bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of Neoantigens and Construction of Immune Subtypes in Prostate Adenocarcinoma
Authors: Gao Yukui , Wang Guixin , Chen Yanzhuo , Zhang Mingpeng , Gao Wenlong , Shang Zhiqun , Niu Yuanjie
Published: April 2022

Background: Messenger ribonucleic acid (mRNA) vaccine has been considered as a potential therapeutic strategy and the next research hotspot, but their efficacy against prostate adenocarcinoma (PRAD) remains undefined. This study aimed to find potential antigens of PRAD for mRNA vaccine development and identify suitable patients for vaccination through immunophenotyping.

Methods: Gene expression profiles and clinical information were obtained from TCGA and ICGC. GEPIA2 was used to calculate the prognostic index of the selected antigens. The genetic alterations were compared on cBioPortal and the correlation between potential antigen and immune infiltrating cells was explored by TIMER. ConsensusClusterPlus was used to construct a consistency matrix, and identify the immune subtypes. Graph learning-based dimensional reduction was performed to depict immune landscape. Boruta algorithm and LASSO logistic analysis were used to screen PRAD patients who may benefit from mRNA vaccine.

Results: Seven potential tumor antigens selected were signiﬁcantly positively associated with poor prognosis and the antigen-presenting immune cells (APCs) in PRAD, including ADA, FYN, HDC, NFKBIZ, RASSF4, SLC6A3, and UPP1. Five immune subtypes of PRAD were identified by differential molecular, cellular, and clinical characteristics in both cohorts. C3 and C5 had immune “hot” and immunosuppressive phenotype, On the contrary, C1&C2 had immune “cold” phenotype. Finally, the immune landscape characterization showed the immune heterogeneity among patients with PRAD.

Conclusions: ADA, FYN, HDC, NFKBIZ, RASSF4, SLC6A3, and UPP1 are potential antigens for mRNA vaccine development against PRAD, and patients in type C1 and C2 are suitable for vaccination.
Identification and Analysis of MYB Gene Family for Discovering Potential Regulators Responding to Abiotic Stresses in Curcuma wenyujin
Authors: Wei Qiuhui , Liu Yuyang , Lan Kaer , Wei Xin , Hu Tianyuan , Chen Rong , Zhao Shujuan , Yin Xiaopu , Xie Tian
Published: April 2022

MYB superfamily is one of the most abundant families in plants, and plays critical role in plant growth, development, metabolism regulation, and stress response. Curcuma wenyujin is the main source plant of three traditional Chinese medicines, which are widely used in clinical treatment due to its diverse pharmacological activities. In present study, 88 CwMYBs were identified and analyzed in C. wenyujin, including 43 MYB-related genes, 42 R2R3-MYB genes, two 3R-MYB genes, and one 4R-MYB gene. Forty-three MYB-related proteins were classified into several types based on conserved domains and specific motifs, including CCA1-like type, R-R type, Myb-CC type, GARP-like type, and TBR-like type. The analysis of motifs in MYB DBD and no-MYB regions revealed the relevance of protein structure and function. Comparative phylogeny analysis divided 42 R2R3-MYB proteins into 19 subgroups and provided a reference for understanding the functions of some CwMYBs based on orthologs of previously characterized MYBs. Expression profile analysis of CwMYB genes revealed the differentially expressed genes responding to various abiotic stresses. Four candidate MYB genes were identified by combining the results of phylogeny analysis and expression analysis. CwMYB10, CwMYB18, CwMYB39, and CwMYB41 were significantly induced by cold, NaCl, and MeJA stress treatments. CwMYB18 and CwMYB41 were proved as regulators with activity of transcriptional activation, whereas CwMYB39 and CwMYB10 were not. They may participate in the response to abiotic stresses through different mechanisms in C. wenyujin. This study was the first step toward understanding the CwMYB family and the response to abiotic stresses in C. wenyujin.
CCN1 Promotes Inflammation by Inducing IL-6 Production via α6β1/PI3K/Akt/NF-κB Pathway in Autoimmune Hepatitis
Authors: Jiang Renquan , Tang Jifeng , Zhang Xuehao , He Yujue , Yu Ziqing , Chen Shuhui , Xia Jinfang , Lin Jinpiao , Ou Qishui
Published: April 2022

Autoimmune hepatitis (AIH) is a chronic inflammatory liver disease with unknown etiology. CCN1, an extracellular matrix-associated protein, is associated with carcinoma, inflammation, liver fibrosis, and even autoimmune diseases. However, the role that CCN1 plays in AIH has remained undetermined. In this study, expression of CCN1 in liver was detected by real-time PCR, western blot and immunohistochemistry (IHC). CCN1 level in serum was detected by ELISA. Diagnostic value of CCN1 was determined by receiver operating characteristic (ROC) curve analysis. CCN1 conditional knockout (CCN1fl/flCre+) mice were generated by mating CCN1fl/fl C57BL/6J and CAG-Cre-ERT C57BL/6J mice. Autoimmune hepatitis mice model was induced by concanavalin A (ConA). IKKα/β, IκBα, NF-κB p65 and Akt phosphorylation were determined by western blot. NF-κB p65 nuclear translocation was examined by immunofluorescence. Here, we found that CCN1 was over-expressed in hepatocytes of AIH patients. CCN1 level also increased in serum of AIH patients compared to healthy controls (HC). ROC curve analysis results showed that serum CCN1 was able to distinguish AIH patients from HD. In ConA induced hepatitis mice model, CCN1 conditional knockout (CCN1fl/flCre+) attenuated inflammation by reducing ALT/AST level and IL-6 expression. In vitro, CCN1 treatment dramatically induced IL-6 production in LO2 cells. Moreover, the production of IL-6 was attenuated by CCN1 knockdown. Furthermore, we showed that CCN1 could activate IL-6 production via the PI3K/Akt/NF-κB signaling pathway by binding to α6β1 receptor. In summary, our results reveal a novel role of CCN1 in promoting inflammation by upregulation of IL-6 production in AIH. Our study also suggests that targeting of CCN1 may represent a novel strategy in AIH treatment.
The Clinical Value of Procalcitonin in the Neutropenic Period After Allogeneic Hematopoietic Stem Cell Transplantation
Authors: Shan Meng , Shen Danya , Song Tiemei , Xu Wenyan , Qiu Huiying , Chen Suning , Han Yue , Tang Xiaowen , Miao Miao , Sun Aining , Wu Depei , Xu Yang
Published: April 2022

