay Kumar , Rathore Abhay P.S. , Wang Lin-Fa , St. John Ashley L. 
Published: September 2022

AbstractCOVID-19 vaccines used in humans are highly effective in limiting disease and death caused by the SARS-CoV-2 virus, yet improved vaccines that provide greater protection at mucosal surfaces, which could reduce break-through infections and subsequent transmission, are still needed. Here we show that intranasal (I.N.) vaccination with the receptor binding domain of Spike antigen of SARS-CoV-2 (S-RBD) in combination with the mucosal adjuvant mastoparan-7 improved systemic T cell responses compared to an equivalent dose of antigen delivered by the sub-cutaneous (S.C.) route, adjuvanted by either M7 or the gold-standard adjuvant, alum. T cell phenotypes induced by I.N. vaccine administration included enhanced polyfunctionality (combined IFN-γ and TNF expression) and greater numbers of T central memory (TCM) cells. These phenotypes were T cell-intrinsic and could be recalled in the lungs and/or brachial LNs upon antigen challenge after adoptive T cell transfer to naïve recipients. Furthermore, mucosal vaccination induced antibody responses that were similarly effective in neutralizing the binding of the parental strain of S-RBD to its ACE2 receptor, but showed greater cross-neutralizing capacity against multiple variants of concern (VOC), compared to S.C. vaccination. These results highlight the role of nasal vaccine administration in imprinting an immune profile associated with long-term T cell retention and diversified neutralizing antibody responses, which could be applied to improve vaccines for COVID-19 and other infectious diseases.
Cellular stress modulates severity of the acute respiratory distress syndrome in COVID-19
Authors: Rico-Llanos Gustavo , Porras-Perales Óscar , Escalante Sandra , Vázquez Daniel , Valiente Lucía , Castillo María I. , Pérez-Tejeiro José Miguel , Baglietto-Vargas David , Becerra José , Reguera José María , Duran Ivan , Csukasi Fabiana 
Published: September 2022

AbstractInflammation is a central pathogenic feature of the acute respiratory distress syndrome (ARDS) in COVID-19. Previous pathologies such as diabetes, autoimmune or cardiovascular diseases become risk factors for the severe hyperinflammatory syndrome. A common feature among these risk factors is the subclinical presence of cellular stress, a finding that has gained attention after the discovery that BiP (GRP78), a master regulator of stress, participates in the SARS-CoV-2 recognition. Here, we show that BiP serum levels are higher in COVID-19 patients who present certain risk factors. Moreover, early during the infection, BiP levels predict severe pneumonia, supporting the use of BiP as a prognosis biomarker. Using a mouse model of pulmonary inflammation, we demonstrate that cell surface BiP (cs-BiP) responds by increasing its levels in leukocytes. Neutrophiles show the highest levels of cs-BiP and respond by increasing their population, whereas alveolar macrophages increase their levels of cs-BiP. The modulation of cellular stress with the use of a clinically approved drug, 4-PBA, resulted in the amelioration of the lung hyperinflammatory response, supporting the anti-stress therapy as a valid therapeutic strategy for patients developing ARDS. Finally, we identified stress-modulated proteins that shed light into the mechanism underlying the cellular stress-inflammation network in lungs.
Protein secretion zones within the Gram-positive cell wall
Authors: Strach Manuel , Koch Felicitas , Fiedler Svenja , Liebeton Klaus , Graumann Peter L. 
Published: September 2022

AbstractWhereas the translocation of proteins across the cell membrane has been thoroughly investigated, it is still unclear how proteins cross the cell wall in Gram positive bacteria, which are widely used for industrial applications. We have studied secretion of α-amylase AmyE within two different Bacillus strains. We show that a C-terminal fusion of AmyE with the fluorescent reporter mCherry is secreted via discrete patches with very low dynamics that are visible at many places within the lateral cell wall, for many minutes. Expression from a high copy number plasmid was required to be able to see these structures we term “secretion zones”. Zones corresponded to visualized AmyE activity on the surface of cells, and frequently overlapped with SecA signals, but did not necessarily co-localize with the secretion ATPase. Single particle tracking showed much higher dynamics of SecA and of SecDF, involved in AmyE secretion, at the cell membrane than AmyE. These experiments suggest that SecA initially translocates AmyE molecules through the cell membrane, and then diffuses to a different translocon. Single molecule tracking of SecA show changes in distinct diffusion states of SecA, but suggest that AmyE overexpression does not overwhelm the system. Because secretion zones were only found during the transition to and within stationary phase, diffusion rather than passive transport based on cell wall growth from inside to outside, releases AmyE and thus probably secreted proteins in general. Our findings suggest active transport through the cell membrane and slow, passive transition through the cell wall in Gram positive bacteria.
Characterization of p38α signaling networks in cancer cells using quantitative proteomics and phosphoproteomics
Authors: Dan Yuzhen , Radic Nevenka , Gay Marina , Fernández-Torras Adrià , Arauz Gianluca , Vilaseca Marta , Aloy Patrick , Canovas Begoña , Nebreda Angel R. 
Published: September 2022

