bluuebunny/crossref_metadata_2025 huggingface dataset:
Complement Factor H Family Proteins Modulate Monocyte and Neutrophil Granulocyte Functions
Authors: Kárpáti Éva , Kremlitzka Mariann , Sándor Noémi , Hajnal Dávid , Schneider Andrea E. , Józsi Mihály
Published: October 2021

Besides being a key effector arm of innate immunity, a plethora of non-canonical functions of complement has recently been emerging. Factor H (FH), the main regulator of the alternative pathway of complement activation, has been reported to bind to various immune cells and regulate their functions, beyond its role in modulating complement activation. In this study we investigated the effect of FH, its alternative splice product FH-like protein 1 (FHL-1), the FH-related (FHR) proteins FHR-1 and FHR-5, and the recently developed artificial complement inhibitor mini-FH, on two key innate immune cells, monocytes and neutrophilic granulocytes. We found that, similar to FH, the other factor H family proteins FHL-1, FHR-1 and FHR-5, as well as the recombinant mini-FH, are able to bind to both monocytes and neutrophils. As a functional outcome, immobilized FH and FHR-1 inhibited PMA-induced NET formation, but increased the adherence and IL-8 production of neutrophils. FHL-1 increased only the adherence of the cells, while FHR-5 was ineffective in altering these functions. The adherence of monocytes was increased on FH, recombinant mini-FH and FHL-1 covered surfaces and, except for FHL-1, the same molecules also enhanced secretion of the inflammatory cytokines IL-1β and TNFα. When monocytes were stimulated with LPS in the presence of immobilized FH family proteins, FH, FHL-1 and mini-FH enhanced whereas FHR-1 and FHR-5 decreased the secretion of TNFα; FHL-1 and mini-FH also enhanced IL-10 release compared to the effect of LPS alone. Our results reveal heterogeneous effects of FH and FH family members on monocytes and neutrophils, altering key features involved in pathogen killing, and also demonstrate that FH-based complement inhibitors, such as mini-FH, may have effects beyond their function of inhibiting complement activation. Thus, our data provide new insight into the non-canonical functions of FH, FHL-1, FHR-1 and FHR-5 that might be exploited during protection against infections and in vaccine development.
Commonalities Between ARDS, Pulmonary Fibrosis and COVID-19: The Potential of Autotaxin as a Therapeutic Target
Authors: Ntatsoulis Konstantinos , Karampitsakos Theodoros , Tsitoura Eliza , Stylianaki Elli-Anna , Matralis Alexios N. , Tzouvelekis Argyrios , Antoniou Katerina , Aidinis Vassilis
Published: October 2021

Severe COVID-19 is characterized by acute respiratory distress syndrome (ARDS)-like hyperinflammation and endothelial dysfunction, that can lead to respiratory and multi organ failure and death. Interstitial lung diseases (ILD) and pulmonary fibrosis confer an increased risk for severe disease, while a subset of COVID-19-related ARDS surviving patients will develop a fibroproliferative response that can persist post hospitalization. Autotaxin (ATX) is a secreted lysophospholipase D, largely responsible for the extracellular production of lysophosphatidic acid (LPA), a pleiotropic signaling lysophospholipid with multiple effects in pulmonary and immune cells. In this review, we discuss the similarities of COVID-19, ARDS and ILDs, and suggest ATX as a possible pathologic link and a potential common therapeutic target.
Applications of Magnetite Nanoparticles in Cancer Immunotherapies: Present Hallmarks and Future Perspectives
Authors: Song Qingle , Javid Amaneh , Zhang Guofang , Li Yang
Published: October 2021

Current immuno-oncotherapeutic protocols that inhibit tumor immune evasion have demonstrated great clinical success. However, the therapeutic response is limited only to a percentage of patients, and the immune-related adverse events can compromise the therapeutic benefits. Therefore, improving cancer immunotherapeutic approaches that pursue high tumor suppression efficiency and low side effects turn out to be a clinical priority. Novel magnetite nanoparticles (MNPs) exhibit great potential for therapeutic and imaging applications by utilizing their properties of superparamagnetism, good biocompatibility, as well as the easy synthesis and modulation/functionalization. In particular, the MNPs can exert magnetic hyperthermia to induce immunogenic cell death of tumor cells for effective antigen release and presentation, and meanwhile polarize tumor-associated macrophages (TAMs) to M1 phenotype for improved tumor killing capability, thus enhancing the anti-tumor immune effects. Furthermore, immune checkpoint antibodies, immune-stimulating agents, or tumor-targeting agents can be decorated on MNPs, thereby improving their selectivity for the tumor or immune cells by the unique magnetic navigation capability of MNPs to promote the tumor killing immune therapeutics with fewer side effects. This mini-review summarizes the recent progress in MNP-based immuno-oncotherapies, including activation of macrophage, promotion of cytotoxic T lymphocyte (CTL) infiltration within tumors and modulation of immune checkpoint blockade, thus further supporting the applications of MNPs in clinical therapeutic protocols.
Adipsin of the Alternative Complement Pathway Is a Potential Predictor for Preeclampsia in Early Pregnancy
Authors: Liu Min , Luo Xiaolei , Xu Qin , Yu Hongbiao , Gao Linbo , Zhou Rong , Wang Tao
Published: October 2021

Objective

The concentrations of complement proteins (adipsin, C3a, and C5a) and soluble endoglin (sENG) in the plasma were measured in this study, and their value as early-pregnancy predictors and potential diagnostic marker of preeclampsia was assessed, respectively.