The diagnostic value of procalcitonin and the prognostic role of PCT clearance remain unclear in neutropenic period after allogeneic hematopoietic stem cell transplantation introduction. This study evaluated 219 febrile neutropenic patients (116, retrospectively; 103, prospectively) who underwent allo-HSCT from April 2014 to March 2016. The area under the receiver operator characteristic curve (AUC) of PCT for detecting documented infection (DI) was 0.637, and that of bloodstream infection (BSI) was 0.811. In multivariate analysis, the inability to decrease PCT by more than 80% within 5–7 days after the onset of fever independently predicted poor 100-day survival following allo-HSCT (P = 0.036). Furthermore, the prognostic nomogram combining PCTc and clinical parameters showed a stable predictive performance, supported by the C-index of 0.808 and AUC of 0.813 in the primary cohort, and C-index of 0.691 and AUC of 0.697 in the validation cohort. This study demonstrated the diagnostic role of PCT in documented and bloodstream infection during the neutropenic period after allo-HSCT. PCTc might serve as a predictive indicator of post-HSCT 100-day mortality. A nomogram based on PCTc and several clinical factors effectively predicted the 100-day survival of febrile patients and may help physicians identify high-risk patients in the post-HSCT neutropenic period.
Advances in the Structural and Physiological Functions of SHARPIN
Authors: Yu Beiming , Wang Feng , Wang Yanfeng
Published: April 2022

SHARPIN was initially found as a SHANK-associated protein. SHARPIN can be used as an important component to form the linear ubiquitin chain assembly complex (LUBAC) with HOIL-1L, HOIP to produce a linear ubiquitin chain connected N-terminal Met1, playing a critical role in various cellular processes including NF-κB signaling, inflammation, embryogenesis and apoptosis. SHARPIN alone can also participate in many critical physiological activities and cause various disorders such as chronic dermatitis, tumor, and Alzheimer’s disease. Mice with spontaneous autosomal recessive mutations in the SHARPIN protein mainly exhibit chronic dermatitis and immunodeficiency with elevated IgM. Additionally, SHARPIN alone also plays a key role in various cellular events, such as B cells activation and platelet aggregation. Structural studies of the SHARPIN or LUBAC have been reported continuously, advancing our understanding of it at the molecular level. However, the full-length structure of the SHARPIN or LUBAC was lagging, and the molecular mechanism underlying these physiological processes is also unclear. Herein, we summarized the currently resolved structure of SHARPIN as well as the emerging physiological role of SHARPIN alone or in LUBAC. Further structural and functional study of SHARPIN will provide insight into the role and underlying mechanism of SHARPIN in disease, as well as its potential application in therapeutic.
Nanobodies Protecting From Lethal SARS-CoV-2 Infection Target Receptor Binding Epitopes Preserved in Virus Variants Other Than Omicron
Authors: Casasnovas José M. , Margolles Yago , Noriega María A. , Guzmán María , Arranz Rocío , Melero Roberto , Casanova Mercedes , Corbera Juan Alberto , Jiménez-de-Oya Nereida , Gastaminza Pablo , Garaigorta Urtzi , Saiz Juan Carlos , Martín-Acebes Miguel Ángel , Fernández Luis Ángel
Published: April 2022

The emergence of SARS-CoV-2 variants that escape from immune neutralization are challenging vaccines and antibodies developed to stop the COVID-19 pandemic. Thus, it is important to establish therapeutics directed toward multiple or specific SARS-CoV-2 variants. The envelope spike (S) glycoprotein of SARS-CoV-2 is the key target of neutralizing antibodies (Abs). We selected a panel of nine nanobodies (Nbs) from dromedary camels immunized with the receptor-binding domain (RBD) of the S, and engineered Nb fusions as humanized heavy chain Abs (hcAbs). Nbs and derived hcAbs bound with subnanomolar or picomolar affinities to the S and its RBD, and S-binding cross-competition clustered them in two different groups. Most of the hcAbs hindered RBD binding to its human ACE2 (hACE2) receptor, blocked cell entry of viruses pseudotyped with the S protein and neutralized SARS-CoV-2 infection in cell cultures. Four potent neutralizing hcAbs prevented the progression to lethal SARS-CoV-2 infection in hACE2-transgenic mice, demonstrating their therapeutic potential. Cryo-electron microscopy identified Nb binding epitopes in and out the receptor binding motif (RBM), and showed different ways to prevent virus binding to its cell entry receptor. The Nb binding modes were consistent with its recognition of SARS-CoV-2 RBD variants; mono and bispecific hcAbs efficiently bound all variants of concern except omicron, which emphasized the immune escape capacity of this latest variant.
Copper Oxide Nanoparticles Stimulate the Immune Response and Decrease Antioxidant Defense in Mice After Six-Week Inhalation
Authors: Tulinska Jana , Mikusova Miroslava Lehotska , Liskova Aurelia , Busova Milena , Masanova Vlasta , Uhnakova Iveta , Rollerova Eva , Alacova Radka , Krivosikova Zora , Wsolova Ladislava , Dusinska Maria , Horvathova Mira , Szabova Michaela , Lukan Norbert , Stuchlikova Martina , Kuba Daniel , Vecera Zbynek , Coufalik Pavel , Krumal Kamil , Alexa Lukas , Vrlikova Lucie , Buchtova Marcela , Dumkova Jana , Piler Pavel , Thon Vojtech , Mikuska Pavel
Published: April 2022