Abstractp38α (encoded by MAPK14) is a protein kinase that regulates cellular responses to almost all types of environmental and intracellular stresses. Upon activation, p38α phosphorylates many substrates both in the cytoplasm and nucleus, allowing this pathway to regulate a wide variety of cellular processes. While the role of p38α in the stress response has been widely investigated, its implication in cell homeostasis is less understood. To investigate the signaling networks regulated by p38α in normally proliferating cancer cells, we performed quantitative proteomic and phosphoproteomic analyses in breast cancer cells in which this pathway had been either genetically targeted or chemically inhibited. Our study identified with high confidence 35 proteins and 82 phosphoproteins (114 phosphosites) that are modulated by p38α, and highlighted the implication of various protein kinases, including MK2 and mTOR, in the p38α-regulated signaling networks. Moreover, functional analyses revealed an important contribution of p38α to the regulation of cell adhesion, DNA replication and RNA metabolism. Indeed, we provide experimental evidence supporting that p38α negatively regulates cell adhesion, and showed that this p38α function is likely mediated by the modulation of the adaptor protein ArgBP2. Collectively, our results illustrate the complexity of the p38α regulated signaling networks, provide valuable information on p38α-dependent phosphorylation events in cancer cells, and document a mechanism by which p38α can regulate cell adhesion.
Anterior hypothalamic parvalbumin neurons are glutamatergic and promote escape behavior
Authors: Laing Brenton T. , Anderson Megan S. , Bonaventura Jordi , Jayan Aishwarya , Sarsfield Sarah , Gajendiran Anjali , Michaelides Michael , Aponte Yeka 
Published: September 2022

ABSTRACTThe anterior hypothalamic area (AHA) is a critical structure for defensive responding. Here, we identified a cluster of parvalbumin-expressing neurons in the AHA (AHAPV) that are glutamatergic with fast-spiking properties and send axonal projections to the dorsal premammillary nucleus (PMD). Using in vivo functional imaging, optogenetics, and behavioral assays, we determined the role of these AHAPV neurons in regulating behaviors essential for survival. We observed that AHAPV neuronal activity significantly increases when mice are exposed to a predator, and in a real-time place preference assay, we found that AHAPV neuron photoactivation is aversive. Moreover, activation of both AHAPV neurons and the AHAPV→PMD pathway triggers escape responding during a predator-looming test. Furthermore, escape responding is impaired after AHAPV neuron ablation, and anxiety-like behavior as measured by the open field and elevated plus maze assays does not seem to be affected by AHAPV neuron ablation. Finally, whole-brain metabolic mapping using positron emission tomography combined with AHAPV neuron photoactivation revealed discrete activation of downstream areas involved in arousal, affective, and defensive behaviors including the amygdala and the substantia nigra. Our results indicate that AHAPV neurons are a functional glutamatergic circuit element mediating defensive behaviors, expanding the identity of genetically defined neurons orchestrating fight-or-flight responses. Together, our work will serve as a foundation for understanding neuropsychiatric disorders such as aggression or fear.
Staphyloxanthin production by Staphylococcus aureus promotes resistance to oxidative stress to delay diabetic wound healing
Authors: McCready-Vangi Amelia R. , Campbell Amy E. , Uberoi Aayushi , Lovins Victoria M. , White Ellen K. , Morgenstern Alexis R. , Gardner Sue E. , Grice Elizabeth A. 
Published: September 2022

