bluuebunny/crossref_metadata_2025 huggingface dataset:
Immune Gene Signatures and Immunotypes in Immune Microenvironment Are Associated With Glioma Prognose
Authors: Wang Xiang-Xu , Cao Haiyan , Zhai Yulong , Deng Shi-Zhou , Chao Min , Hu Yaqin , Mou Yueyang , Guo Shaochun , Zhao Wenjian , Li Chen , Jiao Yang , Xue Guolian , Han Liying , Zhang Hong-Mei , Wang Liang
Published: April 2022

Glioma is the most common primary malignant brain tumor in adults with very poor prognosis. The limited new therapeutic strategies for glioma patients can be partially attributed to the complex tumor microenvironment. However, knowledge about the glioma immune microenvironment and the associated regulatory mechanisms is still lacking. In this study, we found that, different immune subtypes have a significant impact on patient survival. Glioma patients with a high immune response subtype had a shorter survival compared with patients with a low immune response subtype. Moreover, the number of B cell, T cell, NK cell, and in particular, the macrophage in the immune microenvironment of patients with a high immune response subtype were significantly enhanced. In addition, 132 genes were found to be related to glioma immunity. The functional analysis and verification of seven core genes showed that their expression levels were significantly correlated with the prognosis of glioma patients, and the results were consistent at tissue levels. These findings indicated that the glioma immune microenvironment was significantly correlated with the prognosis of glioma patients and multiple genes were involved in regulating the progression of glioma. The identified genes could be used to stratify glioma patients based on immune subgroup analysis, which may guide their clinical treatment regimen.
Cell-Free DNA Promotes Inflammation in Patients With Oral Lichen Planus via the STING Pathway
Authors: Deng Jing , Pan Weiyi , Ji Ning , Liu Na , Chen Qian , Chen Jinhuan , Sun Yutong , Xie Liang , Chen Qianming
Published: April 2022

Background

Damaged and dead cells release cell-free DNA (cfDNA) that activates cyclic GMP–AMP (cGAMP) synthase (cGAS), which leads to the activation of stimulator of interferon genes (STING) via the second messenger cGAMP. STING promotes the production of inflammatory cytokines and type I interferons to induce an inflammatory response. Oral lichen planus (OLP), a chronic autoimmune disease involving oral mucosa characterized by the apoptosis of keratinocytes mediated by T-lymphocytes, is related to the activation of multiple inflammatory signaling pathways. Currently, the relationship between cfDNA and OLP has not been confirmed. We hypothesized that cfDNA may be a potential therapeutic target for OLP.

Methods

cfDNA was extracted from the saliva and plasma of OLP patients; its concentration was measured using the Quanti-iT-PicoGree kit and its relationship with OLP inflammation was assessed. cfDNA of OLP patients (cfDNA-OLP) was transfected into THP-1 macrophages and the expression of inflammatory factors was investigated by performing quantitative real time PCR (qRT-PCR), western blotting, and enzyme-linked immunosorbent assay (ELISA). STING expression was analyzed in the tissues of OLP patients and healthy controls using immunohistochemical staining and western blotting. siRNA was used to knockdown STING expression in THP-1 macrophages, and the inflammatory cytokines tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) secreted by cells following cfDNA-OLP transfection were detected using ELISA. Finally, the effect of the cationic polymer PAMAM-G3 was evaluated on the treatment of inflammation induced by cfDNA-OLP.

Results

The concentration of cfDNA in the saliva and plasma of OLP patients was considerably higher than that of healthy controls, and it positively correlated with the levels of inflammatory cytokines and clinical characteristics. cfDNA-OLP induced an inflammatory response in THP-1 macrophages. STING expression was significantly higher in OLP tissues than in the gingival tissues of healthy controls. STING knockdown suppressed cfDNA-OLP-induced inflammation in THP-1 macrophages. PAMAM-G3 inhibited the inflammatory response caused by cfDNA-OLP.