Copper oxide nanoparticles (CuO NPs) are increasingly used in various industry sectors. Moreover, medical application of CuO NPs as antimicrobials also contributes to human exposure. Their toxicity, including toxicity to the immune system and blood, raises concerns, while information on their immunotoxicity is still very limited. The aim of our work was to evaluate the effects of CuO NPs (number concentration 1.40×106 particles/cm3, geometric mean diameter 20.4 nm) on immune/inflammatory response and antioxidant defense in mice exposed to 32.5 µg CuO/m3 continuously for 6 weeks. After six weeks of CuO NP inhalation, the content of copper in lungs and liver was significantly increased, while in kidneys, spleen, brain, and blood it was similar in exposed and control mice. Inhalation of CuO NPs caused a significant increase in proliferative response of T-lymphocytes after mitogenic stimulation and basal proliferative activity of splenocytes. CuO NPs significantly induced the production of IL-12p70, Th1-cytokine IFN-γ and Th2-cytokines IL-4, IL-5. Levels of TNF-α and IL-6 remained unchanged. Immune assays showed significantly suppressed phagocytic activity of granulocytes and slightly decreased respiratory burst. No significant differences in phagocytosis of monocytes were recorded. The percentage of CD3+, CD3+CD4+, CD3+CD8+, and CD3-CD19+ cell subsets in spleen, thymus, and lymph nodes did not differ between exposed and control animals. No changes in hematological parameters were found between the CuO NP exposed and control groups. The overall antioxidant protection status of the organism was expressed by evaluation of GSH and GSSG concentrations in blood samples. The experimental group exposed to CuO NPs showed a significant decrease in GSH concentration in comparison to the control group. In summary, our results indicate that sub-chronic inhalation of CuO NPs can cause undesired modulation of the immune response. Stimulation of adaptive immunity was indicated by activation of proliferation and secretion functions of lymphocytes. CuO NPs elicited pro-activation state of Th1 and Th2 lymphocytes in exposed mice. Innate immunity was affected by impaired phagocytic activity of granulocytes. Reduced glutathione was significantly decreased in mice exposed to CuO NPs.
The Hidden Side of Complement Regulator C4BP: Dissection and Evaluation of Its Immunomodulatory Activity
Authors: Serrano Inmaculada , Luque Ana , Mitjavila Francesca , Blom Anna M. , Rodríguez de Córdoba Santiago , Vega M. Cristina , Torras Joan , Aran Josep M.
Published: April 2022

C4b-binding protein (C4BP) is a well-known regulator of the complement system that holds additional and important activities unrelated to complement inhibition. Recently, we have described a novel immunomodulatory activity in the minor C4BP(β-) isoform directly acting over inflammatory phagocytes. Here we show that incorporation of the β-chain to the C4BP α-chain oligomer interferes with this immunomodulatory activity of C4BP. Moreover, an oligomeric form including only the complement control protein 6 (CCP6) domain of the C4BP α-chain (PRP6-HO7) is sufficient to “reprogram” monocyte-derived DCs (Mo-DCs) from a pro-inflammatory and immunogenic phenotype to an anti-inflammatory and tolerogenic state. PRP6-HO7 lacks complement regulatory activity but retains full immunomodulatory activity over inflammatory Mo-DCs induced by TLRs, characterized by downregulation of relevant surface markers such as CD83, HLA-DR, co-stimulatory molecules such as CD86, CD80 and CD40, and pro-inflammatory cytokines such as IL-12 and TNF-α. Furthermore, PRP6-HO7-treated Mo-DCs shows increased endocytosis, significantly reduced CCR7 expression and CCL21-mediated chemotaxis, and prevents T cell alloproliferation. Finally, PRP6-HO7 shows also full immunomodulatory activity over Mo-DCs isolated from lupus nephritis patients with active disease, even without further pro-inflammatory stimulation. Therefore PRP6-HO7, retaining the immunomodulatory activity of C4BP(β-) and lacking its complement regulatory activity, might represent a promising and novel alternative to treat autoimmune diseases.
Physicochemical Heuristics for Identifying High Fidelity, Near-Native Structural Models of Peptide/MHC Complexes
Authors: Keller Grant L. J. , Weiss Laura I. , Baker Brian M.
Published: April 2022

There is long-standing interest in accurately modeling the structural features of peptides bound and presented by class I MHC proteins. This interest has grown with the advent of rapid genome sequencing and the prospect of personalized, peptide-based cancer vaccines, as well as the development of molecular and cellular therapeutics based on T cell receptor recognition of peptide-MHC. However, while the speed and accessibility of peptide-MHC modeling has improved substantially over the years, improvements in accuracy have been modest. Accuracy is crucial in peptide-MHC modeling, as T cell receptors are highly sensitive to peptide conformation and capturing fine details is therefore necessary for useful models. Studying nonameric peptides presented by the common class I MHC protein HLA-A*02:01, here we addressed a key question common to modern modeling efforts: from a set of models (or decoys) generated through conformational sampling, which is best? We found that the common strategy of decoy selection by lowest energy can lead to substantial errors in predicted structures. We therefore adopted a data-driven approach and trained functions capable of predicting near native decoys with exceptionally high accuracy. Although our implementation is limited to nonamer/HLA-A*02:01 complexes, our results serve as an important proof of concept from which improvements can be made and, given the significance of HLA-A*02:01 and its preference for nonameric peptides, should have immediate utility in select immunotherapeutic and other efforts for which structural information would be advantageous.
A Minireview on the Use of g-C3N4–Chitosan Biocomposite for Potential Applications
Authors: Santiago-Ramírez C. R , Nair Pooja R , Vela-Monroy C. A , Aba-Guevara C. G , Ramos-Delgado N. A , Gracia-Pinilla M. A
Published: April 2022

