bluuebunny/crossref_metadata_2025 huggingface dataset:
Global Characterization of Metabolic Genes Regulating Survival and Immune Infiltration in Osteosarcoma
Authors: Zhu Zhongpei , Zhang Min , Wang Weidong , Zhang Peng , Wang Yuqiang , Wang Limin
Published: January 2022

Background: The alterations in metabolic profile of tumors have been identified as one of the prognostic hallmarks of cancers, including osteosarcoma. These alterations are majorly controlled by groups of metabolically active genes. However, the regulation of metabolic gene signatures in tumor microenvironment of osteosarcoma has not been well explained.

Objectives: Thus, we investigated the sets of previously published metabolic genes in osteosarcoma patients and normal samples.

Methods: We applied computational techniques to identify metabolic genes involved in the immune function of tumor microenvironment (TME) and survival and prognosis of the osteosarcoma patients. Potential candidate gene PAICS (phosphoribosyl aminoimidazole carboxylase, phosphoribosyl aminoimidazole succino carboxamide synthetase) was chosen for further studies in osteosarcoma cell lines for its role in cell proliferation, migration and apoptosis.

Results: Our analyses identified a list of metabolic genes differentially expressed in osteosarcoma tissues. Next, we scrutinized the list of genes correlated with survival and immune cells, followed by clustering osteosarcoma patients into three categories: C1, C2, and C3. These analyses led us to choose PAICS as potential candidate gene as its expression showed association with poor survival and negative correlation with the immune cells. Furthermore, we established that loss of PAICS induced apoptosis and inhibited proliferation, migration, and wound healing in HOS and MG-63 cell lines. Finally, the results were supported by constructing and validating a prediction model for prognosis of the osteosarcoma patients.

Conclusion: Here, we conclude that metabolic genes specifically PAICS play an integral role in the immune cell infiltration in osteosarcoma TME, as well as cancer development and metastasis.
Multiple Cases of Bacterial Sequence Erroneously Incorporated Into Publicly Available Chloroplast Genomes
Authors: Robinson Aaron J. , Daligault Hajnalka E. , Kelliher Julia M. , LeBrun Erick S. , Chain Patrick S. G.
Published: January 2022

Public sequencing databases are invaluable resources to biological researchers, but assessing data veracity as well as the curation and maintenance of such large collections of data can be challenging. Genomes of eukaryotic organelles, such as chloroplasts and other plastids, are particularly susceptible to assembly errors and misrepresentations in these databases due to their close evolutionary relationships with bacteria, which may co-occur within the same environment, as can be the case when sequencing plants. Here, based on sequence similarities with bacterial genomes, we identified several suspicious chloroplast assemblies present in the National Institutes of Health (NIH) Reference Sequence (RefSeq) collection. Investigations into these chloroplast assemblies reveal examples of erroneous integration of bacterial sequences into chloroplast ribosomal RNA (rRNA) loci, often within the rRNA genes, presumably due to the high similarity between plastid and bacterial rRNAs. The bacterial lineages identified within the examined chloroplasts as the most likely source of contamination are either known associates of plants, or co-occur in the same environmental niches as the examined plants. Modifications to the methods used to process untargeted ‘raw’ shotgun sequencing data from whole genome sequencing efforts, such as the identification and removal of bacterial reads prior to plastome assembly, could eliminate similar errors in the future.
COVID-19 Disease and Dermatomyositis: A Mini-Review
Authors: Qian Jie , Xu Hui
Published: January 2022

The pandemic of coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 has caused a large number of deaths, and there is still no effective treatment. COVID-19 can induce a systemic inflammatory response, and its clinical manifestations are diverse. Recently, it has been reported that COVID-19 patients may develop myositis and interstitial pulmonary disease similar to dermatomyositis (DM). This condition is similar to the rapidly progressive interstitial lung disease associated with MDA5+DM that has a poor prognosis and high mortality, and this poses a challenge for an early identification. Suppression of the immune system can protect COVID-19 patients by preventing the production of inflammatory cytokines. This article attempts to explore the possibility of a relationship between COVID-19 and DM in terms of the potential pathogenesis and clinical features and to analyze the therapeutic effect of the immunosuppressive drugs that are commonly used for the treatment of both DM and COVID-19.
IgA Complexes Induce Neutrophil Extracellular Trap Formation More Potently Than IgG Complexes
Authors: Gimpel Anna-Katharina , Maccataio Antonio , Unterweger Harald , Sokolova Maria V. , Schett Georg , Steffen Ulrike
Published: January 2022

Neutrophil extracellular trap (NET) formation is a powerful instrument to fight pathogens, but may induce collateral damage in the affected tissues. Besides pathogen-derived factors, immune complexes are potent inducers of NET formation. Neutrophils express IgA and IgG specific Fc receptors (FcRs) and therefore respond to complexed IgA and IgG. Especially in the context of autoimmune diseases, IgA and IgG immune complexes have been shown to trigger NET formation, a process that putatively contributes to disease severity. However, it is of question if both antibody classes stimulate neutrophils to the same extent. In this study, we compared the capability of IgA and IgG complexes formed by heat aggregation to induce NET formation. While stimulation of neutrophils with IgA complexes robustly induced NET formation, complexed IgG only marginally increased the amount of NETs compared to the unstimulated control. Mixing IgA with IgG before heat aggregation did not increase the effect of complexed IgA on neutrophils. By contrast, the presence of IgG complexes seemed to disturb neutrophil stimulation by IgA complexes. The capacity of complexed IgG to induce NET formation could not be increased by the addition of autologous serum or the removal of terminal sialic acid in the Fc glycan. Together, our data show that IgA is a much more potent inducer of NET formation than IgG. IgA may thus be the main driving force in (auto)immune complex-mediated NET formation.
ADAM Metalloproteinase Domain 17 Regulates Cholestasis-Associated Liver Injury and Sickness Behavior Development in Mice
Authors: Almishri Wagdi , Swain Liam A. , D’Mello Charlotte , Le Tyson S. , Urbanski Stefan J. , Nguyen Henry H.
Published: January 2022