SUMMARYDiabetic foot ulcers (DFU) are a serious complication of diabetes mellitus that burden patients and health care systems. Staphylococcus aureus is prevalent and abundant in the DFU microbiome, and strain-level differences in S. aureus may drive clinical outcomes. To identify mechanisms underlying strain-specific outcomes in DFU with S. aureus, we performed high-throughput phenotyping screens on a collection of 221 S. aureus cultured isolates from clinically uninfected DFU. Of the 4 phenotypes examined (in vitro biofilm formation and production of staphylokinase, staphyloxanthin, and siderophores), we discovered that isolates from non-healing wounds produced more staphyloxanthin, a carotenoid cell membrane pigment. In a murine diabetic wound healing model, staphyloxanthin-producing isolates delayed wound closure significantly compared to staphyloxanthin-deficient isolates. Staphyloxanthin promoted resistance to oxidative stress in vitro and enhanced bacterial survival in human neutrophils. Comparative genomic and transcriptomic analysis of genetically similar clinical isolates with disparate staphyloxanthin phenotypes revealed a mutation in the Sigma B regulatory pathway that resulted in marked differences in stress response gene expression. Our findings suggest that staphyloxanthin production delays wound healing by protecting S. aureus from neutrophil-mediated oxidative stress, and may provide a target for therapeutic intervention in S. aureus-positive wounds.
Ribosomes as molecular thermometers: metal-binding sites in ribosomal proteins are robust indicators of bacterial adaptation to heat and cold
Authors: van den Elzen Antonia , Helena-Bueno Karla , Brown Charlotte R. , Melnikov Sergey 
Published: September 2022

AbstractRibosomal genes are widely used as “molecular clocks” to infer the evolutionary relatedness of species. It is unclear, however, whether these genes can also serve as “molecular thermometers” to precisely estimate an organism’s optimal growth temperature. Previously, some estimations were made using the average nucleotide content in ribosomal RNA, but the universal application of this approach was prevented by numerous outliers. Here, seeking to bypass this problem, we asked whether ribosomal genes contain additional markers of thermal adaptations, aside from their nucleotide composition. To answer this, we analyzed site-specific variations in sequences of ribosomal proteins from 2,021 bacteria with known optimal growth conditions. We found that ribosomal proteins comprise a few “mutational hotspots”—residues that vary in a temperature-dependent manner and distinguish heat- and cold-adapted bacteria. Most of these residues coordinate metal ions that support protein folding at high temperatures. Using these residues, we then showed that the upper and lower limits of an organism’s optimal growth temperatures can be estimated using just 0.001% of the genome sequence or just two amino residues in the cellular proteome. This finding illustrates that laboratory-independent estimation of optimal growth temperatures can be simplified if we abandon the traditional use of rRNA and protein sequences to assess their content and instead focus on those few residues that are most critical for protein structure. This finding may simplify the analysis of unculturable and extinct species by helping bypass the need for laborious, costly, and at times impossible laboratory experiments.
Serum-dependent recruitment of the chromatin remodeler CHD8 to promoters is mediated by the ERK-ELK pathway
Authors: Subtil-Rodríguez Alicia , Vázquez-Chávez Elena , Guerrero-Martínez Jose A. , Ceballos-Chávez María , Reyes José C. 
Published: September 2022

ABSTRACTChromodomain helicase DNA binding protein 8 (CHD8) is a chromatin remodeler of the SNF2 family involved in gene transcription regulation. It has been shown that CHD8 is required for cell proliferation, cell differentiation and central nervous system development. In fact, CHD8 haploinsufficiency causes a human syndrome characterized by autism, macrocephaly, gastrointestinal complaints and some other clinical characteristics. However, the mechanism by which CHD8 controls transcription and how it is recruited to its targets in the chromatin is still unclear. We have previously shown that serum depletion causes that CHD8 detaches from chromatin. Here we demonstrate that serum-dependent recruitment of CHD8 to promoters requires the extracellular signal-regulated kinase (ERK)/ ETS-like (ELK) branch of the mitogen-activated protein kinase (MAPK) pathway. Our analysis of genomic occupancy data shows that CHD8 binding sites were strongly enriched in ELK1 and ELK4 DNA binding motifs and that CHD8 and ELK1 co-occupy multiple transcription start sites. We show that ELK1 and ELK4 are required for normal recruitment of CHD8 to the promoters of CCNA2, CDC6, CCNE2, BRCA2 and MYC genes. However, CHD8 is dispensable for ELK1 and ELK4 binding. Genome wide transcriptomic analysis evidenced that serum-dependent activation of a subset of immediate early genes, including the well-known ELK1 target gene FOS, was impaired upon depletion of CHD8. In summary, our results uncover the role of the ERK/ELK pathway in CHD8 recruitment to chromatin and provide evidences indicating a role of CHD8 in regulating serum-dependent transcription.
Bacterial Argonaute nucleases reveal different modes of DNA targeting in vitro and in vivo
Authors: Lisitskaya Lidiya , Kropocheva Ekaterina , Agapov Aleksei , Prostova Maria , Panteleev Vladimir , Yudin Denis , Ryazansky Sergey , Kuzmenko Anton , Aravin Alexei A. , Esyunina Daria , Kulbachinskiy Andrey 
Published: September 2022