The novel biocomposite based on graphitic carbon nitride (g-C3N4 (CN)) and Chitosan (CS) has been deeply studied and summarized in key points concerning various applications. The CN material is composed of the earth-abundant nature of C, N, and H and possesses excellent properties due to its two-dimensional structure, good chemical stability, and a narrow bandgap that allows its use in many applications. There is a lot of information on the role of CN as a potential photocatalyst, but not in association with other composites. In contrast, this minireview summarizes its applications not only in the field of photocatalysis but also in all fields reported on the biocomposite of CN with CS. The incorporation of chitosan helps to overcome the existing limitations of CN, like low-surface area, low light absorption, fast recombination of charges, and hydrophobic character. To introduce, CS is an attractive biomaterial, which is a low-cost alternative for the preparation of films and catalysts due to its unique characteristics such as biodegradability, antimicrobial activity, and film-forming properties that increase the popularity of CN. In this current minireview, a comprehensive study was conducted on the properties, synthesis, and applications along with the advancements of CN incorporated with CS. Finally, we hope to stimulate researchers to study the biocomposite of CN and CS to find new portals and ways to develop effective materials.
Rheumatic?—A Digital Diagnostic Decision Support Tool for Individuals Suspecting Rheumatic Diseases: A Multicenter Pilot Validation Study
Authors: Knevel Rachel , Knitza Johannes , Hensvold Aase , Circiumaru Alexandra , Bruce Tor , Evans Sebastian , Maarseveen Tjardo , Maurits Marc , Beaart-van de Voorde Liesbeth , Simon David , Kleyer Arnd , Johannesson Martina , Schett Georg , Huizinga Tom , Svanteson Sofia , Lindfors Alexandra , Klareskog Lars , Catrina Anca
Published: April 2022

Introduction

Digital diagnostic decision support tools promise to accelerate diagnosis and increase health care efficiency in rheumatology. Rheumatic? is an online tool developed by specialists in rheumatology and general medicine together with patients and patient organizations. It calculates a risk score for several rheumatic diseases. We ran a pilot study retrospectively testing Rheumatic? for its ability to differentiate symptoms from existing or emerging immune-mediated rheumatic diseases from other rheumatic and musculoskeletal complaints and disorders in patients visiting rheumatology clinics.

Materials and Methods

The performance of Rheumatic? was tested using in three university rheumatology centers: (A) patients at Risk for RA (Karolinska Institutet, n = 50 individuals with musculoskeletal complaints and anti-citrullinated protein antibody positivity) (B) patients with early joint swelling [dataset B (Erlangen) n = 52]. (C) Patients with early arthritis where the clinician considered it likely to be of auto-immune origin [dataset C (Leiden) n = 73]. In dataset A we tested whether Rheumatic? could predict the development of arthritis. In dataset B and C we tested whether Rheumatic? could predict the development of an immune-mediated rheumatic diseases. We examined the discriminative power of the total score with the Wilcoxon rank test and the area-under-the-receiver-operating-characteristic curve (AUC-ROC). Next, we calculated the test characteristics for these patients passing the first or second expert-based Rheumatic? scoring threshold.

Results

The total test scores differentiated between: (A) Individuals developing arthritis or not, median 245 vs. 163, P < 0.0001, AUC-ROC = 75.3; (B) patients with an immune-mediated arthritic disease or not median 191 vs. 107, P < 0.0001, AUC-ROC = 79.0; but less patients with an immune-mediated arthritic disease or not amongst those where the clinician already considered an immune mediated disease most likely (median 262 vs. 212, P < 0.0001, AUC-ROC = 53.6). Threshold-1 (advising to visit primary care doctor) was highly specific in dataset A and B (0.72, 0.87, and 0.23, respectively) and sensitive (0.67, 0.61, and 0.67). Threshold-2 (advising to visit rheumatologic care) was very specific in all three centers but not very sensitive: specificity of 1.0, 0.96, and 0.91, sensitivity 0.05, 0.07, 0.14 in dataset A, B, and C, respectively.

Conclusion

Rheumatic? is a web-based patient-centered multilingual diagnostic tool capable of differentiating immune-mediated rheumatic conditions from other musculoskeletal problems. The current scoring system needs to be further optimized.
Prevalence and Risk Factors of Gallbladder Stones and Polyps in Liaoning, China
Authors: Zhang Xinhe , Guan Lin , Tian Haoyu , Li Yiling
Published: April 2022

Objective

To investigate the incidence and risk factors of gallbladder stones and polyps in individuals undergoing physical examinations in Liaoning province, China.

Methods

This is a retrospective study of adults who underwent routine health examinations at Xikang Medical Center in Liaoning Province (Shenyang, Dandong, and Dalian) from 01/2016 to 12/2020. The routine health examination included anthropometry, blood tests, and liver ultrasound. Based on liver ultrasound results, patients were grouped into those with gallbladder stones, those with gallbladder polyps, those with both stones and polyps, and those with neither.

