bluuebunny/crossref_metadata_2025 huggingface dataset:
Growing Up Under Constant Light: A Challenge to the Endocrine Function of the Leydig Cells
Authors: Marinkovic Dijana Z. , Medar Marija L. J. , Becin Alisa P. , Andric Silvana A. , Kostic Tatjana S.
Published: March 2021

The factors influencing Leydig cell maturity and the acquisition of functional capacity are incompletely defined. Here we analyzed the constant light (LL) influence on Leydig cells’ endocrine function during reproductive maturation. Rats were exposed to LL from P21 to P90. Data were collected at juvenile (P35), peri/pubertal (P42, P49), and adult (P90) stages of life. The results proved the effect of LL on rats’ physiology by changing of bimodal voluntary activity pattern into free-running. Additionally, the peripheral clock in Leydig cells changed in LL condition, indicating disturbed rhythm: the positive element (Bmal1) increased in pre-/pubertal but decreased in the adult period, while negative elements (Per2 and Reverba) were increased. The effects of LL were most prominent in puberty: pituitary genes encoding gonadotropic hormones (Cga, Lhb, Fshb) decreased; serum corticosterone increased, while serum androgens and mass of testicular and sex accessory organs reduced; markers of Leydig cells maturity/differentiation (Insl3, Lhcgr) and steroidogenesis-related genes (Scarb1, Star, Cyp11a1, Cyp17a1) decreased; the steroidogenic and energetic capacity of the Leydig cell mitochondria decreased; the mtDNA copy number reduced, and mitochondrial dynamics markers changed: fusion decreased (Opa1 and Mfn2), and mitophagy increased (Pink1). In adults, the negative effect of LL on mitochondrial function and steroidogenic capacity persists in adult Leydig cells while other parameters reached control values. Altogether, the results indicate that LL slows down Leydig cells’ maturation by reducing the endocrine and energy capacity of cells leading to the delay of reproductive development.
Network Analysis and Transcriptome Profiling Identify Autophagic and Mitochondrial Dysfunctions in SARS-CoV-2 Infection
Authors: Singh Komudi , Chen Yun-Ching , Hassanzadeh Shahin , Han Kim , Judy Jennifer T. , Seifuddin Fayaz , Tunc Ilker , Sack Michael N. , Pirooznia Mehdi
Published: March 2021

Analyzing host cells' transcriptional response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection will help delineate biological processes underlying viral pathogenesis. First, analysis of expression profiles of lung cell lines A549 and Calu3 revealed upregulation of antiviral interferon signaling genes in response to all three SARS-CoV-2, MERS-CoV, or influenza A virus (IAV) infections. However, perturbations in expression of genes involved in inflammatory, mitochondrial, and autophagy processes were specifically observed in SARS-CoV-2-infected cells. Next, a validation study in infected human nasopharyngeal samples also revealed perturbations in autophagy and mitochondrial processes. Specifically, mTOR expression, mitochondrial ribosomal, mitochondrial complex I, lysosome acidification, and mitochondrial fission promoting genes were concurrently downregulated in both infected cell lines and human samples. SARS-CoV-2 infection impeded autophagic flux either by upregulating GSK3B in lung cell lines or by downregulating autophagy genes, SNAP29, and lysosome acidification genes in human samples, contributing to increased viral replication. Therefore, drugs targeting lysosome acidification or autophagic flux could be tested as intervention strategies. Finally, age-stratified SARS-CoV-2-positive human data revealed impaired upregulation of chemokines, interferon-stimulated genes, and tripartite motif genes that are critical for antiviral signaling. Together, this analysis has revealed specific aspects of autophagic and mitochondrial function that are uniquely perturbed in SARS-CoV-2-infected host cells.
Validation of Differentially Expressed Immune Biomarkers in Latent and Active Tuberculosis by Real-Time PCR
Authors: Perumal Prem , Abdullatif Mohamed Bilal , Garlant Harriet N. , Honeyborne Isobella , Lipman Marc , McHugh Timothy D. , Southern Jo , Breen Ronan , Santis George , Ellappan Kalaiarasan , Kumar Saka Vinod , Belgode Harish , Abubakar Ibrahim , Sinha Sanjeev , Vasan Seshadri S. , Joseph Noyal , Kempsell Karen E.
Published: March 2021

Tuberculosis (TB) remains a major global threat and diagnosis of active TB ((ATB) both extra-pulmonary (EPTB), pulmonary (PTB)) and latent TB (LTBI) infection remains challenging, particularly in high-burden countries which still rely heavily on conventional methods. Although molecular diagnostic methods are available, e.g., Cepheid GeneXpert, they are not universally available in all high TB burden countries. There is intense focus on immune biomarkers for use in TB diagnosis, which could provide alternative low-cost, rapid diagnostic solutions. In our previous gene expression studies, we identified peripheral blood leukocyte (PBL) mRNA biomarkers in a non-human primate TB aerosol-challenge model. Here, we describe a study to further validate select mRNA biomarkers from this prior study in new cohorts of patients and controls, as a prerequisite for further development. Whole blood mRNA was purified from ATB patients recruited in the UK and India, LTBI and two groups of controls from the UK (i) a low TB incidence region (CNTRLA) and (ii) individuals variably-domiciled in the UK and Asia ((CNTRLB), the latter TB high incidence regions). Seventy-two mRNA biomarker gene targets were analyzed by qPCR using the Roche Lightcycler 480 qPCR platform and data analyzed using GeneSpring™ 14.9 bioinformatics software. Differential expression of fifty-three biomarkers was confirmed between MTB infected, LTBI groups and controls, seventeen of which were significant using analysis of variance (ANOVA): CALCOCO2, CD52, GBP1, GBP2, GBP5, HLA-B, IFIT3, IFITM3, IRF1, LOC400759 (GBP1P1), NCF1C, PF4V1, SAMD9L, S100A11, TAF10, TAPBP, and TRIM25. These were analyzed using receiver operating characteristic (ROC) curve analysis. Single biomarkers and biomarker combinations were further assessed using simple arithmetic algorithms. Minimal combination biomarker panels were delineated for primary diagnosis of ATB (both PTB and EPTB), LTBI and identifying LTBI individuals at high risk of progression which showed good performance characteristics. These were assessed for suitability for progression against the standards for new TB diagnostic tests delineated in the published World Health Organization (WHO) technology product profiles (TPPs).
Immune Interaction Map of Human SARS-CoV-2 Target Genes: Implications for Therapeutic Avenues
Authors: Subbarayan Karthikeyan , Ulagappan Kamatchi , Wickenhauser Claudia , Bachmann Michael , Seliger Barbara
Published: March 2021