Experimental Design

Plasma samples were obtained from healthy and preeclampsia pregnant women before delivery for a cross-sectional study. Plasma samples were collected from healthy and preeclampsia pregnant women throughout pregnancy and postpartum for a follow-up study. Enzyme-linked immunosorbent assays were used to detect plasma levels of several complement proteins (adipsin, C3a, and C5a) and sENG.

Results

The plasma levels of adipsin, C5a, and sENG were significantly increased before delivery in pregnant women with preeclampsia. During pregnancy, the plasma adipsin, C5a, and sENG levels were increased from the third trimester in healthy pregnant women; plasma adipsin levels remained stable after delivery, while C3a levels increased in the second trimester and remained stable afterward. Furthermore, levels of adipsin, C5a, and sENG were higher in preeclampsia patients at different stages of pregnancy; the C3a level presents a similar change and no difference was found in the third trimester. In the first trimester, receiver-operating curve (ROC) curve analysis showed that adipsin (AUC, 0.83 ± 0.06, P=0.001) and sENG (AUC, 0.74 ± 0.09, P=0.021) presented high value as predictors of early pregnancy.

Conclusions

Adipsin is likely a novel plasma biomarker to monitor the increased risk of preeclampsia in early pregnancy. Moreover, the increased plasma levels of adipsin, C5a, and sENG before delivery may be associated with preeclampsia.
Induction of High Levels of Specific Humoral and Cellular Responses to SARS-CoV-2 After the Administration of Covid-19 mRNA Vaccines Requires Several Days
Authors: Gil-Manso Sergio , Carbonell Diego , López-Fernández Luis , Miguens Iria , Alonso Roberto , Buño Ismael , Muñoz Patricia , Ochando Jordi , Pion Marjorie , Correa-Rocha Rafael
Published: October 2021

Objectives

In the context of the Covid-19 pandemic, the fast development of vaccines with efficacy of around 95% preventing Covid-19 illness provides a unique opportunity to reduce the mortality associated with the pandemic. However, in the absence of efficacious prophylactic medications and few treatments for this infection, the induction of a fast and robust protective immunity is required for effective disease control, not only to prevent the disease but also the infection and shedding/transmission. The objective of our study was to analyze the level of specific humoral and cellular T-cell responses against the spike protein of SARS-CoV-2 induced by two mRNA-based vaccines (BNT162b2 and mRNA-1273), but also how long it takes after vaccination to induce these protective humoral and cellular immune responses.

Methods

We studied in 40 healthy (not previously infected) volunteers vaccinated with BNT162b2 or mRNA-1273 vaccines the presence of spike-specific IgG antibodies and SARS-CoV-2-specific T cells at 3, 7 and 14 days after receiving the second dose of the vaccine. The specific T-cell response was analyzed stimulating fresh whole blood from vaccinated volunteers with SARS-CoV-2 peptides and measuring the release of cytokines secreted by T cells in response to SARS-CoV-2 stimulation.

Results

Our results indicate that the immunization capacity of both vaccines is comparable. However, although both BNT162b2 and mRNA-1273 vaccines can induce early B-cell and T-cell responses, these vaccine-mediated immune responses do not reach their maximum values until 14 days after completing the vaccination schedule.

Conclusion

This refractory period in the induction of specific immunity observed after completing the vaccination could constitute a window of higher infection risk, which could explain some emerging cases of SARS-CoV-2 infection in vaccinated people.
Computational Inference, Validation, and Analysis of 5’UTR-Leader Sequences of Alleles of Immunoglobulin Heavy Chain Variable Genes
Authors: Huang Yixun , Thörnqvist Linnea , Ohlin Mats
Published: October 2021

Upstream and downstream sequences of immunoglobulin genes may affect the expression of such genes. However, these sequences are rarely studied or characterized in most studies of immunoglobulin repertoires. Inference from large, rearranged immunoglobulin transcriptome data sets offers an opportunity to define the upstream regions (5’-untranslated regions and leader sequences). We have now established a new data pre-processing procedure to eliminate artifacts caused by a 5’-RACE library generation process, reanalyzed a previously studied data set defining human immunoglobulin heavy chain genes, and identified novel upstream regions, as well as previously identified upstream regions that may have been identified in error. Upstream sequences were also identified for a set of previously uncharacterized germline gene alleles. Several novel upstream region variants were validated, for instance by their segregation to a single haplotype in heterozygotic subjects. SNPs representing several sequence variants were identified from population data. Finally, based on the outcomes of the analysis, we define a set of testable hypotheses with respect to the placement of particular alleles in complex IGHV locus haplotypes, and discuss the evolutionary relatedness of particular heavy chain variable genes based on sequences of their upstream regions.
COVID-19 Lung Pathogenesis in SARS-CoV-2 Autopsy Cases
Authors: Valdebenito Silvana , Bessis Simon , Annane Djillali , Lorin de la Grandmaison Geoffroy , Cramer–Bordé Elisabeth , Prideaux Brendan , Eugenin Eliseo A. , Bomsel Morgane
Published: October 2021

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a major public health issue. COVID-19 is considered an airway/multi-systemic disease, and demise has been associated with an uncontrolled immune response and a cytokine storm in response to the virus. However, the lung pathology, immune response, and tissue damage associated with COVID-19 demise are poorly described and understood due to safety concerns. Using post-mortem lung tissues from uninfected and COVID-19 deadly cases as well as an unbiased combined analysis of histology, multi-viral and host markers staining, correlative microscopy, confocal, and image analysis, we identified three distinct phenotypes of COVID-19-induced lung damage. First, a COVID-19-induced hemorrhage characterized by minimal immune infiltration and large thrombus; Second, a COVID-19-induced immune infiltration with excessive immune cell infiltration but no hemorrhagic events. The third phenotype correspond to the combination of the two previous ones. We observed the loss of alveolar wall integrity, detachment of lung tissue pieces, fibroblast proliferation, and extensive fibrosis in all three phenotypes. Although lung tissues studied were from lethal COVID-19, a strong immune response was observed in all cases analyzed with significant B cell and poor T cell infiltrations, suggesting an exhausted or compromised immune cellular response in these patients. Overall, our data show that SARS-CoV-2-induced lung damage is highly heterogeneous. These individual differences need to be considered to understand the acute and long-term COVID-19 consequences.
IFNγ-Producing γ/δ T Cells Accumulate in the Fetal Brain Following Intrauterine Inflammation
Authors: Lewis Emma L. , Tulina Natalia , Anton Lauren , Brown Amy G. , Porrett Paige M. , Elovitz Michal A.
Published: October 2021