Results

Of the 284,129 included subjects, 6,537 (2.30%) were diagnosed with gallbladder stones, and 18,873 (6.64%) were diagnosed with gallbladder polyps. The overall prevalence in Liaoning province increased each year, peaking in 2020. The prevalence of gallbladder stones was higher among females than males (2.39% vs. 2.23%, respectively), while the prevalence of gallbladder polyps was higher among males. The gallbladder polyp group had higher BMI, FBG, SBP, DBP, TG, TC, LDL-C, HDL-C, AST, ALP, GGT, BUN, Scr, SUA. Except for HDL-C, all factors were also higher in the gallbladder stone group. Patients with fatty liver had a higher prevalence of gallbladder stones and polyps than participants without fatty liver.

Conclusion

The prevalence of gallbladder stones and polyps in Liaoning varies by sex, economic status of the city of residence, BMI, and metabolic indicators.
The Coupling Between Cell Wall Integrity Mediated by MAPK Kinases and SsFkh1 Is Involved in Sclerotia Formation and Pathogenicity of Sclerotinia sclerotiorum
Authors: Cong Jie , Xiao Kunqin , Jiao Wenli , Zhang Cheng , Zhang Xianghui , Liu Jinliang , Zhang Yanhua , Pan Hongyu
Published: April 2022

The plant pathogenic fungus Sclerotinia sclerotiorum can survive on a wide range of hosts and cause significant losses on crop yields. FKH, a forkhead box (FOX)-containing protein, functions to regulate transcription and signal transduction. As a transcription factor (TF) with multiple biological functions in eukaryotic organisms, little research has been done on the role of FKH protein in pathogenic fungi. SsFkh1 encodes a protein which has been predicted to contain FOX domain in S. sclerotiorum. In this study, the deletion mutant of SsFkh1 resulted in severe defects in hyphal development, virulence, and sclerotia formation. Moreover, knockout of SsFkh1 lead to gene functional enrichment in mitogen-activated protein kinase (MAPK) signaling pathway in transcriptome analysis and SsFkh1 was found to be involved in the maintenance of the cell wall integrity (CWI) and the MAPK signaling pathway. Yeast two-hybrid and bimolecular fluorescence complementation assays showed that SsFkh1 interacts with SsMkk1. In addition, we explored the conserved MAPK signaling pathway components, including Bck1, Mkk1, Pkc1, and Smk3 in S. sclerotiorum. ΔSsmkk1, ΔSspkc1, ΔSsbck1, and ΔSssmk3knockout mutant strains together with ΔSsmkk1com, ΔSspkc1com, ΔSsbck1com, and ΔSssmk3com complementation mutant strains were obtained. The results indicated that ΔSsmkk1, ΔSspkc1, ΔSsbck1, and ΔSssmk3 displayed similar phenotypes to ΔSsfkh1 in sclerotia formation, compound appressorium development, and pathogenicity. Taken together, SsFkh1 may be the downstream substrate of SsMkk1 and involved in sclerotia formation, compound appressorium development, and pathogenicity in S. sclerotiorum.
Outline, Divergence Times, and Phylogenetic Analyses of Trechisporales (Agaricomycetes, Basidiomycota)
Authors: Liu Zhan-Bo , Wu Ying-Da , Zhao Heng , Lian Ya-Ping , Wang Ya-Rong , Wang Chao-Ge , Mao Wei-Lin , Yuan Yuan
Published: April 2022

Phylogenetic analyses inferred from the nuc rDNA ITS1-5.8S-ITS2 (ITS) data set and the combined 2-locus data set [5.8S + nuc 28S rDNA (nLSU)] of taxa of Trechisporales around the world show that Sistotremastrum family forms a monophyletic lineage within Trechisporales. Bayesian evolutionary and divergence time analyses on two data sets of 5.8S and nLSU sequences indicate an ancient divergence of Sistotremastrum family from Hydnodontaceae during the Triassic period (224.25 Mya). Sistotremastrum family is characterized by resupinate and thin basidiomata, smooth, verruculose, or odontoid-semiporoid hymenophore, a monomitic hyphal structure, and generative hyphae bearing clamp connections, the presence of cystidia and hyphidia in some species, thin-walled, smooth, inamyloid, and acyanophilous basidiospores. In addition, four new species, namely, Trechispora dentata, Trechispora dimitiella, Trechispora fragilis, and Trechispora laevispora, are described and illustrated. In addition, three new combinations, namely, Brevicellicium daweishanense, Brevicellicium xanthum, and Sertulicium limonadense, are also proposed.
Metagenomic Insights Into Competition Between Denitrification and Dissimilatory Nitrate Reduction to Ammonia Within One-Stage and Two-Stage Partial-Nitritation Anammox Bioreactor Configurations
Authors: Bryson Samuel J. , Hunt Kristopher A. , Stahl David A. , Winkler Mari-Karoliina H.
Published: April 2022