There exists increasing evidence that people with preceding medical conditions, such as diabetes and cancer, have a higher risk of infection with SARS-CoV-2 and are more vulnerable to severe disease. To get insights into the possible role of the immune system upon COVID-19 infection, 2811 genes of the gene ontology term “immune system process GO: 0002376” were selected for coexpression analysis of the human targets of SARS-CoV-2 (HT-SARS-CoV-2) ACE2, TMPRSS2, and FURIN in tissue samples from patients with cancer and diabetes mellitus. The network between HT-SARS-CoV-2 and immune system process genes was analyzed based on functional protein associations using STRING. In addition, STITCH was employed to determine druggable targets. DPP4 was the only immune system process gene, which was coexpressed with the three HT-SARS-CoV-2 genes, while eight other immune genes were at least coexpressed with two HT-SARS-CoV-2 genes. STRING analysis between immune and HT-SARS-CoV-2 genes plotted 19 associations of which there were eight common networking genes in mixed healthy (323) and pan-cancer (11003) tissues in addition to normal (87), cancer (90), and diabetic (128) pancreatic tissues. Using this approach, three commonly applicable druggable connections between HT-SARS-CoV-2 and immune system process genes were identified. These include positive associations of ACE2—DPP4 and TMPRSS2—SRC as well as a negative association of FURIN with ADAM17. Furthermore, 16 drugs were extracted from STITCH (score <0.8) with 32 target genes. Thus, an immunological network associated with HT-SARS-CoV-2 using bioinformatics tools was identified leading to novel therapeutic opportunities for COVID-19.
Assessing the Function of the ZFP90 Variant rs1170426 in SLE and the Association Between SLE Drug Target and Susceptibility Genes
Authors: Zhu Tingting , Huang Yuandi , Qian Danfeng , Sheng Yuming , Zhang Chaowen , Chen Shirui , Zhang Hui , Wang Hui , Zhang Xuejun , Liu Junlin , Ding Changhai , Liu Lu
Published: March 2021

A genome-wide association study (GWAS) has discovered that a polymorphism in the ZFP90 gene is associated with systemic lupus erythematosus (SLE). In this study, we explored the candidate function of a ZFP90 variant (rs1170426) in the context of SLE and detected the relationship between SLE susceptible genes and SLE drug target genes. First, we investigated the regulatory role of rs1170426 on ZFP90 expression by expression quantitative trait loci (eQTL) analysis in peripheral blood mononuclear cells (PBMCs), T, B, and monocytes cells and annotated the regulatory function of rs1170426 using bioinformatic databases. Second, we compared the case-control difference in ZFP90 expression levels. Third, we analyzed the association of genotype and ZFP90 expression levels with SLE clinical characters. Last, we showed the interaction of SLE susceptibility genes with SLE drug target genes. Subjects with the risk allele “C” of rs1170426 had lower expression levels of ZFP90 in PBMCs (P = 0.006) and CD8+ T cells (P = 0.003) from controls. SLE cases also had lower expression levels compared with controls (P = 2.78E-9). After correction for multiple testing, the ZFP90 expression levels were related to serositis (FDR p = 0.004), arthritis (FDR p = 0.020), hematological involvement (FDR p = 0.021), and increased C-reactive protein (CRP) (FDR p = 0.005) in cases. Furthermore, the SLE susceptible genes and the recognized SLE drug target genes were more likely to act upon each other compared with non-SLE genetic genes (OR = 2.701, P = 1.80E-5). These findings suggest that ZFP90 might play a role in the pathogenesis of SLE, and SLE genetics would contribute to therapeutic drug discovery.
Chitotriosidase Activity Is Counterproductive in a Mouse Model of Systemic Candidiasis
Authors: Schmitz Nicholas A. , Thakare Ritesh P. , Chung Chun-Shiang , Lee Chang-Min , Elias Jack A. , Lee Chun Geun , LeBlanc Brian W.
Published: March 2021

Mammalian cells do not produce chitin, an insoluble polymer of N-acetyl-D-glucosamine (GlcNAc), although chitin is a structural component of the cell wall of pathogenic microorganisms such as Candida albicans. Mammalian cells, including cells of the innate immune system elaborate chitinases, including chitotriosidase (Chit1), which may play a role in the anti-fungal immune response. In the current study, using knockout mice, we determined the role of Chit1 against systemic candidiasis. Chit1-deficient mice showed significant decrease in kidney fungal burden compared to mice expressing the functional enzyme. Usingin vitroanti-candidal neutrophil functional assays, the introduction of the Chit1:chitin digestion end-product, chitobiose (N-acetyl-D-glucosamine dimer, GlcNAc2), decreased fungal-induced neutrophil swarming and Candida killingin vitro. Also, a role for the lectin-like binding site on the neutrophil integrin CR3 (Mac-1, CD11b/CD18) was found through physiological competitive interference by chitobiose. Furthermore, chitobiose treatment of wild type mice during systemic candidiasis resulted in the significant increase in fungal burden in the kidney. These data suggest a counterproductive role of Chit1 in mounting an efficient anti-fungal defense against systemic candidiasis.
Staphylococcus aureus-Specific Tissue-Resident Memory CD4+ T Cells Are Abundant in Healthy Human Skin
Authors: Hendriks Astrid , Mnich Malgorzata Ewa , Clemente Bruna , Cruz Ana Rita , Tavarini Simona , Bagnoli Fabio , Soldaini Elisabetta
Published: March 2021