Conclusion

The cfDNA level is increased in OLP patients, and the STING pathway activated by cfDNA-OLP might play a critical role in OLP pathogenesis. Treatment with PAMAM-G3 reduced the inflammation induced by cfDNA-OLP, and therefore, may be a potential treatment strategy for OLP.
Non-Muscle Myosin II Is Essential for the Negative Regulation of B-Cell Receptor Signaling and B-Cell Activation
Authors: Seeley-Fallen Margaret K. , Lazzaro Michelle , Liu Chaohong , Li Quan-Zhen , Upadhyaya Arpita , Song Wenxia
Published: April 2022

Antigen (Ag)-triggered B-cell receptor (BCR) signaling initiates antibody responses. However, prolonged or uncontrolled BCR signaling is associated with the development of self-reactive B-cells and autoimmune diseases. We previously showed that actin-mediated B-cell contraction on Ag-presenting surfaces negatively regulates BCR signaling. Non-muscle myosin II (NMII), an actin motor, is involved in B-cell development and antibody responses by mediating B-cell migration, cytokinesis, and Ag extraction from Ag-presenting cells. However, whether and how NMII regulates humoral responses through BCR signaling remains elusive. Utilizing a B-cell-specific, partial NMIIA knockout (cIIAKO) mouse model and NMII inhibitors, this study examined the role of NMII in BCR signaling. Upon BCR binding to antibody-coated planar lipid bilayers (PLB), NMIIA was recruited to the B-cell contact membrane and formed a ring-like structure during B-cell contraction. NMII recruitment depended on phosphatidylinositol 5-phosphatase (SHIP1), an inhibitory signaling molecule. NMII inhibition by cIIAKO did not affect B-cell spreading on PLB but delayed B-cell contraction and altered BCR clustering. Surface BCR “cap” formation induced by soluble stimulation was enhanced in cIIAKO B-cells. Notably, NMII inhibition by cIIAKO and inhibitors up-regulated BCR signaling in response to both surface-associated and soluble stimulation, increasing phosphorylated tyrosine, CD79a, BLNK, and Erk and decreasing phosphorylated SHIP1. While cIIAKO did not affect B-cell development, the number of germinal center B-cells was significantly increased in unimmunized cIIAKO mice, compared to control mice. While cIIAKO mice mounted similar antibody responses when compared to control mice upon immunization, the percentages of high-affinity antibodies, Ag-specific germinal center B-cells and isotype switched B-cells were significantly lower in cIIAKO mice than in control mice. Furthermore, autoantibody levels were elevated in cIIAKO mice, compared to control mice. Collectively, our results reveal that NMII exerts a B-cell-intrinsic inhibition on BCR signaling by regulating B-cell membrane contraction and surface BCR clustering, which curtails the activation of non-specific and self-reactive B-cells.
CD33 Expression on Peripheral Blood Monocytes Predicts Efficacy of Anti-PD-1 Immunotherapy Against Non-Small Cell Lung Cancer
Authors: Olingy Claire , Alimadadi Ahmad , Araujo Daniel J. , Barry David , Gutierrez Norma A. , Werbin Max Hardy , Arriola Edurne , Patel Sandip Pravin , Ottensmeier Christian H. , Dinh Huy Q. , Hedrick Catherine C.
Published: April 2022

Non-small cell lung carcinoma (NSCLC) is the leading cause of cancer-related deaths globally. Immune checkpoint blockade (ICB) has transformed cancer medicine, with anti-programmed cell death protein 1 (anti-PD-1) therapy now well-utilized for treating NSCLC. Still, not all patients with NSCLC respond positively to anti-PD-1 therapy, and some patients acquire resistance to treatment. There remains an urgent need to find markers predictive of anti-PD-1 responsiveness. To this end, we performed mass cytometry on peripheral blood mononuclear cells from 26 patients with NSCLC during anti-PD-1 treatment. Patients who responded to anti-PD-1 ICB displayed significantly higher levels of antigen-presenting myeloid cells, including CD9+ nonclassical monocytes, and CD33hi classical monocytes. Using matched pre-post treatment samples, we found that the baseline pre-treatment frequencies of CD33hi monocytes predicted patient responsiveness to anti-PD-1 therapy. Moreover, some of these classical and nonclassical monocyte subsets were associated with reduced immunosuppression by T regulatory (CD4+FOXP3+CD25+) cells in the same patients. Our use of machine learning corroborated the association of specific monocyte markers with responsiveness to ICB. Our work provides a high-dimensional profile of monocytes in NSCLC and links CD33 expression on monocytes with anti-PD-1 effectiveness in patients with NSCLC.
PAMPs of Piscirickettsia salmonis Trigger the Transcription of Genes Involved in Nutritional Immunity in a Salmon Macrophage-Like Cell Line
Authors: Martínez Danixa Pamela , Oliver Cristian , Santibañez Natacha , Coronado José Leonardo , Oyarzún-Salazar Ricardo , Enriquez Ricardo , Vargas-Chacoff Luis , Romero Alex
Published: April 2022