Anaerobic ammonia oxidizing bacteria (Anammox) are implemented in high-efficiency wastewater treatment systems operated in two general configurations; one-stage systems combine aerobic ammonia oxidizing bacteria (AOB) and Anammox within a single aerated reactor, whereas two-stage configurations separate these processes into discrete tanks. Within both configurations heterotrophic populations that perform denitrification or dissimilatory nitrate reduction to ammonia (DNRA) compete for carbon and nitrate or nitrite and can impact reactor performance because DNRA retains nitrogen in the system. Therefore, it is important to understand how selective pressures imposed by one-stage and two-stage reactor configurations impact the microbial community structure and associated nitrogen transforming functions. We performed 16S rRNA gene and metagenomic sequencing on different biomass fractions (granules, flocs, and suspended biomass) sampled from two facilities treating sludge dewatering centrate: a one-stage treatment facility (Chambers Creek, Tacoma, WA) and a two-stage system (Rotterdam, Netherlands). Similar microbial populations were identified across the different samples, but relative abundances differed between reactor configurations and biomass sources. Analysis of metagenome assembled genomes (MAGs) indicated different lifestyles for abundant heterotrophic populations. Acidobacteria, Bacteroidetes, and Chloroflexi MAGs had varying capacity for DNRA and denitrification. Acidobacteria MAGs possessed high numbers of glycosyl hydrolases and glycosyl transferases indicating a role in biomass degradation. Ignavibacteria and Phycosphaerae MAGs contributed to the greater relative abundance of DNRA associated nrf genes in the two-stage granules and contained genomic features suggesting a preference for an anoxic or microoxic niche. In the one-stage granules a MAG assigned to Burkholderiales accounted for much of the abundant denitrification genes and had genomic features, including the potential for autotrophic denitrification using reduced sulfur, that indicate an ability to adapt its physiology to varying redox conditions. Overall, the competition for carbon substrates between denitrifying and DNRA performing heterotrophs may be impacted by configuration specific selective pressures. In one-stage systems oxygen availability in the bulk liquid and the oxygen gradient within granules would provide a greater niche space for heterotrophic populations capable of utilizing both oxygen and nitrate or nitrite as terminal electron acceptors, compared to two-stage systems where a homogeneous anoxic environment would favor heterotrophic populations primarily adapted to anaerobic metabolism.
In vivo Antiphytoviral Activity of Essential Oils and Hydrosols From Origanum vulgare, Thymus vulgaris, and Rosmarinus officinalis to Control Zucchini Yellow Mosaic Virus and Tomato Leaf Curl New Delhi Virus in Cucurbita pepo L.
Authors: Taglienti Anna , Donati Livia , Ferretti Luca , Tomassoli Laura , Sapienza Filippo , Sabatino Manuela , Di Massimo Gaia , Fiorentino Simona , Vecchiarelli Valerio , Nota Paolo , Ragno Rino
Published: April 2022

In the last decades, the interest in biological activity of natural compounds has been growing. In plant protection, essential oils have been reported to exhibit antiviral, antimycotic, and antiparasitic activities, and are regarded as promising for the formulation of safe antimicrobial agents. Attention has also been focused on hydrosols, the by-products of hydro-distillation of essential oils. Their production is easy, fast, and cheap, and they seem to arise less concern for human health than essential oils. Plant viruses represent a major concern for agricultural crops since no treatment compound is available for virus control. This work was aimed at evaluating the antiphytoviral effectiveness of treatments with three essential oils and corresponding hydrosols extracted from Origanum vulgare, Thymus vulgaris, and Rosmarinus officinalis on Cucurbita pepo plants infected by zucchini yellow mosaic virus or tomato leaf curl New Delhi virus. Treatments were applied either concurrently or after virus inoculation to ascertain an inhibition or curative activity, respectively. Symptoms were observed and samplings were performed weekly. Virus titer and expression levels of phenylalanine ammonia lyase gene (PAL) were measured on treated and untreated infected plants by real-time PCR. PAL gene plays an important role in plant defense response as it is involved in tolerance/resistance to phytopathogens. Results indicated that treatments were effective against tomato leaf curl New Delhi virus whether applied simultaneously with the inoculation or after. A major inhibition was observed with O. vulgare essential oil and hydrosol, resulting in 10–4-fold decrease of virus titer 3 weeks after treatment. Curative activity gave maximum results with all three essential oils and T. vulgaris and R. officinalis hydrosols, recording from 10–2-fold decrease to virus not detected 4 weeks after treatment. An induction of PAL gene expression was recorded at 12 d.p.i. and then was restored to the levels of untreated control. This allows to hypothesize an early plant defense response to virus infection, possibly boosted by treatments. Plant extracts’ composition was characterized by gas chromatography-mass spectrometry. Phenols were largely main components of O. vulgare and T. vulgaris extracts (carvacrol and thymol, respectively), while extracts from R. officinalis were based on monoterpene hydrocarbons (essential oil) and oxygenated monoterpenes (hydrosol).
Effectiveness of Endobronchial Ultrasound-Guided Transbronchial Biopsy Combined With Tissue Culture for the Diagnosis of Sputum Smear-Negative Pulmonary Tuberculosis
Authors: Lin Ching-Kai , Fan Hung-Jen , Yu Kai-Lun , Chang Lih-Yu , Wen Yueh-Feng , Keng Li-Ta , Ho Chao-Chi
Published: April 2022

Background

Microorganisms of tuberculosis (TB) are frequently difficult to identify from the airway specimen; therefore, lung biopsy for further histologic and microbiologic study is required. Endobronchial ultrasound-guided transbronchial biopsy (EBUS-TBB) is used for the diagnosis of pulmonary malignancy, but is rarely in the TB population. The purpose of this study was to verify the effectiveness and safety of EBUS-TBB with histologic study and tissue culture in the diagnosis of sputum smear-negative pulmonary TB.

Methods

Patients who underwent EBUS-TBB with histologic study and TB tissue culture for clinically suspected, but sputum smear-negative pulmonary TB from January 2016 to December 2018, were included. The accuracy of each diagnostic modality was calculated, respectively. Factors that might influence the positive rate of TB culture (washing fluid and tissue specimen) were also evaluated.