The skin is an immunocompetent tissue that harbors several kinds of immune cells and a plethora of commensal microbes constituting the skin microbiome. Staphylococcus aureus is a prominent skin pathogen that colonizes a large proportion of the human population. We currently have an incomplete understanding of the correlates of protection against S. aureus infection, however genetic and experimental evidence has shown that CD4+ T cells play a key role in orchestrating a protective anti-S. aureus immune response. A high S. aureus-specific memory CD4+ T cell response has been reported in the blood of healthy subjects. Since T cells are more abundant in the skin than in blood, we hypothesized that S. aureus-specific CD4+ T cells could be present in the skin of healthy individuals. Indeed, we observed proliferation of tissue-resident memory CD4+ T cells and production of IL-17A, IL-22, IFN-γ and TNF-β by cells isolated from abdominal skin explants in response to heat-killed S. aureus. Remarkably, these cytokines were produced also during an ex vivo epicutaneous S. aureus infection of human skin explants. These findings highlight the importance of tissue-resident memory CD4+ T cells present at barrier sites such as the skin, a primary entry site for S. aureus. Further phenotypical and functional characterization of these cells will ultimately aid in the development of novel vaccine strategies against this elusive pathogen.
Frequency of Gluten-Reactive T Cells in Active Celiac Lesions Estimated by Direct Cell Cloning
Authors: Qiao Shuo-Wang , Dahal-Koirala Shiva , Eggesbø Linn M. , Lundin Knut E. A. , Sollid Ludvig M.
Published: March 2021

Chronic inflammation of the small intestine in celiac disease is driven by activation of CD4+ T cells that recognize gluten peptides presented by disease-associated HLA-DQ molecules. We have performed direct cell cloning of duodenal biopsies from five untreated and one refractory celiac disease patients, and three non-celiac disease control subjects in order to assess, in an unbiased fashion, the frequency of gluten-reactive T cells in the disease-affected tissue as well as the antigen fine specificity of the responding T cells. From the biopsies of active disease lesions of five patients, 19 T-cell clones were found to be gluten-reactive out of total 1,379 clones tested. This gave an average of 1.4% (range 0.7% - 1.9%) of gluten-reactive T cells in lamina propria of active celiac lesions. Interestingly, also the patient with refractory celiac disease had gluten-reactive T cell clones in the lamina propria (5/273; 1.8%). In comparison, we found no gluten-reactive T cells in any of the total 984 T-cell clones screened from biopsies from three disease control donors. Around two thirds of the gluten-reactive clones were reactive to a panel of peptides representing known gluten T-cell epitopes, of which two thirds were reactive to the immunodominant DQ2.5-glia-α1/DQ2.5-glia-α2 and DQ2.5-glia-ω1/DQ2.5-glia-ω2 epitopes. This study shows that gluten-reactive T cells in the inflamed duodenal tissue are prevalent in the active disease lesion, and that many of these T cells are reactive to T-cell epitopes that are not yet characterized. Knowledge of the prevalence and epitope specificity of gluten-specific T cells is a prerequisite for therapeutic efforts that target disease-specific T cells in celiac disease.
Serum Neurofilament Light and GFAP Are Associated With Disease Severity in Inflammatory Disorders With Aquaporin-4 or Myelin Oligodendrocyte Glycoprotein Antibodies
Authors: Chang Xuechun , Huang Wenjuan , Wang Liang , ZhangBao Jingzi , Zhou Lei , Lu Chuanzhen , Wang Min , Yu Jian , Li Haiqing , Li Yuxin , Zhao Chongbo , Lu Jiahong , Quan Chao
Published: March 2021

Objective: To evaluate the potential of serum neurofilament light (sNfL) and serum glial fibrillary acidic protein (sGFAP) as disease biomarkers in neuromyelitis optica spectrum disorder (NMOSD) with aquaporin-4 antibody (AQP4-ab) or myelin oligodendrocyte glycoprotein-antibody-associated disease (MOGAD).

Methods: Patients with AQP4-ab-positive NMOSD (n = 51), MOGAD (n = 42), and relapsing-remitting multiple sclerosis (RRMS) (n = 31 for sNfL and n = 22 for sGFAP testing), as well as healthy controls (HCs) (n = 28), were enrolled prospectively. We assessed sNfL and sGFAP levels using ultrasensitive single-molecule array assays. Correlations of sNfL and sGFAP levels with clinical parameters were further examined in AQP4-ab-positive NMOSD and MOGAD patients.

Results: sNfL levels were significantly higher in patients with AQP4-ab-positive NMOSD (median 17.6 pg/mL), MOGAD (27.2 pg/mL), and RRMS (24.5 pg/mL) than in HCs (7.4 pg/mL, all p < 0.001). sGFAP levels were remarkably increased in patients with AQP4-ab-positive NMOSD (274.1 pg/mL) and MOGAD (136.7 pg/mL) than in HCs (61.4 pg/mL, both p < 0.001). Besides, sGFAP levels were also significantly higher in patients with AQP4-ab-positive NMOSD compared to those in RRMS patients (66.5 pg/mL, p < 0.001). The sGFAP/sNfL ratio exhibited good discrimination among the three disease groups. sNfL levels increased during relapse in patients with MOGAD (p = 0.049) and RRMS (p < 0.001), while sGFAP levels increased during relapse in all three of the disease groups (all p < 0.05). Both sNfL and sGFAP concentrations correlated positively with Expanded Disability Status Scale scores in AQP4-ab-positive NMOSD (β = 1.88, p = 0.018 and β = 2.04, p = 0.032) and MOGAD patients (β = 1.98, p = 0.013 and β = 1.52, p = 0.008).