AbstractProkaryotic Argonaute proteins (pAgos) are homologs of eukaryotic Argonautes (eAgos) that were similarly proposed to play a role in cell defense against invaders. However, pAgos are much more diverse than eAgos and very little is known about their functional activity and target specificity in vivo. Here, we describe five pAgo proteins from mesophilic bacteria that act as DNA-guided DNA endonucleases and analyze their ability to target chromosomal and invader DNA. In vitro, the analyzed proteins use small guide DNAs for precise cleavage of single-stranded DNA at a wide range of temperatures. Upon their expression in Escherichia coli, all five pAgos are loaded with small DNAs preferentially produced from plasmid DNA and from chromosomal regions of replication termination. One of the tested pAgos, EmaAgo from Exiguobacterium marinum can induce DNA interference between multicopy sequences resulting in targeted processing of homologous plasmid and chromosomal loci. EmaAgo also protects bacteria from bacteriophage infection and is preferentially loaded with phage guide DNAs suggesting that the ability of pAgos to target multicopy elements may be crucial for their protective function. The wide spectrum of pAgo activities suggests that they may have diverse functions in vivo and paves the way for their use in biotechnology.
Expression profiling of immune-response genes common in SARS-CoV-1 and influenza A virus disease, viz-a-viz neutropenia disorder, using integrated bioinformatics tools
Authors: Olaniyi Ayinde , Oluwadamilola Obasanmi , Oluwabunmi Alabi 
Published: September 2022

AbstractViral diseases have proven to be an existential threat to man due to its fatality and its consistent emergence and re-emergence, so the need for novel ideas in combating this menace. Advances in genetic studies has proven to be indispensable in this fight as knowledge of organismal genetic variability has been useful in therapy development, as well as in mounting defense against the treacherous infectious agents. However, there are still fallow grounds needing to be explored in this war which informed this study, with focus on expression profiling of similar immune-responsegenes in SARS-COV-1 and influenza A virus (AIV) in respect to neutropenia (NP), using integrated bioinformatics techniques such as extraction of microarray dataset in the gene expression omnibus (GEO) database, generation of DEGs using GEO2R tool, construction of protein-protein interaction (PPI) network using string and Cytoscape software, Venn diagram analysis and then gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) for enrichment and pathway analysis respectively. Ten genes which includes ELANE, ITGA2B, CXCR1, CSF3R, SPI1, MS4A3, MMP8, CEACAM8, RNASE3, and DEFA4 were identified, with ELANE gene moreover identified as a key gene, which might be responsible in the regulation of immune response during viral infection, based on its characteristic feature in the PPI network.
A new and highly effective method for predicting T-cell response targets implemented on SARS-CoV-2 data
Authors: Flegr Jaroslav , Zahradník Daniel 
Published: September 2022

AbstractComputational T-cell epitope prediction is essential in many immunological projects, including the development of vaccines. T-cells of immunocompetent vertebrate hosts can recognize as non-self only peptides which are present in the parasite’s proteins and absent in the host’s proteins. This basic principle allows us to predict which peptides can elicit T-cells’ response. We built on the fact that the specificity of T-cells reacting to SARS-CoV-2 antigens has been recently mapped in detail. Using Monte Carlo tests, we found that empirically confirmed peptides that stimulate T-cells contain an increased fraction of pentapeptides, hexapeptides, and heptapeptides which are not found in the human proteome (p < 0.0001). Similarly, hexapeptides absent in human proteins were overrepresented in peptides that elicited T-cell response in a published empirical study (p = 0.027). The new theory-based method predicted T-cell immunogenicity of SARS-CoV-2 peptides four times more effectively than current empirically based methods.
Identification of regulatory elements in primary sensory neurons involved in neuropathic pain
Authors: Stephens Kimberly E. , Moore Cedric , Vinson David A. , White Bryan E. , Renfro Zachary , Zhou Weiqiang , Ji Zhicheng , Ji Hongkai , Zhu Heng , Guan Yun , Taverna Sean D. 
Published: September 2022