Intrauterine inflammation impacts prenatal neurodevelopment and is linked to adverse neurobehavioral outcomes ranging from cerebral palsy to autism spectrum disorder. However, the mechanism by which a prenatal exposure to intrauterine inflammation contributes to life-long neurobehavioral consequences is unknown. To address this gap in knowledge, this study investigates how inflammation transverses across multiple anatomic compartments from the maternal reproductive tract to the fetal brain and what specific cell types in the fetal brain may cause long-term neuronal injury. Utilizing a well-established mouse model, we found that mid-gestation intrauterine inflammation resulted in a lasting neutrophil influx to the decidua in the absence of maternal systemic inflammation. Fetal immunologic changes were observed at 72-hours post-intrauterine inflammation, including elevated neutrophils and macrophages in the fetal liver, and increased granulocytes and activated microglia in the fetal brain. Through unbiased clustering, a population of Gr-1+ γ/δ T cells was identified as the earliest immune cell shift in the fetal brain of fetuses exposed to intrauterine inflammation and determined to be producing high levels of IFNγ when compared to γ/δ T cells in other compartments. In a case-control study of term infants, IFNγ was found to be elevated in the cord blood of term infants exposed to intrauterine inflammation compared to those without this exposure. Collectively, these data identify a novel cellular immune mechanism for fetal brain injury in the setting of intrauterine inflammation.
Modeling Plasmodium falciparum Diagnostic Test Sensitivity Using Machine Learning With Histidine-Rich Protein 2 Variants
Authors: Ford Colby T. , Alemayehu Gezahegn Solomon , Blackburn Kayla , Lopez Karen , Dieng Cheikh Cambel , Golassa Lemu , Lo Eugenia , Janies Daniel
Published: October 2021

Malaria, predominantly caused by Plasmodium falciparum, poses one of largest and most durable health threats in the world. Previously, simplistic regression-based models have been created to characterize malaria rapid diagnostic test performance, though these models often only include a couple genetic factors. Specifically, the Baker et al., 2005 model uses two types of particular repeats in histidine-rich protein 2 (PfHRP2) to describe a P. falciparum infection, though the efficacy of this model has waned over recent years due to genetic mutations in the parasite. In this work, we use a dataset of 100 P. falciparum PfHRP2 genetic sequences collected in Ethiopia and derived a larger set of motif repeat matches for use in generating a series of diagnostic machine learning models. Here we show that the usage of additional and different motif repeats in more sophisticated machine learning methods proves effective in characterizing PfHRP2 diversity. Furthermore, we use machine learning model explainability methods to highlight which of the repeat types are most important with regards to rapid diagnostic test sensitivity, thereby showcasing a novel methodology for identifying potential targets for future versions of rapid diagnostic tests.
MBD2 as a Potential Novel Biomarker for Identifying Severe Asthma With Different Endotypes
Authors: Chen Zhifeng , Yuan Yu , He Yi , Wasti Binaya , Duan Wentao , Jia Jingsi , Li Danhong , Xiao Bing , Zhang Dongshan , Ma Libing , Li Jianmin , Liu Yi , Zeng Qingping , Xiang Xudong , Zhang Xiufeng , Liu Shaokun
Published: October 2021

Background: Studies have shown that methyl-CpG binding domain protein 2 (MBD2) expression is significantly elevated in a neutrophil-dominant severe asthma mouse model. It also regulates Th17 cell differentiation. The objective of this study was to investigate the relationship between serum MBD2 levels in patients with severe asthma with different endotypes.

Methods: Eligible adults with confirmed asthma (n = 63) underwent a clinical assessment, asthma control test and pulmonary function test and were classified as having mild, moderate or severe asthma. Severe asthma endotypes were defined according to the percentage of Th2 and Th17 cells in the peripheral blood and by the type of inflammation. The percentage of Th2 and Th17 cells in the peripheral blood was determined by flow cytometry. Serum MBD2, eosinophilic cationic protein and myeloperoxidase were measured by enzyme-linked immunosorbent assay. Correlations of MBD2 expression with clinical parameters were evaluated using Spearman's rank correlation analysis.

Results: Serum MBD2 levels were upregulated in patients with severe asthma compared to healthy controls and patients with mild to moderate asthma. MBD2 was also significantly increased in patients with Th17 severe asthma compared to patients with type 2 severe asthma. Furthermore, MBD2 was positively correlated with MPO and Th17 cells but negatively correlated with ECP and Th2 cells in patients with severe asthma.