Conclusion: sNfL and sGFAP levels are associated with disease severity in AQP4-ab-positive NMOSD and MOGAD patients, and the sGFAP/sNfL ratio may reflect distinct disease pathogenesis.
Small Molecule Analysis of Extracellular Vesicles Produced by Cryptococcus gattii: Identification of a Tripeptide Controlling Cryptococcal Infection in an Invertebrate Host Model
Authors: Reis Flavia C. G. , Costa Jonas H. , Honorato Leandro , Nimrichter Leonardo , Fill Taícia P. , Rodrigues Marcio L.
Published: March 2021

The small molecule (molecular mass <900 Daltons) composition of extracellular vesicles (EVs) produced by the pathogenic fungus Cryptococcus gattii is unknown, which limits the understanding of the functions of cryptococcal EVs. In this study, we analyzed the composition of small molecules in samples obtained from solid cultures of C. gattii by a combination of chromatographic and spectrometric approaches, and untargeted metabolomics. This analysis revealed previously unknown components of EVs, including small peptides with known biological functions in other models. The peptides found in C. gattii EVs had their chemical structure validated by chemical approaches and comparison with authentic standards, and their functions tested in a Galleria mellonella model of cryptococcal infection. One of the vesicular peptides (isoleucine-proline-isoleucine, Ile-Pro-Ile) improved the survival of G. mellonella lethally infected with C. gattii or C. neoformans. These results indicate that small molecules exported in EVs are biologically active in Cryptococcus. Our study is the first to characterize a fungal EV molecule inducing protection, pointing to an immunological potential of extracellular peptides produced by C. gattii.
Flexible Perovskite Solar Cells: Progress and Prospects
Authors: Liang Xiao , Ge Chuangye , Fang Qianru , Deng Wanyuan , Dey Sukumar , Lin Haoran , Zhang Yong , Zhang Xintao , Zhu Quanyao , Hu Hanlin
Published: March 2021

Flexible perovskite solar cells (FPSCs) have shown great potential in the field of wearable power supply and integration with architectures in the future due to their advantages of high flexibility, light weight, portability, and compatibility with irregular electronic products. As a promising photovoltaic technology compatible with roll-to-roll manufacturing process, FPSCs have made significant progress in the past several years through composition engineering, interface modification, optimization of fabrication process, and exploitation of new charge transport materials. As a result, the light-to-electricity power conversion efficiency of FPSCs has exceeded 20% recently. In this mini review, the latest developments of FPSCs are systematically summarized and discussed, including the flexible substrates and electrodes, as well as the fabrication of high-quality perovskite films. Finally, a prospect on the massive manufacturing of FPSCs as well as the challenge is also discussed.
Rubber Adhesion and Friction: Role of Surface Energy and Contamination Films
Authors: Tiwari A. , Tolpekina T. , Benthem Hans van , Gunnewiek M. K. , Persson B. N. J.
Published: March 2021

We study the influence of the surface energy and contamination films on rubber adhesion and sliding friction. We find that there is a transfer of molecules from the rubber to the substrate which reduces the work of adhesion and makes the rubber friction insensitive to the substrate surface energy. We show that there is no simple relation between adhesion and friction: adhesion is due to (vertical) detachment processes at the edge of the contact regions (opening crack propagation), while friction in many cases is determined mainly by (tangential) stick-slip instabilities of nanosized regions, within the whole sliding contact. Thus while the pull-off force in fluids may be strongly reduced (due to a reduction of the work of adhesion), the sliding friction may be only slightly affected as the area of real contact may be dry, and the frictional shear stress in the contact area nearly unaffected by the fluid.
Critical Ignition Conditions of Wood by Cylindrical Firebrands
Authors: Salehizadeh Hamed , Hakes Raquel S. P. , Gollner Michael J.
Published: March 2021

This study investigated the thermal conditions preceding ignition of three dense woody fuels often found on structures by firebrands, a major cause of home ignition during wildland-urban interface (WUI) fires. Piles of smoldering cylindrical firebrands, fabricated from wooden dowels, were deposited either on a flat inert surface instrumented with temperature and heat flux sensors or on a target fuel (marine-grade plywood, oriented-strand board, or cedar shingles) to investigate critical conditions at ignition. The former provided thermal data to characterize the time before and at ignition, while the latter provided smoldering and flaming ignition times. Tests were conducted in a small-scale wind tunnel. Larger firebrand piles produced higher temperatures at the center of the pile, thought to be due to re-radiation within the pile. Ignition was found to be dependent on target fuel density; flaming ignition was additionally found to be dependent on wind speed. Higher wind speeds increased the rate of oxidation and led to higher temperatures and heat fluxes measured on the test surface. The heat flux at ignition was determined by combining results of inert and ignition tests, showing that ignition occurred while transient heating from the firebrand pile was increasing. Ultimately, critical ignition conditions from firebrand pile exposure are needed to design appropriate fire safety standards and WUI fire modeling.
The Unique Impact of COVID-19 on Human Gut Microbiome Research
Authors: Burchill Ella , Lymberopoulos Eva , Menozzi Elisa , Budhdeo Sanjay , McIlroy James R. , Macnaughtan Jane , Sharma Nikhil
Published: March 2021