AbstractChronic pain is a significant public health issue that is often refractory to existing therapies. Here we use a multiomic approach to identify cis-regulatory elements that show differential chromatin accessibility, and reveal transcription factor (TF) binding motifs with functional regulation in the dorsal root ganglion (DRG), which contain cell bodies of primary sensory neurons, after nerve injury. We integrated RNA-seq to understand how differential chromatin accessibility after nerve injury may influence gene expression. Using TF protein arrays and chromatin immunoprecipitation-qPCR, we confirmed C/EBPγ binding to a differentially accessible sequence and used RNA-seq to identify processes in which C/EBPγ plays an important role. Our findings offer insights into TF motifs that are associated with chronic pain. These data show how interactions between chromatin landscapes and TF expression patterns may work together to determine gene expression programs in DRG neurons after nerve injury.
Tethered agonist activated ADGRF1 structure reveals molecular preference for Gαq signalling
Authors: Jones Daniel T. D. , Dates Andrew N. , Rawson Shaun D. , Burruss Maggie M. , Lipper Colin H. , Blacklow Stephen C. 
Published: September 2022

AbstractAdhesion G-Protein Coupled Receptors (aGPCRs) have evolved an activation mechanism to translate extracellular force into liberation of a tethered agonist (TA) to modulate cell signalling. We report here that ADGRF1 is the first class B GPCR shown to signal through all major G-protein classes and identify the structural basis for its Gαq preference by cryo-EM. Our structure shows that Gαq over Gαs preference in ADGRF1 derives from tighter packing at the conserved F569 of the TA, altering contacts between TM helix I and VII, with a concurrent rearrangement of TM helices VII and VIII at the site of Gα recruitment. Gαs signalling is also more sensitive to mutation of TA or binding site residues than Gαq. Our work advances the understanding of aGPCR TA activation in molecular detail, identifying structural features that potentially explain preferential signal modulation.
The effect of transformational, transactional and authentic leadership on innovation: the mediating role of organizational culture
Authors: Rashwan Kareem A. , Ghaly Meril 
Published: September 2022

PurposeThis study aims to investigate the effects of different leadership styles, transformational, transactional and authentic leadership, on travel agents’ innovational behavior, with organizational culture as a mediator.Design/methodology/approachThe study aim was achieved by using an integrative model using LISREL 8.80. Quantitative research was used using a questionnaire. A convenient sampling technique was used to select the sample. A total of 500 questionnaires were distributed to travel agents, out of which 415 were returned, and 376 usable ones were statistically handled (75.2% response rate).FindingsTransformational leadership has a significant impact on organizational culture (ß = 0.34) and innovational behavior (ß = 0.46). Authentic leadership has a significant impact on both organizational culture (ß = 0.38) and innovational behavior (ß = 0.52). Transactional leadership significantly impacts organizational culture (ß = 0.38); however, it has no significant impact on innovational behavior (ß = 0.31). The positive influence of leadership styles on innovative behavior is mediated by innovative organizational culture (ß = 0.92).Research limitations/implicationsFurther research should explore the relationship between other leadership styles and innovation. Additionally, investigates the relationship between organizational culture factors and innovation. This study targeted category “A” travel agencies. Therefore, to generalize the study findings, the study should be replicated with other categories of travel agencies.Practical implicationsTravel agencies organizations should invest in managers who adopt authentic and transformational leadership, whereas transactional leaders are urged to be open to new ideas, invest in the knowledge and skills of their employees, encourage friendly communication with their employees and ensure that there are reasonable punishment and reward systems within the organization.Originality/valueThis study presents new insights into tourism field by integrating the study variables (organizational culture, innovative behavior and leadership style), into one framework, particularly in developing countries’ contexts.