Conclusions: These findings suggest that serum MBD2 may be a potential new biomarker for identifying severe asthma, Th17 severe asthma and the type of airway inflammation. However, these findings are still preliminary and need to be further investigated.
Ferroptosis-Related Genes in Bronchoalveolar Lavage Fluid Serves as Prognostic Biomarkers for Idiopathic Pulmonary Fibrosis
Authors: Li Meng , Wang Ke , Zhang Yanpeng , Fan Meng , Li Anqi , Zhou Jiejun , Yang Tian , Shi Puyu , Li Dan , Zhang Guangjian , Chen Mingwei , Ren Hui
Published: October 2021

Background: Idiopathic pulmonary fibrosis (IPF) is a chronic progressive disease with unknown etiology and unfavorable prognosis. Ferroptosis is a form of regulated cell death with an iron-dependent way that is involved in the development of various diseases. Whereas the prognostic value of ferroptosis-related genes (FRGs) in IPF remains uncertain and needs to be further elucidated.

Methods: The FerrDb database and the previous studies were screened to explore the FRGs. The data of patients with IPF were obtained from the GSE70866 dataset. Wilcoxon's test and univariate Cox regression analysis were applied to identify the FRGs that are differentially expressed between normal and patients with IPF and associated with prognosis. Next, a multigene signature was constructed by the least absolute shrinkage and selection operator (LASSO)-penalized Cox model in the training cohort and evaluated by using calibration and receiver operating characteristic (ROC) curves. Then, 30% of the dataset samples were randomly selected for internal validation. Finally, the potential function and pathways that might be affected by the risk score-related differently expressed genes (DEGs) were further explored.

Results: A total of 183 FRGs were identified by the FerrDb database and the previous studies, and 19 of them were differentially expressed in bronchoalveolar lavage fluid (BALF) between IPF and healthy controls and associated with prognosis (p < 0.05). There were five FRGs (aconitase 1 [ACO1], neuroblastoma RAS viral (v-ras) oncogene homolog [NRAS], Ectonucleotide pyrophosphatase/phosphodiesterase 2 [ENPP2], Mucin 1 [MUC1], and ZFP36 ring finger protein [ZFP36]) identified as risk signatures and stratified patients with IPF into the two risk groups. The overall survival rate in patients with high risk was significantly lower than that in patients with low risk (p < 0.001). The calibration and ROC curve analysis confirmed the predictive capacity of this signature, and the results were further verified in the validation group. Risk score-related DEGs were found enriched in ECM-receptor interaction and focal adhesion pathways.

Conclusion: The five FRGs in BALF can be used for prognostic prediction in IPF, which may contribute to improving the management strategies of IPF.
HBV/HIV Coinfection: Impact on the Development and Clinical Treatment of Liver Diseases
Authors: Cheng Zhimeng , Lin Panpan , Cheng Nansheng
Published: October 2021

Hepatitis B virus (HBV) infection is a common contributor to chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. Approximately 10% of people with human immunodeficiency virus (HIV) also have chronic HBV co-infection, owing to shared transmission routes. HIV/HBV coinfection accelerates the progression of chronic HBV to cirrhosis, end-stage liver disease, or hepatocellular carcinoma compared to chronic HBV mono-infection. HBV/HIV coinfection alters the natural history of hepatitis B and renders the antiviral treatment more complex. In this report, we conducted a critical review on the epidemiology, natural history, and pathogenesis of liver diseases related to HBV/HIV coinfection. We summarized the novel therapeutic options for these coinfected patients.
Metagenomic Next-Generation Sequencing in the Diagnosis of HHV-1 Reactivation in a Critically Ill COVID-19 Patient: A Case Report
Authors: Shi Lei , Xia Han , Moore Matthew D. , Deng Chao , Li Na , Ren Hui , Chen Yunru , Liu Jinfeng , Du Fenjing , Zheng Gezhi , Li Jing , Han Qunying , Fan Wanhu , Ye Feng , Lin Shumei , Liu Zhengwen , Liu Hongjuan , Wang Yawen , Yang Jian , Liu Qingguang , Zhao Yingren , Chen Tianyan
Published: October 2021

Background: Secondary infections pose tremendous challenges in Coronavirus disease 2019 (COVID-19) treatment and are associated with higher mortality rates. Clinicians face of the challenge of diagnosing viral infections because of low sensitivity of available laboratory tests.

Case Presentation: A 66-year-old woman initially manifested fever and shortness of breath. She was diagnosed as critically ill with COVID-19 using quantitative reverse transcription PCR (RT-qPCR) and treated with antiviral therapy, ventilator and extracorporeal membrane oxygenation (ECMO). However, after the condition was relatively stabled for a few days, the patient deteriorated with fever, frequent cough, increased airway secretions, and increased exudative lesions in the lower right lung on chest X-rays, showing the possibility of a newly acquired infection, though sputum bacterial and fungal cultures and smears showed negative results. Using metagenomic next-generation sequencing (mNGS), we identified a reactivation of latent human herpes virus type 1 (HHV-1) in the respiratory tract, blood and gastrointestinal tract, resulting in a worsened clinical course in a critically ill COVID-19 patient on ECMO. Anti-HHV-1 therapy guided by these sequencing results effectively decreased HHV-1 levels, and improved the patient's clinical condition. After 49 days on ECMO and 67 days on the ventilator, the 66-year-old patient recovered and was discharged.