The coronavirus (COVID-19) pandemic has disrupted clinical trials globally, with unique implications for research into the human gut microbiome. In this mini-review, we explore the direct and indirect influences of the pandemic on the gut microbiome and how these can affect research and clinical trials. We explore the direct bidirectional relationships between the COVID-19 virus and the gut and lung microbiomes. We then consider the significant indirect effects of the pandemic, such as repeated lockdowns, increased hand hygiene, and changes to mood and diet, that could all lead to longstanding changes to the gut microbiome at an individual and a population level. Together, these changes may affect long term microbiome research, both in observational as well as in population studies, requiring urgent attention. Finally, we explore the unique implications for clinical trials using faecal microbiota transplants (FMT), which are increasingly investigated as potential treatments for a range of diseases. The pandemic introduces new barriers to participation in trials, while the direct and indirect effects laid out above can present a confounding factor. This affects recruitment and sample size, as well as study design and statistical analyses. Therefore, the potential impact of the pandemic on gut microbiome research is significant and needs to be specifically addressed by the research community and funders.
Modulation of Gene Expression in Actinobacteria by Translational Modification of Transcriptional Factors and Secondary Metabolite Biosynthetic Enzymes
Authors: Martín Juan F. , Liras Paloma , Sánchez Sergio
Published: March 2021

Different types of post-translational modifications are present in bacteria that play essential roles in bacterial metabolism modulation. Nevertheless, limited information is available on these types of modifications in actinobacteria, particularly on their effects on secondary metabolite biosynthesis. Recently, phosphorylation, acetylation, or phosphopantetheneylation of transcriptional factors and key enzymes involved in secondary metabolite biosynthesis have been reported. There are two types of phosphorylations involved in the control of transcriptional factors: (1) phosphorylation of sensor kinases and transfer of the phosphate group to the receiver domain of response regulators, which alters the expression of regulator target genes. (2) Phosphorylation systems involving promiscuous serine/threonine/tyrosine kinases that modify proteins at several amino acid residues, e.g., the phosphorylation of the global nitrogen regulator GlnR. Another post-translational modification is the acetylation at the epsilon amino group of lysine residues. The protein acetylation/deacetylation controls the activity of many short and long-chain acyl-CoA synthetases, transcriptional factors, key proteins of bacterial metabolism, and enzymes for the biosynthesis of non-ribosomal peptides, desferrioxamine, streptomycin, or phosphinic acid-derived antibiotics. Acetyltransferases catalyze acetylation reactions showing different specificity for the acyl-CoA donor. Although it functions as acetyltransferase, there are examples of malonylation, crotonylation, succinylation, or in a few cases acylation activities using bulky acyl-CoA derivatives. Substrates activation by nucleoside triphosphates is one of the central reactions inhibited by lysine acetyltransferases. Phosphorylation/dephosphorylation or acylation/deacylation reactions on global regulators like PhoP, GlnR, AfsR, and the carbon catabolite regulator glucokinase strongly affects the expression of genes controlled by these regulators. Finally, a different type of post-translational protein modification is the phosphopantetheinylation, catalized by phosphopantetheinyl transferases (PPTases). This reaction is essential to modify those enzymes requiring phosphopantetheine groups like non-ribosomal peptide synthetases, polyketide synthases, and fatty acid synthases. Up to five PPTases are present in S. tsukubaensis and S. avermitilis. Different PPTases modify substrate proteins in the PCP or ACP domains of tacrolimus biosynthetic enzymes. Directed mutations of genes encoding enzymes involved in the post-translational modification is a promising tool to enhance the production of bioactive metabolites.
Improved Detection of HIV Gag p24 Protein Using a Combined Immunoprecipitation and Digital ELISA Method
Authors: Wu Guoxin , Cheney Carol , Huang Qian , Hazuda Daria J. , Howell Bonnie J. , Zuck Paul
Published: March 2021

Greater than 90% of HIV-1 proviruses are thought to be defective and incapable of viral replication. While replication competent proviruses are of primary concern with respect to disease progression or transmission, studies have shown that even defective proviruses are not silent and can produce viral proteins, which may contribute to inflammation and immune responses. Viral protein expression also has implications for immune-based HIV-1 clearance strategies, which rely on antigen recognition. Thus, sensitive assays aimed at quantifying both replication-competent proviruses and defective, yet translationally competent proviruses are needed to understand the contribution of viral protein to HIV-1 pathogenesis and determine the effectiveness of HIV-1 cure interventions. Previously, we reported a modified HIV-1 gag p24 digital enzyme-linked immunosorbent assay with single molecule array (Simoa) detection of cell-associated viral protein. Here we report a novel p24 protein enrichment method coupled with the digital immunoassay to further extend the sensitivity and specificity of viral protein detection. Immunocapture of HIV gag p24 followed by elution in a Simoa-compatible format resulted in higher protein recovery and lower background from various biological matrices and sample volumes. Quantification of as little as 1 fg of p24 protein from cell lysates from cells isolated from peripheral blood or tissues from ART-suppressed HIV participants, as well as simian–human immunodeficiency virus–infected non-human primates (NHPs), with high recovery and reproducibility is demonstrated here. The application of these enhanced methods to patient-derived samples has potential to further the study of the persistent HIV state and examine in vitro response to therapies, as well as ex vivo study of translationally competent cells from a variety of donors.
Characterization and Diversity Analysis of the Extracellular Proteases of Thermophilic Anoxybacillus caldiproteolyticus 1A02591 From Deep-Sea Hydrothermal Vent Sediment
Authors: Cheng Jun-Hui , Wang Yan , Zhang Xiao-Yu , Sun Mei-Ling , Zhang Xia , Song Xiao-Yan , Zhang Yu-Zhong , Zhang Yi , Chen Xiu-Lan
Published: March 2021