Disintegrin and metalloproteinase domain-containing protein 17 (ADAM17) is a ubiquitously expressed membrane-bound enzyme that mediates shedding of a wide variety of important regulators in inflammation including cytokines and adhesion molecules. Hepatic expression of numerous cytokines and adhesion molecules are increased in cholestatic liver diseases including primary biliary cholangitis (PBC) and primary sclerosing cholangitis (PSC), however, the pathophysiological role of ADAM17 in regulating these conditions remains unknown. Therefore, we evaluated the role of ADAM17 in a mouse model of cholestatic liver injury due to bile duct ligation (BDL). We found that BDL enhanced hepatic ADAM17 protein expression, paralleled by increased ADAM17 bioactivity. Moreover, inhibition of ADAM17 bioactivity with the specific inhibitor DPC 333 significantly improved both biochemical and histological evidence of liver damage in BDL mice. Patients with cholestatic liver disease commonly experience adverse behavioral symptoms, termed sickness behaviors. Similarly, BDL in mice induces reproducible sickness behavior development, driven by the upregulated expression of cytokines and adhesion molecules that are in turn regulated by ADAM17 activity. Indeed, inhibition of ADAM17 activity significantly ameliorated BDL-associated sickness behavior development. In translational studies, we evaluated changes in ADAM17 protein expression in liver biopsies obtained from patients with PBC and PSC, compared to normal control livers. PSC and PBC patients demonstrated increased hepatic ADAM17 expression in hepatocytes, cholangiocytes and in association with liver-infiltrating immune cells compared to normal controls. In summary, cholestatic liver injury in mice and humans is associated with increased hepatic ADAM17 expression. Furthermore, inhibition of ADAM17 activity improves both cholestatic liver injury and associated sickness behavior development, suggesting that ADAM17 inhibition may represent a novel therapeutic approach for treating patients with PBC/PSC.
Differential Virus-Specific IFN-Gamma Producing T Cell Responses to Marek’s Disease Virus in Chickens With B19 and B21 MHC Haplotypes
Authors: Boodhoo Nitish , Behboudi Shahriar
Published: January 2022

Marek’s disease virus (MDV), the etiologic agent for Marek’s disease (MD), causes a deadly lymphoproliferative disease in chickens. Causes of the well-documented association between genetically defined lines of chicken and resistance to MD remain unknown. Here, the frequencies of IFN-gamma producing pp38 and MEQ-specific T cell responses were determined in line N (B21 haplotype; MD-resistant) and line P2a (B19 haplotype, MD-susceptible) chickens after infection with vaccine and/or virulent (RB1B) strains of MDV using both standard ex vivo and cultured chIFN-gamma ELISPOT assays. Notably, MDV infection of naïve and vaccinated MD-resistant chickens induced higher frequencies of IFN-gamma producing MDV-specific T cell responses using the cultured and ex vivo ELISPOT assay, respectively. Remarkably, vaccination did not induce or boost MEQ-specific effector T cells in the susceptible chickens, while it boosted both pp38-and MEQ-specific response in resistant line. Taken together, our results revealed that there is a direct association between the magnitude of T cell responses to pp38 and MEQ of MDV antigens and resistance to the disease.
Low-Molecular-Weight Heparin Enhanced Therapeutic Effects of Human Adipose-Derived Stem Cell Administration in a Mouse Model of Lupus Nephritis
Authors: Matsuda Shogo , Kotani Takuya , Saito Takashi , Suzuka Takayasu , Mori Tatsuhiko , Takeuchi Tohru
Published: January 2022

Background

Lupus nephritis is a life-threatening complication in systemic lupus erythematosus (SLE), but the efficiency of current therapies involving corticosteroids, immunosuppressants, and biological agents is limited. Adipose-derived mesenchymal stem cells (ASCs) are gaining attention as a novel treatment for inflammation in SLE. Low-molecular-weight heparin (LMWH) exhibits multiple functions including anti-inflammatory, anti-fibrotic, and cell function-promoting effects. LMWH stimulation is expected to increase the therapeutic effect of ASCs by promoting cellular functions. In this study, we investigated the effects of LMWH on ASC functions and the therapeutic effect of LMWH-activated human-ASCs (hep-hASCs) in an SLE mouse model.

Methods

The cellular functions of human-derived ASCs stimulated with different LMWH concentrations were observed, and the optimum LMWH dose was selected. The mice were assigned to control, human-ASC, and hep-hASC groups; treatments were performed on week 20. Twenty-six week-old mice were sacrificed, and urine protein score, serum blood urea nitrogen, creatinine (Cr), anti-ds DNA IgG antibody, and serum IL-6 levels were analyzed in each group. Mice kidneys were evaluated via histological examination, immunohistochemical staining, and gene expression levels.