Results

One hundred sixty-one patients who underwent EBUS-TBB for clinically suspected, but sputum smear-negative pulmonary TB, were enrolled, and 43 of them were finally diagnosed as having pulmonary TB. The sensitivity of washing fluid (a combination of smear, culture, and polymerase chain reaction for TB) and tissue specimen (a combination of pathology and tissue culture) via EBUS-TBB for TB diagnosis were 48.8 and 55.8%, respectively. The sensitivity for TB diagnosis would be elevated to 67.4% when both washing fluid and tissue specimens are used. The positive TB culture rate would not statistically increase with a combination of tissue specimens and washing fluid. Univariate analysis revealed that TB microorganisms would be more easily cultivated when lesions had an abscess or cavity on the computed tomography (CT) image (presence vs. absence; 62.5 vs. 26.3%, p = 0.022), heterogeneous echogenicity on the EBUS finding (heterogeneous vs. homogeneous; 93.3 vs. 21.4%, p = 0.001), or a necrotic pattern via histologic study (presence vs. absence; 70.6 vs. 30.8%, p = 0.013). Heterogeneous echogenicity in the EBUS finding was the independent predictor according to the results of multivariate analysis. None of our patients encountered major adverse events or received further intensive care after EBUS-TBB.

Conclusion

Endobronchial ultrasound-guided transbronchial biopsy is safe and effective for use in diagnosing sputum smear-negative pulmonary TB. EBUS echoic feature is also a predictor of the positive TB culture rate in pulmonary TB. However, tissue culture via EBUS-TBB has little effect in improving the positive TB culture rate.
The Effects of Helicobacter pylori Infection on Gastric Microbiota in Children With Duodenal Ulcer
Authors: Zheng Wei , Zhu Zhenya , Ying Jingjing , Long Gao , Chen Bo , Peng Kerong , Li Fubang , Zhao Hong , Jiang Mizu
Published: April 2022

Background

Helicobacter pylori (H. pylori) infection is the main cause of chronic gastritis and duodenal ulcer in children. Little is known about the effect of H. pylori on gastric microbiota in children with duodenal ulcer. This study is aimed at the characteristics of gastric microbiota in children with duodenal ulcer on H. pylori infection.

Methods

We studied 23 children diagnosed with duodenal ulcer by gastric endoscopy because of the gastrointestinal symptoms, 15 children were diagnosed with H. pylori infection, while 8 children were without H. pylori infection. Endoscopic mucosal biopsy samples were obtained for DNA extraction. Microbiomes were analyzed by 16S rRNA profiling and microbial functions were predicted using the software Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt).

Results

Bacterial richness and diversity of gastric microbiota in duodenal ulcer with H. pylori-positive were lower than those negative. The gastric microbiota in H. pylori-positive group significantly reduced proportions of six phyla and fifteen genera; only Helicobacter taxa were more abundant in H. pylori-positive group. Co-expression network analysis showed a more complex network of interactions in the H. pylori-positive group than that in the H. pylori-negative group. For the predicted functions, lower abundance in the pathways of carbohydrate metabolism, signal transduction, amino acid metabolism, and lipid metabolism were found in H. pylori-positive group than the H. pylori-negative group. H. pylori colonization reduces a microbial community with genotoxic potential in the gastric mucosa of children with duodenal ulcer.

Conclusions

The presence of H. pylori significantly influences gastric microbiota and results in a lower abundance of multiple taxonomic levels in children with duodenal ulcer. Children with duodenal ulcer exhibit a dysbiotic microbial community with genotoxic potential, which is distinct from that of children with H. pylori infection.

Clinical Trial Registration

[http://www.chictr.org.cn], identifier [ChiCTR1800015190].
Overview of Diverse Methyl/Alkyl-Coenzyme M Reductases and Considerations for Their Potential Heterologous Expression
Authors: Gendron Aleksei , Allen Kylie D.
Published: April 2022

Methyl-coenzyme M reductase (MCR) is an archaeal enzyme that catalyzes the final step of methanogenesis and the first step in the anaerobic oxidation of methane, the energy metabolisms of methanogens and anaerobic methanotrophs (ANME), respectively. Variants of MCR, known as alkyl-coenzyme M reductases, are involved in the anaerobic oxidation of short-chain alkanes including ethane, propane, and butane as well as the catabolism of long-chain alkanes from oil reservoirs. MCR is a dimer of heterotrimers (encoded by mcrABG) and requires the nickel-containing tetrapyrrole prosthetic group known as coenzyme F430. MCR houses a series of unusual post-translational modifications within its active site whose identities vary depending on the organism and whose functions remain unclear. Methanogenic MCRs are encoded in a highly conserved mcrBDCGA gene cluster, which encodes two accessory proteins, McrD and McrC, that are believed to be involved in the assembly and activation of MCR, respectively. The requirement of a unique and complex coenzyme, various unusual post-translational modifications, and many remaining questions surrounding assembly and activation of MCR largely limit in vitro experiments to native enzymes with recombinant methods only recently appearing. Production of MCRs in a heterologous host is an important step toward developing optimized biocatalytic systems for methane production as well as for bioconversion of methane and other alkanes into value-added compounds. This review will first summarize MCR catalysis and structure, followed by a discussion of advances and challenges related to the production of diverse MCRs in a heterologous host.
Chicken Feather Waste Valorization Into Nutritive Protein Hydrolysate: Role of Novel Thermostable Keratinase From Bacillus pacificus RSA27
Authors: Sharma Chhavi , Timorshina Svetlana , Osmolovskiy Alexander , Misri Jyoti , Singh Rajni
Published: April 2022