Protease-producing bacteria play key roles in the degradation of marine organic nitrogen. Although some deep-sea bacteria are found to produce proteases, there has been no report on protease-secreting Anoxybacillus from marine hydrothermal vent regions. Here, we analyzed the diversity and functions of the proteases, especially the extracellular proteases, of Anoxybacillus caldiproteolyticus 1A02591, a protease-secreting strain isolated from a deep-sea hydrothermal vent sediment of the East Pacific Ocean. Strain 1A02591 is a thermophilic bacterium with a strong protease-secreting ability, which displayed the maximum growth rate (0.139 h–1) and extracellular protease production (307.99 U/mL) at 55°C. Strain 1A02591 contains 75 putative proteases, including 65 intracellular proteases and 10 extracellular proteases according to signal peptide prediction. When strain 1A02591 was cultured with casein, 12 proteases were identified in the secretome, in which metalloproteases (6/12) and serine proteases (4/12) accounted for the majority, and a thermolysin-like protease of the M4 family was the most abundant, suggesting that strain 1A02591 mainly secreted a thermophilic metalloprotease. Correspondingly, the secreted proteases of strain 1A02591 showed the highest activity at the temperature as high as 70°C, and was inhibited 70% by metalloprotease inhibitor o-phenanthroline and 50% by serine protease inhibitor phenylmethylsulfonyl fluoride. The secreted proteases could degrade different proteins, suggesting the role of strain 1A02591 in organic nitrogen degradation in deep-sea hydrothermal ecosystem. These results provide the first insight into the proteases of an Anoxybacillus strain from deep-sea hydrothermal ecosystem, which is helpful in understanding the function of Anoxybacillus in the marine biogeochemical cycle.
Ultraviolet Radiation Stimulates Activity of CO2 Concentrating Mechanisms in a Bloom-Forming Diatom Under Reduced CO2 Availability
Authors: Gao Guang , Liu Wei , Zhao Xin , Gao Kunshan
Published: March 2021

The diatom Skeletonema costatum is cosmopolitan and forms algal blooms in coastal waters, being exposed to varying levels of solar UV radiation (UVR) and reduced levels of carbon dioxide (CO2). While reduced CO2 availability is known to enhance CO2 concentrating mechanisms (CCMs) in this diatom and others, little is known on the effects of UV on microalgal CCMs, especially when CO2 levels fluctuate in coastal waters. Here, we show that S. costatum upregulated its CCMs in response to UVR (295–395 nm), especially to UVA (320–395 nm) in the presence and absence of photosynthetically active radiation (PAR). The intensity rise of UVA and/or UVR alone resulted in an increase of the activity of extracellular carbonic anhydrase (CAe); and the addition of UVA enhanced the activity of CCMs-related CAe by 23–27% when PAR levels were low. Such UV-stimulated CCMs activity was only significant at the reduced CO2 level (3.4 μmol L−1). In addition, UVA alone drove active HCO3− uptake although it was not as obvious as CAe activity, another evidence for its role in enhancing CCMs activity. In parallel, the addition of UVA enhanced photosynthetic carbon fixation only at the lower CO2 level compared to PAR alone. In the absence of PAR, carbon fixation increased linearly with increased intensities of UVA or UVR regardless of the CO2 levels. These findings imply that during S. costatum blooming period when CO2 and PAR availability becomes lower, solar UVR (mainly UVA) helps to upregulate its CCMs and thus carbon fixation, enabling its success of frequent algal blooms.
An Overview of Spike Surface Glycoprotein in Severe Acute Respiratory Syndrome–Coronavirus
Authors: Kathiravan Muthu Kumaradoss , Radhakrishnan Srimathi , Namasivayam Vigneshwaran , Palaniappan Senthilkumar
Published: March 2021

The novel coronavirus originated in December 2019 in Hubei, China. This contagious disease named as COVID-19 resulted in a massive expansion within 6 months by spreading to more than 213 countries. Despite the availability of antiviral drugs for the treatment of various viral infections, it was concluded by the WHO that there is no medicine to treat novel CoV, SARS-CoV-2. It has been confirmed that SARS-COV-2 is the most highly virulent human coronavirus and occupies the third position following SARS and MERS with the highest mortality rate. The genetic assembly of SARS-CoV-2 is segmented into structural and non-structural proteins, of which two-thirds of the viral genome encodes non-structural proteins and the remaining genome encodes structural proteins. The most predominant structural proteins that make up SARS-CoV-2 include spike surface glycoproteins (S), membrane proteins (M), envelope proteins (E), and nucleocapsid proteins (N). This review will focus on one of the four major structural proteins in the CoV assembly, the spike, which is involved in host cell recognition and the fusion process. The monomer disintegrates into S1 and S2 subunits with the S1 domain necessitating binding of the virus to its host cell receptor and the S2 domain mediating the viral fusion. On viral infection by the host, the S protein is further cleaved by the protease enzyme to two major subdomains S1/S2. Spike is proven to be an interesting target for developing vaccines and in particular, the RBD-single chain dimer has shown initial success. The availability of small molecules and peptidic inhibitors for host cell receptors is briefly discussed. The development of new molecules and therapeutic druggable targets for SARS-CoV-2 is of global importance. Attacking the virus employing multiple targets and strategies is the best way to inhibit the virus. This article will appeal to researchers in understanding the structural and biological aspects of the S protein in the field of drug design and discovery.
Impact of the Whole Genome Duplication Event on PYK Activity and Effects of a PYK1 Mutation on Metabolism in S. cerevisiae
Authors: Chen Hong , Blum Jamie E. , Thalacker-Mercer Anna , Gu Zhenglong
Published: March 2021

Background: Evolution of aerobic fermentation (crabtree effect) in yeast is associated with the whole genome duplication (WGD) event, suggesting that duplication of certain genes may have altered yeast metabolism. The pyruvate kinase (PYK) gene is associated with alterations in cell metabolism, and duplicated during the WGD, generating PYK1 and PYK2. Thus, the impact of WGD on PYK activity and role of PYK in yeast metabolism were explored.