Results

LMWH significantly promoted ASC migration and proliferation and hepatocyte growth factor production and upregulated immunomodulatory factors in vitro. Hep-hASC administration resulted in significant disease activity improvement including proteinuria, serum Cr and IL-6 levels, anti-ds DNA IgG antibody, glomerulonephritis, and immune complex in mice. Inflammation and fibrosis in kidneys was significantly suppressed in the hep-hASC group; the gene expression levels of TNF-alpha, TIMP-2, and MMP-2 was significantly downregulated in the hep-hASC group compared with the control group.

Conclusions

Hep-hASC exhibited higher anti-inflammatory and anti-fibrotic effects than hASCs and may be a candidate tool for SLE treatment in future.
Monolaurin Confers a Protective Effect Against Porcine Epidemic Diarrhea Virus Infection in Piglets by Regulating the Interferon Pathway
Authors: Zhang Qian , Yi Dan , Ji Changzheng , Wu Tao , Wang Manli , Guo Shuangshuang , Wang Lei , Zhao Di , Hou Yongqing
Published: January 2022

Porcine epidemic diarrhea virus (PEDV) has reemerged as the main pathogen of piglets due to its high mutation feature. Monolaurin (ML) is a natural compound with a wide range of antibacterial and antiviral activities. However, the role of ML in PEDV infection is still unknown. This study aimed to evaluate the effect of ML on the growth performance, intestinal function, virus replication and cytokine response in piglets infected with PEDV, and to reveal the mechanism through proteomics analysis. Piglets were orally administrated with ML at a dose of 100 mg/kg·BW for 7 days before PEDV infection. Results showed that although there was no significant effect on the growth performance of piglets, ML administration alleviated the diarrhea caused by PEDV infection. ML administration promoted the recovery of intestinal villi, thereby improving intestinal function. Meanwhile, PEDV replication was significantly inhibited, and PEDV-induced expression of IL-6 and IL-8 were decreased with ML administration. Proteomics analyses showed that 38 proteins were differentially expressed between PEDV and ML+PEDV groups and were significantly enriched in the interferon-related pathways. This suggests ML could promote the restoration of homeostasis by regulating the interferon pathway. Overall, the present study demonstrated ML could confer a protective effect against PEDV infection in piglets and may be developed as a drug or feed additive to prevent and control PEDV disease.
Emerging Molecular Markers Towards Potential Diagnostic Panels for Lupus
Authors: Tan Gongjun , Baby Binila , Zhou Yuqiu , Wu Tianfu
Published: January 2022

Systemic lupus erythematosus (SLE) is a multifactorial autoimmune disease which can affect various tissues and organs, posing significant challenges for clinical diagnosis and treatment. The etiology of SLE is highly complex with contributions from environmental factors, stochastic factors as well as genetic susceptibility. The current criteria for diagnosing SLE is based primarily on a combination of clinical presentations and traditional lab testing. However, these tests have suboptimal sensitivity and specificity. They are unable to indicate disease cause or guide physicians in decision-making for treatment. Therefore, there is an urgent need to develop a more accurate and robust tool for effective clinical management and drug development in lupus patients. It is fortunate that the emerging Omics have empowered scientists in the discovery and identification of potential novel biomarkers of SLE, especially the markers from blood, urine, cerebrospinal fluids (CSF), and other bodily fluids. However, many of these markers have not been carefully validated for clinical use. In addition, it is apparent that individual biomarkers lack sensitivity or specificity. This review summarizes the sensitivity, specificity and diagnostic value of emerging biomarkers from recent studies, and discusses the potential of these markers in the development of biomarker panel based diagnostics or disease monitoring system in SLE.
Inflammasome and Its Therapeutic Targeting in Rheumatoid Arthritis
Authors: Jiang Qi , Wang Xin , Huang Enyu , Wang Qiao , Wen Chengping , Yang Guocan , Lu Liwei , Cui Dawei
Published: January 2022

Inflammasome is a cytoplasmic multiprotein complex that facilitates the clearance of exogenous microorganisms or the recognition of endogenous danger signals, which is critically involved in innate inflammatory response. Excessive or abnormal activation of inflammasomes has been shown to contribute to the development of various diseases including autoimmune diseases, neurodegenerative changes, and cancers. Rheumatoid arthritis (RA) is a chronic and complex autoimmune disease, in which inflammasome activation plays a pivotal role in immune dysregulation and joint inflammation. This review summarizes recent findings on inflammasome activation and its effector mechanisms in the pathogenesis of RA and potential development of therapeutic targeting of inflammasome for the immunotherapy of RA.
Dosimetric Risk Factors for Acute Radiation Pneumonitis in Patients With Prior Receipt of Immune Checkpoint Inhibitors
Authors: Bi Jianping , Qian Jing , Yang Dongqin , Sun Lu , Lin Shouyu , Li Ying , Xue Xudong , Nie Tingting , Verma Vivek , Han Guang
Published: January 2022

Purpose

Dosimetric parameters (e.g., mean lung dose (MLD), V20, and V5) can predict radiation pneumonitis (RP). Constraints thereof were formulated before the era of combined immune checkpoint inhibitors (ICIs) and radiotherapy, which could amplify the RP risk. Dosimetric predictors of acute RP (aRP) in the context of ICIs are urgently needed because no data exist thus far.