Conclusions: This case report demonstrates the potential value of mNGS for evidence-based treatment, and suggests that potential reactivation of latent viruses should be considered in critically ill COVID-19 patients.
Recent Advances of WEE1 Inhibitors and Statins in Cancers With p53 Mutations
Authors: Meng Xiangbing , Gao Jason Z. , Gomendoza Sean Michael T. , Li John W. , Yang Shujie
Published: October 2021

p53 is among the most frequently mutated tumor suppressor genes given its prevalence in >50% of all human cancers. One critical tumor suppression function of p53 is to regulate transcription of downstream genes and maintain genomic stability by inducing the G1/S checkpoint in response to DNA damage. Tumor cells lacking functional p53 are defective in the G1/S checkpoint and become highly dependent on the G2/M checkpoint to maintain genomic stability and are consequently vulnerable to Wee1 inhibitors, which override the cell cycle G2/M checkpoint and induce cell death through mitotic catastrophe. In addition to the lost tumor suppression function, many mutated p53 (Mutp53) proteins acquire gain-of-function (GOF) activities as oncogenes to promote cancer progression, which manifest through aberrant expression of p53. In cancer cells with GOF Mutp53, statins can induce CHIP-mediated degradation of Mutp53 within the mevalonate pathway by blocking the interaction between mutp53 and DNAJA1. Therefore, targeting critical downstream pathways of Mutp53 provides an alternative strategy for treating cancers expressing Mutp53. In this review, we summarize recent advances with Wee1 inhibitors, statins, and mevalonate pathway inhibitors in cancers with p53 mutations.
68Ga-DOTA-FAPI-04 PET/CT as a Promising Tool for Differentiating Ovarian Physiological Uptake: Preliminary Experience of Comparative Analysis With 18F-FDG
Authors: Wang Qixin , Yang Songsong , Tang Wenxin , Liu Lin , Chen Yue
Published: October 2021

Objectives: This study aimed to investigate the physiological distribution characteristics of 68Ga-DOTA-FAPI-04 in the ovary, and assess the feasibility of early diagnosis of primary ovarian disease with 68Ga-DOTA-FAPI-04 PET/CT.

Methods: We retrospectively analyzed the data of patients who received 18F-FDG and 68Ga-DOTA-FAPI-04 PET/CT scanning in the Nuclear Medicine Department of our hospital within 3 days from September 2020 to January 2021. We selected the data in which ovaries showed abnormal FDG activity. Patients with abnormal ovarian FDG uptake with focus confirmed by pathological biopsy or clinical follow-up as pathological changes were excluded. The uptake of tracers (18F-FDG and 68Ga-FAPI) was semi-quantitatively analyzed.

Results: This study included 14 patients (average age was 38.6). Physiological ovarian uptake was mostly unilateral, and there was no significant difference in SUVmax between the left and right sides (FDGt = 0.272, FAPIt = 0.592). The ovary SUVmax of FDG (4.89 ± 1.84) was statistically significantly higher than that of FAPI (1.53 ± 0.37). The Le/Li ratio on FDG is 3.38 ± 1.81, TBR is 5.81 ± 1.98, while the Le/Li ratio on FAPI is 3.57 ± 1.26, TBR is 0.94 ± 0.19.

Conclusion: Our research shows that ovarian functional or pathological changes can be manifested as FDG avid, while 68Ga-DOTA-FAPI-04 has no physiological accumulation in the ovary and is not affected by the menstrual cycle. Therefore, 68Ga-DOTA-FAPI-04 has unique advantages in the diagnosis of ovarian diseases, and can identify them early and accurately.
The Role of Hippo/YAP Signaling in Alveolar Repair and Pulmonary Fibrosis
Authors: Gokey Jason J. , Patel Saawan D. , Kropski Jonathan A.
Published: October 2021

Pulmonary fibrosis is characterized by loss of normal alveoli, accumulation of pathologic activated fibroblasts, and exuberant extracellular matrix deposition that over time can lead to progressive loss of respiratory function and death. This loss of respiratory function is associated with the loss of alveolar type 1 cells (AT1) that play a crucial role in gas exchange and the depletion of the alveolar type 2 cells (AT2) that act as progenitor cells to regenerate the AT1 and AT2 cell populations during repair. Understanding the mechanisms that regulate normal alveolar repair and those associated with pathologic repair is essential to identify potential therapeutic targets to treat or delay progression of fibrotic diseases. The Hippo/YAP developmental signaling pathway has been implicated as a regulator of normal alveolar development and repair. In idiopathic pulmonary fibrosis, aberrant activation of YAP/TAZ has been demonstrated in both the alveolar epithelium and activated fibroblasts associated with increased fibrotic remodeling, and there is emerging interest in this pathway as a target for antifibrotic therapies. In this review, we summarize current evidence as to the role of the Hippo-YAP/TAZ pathway in alveolar development, homeostasis, and repair, and highlight key questions that must be resolved to determine effective strategies to modulate YAP/TAZ signaling to prevent progressive pulmonary fibrosis and enhance adaptive alveolar repair.
Prevalence of ExoY Activity in Pseudomonas aeruginosa Reference Panel Strains and Impact on Cytotoxicity in Epithelial Cells
Authors: Silistre Hazel , Raoux-Barbot Dorothée , Mancinelli Federica , Sangouard Flora , Dupin Alice , Belyy Alexander , Deruelle Vincent , Renault Louis , Ladant Daniel , Touqui Lhousseine , Mechold Undine
Published: October 2021

ExoY is among the effectors that are injected by the type III secretion system (T3SS) of Pseudomonas aeruginosa into host cells. Inside eukaryotic cells, ExoY interacts with F-actin, which stimulates its potent nucleotidyl cyclase activity to produce cyclic nucleotide monophosphates (cNMPs). ExoY has broad substrate specificity with GTP as a preferential substrate in vitro. How ExoY contributes to the virulence of P. aeruginosa remains largely unknown. Here, we examined the prevalence of active ExoY among strains from the international P. aeruginosa reference panel, a collection of strains that includes environmental and clinical isolates, commonly used laboratory strains, and sequential clonal isolates from cystic fibrosis (CF) patients and thus represents the large diversity of this bacterial species. The ability to secrete active ExoY was determined by measuring the F-actin stimulated guanylate cyclase (GC) activity in bacterial culture supernatants. We found an overall ExoY activity prevalence of about 60% among the 40 examined strains with no significant difference between CF and non-CF isolates. In parallel, we used cellular infection models of human lung epithelial cells to compare the cytotoxic effects of isogenic reference strains expressing active ExoY or lacking the exoY gene. We found that P. aeruginosa strains lacking ExoY were in fact more cytotoxic to the epithelial cells than those secreting active ExoY. This suggests that under certain conditions, ExoY might partly alleviate the cytotoxic effects of other virulence factors of P. aeruginosa.
A Novel Polyphenol Oxidoreductase OhLac from Ochrobactrum sp. J10 for Lignin Degradation
Authors: Yang Chenxian , Ma Lingling , Wang Xin , Xing Yuqi , Lü Xin
Published: October 2021