Methods: PYK activity in the presence or absence of fructose-1,6-bisphosphate (FBP) was compared between pre- and post-WGD yeast. Glucose consumption, ethanol production, and oxygen consumption were measured in wildtype yeast and yeast with a T403E point mutation, which alters FBP binding affinity.

Results: FBP stimulated increased PYK activity in pre-WGD yeast and in the PYK1 isoforms of post-WGD yeast, but not in the PYK2 isoforms of post-WGD yeast. Compared to wildtype, T403E mutant yeast displayed reduced glucose consumption, reduced ethanol production, and increased mitochondrial metabolism.

Conclusion: The WGD event impacted the sensitivity of PYK activity to FBP. Mutations in the FBP binding domain of PYK induce metabolic shifts that favor respiration and suppress fermentation.
The Delayed Neuropathological Consequences of Traumatic Brain Injury in a Community-Based Sample
Authors: Postupna Nadia , Rose Shannon E. , Gibbons Laura E. , Coleman Natalie M. , Hellstern Leanne L. , Ritchie Kayla , Wilson Angela M. , Cudaback Eiron , Li Xianwu , Melief Erica J. , Beller Allison E. , Miller Jeremy A. , Nolan Amber L. , Marshall Desiree A. , Walker Rod , Montine Thomas J. , Larson Eric B. , Crane Paul K. , Ellenbogen Richard G. , Lein Edward S. , Dams-O'Connor Kristen , Keene C. Dirk
Published: March 2021

The late neuropathological effects of traumatic brain injury have yet to be fully elucidated, particularly with respect to community-based cohorts. To contribute to this critical gap in knowledge, we designed a multimodal neuropathological study, integrating traditional and quantitative approaches to detect pathologic changes in 532 consecutive brain autopsies from participants in the Adult Changes in Thought (ACT) study. Diagnostic evaluation including assessment for chronic traumatic encephalopathy (CTE) and quantitative immunoassay-based methods were deployed to examine levels of pathological (hyperphosphorylated) tau (pTau) and amyloid (A) β in brains from ACT participants with (n = 107) and without (n = 425) history of remote TBI with loss of consciousness (w/LOC). Further neuropathological assessments included immunohistochemistry for α-synuclein and phospho-TDP-43 pathology and astro- (GFAP) and micro- (Iba1) gliosis, mass spectrometry analysis of free radical injury, and gene expression evaluation (RNA sequencing) in a smaller sub-cohort of matched samples (49 cases with TBI and 49 non-exposed matched controls). Out of 532 cases, only 3 (0.6%–none with TBI w/LOC history) showed evidence of the neuropathologic signature of chronic traumatic encephalopathy (CTE). Across the entire cohort, the levels of pTau and Aβ showed expected differences for brain region (higher levels in temporal cortex), neuropathological diagnosis (higher in participants with Alzheimer's disease), and APOE genotype (higher in participants with one or more APOE ε4 allele). However, no differences in PHF-tau or Aβ1−42 were identified by Histelide with respect to the history of TBI w/LOC. In a subset of TBI cases with more carefully matched control samples and more extensive analysis, those with TBI w/LOC history had higher levels of hippocampal pTau but no significant differences in Aβ, α-synuclein, pTDP-43, GFAP, Iba1, or free radical injury. RNA-sequencing also did not reveal significant gene expression associated with any measure of TBI exposure. Combined, these findings suggest long term neuropathological changes associated with TBI w/LOC may be subtle, involve non-traditional pathways of neurotoxicity and neurodegeneration, and/or differ from those in autopsy cohorts specifically selected for neurotrauma exposure.
Sleep-Related Problems in Night Shift Nurses: Towards an Individualized Interventional Practice
Authors: Alfonsi Valentina , Scarpelli Serena , Gorgoni Maurizio , Pazzaglia Mariella , Giannini Anna Maria , De Gennaro Luigi
Published: March 2021

Rotating shifts (mostly 8- or 12-h) are common among nurses to ensure continuity of care. This scheduling system encompasses several adverse health and performance consequences. One of the most injurious effects of night-time shift work is the deterioration of sleep patterns due to both circadian rhythm disruption and increased sleep homeostatic pressure. Sleep problems lead to secondary effects on other aspects of wellbeing and cognitive functioning, increasing the risk of errors and workplace accidents. A wide range of interventions has been proposed to improve the sleep quality of nurses and promote an increase in attention levels. In recent years, particular attention has been paid to individual and environmental factors mediating the subjective ability to cope with sleep deprivation during the night shift. Given the predictive role of these factors on the negative impact of a night shift, an individualized intervention could represent an effective countermeasure by ensuring suitable management of shift schedules. Therefore, the aims of this mini-review are to: (a) provide an updated overview of the literature on sleep problems in night shift nurses and their adverse consequences; and (b) critically analyze the psychosocial factors that mediate the negative impact of shift work with the ultimate goal of defining an effective countermeasure based on an individualized approach.
Iron Metabolism Disorders for Cognitive Dysfunction After Mild Traumatic Brain Injury
Authors: Huang Suna , Li Su , Feng Hua , Chen Yujie
Published: March 2021