Methods and Materials

All included patients underwent thoracic intensity-modulated radiotherapy, previously received ICIs, and followed-up at least once. Logistic regression models examined predictors of aRP (including a priori evaluation of MLD, V20, and V5), and their discriminative capacity was assessed by receiver operating characteristic analysis.

Results

Median follow-up of the 40 patients was 5.3 months. Cancers were lung (80%) or esophageal (20%). ICIs were PD-1 (85%) or PD-L1 (15%) inhibitors (median 4 cycles). Patients underwent definitive (n=19), consolidative (n=14), or palliative (n=7) radiotherapy; the median equivalent dose in 2 Gy fractions (EQD2) was 60 Gy (IQR, 51.8-64 Gy). Grades 1-5 aRP occurred in 25%, 17.5%, 15%, 2.5%, and 5%, respectively. The only variables associated with any-grade aRP were V20 (p=0.014) and MLD (p=0.026), and only V20 with grade ≥2 aRP (p=0.035). Neither the number of prior ICI cycles nor the delivery of concurrent systemic therapy significantly associated with aRP risk. Graphs were constructed showing the incrementally increasing risk of aRP based on V20 and MLD (continuous variables).

Conclusions

This is the first study illustrating that V20 and MLD may impact aRP in the setting of prior ICIs. However, these data should not be extrapolated to patients without pre-radiotherapy receipt of prior ICIs, or to evaluate the risk of chronic pulmonary effects. If these results are validated by larger studies with more homogeneous populations, the commonly accepted V20/MLD dose constraints could require revision if utilized in the setting of ICIs.
Circulating Exosomal circRNAs Contribute to Potential Diagnostic Value of Large Artery Atherosclerotic Stroke
Authors: Xiao Qi , Hou Rongyao , Li Hong , Zhang Shuai , Zhang Fuzhi , Zhu Xiaoyan , Pan Xudong
Published: January 2022

Large artery atherosclerotic (LAA) stroke is closely associated with atherosclerosis, characterized by the accumulation of immune cells. Early recognition of LAA stroke is crucial. Circulating exosomal circRNAs profiling represents a promising, noninvasive approach for the detection of LAA stroke. Exosomal circRNA sequencing was used to identify differentially expressed circRNAs between LAA stroke and normal controls. From a further validation stage, the results were validated using RT-qPCR. We then built logistic regression models of exosomal circRNAs based on a large replication stage, and receiver operating characteristic (ROC) curves were constructed to assess the diagnostic efficacy. Using exosomal circRNA sequencing, large sample validation, and diagnostic model construction revealed that exosomal circ_0043837 and circ_ 0001801were independent predictive factors for LAA stroke, and had better diagnostic efficacy than plasma circRNAs. In the atherosclerotic group (AS), we developed a nomogram for clinical use that integrated the two-circRNA-based risk factors to predict which patients might have the risk of plaque rupture. Circulating exosomal circRNAs profiling identifies novel predictive biomarkers for the LAA stroke and plaque rupture, with superior diagnostic value than plasma circRNAs. It might facilitate the prevention and better management of this disease.
A Warmer Arctic Compromises Winter Survival of Habitat-Forming Seaweeds
Authors: Gordillo Francisco J. L. , Carmona Raquel , Jiménez Carlos
Published: January 2022

Continuous winter darkness at a latitude of 79°N was simulated in cultures of four species of Arctic seaweeds at 3 and 8°C. The laminarians Saccharina latissima and Alaria esculenta, and the rhodophytes Phycodrys rubens and Ptilota gunneri were monitored for 4 months in total darkness and after 1 week following light return in early spring, under controlled laboratory conditions. Biomass loss during darkness was enhanced by the high temperature in all species. At 8°C, the two laminarians were unable to resume growth upon re-illumination. Alaria esculenta showed new blade production by the end of the dark period, but only at 3°C. In all species, the photosynthetic ability was sustained, not suspended, during the whole dark period. P. rubens exhibited lower photosynthetic potential at 8°C than at 3°C during the darkness period, but it was able to recover its O2 evolving potential upon re-illumination, as P. gunneri and S. latissima did, but the latter only at 3°C. The reactivation of photosynthesis seemed to involve photosystem II over photosystem I, as 7 d of photoperiod after the prolonged darkness was not enough to fully recover the PAM-related photosynthetic parameters. Only small changes were recorded in the internal chemical composition (total C, total N, carbohydrates, proteins, and lipids), but species-specific differences were observed. Unlike subarctic areas with an operating photoperiod along the year, a warmer polar night might pose a limit to the ability of multi-year seaweeds to occupy the new ice-free illuminated areas of the Arctic coasts, so that newcomers will potentially be restricted to the spring-summer season.
Estimating Bycatch From Non-representative Samples (II): A Case Study of Pair Trawlers and Common Dolphins in the Bay of Biscay
Authors: Rouby Etienne , Dubroca Laurent , Cloâtre Thomas , Demanèche Sebastien , Genu Mathieu , Macleod Kelly , Peltier Hélène , Ridoux Vincent , Authier Matthieu
Published: January 2022