Identifying the enzymes involved in lignin degradation by bacteria is important in studying lignin valorization to produce renewable chemical products. In this paper, the catalytic oxidation of lignin by a novel multi-copper polyphenol oxidoreductase (OhLac) from the lignin degrader Ochrobactrum sp. J10 was explored. Following its expression, reconstitution, and purification, a recombinant enzyme OhLac was obtained. The OhLac enzyme was characterized kinetically against a range of substrates, including ABTS, guaiacol, and 2,6-DMP. Moreover, the effects of pH, temperature, and Cu2+ on OhLac activity and stability were determined. Gas chromatography-mass spectrometer (GC-MS) results indicated that the β-aryl ether lignin model compound guaiacylglycerol-β-guaiacyl ether (GGE) was oxidized by OhLac to generate guaiacol and vanillic acid. Molecular docking analysis of GGE and OhLac was then used to examine the significant amino residues and hydrogen bonding sites in the substrate–enzyme interaction. Altogether, we were able to investigate the mechanisms involved in lignin degradation. The breakdown of the lignocellulose materials wheat straw, corn stalk, and switchgrass by the recombinant OhLac was observed over 3 days, and the degradation results revealed that OhLac plays a key role in lignin degradation.
Extended-Spectrum Beta-Lactamase Producing-Escherichia coli Isolated From Irrigation Waters and Produce in Ecuador
Authors: Montero Lorena , Irazabal Jorge , Cardenas Paul , Graham Jay P. , Trueba Gabriel
Published: October 2021

In cities across the globe, the majority of wastewater – that includes drug resistant and pathogenic bacteria among other contaminants – is released into streams untreated. This water is often subsequently used for irrigation of pastures and produce. This use of wastewater-contaminated streams allows antibiotic-resistant bacteria to potentially cycle back to humans through agricultural products. In this study, we investigated the prevalence of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolated from produce and irrigation water across 17 provinces of Ecuador. A total of 117 vegetable samples, 119 fruit samples, and 38 irrigation water samples were analyzed. Results showed that 11% of the samples were positive for E. coli including 11 irrigation water samples (29%), and samples of 13 vegetables (11%), and 11 fruits (9%). Among the 165 E. coli isolates cultured, 96 (58%) had the ESBL phenotype, and 58% of ESBL producing E. coli came from irrigation water samples, 11% from vegetables, and 30% from fruits. The blaCTX–M–55, blaCTX–M 65, and blaCTX–M 15 genes were the most frequently found gene associated with the ESBL phenotype and coincided with the blaCTX–M alleles associated with human infections in Ecuador. Three isolates had the mcr-1 gene which is responsible for colistin resistance. This report provides evidence of the potential role of irrigation water in the growing antimicrobial resistance crisis in Ecuador.
Genomic Changes and Genetic Divergence of Vibrio alginolyticus Under Phage Infection Stress Revealed by Whole-Genome Sequencing and Resequencing
Authors: Zhou Wenjie , Li Yingying , Li Zhuobo , Ma Bo , Jiang Xiao , Hu Chaoqun , Ai Yongxing , Luo Peng
Published: October 2021

Bacteriophages (phages) and their bacterial hosts were the most abundant and genetically highly diverse organisms on the earth. In this study, a series of phage-resistant mutant (PRM) strains derived from Vibrio alginolyticus were isolated and Infrequent-restriction-site PCR (IRS-PCR) was used to investigate the genetic diversity of the PRM strains. Phenotypic variations of eight PRM strains were analyzed using profiles of utilizing carbon sources and chemical sensitivity. Genetic variations of eight PRM strains and coevolved V. alginolyticus populations with phages were analyzed by whole-genome sequencing and resequencing, respectively. The results indicated that eight genetically discrepant PRM stains exhibited abundant and abundant phenotypic variations. Eight PRM strains and coevolved V. alginolyticus populations (VE1, VE2, and VE3) contained numerous single nucleotide variations (SNVs) and insertions/indels (InDels) and exhibited obvious genetic divergence. Most of the SNVs and InDels in coding genes were related to the synthesis of flagellar, extracellular polysaccharide (EPS), which often served as the receptors of phage invasion. The PRM strains and the coevolved cell populations also contained frequent mutations in tRNA and rRNA genes. Two out of three coevolved populations (VE1 and VE2) contained a large mutation segment severely deconstructing gene nrdA, which was predictably responsible for the booming of mutation rate in the genome. In summary, numerous mutations and genetic divergence were detected in the genomes of V. alginolyticus PRM strains and in coevolved cell populations of V. alginolyticus under phage infection stress. The phage infection stress may provide an important force driving genomic evolution of V. alginolyticus.
The Importance of Environmentally Acquired Bacterial Symbionts for the Squash Bug (Anasa tristis), a Significant Agricultural Pest
Authors: Acevedo Tarik S. , Fricker Gregory P. , Garcia Justine R. , Alcaide Tiffanie , Berasategui Aileen , Stoy Kayla S. , Gerardo Nicole M.
Published: October 2021