The innate immune system can limit the growth of invading pathogens by depleting micronutrients at a cellular and tissue level. However, it is not known whether nutrient depletion mechanisms discriminate between living pathogens (which require nutrients) and pathogen-associated molecular patterns (PAMPs) (which do not). We stimulated SHK-1 cells with different PAMPs (outer membrane vesicles of Piscirickettsia salmonis “OMVs”, protein extract of P. salmonis “TP” and lipopolysaccharides of P. salmonis “LPS”) isolated from P. salmonis and evaluated transcriptional changes in nutritional immunity associated genes. Our experimental treatments were: Control (SHK-1 stimulated with bacterial culture medium), OMVs (SHK-1 stimulated with 1μg of outer membrane vesicles), TP (SHK-1 stimulated with 1μg of total protein extract) and LPS (SHK-1 stimulated with 1μg of lipopolysaccharides). Cells were sampled at 15-, 30-, 60- and 120-minutes post-stimulation. We detected increased transcription of zip8, zip14, irp1, irp2 and tfr1 in all three experimental conditions and increased transcription of dmt1 in cells stimulated with OMVs and TP, but not LPS. Additionally, we observed generally increased transcription of ireg-1, il-6, hamp, irp1, ft-h and ft-m in all three experimental conditions, but we also detected decreased transcription of these markers in cells stimulated with TP and LPS at specific time points. Our results demonstrate that SHK-1 cells stimulated with P. salmonis PAMPs increase transcription of markers involved in the transport, uptake, storage and regulation of micronutrients such as iron, manganese and zinc.
Differences in Humoral and Cellular Vaccine Responses to SARS-CoV-2 in Kidney and Liver Transplant Recipients
Authors: Furian Lucrezia , Russo Francesco Paolo , Zaza Gianluigi , Burra Patrizia , Hartzell Susan , Bizzaro Debora , Di Bello Marianna , Di Bella Caterina , Nuzzolese Erica , Agnolon Clara , Florman Sander , Rana Meenakshi , Lee Jar-How , Kim Yesl , Maggiore Umberto , Maltzman Jonathan S. , Cravedi Paolo
Published: April 2022

The antibody and T cell responses after SARS-CoV-2 vaccination have not been formally compared between kidney and liver transplant recipients. Using a multiplex assay, we measured IgG levels against 4 epitopes of SARS-CoV-2 spike protein and nucleocapsid (NC) antigen, SARS-CoV-2 variants, and common coronaviruses in serial blood samples from 52 kidney and 50 liver transplant recipients undergoing mRNA SARS-CoV-2 vaccination. We quantified IFN-γ/IL-2 T cells reactive against SARS-CoV-2 spike protein by FluoroSpot. We used multivariable generalized linear models to adjust for the differences in immunosuppression between groups. In liver transplant recipients, IgG levels against every SARS-CoV-2 spike epitope increased significantly more than in kidney transplant recipients (MFI: 19,617 vs 6,056; P<0.001), a difference that remained significant after adjustments. Vaccine did not affect IgG levels against NC nor common coronaviruses. Elicited antibodies recognized all variants tested but at significantly lower strength than the original Wuhan strain. Anti-spike IFN-γ-producing T cells increased significantly more in liver than in kidney transplant recipients (IFN-γ-producing T cells 28 vs 11 spots/5x105 cells), but this difference lost statistical significance after adjustments. SARS-CoV-2 vaccine elicits a stronger antibody response in liver than in kidney transplant recipients, a phenomenon that is not entirely explained by the different immunosuppression.
Clinical and Renal Histology Findings and Different Responses to Induction Treatment Affecting the Long-Term Renal Outcomes of Children With ANCA-Associated Vasculitis: a Single-Center Cohort Analysis
Authors: Yang Jing , Yang Yuan , Xu Yongli , Zhou Lanqi , Zhou Luowen , Yin Xiaoling , Pu Jinyun , Yang Fengjie , Liu Yaping , He Yonghua , Chen Yaxian , Yuan Huiqing , Qiu Liru , Zhang Yu , Chen Yu , Liu Tonglin , Tang Jinhui , Zhou Jianhua
Published: April 2022

Introduction

Antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) is relatively rare in children. This article aimed to analyze clinical and renal histology findings and different responses to induction treatment associated with the long-term renal outcomes in children with AAV in a single center.