Traumatic brain injury (TBI) is one of the most harmful forms of acute brain injury and predicted to be one of the three major neurological diseases that cause neurological disabilities by 2030. A series of secondary injury cascades often cause cognitive dysfunction of TBI patients leading to poor prognosis. However, there are still no effective intervention measures, which drive us to explore new therapeutic targets. In this process, the most part of mild traumatic brain injury (mTBI) is ignored because its initial symptoms seemed not serious. Unfortunately, the ignored mTBI accounts for 80% of the total TBI, and a large part of the patients have long-term cognitive dysfunction. Iron deposition has been observed in mTBI patients and accompanies the whole pathological process. Iron accumulation may affect long-term cognitive dysfunction from three pathways: local injury, iron deposition induces tau phosphorylation, the formation of neurofibrillary tangles; neural cells death; and neural network damage, iron deposition leads to axonal injury by utilizing the iron sensibility of oligodendrocytes. Thus, iron overload and metabolism dysfunction was thought to play a pivotal role in mTBI pathophysiology. Cerebrospinal fluid-contacting neurons (CSF-cNs) located in the ependyma have bidirectional communication function between cerebral–spinal fluid and brain parenchyma, and may participate in the pathway of iron-induced cognitive dysfunction through projected nerve fibers and transmitted factor, such as 5-hydroxytryptamine, etc. The present review provides an overview of the metabolism and function of iron in mTBI, and to seek a potential new treatment target for mTBI with a novel perspective through combined iron and CSF-cNs.
The Extracellular Domains of GluN Subunits Play an Essential Role in Processing NMDA Receptors in the ER
Authors: Horak Martin , Barackova Petra , Langore Emily , Netolicky Jakub , Rivas-Ramirez Paula , Rehakova Kristyna
Published: March 2021

N-methyl-D-aspartate receptors (NMDARs) belong to a family of ionotropic glutamate receptors that play essential roles in excitatory neurotransmission and synaptic plasticity in the mammalian central nervous system (CNS). Functional NMDARs consist of heterotetramers comprised of GluN1, GluN2A-D, and/or GluN3A-B subunits, each of which contains four membrane domains (M1 through M4), an intracellular C-terminal domain, a large extracellular N-terminal domain composed of the amino-terminal domain and the S1 segment of the ligand-binding domain (LBD), and an extracellular loop between M3 and M4, which contains the S2 segment of the LBD. Both the number and type of NMDARs expressed at the cell surface are regulated at several levels, including their translation and posttranslational maturation in the endoplasmic reticulum (ER), intracellular trafficking via the Golgi apparatus, lateral diffusion in the plasma membrane, and internalization and degradation. This review focuses on the roles played by the extracellular regions of GluN subunits in ER processing. Specifically, we discuss the presence of ER retention signals, the integrity of the LBD, and critical N-glycosylated sites and disulfide bridges within the NMDAR subunits, each of these steps must pass quality control in the ER in order to ensure that only correctly assembled NMDARs are released from the ER for subsequent processing and trafficking to the surface. Finally, we discuss the effect of pathogenic missense mutations within the extracellular domains of GluN subunits with respect to ER processing of NMDARs.
Treatment Response, Survival, and Safety of Transarterial Chemoembolization With CalliSpheres® Microspheres Versus Conventional Transarterial Chemoembolization in Hepatocellular Carcinoma: A Meta-Analysis
Authors: Liang Bin , Makamure Joyman , Shu Shenglei , Zhang Lijie , Sun Tao , Zheng Chuansheng
Published: March 2021

Background

Drug-eluting embolic transarterial chemoembolization (DEE-TACE) is an advance in TACE technique. However, at present there is insufficient evidence to support that DEE-TACE is superior to conventional TACE (cTACE) for hepatocellular carcinoma (HCC). The aim of this meta-analysis is to evaluate the efficacy and safety of TACE with CalliSpheres® microspheres (CSM-TACE) compared with cTACE in patients with HCC.

Data Sources

PubMed, Embase, Web of Science, CNKI and Wanfang Databases were searched to identify relevant articles published before March 26, 2020. The data regarding treatment response, survival profile, adverse events and liver function indexes were retrieved.

Results

A total of 16 studies with 1454 HCC patients (722 treated with CSM-TACE and 732 with cTACE) were included. Patients receiving CSM-TACE had higher 1-month complete response (CR), objective response rate (ORR), disease control rate (DCR) (odds ratio (OR): 2.00, 95% confidence interval (95% CI): 1.29–3.09; OR: 2.87, 95% CI: 2.15–3.83; OR: 2.01, 95% CI: 1.37–2.95, respectively), 3-month CR, ORR, DCR (OR: 4.04, 95%CI: 2.46–6.64; OR: 3.39, 95%CI: 2.45–4.70; OR: 1.71, 95%CI: 1.14–2.55 respectively), and 6-month CR, ORR, DCR (OR: 4.02, 95%CI: 2.26–7.16; OR: 3.00, 95%CI: 2.05–4.38; OR: 2.66, 95%CI: 1.70–4.16 respectively) than those treated with cTACE. Furthermore, CSM-TACE exhibited a trend toward improved progression free survival (hazard ratio (HR): 0.86, 95%CI: 0.67–1.11) and overall survival (HR: 0.79, 95%CI: 0.59–1.07) over cTACE although these differences did not reach statistical significance. In terms of safety, the two TACE treatments showed similar post-treatment pain (OR: 0.84, 95%CI: 0.55–1.28), fever (OR: 0.99, 95%CI: 0.60–1.63), nausea/vomiting (OR: 0.84, 95% CI: 0.60–1.17), as well as 1-month follow-up alanine aminotransferase (Mean difference (MD): −3.66, 95%CI: −10.38–3.07), aspartate aminotransferase (MD: −2.30, 95%CI: −8.91–4.31) and total bilirubin (MD: −0.15, 95%CI: −2.26–1.96).

Conclusion

CSM-TACE displays superior treatment response, non-inferior survival profile and safety over cTACE in HCC patients.