Most insects maintain associations with microbes that shape their ecology and evolution. Such symbioses have important applied implications when the associated insects are pests or vectors of disease. The squash bug, Anasa tristis (Coreoidea: Coreidae), is a significant pest of human agriculture in its own right and also causes damage to crops due to its capacity to transmit a bacterial plant pathogen. Here, we demonstrate that complete understanding of these insects requires consideration of their association with bacterial symbionts in the family Burkholderiaceae. Isolation and sequencing of bacteria housed in the insects’ midgut crypts indicates that these bacteria are consistent and dominant members of the crypt-associated bacterial communities. These symbionts are closely related to Caballeronia spp. associated with other true bugs in the superfamilies Lygaeoidea and Coreoidea. Fitness assays with representative Burkholderiaceae strains indicate that the association can significantly increase survival and decrease development time, though strains do vary in the benefits that they confer to their hosts, with Caballeronia spp. providing the greatest benefit. Experiments designed to assess transmission mode indicate that, unlike many other beneficial insect symbionts, the bacteria are not acquired from parents before or after hatching but are instead acquired from the environment after molting to a later developmental stage. The bacteria do, however, have the capacity to escape adults to be transmitted to later generations, leaving the possibility for a combination of indirect vertical and horizontal transmission.
Sequence Analyses and Phenotypic Characterization Revealed Multidrug Resistant Gene Insertions in the Genomic Region Encompassing Phase 2 Flagellin Encoding fljAB Genes in Monophasic Variant Salmonella enterica Serovar 4,5,12:i:- Isolates From Various Sources in Thailand
Authors: Win Aye Thida , Supa-amornkul Sirirak , Orsi Renato H. , Carey Jaclyn H. , Wolfgang William J. , Chaturongakul Soraya
Published: October 2021

Salmonella enterica serovar 4,5,12:i:- (S. 4,5,12:i:-), a monophasic variant of Salmonella Typhimurium (STm) lacking the phase 2 flagellin encoding genes fljAB, has become increasingly prevalent worldwide. The increasing trends in multidrug resistant (MDR) S. 4,5,12:i:- prevalence also pose an important global health threat. Though many reports have characterized phenotypic and genotypic drug resistance of this serovar, few studies have characterized antimicrobial resistance of this serovar in Thailand. In this study, 108 S. 4,5,12:i:- isolates from various sources in Thailand and four international S. 4,5,12:i:- isolates were screened using polymerase chain reaction (PCR) to detect the presence of five target regions which are associated with antimicrobial resistant (AMR) genes, in the genomic region that contained fljAB genes in STm. We determined AMR phenotypes of all isolates by Kirby-Bauer disk diffusion method. Whole genome sequencing (WGS) was performed on 53 representative isolates (based on differences in the pulsed filed gel electrophoresis profiles, the sources of isolate, and the PCR and AMR patterns) to characterize the genetic basis of AMR phenotype and to identify the location of AMR determinants. Based on PCR screening, nine PCR profiles showing distinct deletion patterns of the five target regions have been observed. Approximately 76% of isolates (or 85 of 112 isolates), all of which were Thai isolates, contained five target regions inserted between STM2759 and iroB gene. A total of 21 phenotypic AMR patterns were identified with the predominant AmpST resistant phenotype [i.e., 84% (or 94 of 112) tested positive for resistance to ampicillin, streptomycin, and tetracycline], and 89% (or 100 of 112) were found to be MDR (defined here as resistant to at least three classes of tested antimicrobials). Using WGS data, a total of 24 genotypic AMR determinants belonging to seven different antimicrobial groups were found. AMR determinants (i.e., blaTEM–1, strB-A, sul2, and tetB, conferring resistance to ampicillin, streptomycin, sulfonamides, and tetracycline, respectively) were found to be inserted in a region typically occupied by the phase 2 flagellin encoding genes in STm. These resistant genes were flanked by a number of insertion sequences (IS), and co-localized with mercury tolerance genes. Our findings identify AMR genes, possibly associated with multiple IS26 copies, in the genetic region between STM2759 and iroB genes replacing phase 2 flagellin encoding fljAB genes in Thai S. 4,5,12:i:- isolates.
Genomic Characterization of Endemic and Ecdemic Non-typhoidal Salmonella enterica Lineages Circulating Among Animals and Animal Products in South Africa
Authors: Carroll Laura M. , Pierneef Rian , Mathole Masenyabu , Matle Itumeleng
Published: October 2021