Methods

All pediatric patients with AAV admitted to Tongji Hospital from January 2002 to January 2021 were included in the study. The demographic, clinical, pathological, laboratory, and treatment data and outcomes were collected and analyzed to identify predictors associated with response to induction treatment and progression to end-stage renal disease (ESRD).

Results

In total, 48 children with AAV were included in this cohort; 81.25% of them were women, and 91.7% were microscopic polyangiitis (MPA). Kidney involvement was found in 45 patients (93.75%). The most common histopathological subtype was crescentic form in this cohort according to Berden’s classification. In total, 34 patients (70.8%) showed eGFR <60 ml/min/1.73 m2 at the time of diagnosis. Complete and partial remission was achieved in 8 patients (16.7%) and 19 patients (39.6%), respectively, following 6-month induction treatment. Half of the patients eventually progressed to ESRD at a mean time of (13.04 ± 15.83) months after diagnosis. The independent predictors of nonremission following induction treatment and progression to ESRD were baseline eGFR <60 ml/min/1.73 m2 and hypertension at diagnosis. Renal survival significantly decreased over time in patients with renal sclerotic subtypes or those with nonremission following induction treatment by Kaplan–Meier curve estimation.

Conclusions

Our study demonstrates that women, MPA, and crescentic subtypes are predominant in pediatric AAV in China. Initial renal failure (eGFR <60 ml/min/1.73 m2), hypertension, sclerotic pathological subtype, and nonremission following induction treatment are predictive of long-term renal outcomes.
Persistence of SARS-CoV-2 Infection in Severely Immunocompromised Patients With Complete Remission B-Cell Lymphoma and Anti-CD20 Monoclonal Antibody Therapy: A Case Report of Two Cases
Authors: Martínez-Chinchilla Carlos , Vazquez-Montero Lucía , Palazón-Carrión Natalia , Fernández-Román Isabel M. , López-Barba José , de la Cruz-Merino Luis , Rodríguez-Baño Jesús , Palacios-Baena Zaira R.
Published: April 2022

Immunosuppressant conditions such as hematological malignancies increase the risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. It has been described in the literature that patients on anti-CD20 maintenance therapies for lymphoid malignancies are susceptible to having recurrent flares together with viral replication or reinfections, although these cases are scarce. These patients are not well represented in randomized controlled trials, and as a consequence, the evidence for the use of certain treatments in this scenario is lacking. We present two cases of patients with B-cell lymphoma on remission and treated with rituximab on maintenance. They developed at least 1 flare of coronavirus disease 2019 (COVID-19) after acute infection and always after receiving rituximab. RT-PCR was positive in the nasopharyngeal swab and also in plasma. Patients were treated during flares with remdesivir, hyperimmune plasma, and corticosteroids. These two cases showed the unresolved problem of COVID-19 in immunosuppressant patients and showed that despite the vast amount of information available on SARS-CoV-2, information in this subgroup of patients is lacking.
Elevated Expression of TLR2 in Aging Hearts Exacerbates Cardiac Inflammatory Response and Adverse Remodeling Following Ischemia and Reperfusion Injury
Authors: Zhai Yufeng , Ao Lihua , Yao Qingzhou , The Erlinda , Fullerton David A. , Meng Xianzhong
Published: April 2022

This study tested the hypothesis that Toll-like receptor 2 (TLR2) augments the inflammatory responses and adverse remodeling in aging hearts to exacerbate myocardial injury and cardiac dysfunction.