Microbial keratinases exhibit a momentous role in converting keratin biowastes into exceedingly valuable protein supplements. This study reports a novel, highly stable keratinase fromBacillus pacificusRSA27 for the production of pure peptides rich in essential amino acids from chicken feathers. Purified keratinase showed a specific activity of 38.73 U/mg, 2.58-fold purification, and molecular weight of 36 kDa. Kinetic studies using a chicken feather as substrate reportKmandVmaxvalues of 5.69 mg/ml and 142.40 μg/ml/min, respectively, suggesting significant enzyme-substrate affinity/biocatalysis. Identification andin silicostructural-functional analysis of keratinase discovered the presence of distinct amino acid residues and their positions. Besides, keratinase possesses a high-affinity calcium-binding site (Asp128, Leu162, Asn164, Ile166, and Val168) and a catalytic triad of Asp119, His151, and Ser308, known attributes of serine protease (subtilisin family). Furthermore, a scale-up to 5 L fermenter revealed complete feather hydrolysis (94.5%) within 24 h with high activity (789 U/ml) and total amino acid of 153.97 μmol/ml. Finally, cytotoxicity evaluation of protein hydrolysate resulted in negligible cytotoxic effects (1.02%) on the mammalian hepatoblastoma cell line, signifying its potential biotechnological applications.
Development in Detection Methods for the Expression of Surface-Displayed Proteins
Authors: Ma Chenglong , Jiang Chunyang , Zhao Dongping , Li Shuhao , Li Ronggui , Li Lei
Published: April 2022

Directed evolution is a widely-used engineering strategy for improving the stabilities or biochemical functions of proteins by repeated rounds of mutation and selection. A protein of interest is selected as the template and expressed on a molecular display platform such as a bacteriophage for engineering. Initially, the surface-displayed protein template needs to be checked against the desired target via ELISA to examine whether the functions of the displayed template remain intact. The ELISA signal is subject to the protein-target binding affinity. A low-affinity results in a weak ELISA signal which makes it difficult to determine whether the weak signal is because of low affinity or because of poor expression of the protein. Using a methyllysine-binding chromodomain protein Cbx1 that weakly binds to the histone H3K9me3 peptide, we developed and compared three different approaches to increase the signal-to-background ratio of ELISA measurements. We observed that the specific peptide-binding signal was enhanced by increasing the Cbx1 phage concentration on the ELISA plate. The introduction of previously known gain-of-function mutations to the Cbx1 protein significantly increased the ELISA signals. Moreover, we demonstrated that the H3K9me3-specific binding signal was enhanced by fusing Cbx1 with a high-affinity phosphotyrosine-binding protein and by coating the ELISA plate with a mixture of H3K9me3 and phosphotyrosine peptides. This approach also worked with binding to a lower affinity momomethyllysine peptide H3K9me1. These approaches may help improve ELISA experiments when dealing with low-affinity ligand-protein interactions.
Expression Pattern of p62 in Primary Age-Related Tauopathy: Staging of p62 in PART
Authors: Wang Xin , Zhang Lei , Lu Hui , Wu Juanli , Liang Huazheng , Sun Bing , Zhu Keqing
Published: April 2022

The present study analyzed the distribution pattern of p62 immunoreactivity in brains of primary age-related tauopathy (PART) and Braak NFT matched pre-AD and Alzheimer’s disease (AD) patients using immunohistochemistry in combination with semi-quantitative evaluation. In PART and AD brains, p62 was found positive in seven regions, including the neocortex, thalamus, basal ganglia, hippocampus, brainstem, cerebellar dentate nucleus, and the cervical spinal cord. There was a positive correlation between the Braak NFT stage and the distribution of p62 expression. Six stages of expression of p62 were proposed from the present study. Expression of p62 in the hippocampus of PART and AD was classified stage I, the brainstem stage II, the thalamus stage I _I _I, the basal ganglia stage IV, the neocortex stage V, the cerebellum and the cervical spinal cord stage VI. The hippocampus was the site initially affected by p62, especially the CA1 and the subiculum. They might be the earliest accumulation site of p62.
Anxiety-Induced Sleep Disturbance and Associated Lifestyle Behaviors According to Sex in Argentine Adolescents
Authors: López-Gil José Francisco , Cavero-Redondo Iván , Tárraga López Pedro J. , Jiménez-López Estela , González Alberto Durán , Sequí-Domínguez Irene , Mesas Arthur Eumann
Published: April 2022

Purpose

The aim of the current study was twofold: first, to determine the prevalence of anxiety-induced sleep disturbances among Argentine adolescents according to sex, and second, to identify the association between these sleep disturbances and lifestyle behaviors in this population.

Methods

This is a cross-sectional study with data from the Global School-based Student Health Survey (GSHS) in Argentina (2018). A total of 32,393 adolescents (aged 12–17 years; 53.4% girls) were included in the final analysis. Anxiety-induced sleep disturbances were assessed with the question “During the past 12 months, how often have you been so worried about something that you could not sleep at night?”

Results

The prevalence of anxiety-induced sleep disturbances was higher in girls (17.4%) than in boys (7.9%) (p < 0.001). In boys, results indicated that those who used marijuana (cannabis) (odds ratio [OR] = 1.46, 95% confidence interval [CI] 1.08–1.98), used amphetamine or methamphetamine (OR = 2.19, 95% CI 1.28–3.77), walked or biked to or from school (OR = 1.53, 95% CI 1.19–1.96), and spent 3 h or more in sedentary behaviors (OR = 1.35, 95% CI 1.05–1.74) were more likely to report anxiety-induced sleep disturbances. In girls, those who ate from a fast-food restaurant (OR = 1.24, 95% CI 1.05–1.47), consumed alcoholic beverages (OR = 1.45, 95% CI 1.19–1.75), smoked cigarettes (OR = 2.09, 95%CI 1.05–4.14), consumed any tobacco product (OR = 1.47, 95% CI 1.19–1.82), used amphetamine or methamphetamine (OR = 2.08, 95% CI 1.33–3.26), and those who spent 3 h or more in sedentary behaviors (OR = 1.32, 95% CI 1.11–1.57) were more likely to report frequent anxiety-induced sleep disturbances.

Conclusion

In conclusion, considerable sex differences were observed with respect to the prevalence of anxiety-related sleep disturbances and associated lifestyle aspects.