Marine megafauna plays an important functional role in marine ecosystems as top predators but are threatened by a wide range of anthropogenic activities. Bycatch, the incidental capture of non-targeted species in commercial and recreational fisheries, is of particular concern for small cetacean species, such as dolphins and porpoises. In the North-East Atlantic, common dolphin (Delphinus delphis, Linné 1758) bycatch has been increasing and associated with large numbers of animals stranding during winter on the French Atlantic seashore since at least 2017. However, uncertainties around the true magnitude of common dolphin bycatch and the fisheries involved have led to delays in the implementation of mitigation measures. Current data collection on dolphin bycatch in France is with non-dedicated observers deployed on vessels for the purpose of national fisheries sampling programmes. These data cannot be assumed representative of the whole fisheries' bycatch events. This feature makes it difficult to use classic ratio estimators since they require a truly randomised sample of the fishery by dedicated observers. We applied a newly developed approach, regularised multilevel regression with post-stratification, to estimate total bycatch from unrepresentative samples and total fishing effort. The latter is needed for post-stratification and the former is analysed in a Bayesian framework with multilevel regression to regularise and better predict bycatch risk. We estimated the number of bycaught dolphins for each week and 10 International Council for the Exploration of the Sea (ICES) divisions from 2004 to 2020 by estimating jointly bycatch risk, haul duration, and the number of hauls per days at sea (DaS). Bycatch risk in pair trawlers flying the French flag was the highest in winter 2017 and 2019 and was associated with the longest haul durations. ICES divisions 8.a and 8.b (shelf part of the Bay of Biscay) were estimated to have the highest common dolphin bycatch. Our results were consistent with independent estimates of common dolphin bycatch from strandings. Our method show cases how non-representative observer data can nevertheless be analysed to estimate fishing duration, bycatch risk and, ultimately, the number of bycaught dolphins. These weekly-estimates improve upon current knowledge of the nature of common dolphin bycatch and can be used to inform management and policy decisions at a finer spatio-temporal scale than has been possible to date. Our results suggest that limiting haul duration, especially in winter, could serve as an effective mitigation strategy.
The Current Status and Future Direction of Clinical Research in Japan From a Regulatory Perspective
Authors: Maeda Hideki
Published: January 2022

In Japan, a law called the Clinical Trials Act went into being effective on April 1, 2018, and clinical research on human subjects conducted in Japan has been undergone major changes. Those other than clinical trials for marketing approval of drugs or medical devices are broadly classified into “specific clinical trials” and others, and regulations have been tightened for each. As a result, clinical interventional study was drastically reduced, and observational clinical study increased. For the observational clinical study, the two previous ethical guidelines were merged into the “Ethical Guidelines for Medical and Biological Research Involving Human Subjects,” which was enacted in March 2021. The observational clinical study is now subjected to these ethical guidelines. In addition, changes are planned for the Act on the Protection of Personal Information, which greatly affects data collection in clinical research. Clinical research in Japan must be conducted appropriately while adapting to these various changes in the external environment and legal framework. Adapting to these changes is not an easy task, as it requires increased financial and human resources for all stakeholders.
Emerging Parasitic Protists: The Case of Perkinsea
Authors: Itoïz Sarah , Metz Sebastian , Derelle Evelyne , Reñé Albert , Garcés Esther , Bass David , Soudant Philippe , Chambouvet Aurélie
Published: January 2022

The last century has witnessed an increasing rate of new disease emergence across the world leading to permanent loss of biodiversity. Perkinsea is a microeukaryotic parasitic phylum composed of four main lineages of parasitic protists with broad host ranges. Some of them represent major ecological and economical threats because of their geographically invasive ability and pathogenicity (leading to mortality events). In marine environments, three lineages are currently described, the Parviluciferaceae, the Perkinsidae, and the Xcellidae, infecting, respectively, dinoflagellates, mollusks, and fish. In contrast, only one lineage is officially described in freshwater environments: the severe Perkinsea infectious agent infecting frog tadpoles. The advent of high-throughput sequencing methods, mainly based on 18S rRNA assays, showed that Perkinsea is far more diverse than the previously four described lineages especially in freshwater environments. Indeed, some lineages could be parasites of green microalgae, but a formal nature of the interaction needs to be explored. Hence, to date, most of the newly described aquatic clusters are only defined by their environmental sequences and are still not (yet) associated with any host. The unveiling of this microbial black box presents a multitude of research challenges to understand their ecological roles and ultimately to prevent their most negative impacts. This review summarizes the biological and ecological traits of Perkinsea—their diversity, life cycle, host preferences, pathogenicity, and highlights their diversity and ubiquity in association with a wide range of hosts.
Structural Insights for Core Scaffold and Substrate Specificity of B1, B2, and B3 Metallo-β-Lactamases
Authors: Yun Yeongjin , Han Sangjun , Park Yoon Sik , Park Hyunjae , Kim Dogyeong , Kim Yeseul , Kwon Yongdae , Kim Sumin , Lee Jung Hun , Jeon Jeong Ho , Lee Sang Hee , Kang Lin-Woo
Published: January 2022