In Africa, the burden of illness caused by non-typhoidal Salmonella enterica is disproportionally high; however, whole-genome sequencing (WGS) efforts are overwhelmingly concentrated in world regions with lower burdens. While WGS is being increasingly employed in South Africa to characterize Salmonella enterica, the bulk of these efforts have centered on characterizing human clinical strains. Thus, very little is known about lineages circulating among animals in the country on a genomic scale. Here, we used WGS to characterize 63 Salmonella enterica strains isolated from livestock, companion animals, wildlife, and animal products in South Africa over a 60-year period. Genomes were assigned to serotypes Dublin, Hadar, Enteritidis, and Typhimurium (n = 18, 8, 13, and 24 strains, respectively) and sequence types (STs) ST10 (all S. Dublin), ST33 (all S. Hadar), ST11/ST366 (n = 12 and 1 S. Enteritidis, respectively), and ST19/ST34 (n = 23 and 1 S. Typhimurium, respectively; via seven-gene multi-locus sequence typing). Within-ST phylogenies were constructed using genomes sequenced in this study, plus publicly available genomes representative of each ST’s (i) global (n = 2,802 and 1,569 S. Dublin and Hadar genomes, respectively) and (ii) African (n = 716 and 343 S. Enteritidis and Typhimurium genomes, respectively) population. For S. Dublin ST10, a largely antimicrobial-susceptible, endemic lineage circulating among humans, animals, and food in South Africa was identified, as well as a lineage that was likely recently introduced from the United States. For S. Hadar ST33, multiple South African lineages harboring streptomycin and tetracycline resistance-conferring genes were identified. African S. Enteritidis ST11 could be primarily partitioned into one largely antimicrobial-susceptible and one largely multidrug-resistant (MDR) clade, with South African isolates confined to the largely antimicrobial-susceptible clade. S. Typhimurium ST19/ST34 strains sequenced here were distributed across the African S. Typhimurium ST19/ST34 phylogeny, representing a diverse range of lineages, including numerous MDR lineages. Overall, this study provides critical insights into endemic and ecdemic non-typhoidal Salmonella enterica lineages circulating among animals, foods, and humans in South Africa and showcases the utility of WGS in characterizing animal-associated strains from a world region with a high salmonellosis burden.
Isolation, Identification, and Selection of Bacteria With Proof-of-Concept for Bioaugmentation of Whitewater From Wood-Free Paper Mills
Authors: Verdel Nada , Rijavec Tomaž , Rybkin Iaroslav , Erzin Anja , Velišček Žiga , Pintar Albin , Lapanje Aleš
Published: October 2021

In the wood-free paper industry, whitewater is usually a mixture of additives for paper production. We are currently lacking an efficient, cost-effective purification technology for their removal. In closed whitewater cycles the additives accumulate, causing adverse production problems, such as the formation of slime and pitch. The aim of our study was to find an effective bio-based strategy for whitewater treatment using a selection of indigenous bacterial isolates. We first obtained a large collection of bacterial isolates and then tested them individually by simple plate and spectrophotometric methods for their ability to degrade the papermaking additives, i.e., carbohydrates, resin acids, alkyl ketene dimers, polyvinyl alcohol, latex, and azo and fluorescent dyes. We examined correlation between carbon source use, genera, and inoculum source of isolates using two multivariate methods: principal component analysis and FreeViz projection. Of the 318 bacterial isolates, we selected a consortium of four strains (Xanthomonadales bacterium sp. CST37-CF, Sphingomonas sp. BLA14-CF, Cellulosimicrobium sp. AKD4-BF and Aeromonas sp. RES19-BTP) that degrade the entire spectrum of tested additives by means of dissolved organic carbon measurements. A proof-of-concept study on a pilot scale was then performed by immobilizing the artificial consortium of the four strains and inserting them into a 33-liter, tubular flow-through reactor with a retention time of < 15 h. The consortium caused an 88% reduction in the COD of the whitewater, even after 21 days.
Optimal Extracellular Matrix Niches for Neurogenesis: Identifying Glycosaminoglycan Chain Composition in the Subventricular Neurogenic Zone
Authors: Kerever Aurelien , Arikawa-Hirasawa Eri
Published: October 2021

In the adult mammalian brain, new neurons are generated in a restricted region called the neurogenic niche, which refers to the specific regulatory microenvironment of neural stem cells (NSCs). Among the constituents of neurogenic niches, the extracellular matrix (ECM) has emerged as a key player in NSC maintenance, proliferation, and differentiation. In particular, heparan sulfate (HS) proteoglycans are capable of regulating various growth factor signaling pathways that influence neurogenesis. In this review, we summarize our current understanding of the ECM niche in the adult subventricular zone (SVZ), with a special focus on basement membrane (BM)-like structures called fractones, and discuss how fractones, particularly their composition of glycosaminoglycans (GAGs), may influence neurogenesis.
Higher-Order Conditioning and Dopamine: Charting a Path Forward
Authors: Seitz Benjamin M. , Blaisdell Aaron P. , Sharpe Melissa J.
Published: October 2021

Higher-order conditioning involves learning causal links between multiple events, which then allows one to make novel inferences. For example, observing a correlation between two events (e.g., a neighbor wearing a particular sports jersey), later helps one make new predictions based on this knowledge (e.g., the neighbor’s wife’s favorite sports team). This type of learning is important because it allows one to benefit maximally from previous experiences and perform adaptively in complex environments where many things are ambiguous or uncertain. Two procedures in the lab are often used to probe this kind of learning, second-order conditioning (SOC) and sensory preconditioning (SPC). In second-order conditioning (SOC), we first teach subjects that there is a relationship between a stimulus and an outcome (e.g., a tone that predicts food). Then, an additional stimulus is taught to precede the predictive stimulus (e.g., a light leads to the food-predictive tone). In sensory preconditioning (SPC), this order of training is reversed. Specifically, the two neutral stimuli (i.e., light and tone) are first paired together and then the tone is paired separately with food. Interestingly, in both SPC and SOC, humans, rodents, and even insects, and other invertebrates will later predict that both the light and tone are likely to lead to food, even though they only experienced the tone directly paired with food. While these processes are procedurally similar, a wealth of research suggests they are associatively and neurobiologically distinct. However, midbrain dopamine, a neurotransmitter long thought to facilitate basic Pavlovian conditioning in a relatively simplistic manner, appears critical for both SOC and SPC. These findings suggest dopamine may contribute to learning in ways that transcend differences in associative and neurological structure. We discuss how research demonstrating that dopamine is critical to both SOC and SPC places it at the center of more complex forms of cognition (e.g., spatial navigation and causal reasoning). Further, we suggest that these more sophisticated learning procedures, coupled with recent advances in recording and manipulating dopamine neurons, represent a new path forward in understanding dopamine’s contribution to learning and cognition.