Metallo-β-lactamases (MBLs) hydrolyze almost all β-lactam antibiotics, including penicillins, cephalosporins, and carbapenems; however, no effective inhibitors are currently clinically available. MBLs are classified into three subclasses: B1, B2, and B3. Although the amino acid sequences of MBLs are varied, their overall scaffold is well conserved. In this study, we systematically studied the primary sequences and crystal structures of all subclasses of MBLs, especially the core scaffold, the zinc-coordinating residues in the active site, and the substrate-binding pocket. We presented the conserved structural features of MBLs in the same subclass and the characteristics of MBLs of each subclass. The catalytic zinc ions are bound with four loops from the two central β-sheets in the conserved αβ/βα sandwich fold of MBLs. The three external loops cover the zinc site(s) from the outside and simultaneously form a substrate-binding pocket. In the overall structure, B1 and B2 MBLs are more closely related to each other than they are to B3 MBLs. However, B1 and B3 MBLs have two zinc ions in the active site, while B2 MBLs have one. The substrate-binding pocket is different among all three subclasses, which is especially important for substrate specificity and drug resistance. Thus far, various classes of β-lactam antibiotics have been developed to have modified ring structures and substituted R groups. Currently available structures of β-lactam-bound MBLs show that the binding of β-lactams is well conserved according to the overall chemical structure in the substrate-binding pocket. Besides β-lactam substrates, B1 and cross-class MBL inhibitors also have distinguished differences in the chemical structure, which fit well to the substrate-binding pocket of MBLs within their inhibitory spectrum. The systematic structural comparison among B1, B2, and B3 MBLs provides in-depth insight into their substrate specificity, which will be useful for developing a clinical inhibitor targeting MBLs.
Responses of Phosphate-Solubilizing Microorganisms Mediated Phosphorus Cycling to Drought-Flood Abrupt Alternation in Summer Maize Field Soil
Authors: Bi Wuxia , Weng Baisha , Yan Denghua , Wang Hao , Wang Mengke , Yan Siying , Jing Lanshu , Liu Tiejun , Chang Wenjuan
Published: January 2022

Soil microbial communities are essential to phosphorus (P) cycling, especially in the process of insoluble phosphorus solubilization for plant P uptake. Phosphate-solubilizing microorganisms (PSM) are the dominant driving forces. The PSM mediated soil P cycling is easily affected by water condition changes due to extreme hydrological events. Previous studies basically focused on the effects of droughts, floods, or drying-rewetting on P cycling, while few focused on drought-flood abrupt alternation (DFAA), especially through microbial activities. This study explored the DFAA effects on P cycling mediated by PSM and P metabolism-related genes in summer maize field soil. Field control experiments were conducted to simulate two levels of DFAA (light drought-moderate flood, moderate drought-moderate flood) during two summer maize growing periods (seeding-jointing stage, tasseling-grain filling stage). Results showed that the relative abundance of phosphate-solubilizing bacteria (PSB) and phosphate-solubilizing fungi (PSF) increased after DFAA compared to the control system (CS), and PSF has lower resistance but higher resilience to DFAA than PSB. Significant differences can be found on the genera Pseudomonas, Arthrobacter, and Penicillium, and the P metabolism-related gene K21195 under DFAA. The DFAA also led to unstable and dispersed structure of the farmland ecosystem network related to P cycling, with persistent influences until the mature stage of summer maize. This study provides references for understanding the micro process on P cycling under DFAA in topsoil, which could further guide the DFAA regulations.
Lactiplantibacillus plantarum AR113 Exhibit Accelerated Liver Regeneration by Regulating Gut Microbiota and Plasma Glycerophospholipid
Authors: Xie Chunliang , Zhang Zhoumei , Yang Manyi , Cao Cha , Zhou Yingjun , Zhu Zuohua , Gong Wenbing , Xu Chao , Yan Li , Hu Zhenxiu , Ai Lianzhong , Peng Yuande
Published: January 2022

Emerging evidence indicates that probiotics have been proved to influence liver injury and regeneration. In the present study, the effects of Lactiplantibacillus plantarum AR113 on the liver regeneration were investigated in 70% partial hepatectomy (PHx) rats. Sprague-Dawley (SD) rats were gavaged with L. plantarum AR113 suspensions (1 × 1010 CFU/mL) both before and after partial hepatectomy. The results showed that L. plantarum AR113 administration 2 weeks before partial hepatectomy can accelerate liver regeneration by increased hepatocyte proliferation and tumor necrosis factor-α (TNF-α), hepatocyte growth factor (HGF), and transforming growth factor-β (TGF-β) expression. Probiotic administration enriched Lactobacillus and Bacteroides and depleted Flavonifractor and Acetatifactor in the gut microbiome. Meanwhile, L. plantarum AR113 showed decline of phosphatidylethanolamine (PE), phosphatidylcholine (PC), phosphatidyl serine (PS), and lysophosphatidyl choline (LysoPC) levels in the serum of the rats after the L. plantarum AR113 administration. Moreover, L. plantarum AR113 treated rats exhibited higher concentrations of L-leucine, L-isoleucine, mevalonic acid, and lower 7-oxo-8-amino-nonanoic acid in plasma than that in PHx. Spearman correlation analysis revealed a significant correlation between changes in gut microbiota composition and glycerophospholipid. These results indicate that L. plantarum AR113 is promising for accelerating liver regeneration and provide new insights regarding the correlations among the microbiome, the metabolome, and liver regeneration.
Nosocomial Outbreak of Carbapenemase-Producing Proteus mirabilis With Two Novel Salmonella Genomic Island 1 Variants Carrying Different blaNDM–1 Gene Copies in China
Authors: Yang Lang , He Hong , Chen Qichao , Wang Kaiying , Lin Yanfeng , Li Peihan , Li Jinhui , Liu Xiong , Jia Leili , Song Hongbin , Li Peng
Published: January 2022

NDM-1-producing multidrug-resistant Proteus mirabilis brings formidable clinical challenges. We report a nosocomial outbreak of carbapenem-resistant P. mirabilis in China. Six P. mirabilis strains collected in the same ward showed close phylogenetic relatedness, indicating clonal expansion. Illumina and MinION sequencing revealed that three isolates harbored a novel Salmonella genomic island 1 carrying a blaNDM–1 gene (SGI1-1NDM), while three other isolates showed elevated carbapenem resistance and carried a similar SGI1 but with two blaNDM–1 gene copies (SGI1-2NDM). Four new single nucleotide mutations were present in the genomes of the two-blaNDM–1-harboring isolates, indicating later emergence of the SGI1-2NDM structure. Passage experiments indicated that both SGI variants were stably persistent in this clone without blaNDM–1 copy number changes. This study characterizes two novel blaNDM–1-harboring SGI1 variants in P. mirabilis and provides a new insight into resistance gene copy number variation in bacteria.
Mechanism of a Volatile Organic Compound (6-Methyl-2-Heptanone) Emitted From Bacillus subtilis ZD01 Against Alternaria solani in Potato
Authors: Zhang Dai , Qiang Ran , Zhao Jing , Zhang Jinglin , Cheng Jianing , Zhao Dongmei , Fan Yaning , Yang Zhihui , Zhu Jiehua
Published: January 2022

The antagonistic mechanisms of soluble non-volatile bioactive compounds, such as proteins and lipopeptides emitted from Bacillus have been widely studied. However, there are limited studies on the antifungal mechanisms of volatile organic compounds (VOCs) produced by Bacillus against plant fungal diseases. In this study, the antagonistic mechanisms of one specific VOC, 6-methyl-2-heptanone, against Alternaria solani were investigated. To optimize the extraction conditions of headspace solid-phase microextraction, a 50/30-μm divinylbenzene/carboxen/polydimethylsiloxane fiber at 50°C for 40 min was used. For gas chromatography-mass spectrometry using a free fatty acid phase capillary column, 6-methyl-2-heptanone accounted for the highest content, at 22.27%, of the total VOCs from Bacillus subtilis ZD01, which inhibited A. solani mycelial growth strongly in vitro. Therefore, 6-methyl-2-heptanone was selected as the main active chemical to elucidate the action mechanisms against A. solani. Scanning and transmission electron microscopy analyses revealed that after exposure to an EC50 dose of 6-methyl-2-heptanone, A. solani hyphal cells had a wide range of abnormalities. 6-Methyl-2-heptanone also caused the capture of cellular fluorescent green label and the release of adenosine triphosphate (ATP) from outer membranes A. solani cells, which may enhance 6-methyl-2-heptanone ability to reach the cytoplasmic membrane. In addition, 6-methyl-2-heptanone showed strong inhibitory effect on A. solani conidial germination. It also damaged conidial internal structures, with the treated group having collapsed shrunken small vesicles as observed by transmission electron microscopy. Because 6-methyl-2-heptanone showed strong effects on mycelial integrity and conidial structure, the expression levels of related pathogenic genes in A. solani treated with 6-methyl-2-heptanone were investigated. The qRT-PCR results showed that transcriptional expression levels of slt2 and wetA genes were strongly down-regulated after exposure to 6-methyl-2-heptanone. Finally, because identifying the functions of pathogenic genes will be important for the biological control of A. solani, the wetA gene was identified as a conidia-associated gene that plays roles in regulating sporulation yield and conidial maturation. These findings provide further insights into the mechanisms of VOCs secreted by Bacillus against A. solani.
Wheat Microbiome: Structure, Dynamics, and Role in Improving Performance Under Stress Environments
Authors: Chen Jian , Sharifi Rouhallah , Khan Muhammad Saad Shoaib , Islam Faisal , Bhat Javaid Akhter , Kui Ling , Majeed Aasim
Published: January 2022

Wheat is an important cereal crop species consumed globally. The growing global population demands a rapid and sustainable growth of agricultural systems. The development of genetically efficient wheat varieties has solved the global demand for wheat to a greater extent. The use of chemical substances for pathogen control and chemical fertilizers for enhanced agronomic traits also proved advantageous but at the cost of environmental health. An efficient alternative environment-friendly strategy would be the use of beneficial microorganisms growing on plants, which have the potential of controlling plant pathogens as well as enhancing the host plant’s water and mineral availability and absorption along with conferring tolerance to different stresses. Therefore, a thorough understanding of plant-microbe interaction, identification of beneficial microbes and their roles, and finally harnessing their beneficial functions to enhance sustainable agriculture without altering the environmental quality is appealing. The wheat microbiome shows prominent variations with the developmental stage, tissue type, environmental conditions, genotype, and age of the plant. A diverse array of bacterial and fungal classes, genera, and species was found to be associated with stems, leaves, roots, seeds, spikes, and rhizospheres, etc., which play a beneficial role in wheat. Harnessing the beneficial aspect of these microbes is a promising method for enhancing the performance of wheat under different environmental stresses. This review focuses on the microbiomes associated with wheat, their spatio-temporal dynamics, and their involvement in mitigating biotic and abiotic stresses.
Characterization of an Aging-Based Diagnostic Gene Signature and Molecular Subtypes With Diverse Immune Infiltrations in Atherosclerosis
Authors: Zhao Lei , Lv Fengfeng , Zheng Ye , Yan Liqiu , Cao Xufen
Published: January 2022

Objective: Advancing age is a major risk factor of atherosclerosis (AS). Nevertheless, the mechanism underlying this phenomenon remains indistinct. Herein, this study conducted a comprehensive analysis of the biological implications of aging-related genes in AS.

Methods: Gene expression profiles of AS and non-AS samples were curated from the GEO project. Differential expression analysis was adopted for screening AS-specific aging-related genes. LASSO regression analysis was presented for constructing a diagnostic model, and the discriminatory capacity was evaluated with ROC curves. Through consensus clustering analysis, aging-based molecular subtypes were conducted. Immune levels were estimated based on the expression of HLAs, immune checkpoints, and immune cell infiltrations. Key genes were then identified via WGCNA. The effects of CEBPB knockdown on macrophage polarization were examined with western blotting and ELISA. Furthermore, macrophages were exposed to 100 mg/L ox-LDL for 48 h to induce macrophage foam cells. After silencing CEBPB, markers of cholesterol uptake, esterification and hydrolysis, and efflux were detected with western blotting.

Results: This study identified 28 AS-specific aging-related genes. The aging-related gene signature was developed, which could accurately diagnose AS in both the GSE20129 (AUC = 0.898) and GSE43292 (AUC = 0.685) datasets. Based on the expression profiling of AS-specific aging-related genes, two molecular subtypes were clustered, and with diverse immune infiltration features. The molecular subtype–relevant genes were obtained with WGCNA, which were markedly associated with immune activation. Silencing CEBPB triggered anti-inflammatory M2-like polarization and suppressed foam cell formation.

Conclusion: Our findings suggest the critical implications of aging-related genes in diagnosing AS and modulating immune infiltrations.
Brain Activity and Functional Connectivity Patterns Associated With Fast and Slow Motor Sequence Learning in Late Middle Adulthood
Authors: Aznárez-Sanado Maite , Eudave Luis , Martínez Martín , Luis Elkin O. , Villagra Federico , Loayza Francis R. , Fernández-Seara María A. , Pastor María A.
Published: January 2022

The human brain undergoes structural and functional changes across the lifespan. The study of motor sequence learning in elderly subjects is of particularly interest since previous findings in young adults might not replicate during later stages of adulthood. The present functional magnetic resonance imaging (fMRI) study assessed the performance, brain activity and functional connectivity patterns associated with motor sequence learning in late middle adulthood. For this purpose, a total of 25 subjects were evaluated during early stages of learning [i.e., fast learning (FL)]. A subset of these subjects (n = 11) was evaluated after extensive practice of a motor sequence [i.e., slow learning (SL) phase]. As expected, late middle adults improved motor performance from FL to SL. Learning-related brain activity patterns replicated most of the findings reported previously in young subjects except for the lack of hippocampal activity during FL and the involvement of cerebellum during SL. Regarding functional connectivity, precuneus and sensorimotor lobule VI of the cerebellum showed a central role during improvement of novel motor performance. In the sample of subjects evaluated, connectivity between the posterior putamen and parietal and frontal regions was significantly decreased with aging during SL. This age-related connectivity pattern may reflect losses in network efficiency when approaching late adulthood. Altogether, these results may have important applications, for instance, in motor rehabilitation programs.
Validation of a System xc– Functional Assay in Cultured Astrocytes and Nervous Tissue Samples
Authors: Beckers Pauline , Lara Olaya , Belo do Nascimento Ines , Desmet Nathalie , Massie Ann , Hermans Emmanuel
Published: January 2022

Disruption of the glutamatergic homeostasis is commonly observed in neurological diseases and has been frequently correlated with the altered expression and/or function of astrocytic high-affinity glutamate transporters. There is, however, a growing interest for the role of the cystine-glutamate exchanger system xc– in controlling glutamate transmission. This exchanger is predominantly expressed in glial cells, especially in microglia and astrocytes, and its dysregulation has been documented in diverse neurological conditions. While most studies have focused on measuring the expression of its specific subunit xCT by RT-qPCR or by Western blotting, the activity of this exchanger in tissue samples remains poorly examined. Indeed, the reported use of sulfur- and carbon-radiolabeled cystine in uptake assays shows several drawbacks related to its short radioactive half-life and its relatively high cost. We here report on the elaborate validation of a method using tritiated glutamate as a substrate for the reversed transport mediated by system xc–. The uptake assay was validated in primary cultured astrocytes, in transfected cells as well as in crude synaptosomes obtained from fresh nervous tissue samples. Working in buffers containing defined concentrations of Na+, allowed us to differentiate the glutamate uptake supported by system xc– or by high-affinity glutamate transporters, as confirmed by using selective pharmacological inhibitors. The specificity was further demonstrated in primary astrocyte cultures from transgenic mice lacking xCT or in cell lines where xCT expression was genetically induced or reduced. As such, this assay appears to be a robust and cost-efficient solution to investigate the activity of this exchanger in physiological and pathological conditions. It also provides a reliable tool for the screening and characterization of new system xc– inhibitors which have been frequently cited as valuable drugs for nervous disorders and cancer.