Methods

Old (20-22 months old) and adult (4-6 months old) mice of C57BL/6 wild-type and TLR2 knockout (KO) were subjected to coronary artery ligation (30 minutes) and reperfusion (3 or 14 days). Left ventricle function was assessed using a pressure-volume microcatheter. Cardiac infarct size was determined by histology. Levels of vascular cell adhesion molecule-1 (VCAM-1), intercellular adhesion molecule-1 (ICAM-1), matrix metalloproteinase 9 (MMP 9), and collagen I in non-ischemic myocardium were assessed by immunoblotting. Monocyte chemoattractant protein-1 (MCP-1), keratinocyte chemoattractant (KC), and interleukin-6 (IL-6) levels in ischemic and non-ischemic myocardium were measured by enzyme-linked immunosorbent assay (ELISA). TLR2 expression in the myocardium of untreated wild type mice was also measured by immunoblotting.

Results

Higher levels of MCP-1, KC, IL-6 were induced in both ischemic and non-ischemic myocardium of old wild type mice at day 3 and 14 following ischemia/reperfusion (I/R) than those of adult wild type mice. The hyper-inflammatory responses to I/R in aging hearts were associated with elevated levels of myocardial TLR2. TLR2 KO markedly down-regulated the expression of MCP-1, KC, IL-6, ICAM-1 and VCAM-1 in aging hearts at day 3 and 14 following I/R. The down-regulated inflammatory activity in aging TLR2 KO hearts was associated with attenuated production of MMP 9 and collagen I at day 14 and resulted in reduced infarct size and improved cardiac function.

Conclusion

Elevated expression of myocardial TLR2 contributes to the mechanism by which aging exacerbates the inflammatory responses, adverse remodeling and cardiac dysfunction following myocardial I/R in aging.
Evolution of the Distribution and Dynamic of Microplastic in Water and Biota: A Study Case From the Gulf of Gabes (Southern Mediterranean Sea)
Authors: Ben Ismail Sana , Costa Elisa , Jaziri Hela , Morgana Silvia , Boukthir Moncef , Ben Ismail Mohamed Anis , Minetti Roberta , Montarsolo Alessio , Narizzano Riccardo , Sammari Cherif , Faimali Marco , Garaventa Francesca
Published: April 2022

Marine plastic pollution represents a major problem owing to its increasing presence in the environment, persistence and ability to spread in every compartment in the form of small plastic particles, namely microplastics (MPs). Studies concerning MPs abundance in the Mediterranean Sea are growing, but their occurrence in the Southern regions remains largely unexplored. In this study, distribution, abundance, size, and polymer type of microplastics were investigated in surface water samples collected with a Manta net (200 μm mesh size) and in 118 marine specimens of commercial interests, including fishes, crustaceans, and mollusks, during Spring and Autumn 2019 EU H2020 Claim Project sampling Campaigns in the Gulf of Gabes (Southern Mediterranean Sea). Laboratory characterization showed significant plastic pollution concentrations, with an average abundance of 312,887 and 77,110 items/km2 in surface water samples collected in Spring and Autumn, respectively. A 3D hydrodynamic and Tracking Model was used to identify dispersal and transport pathways of the floating plastics, reporting a seasonal variability observed in MPs distribution between I (Spring) and II Campaign (Autumn). Despite the high values of MPs abundance found in surface water samples, an overall low frequency of ingestion among studied species was observed, with a maximum value of 20% of individuals (in Scomber scombrus) found with ingested MPs. The present study contributes to expand our state of knowledge regarding MPs pollution level in water and biota samples collected in the Gulf of Gabes, an area of particular interest for its biological resources, but still little investigated.
Novel Methodologies for Providing In Situ Data to HAB Early Warning Systems in the European Atlantic Area: The PRIMROSE Experience
Authors: Ruiz-Villarreal Manuel , Sourisseau Marc , Anderson Phil , Cusack Caroline , Neira Patricia , Silke Joe , Rodriguez Francisco , Ben-Gigirey Begoña , Whyte Callum , Giraudeau-Potel Solene , Quemener Loic , Arthur Gregg , Davidson Keith
Published: April 2022

Harmful algal blooms (HABs) cause harm to human health or hinder sustainable use of the marine environment in Blue Economy sectors. HABs are temporally and spatially variable and hence their mitigation is closely linked to effective early warning. The European Union (EU) Interreg Atlantic Area project “PRIMROSE”, Predicting Risk and Impact of Harmful Events on the Aquaculture Sector, was focused on the joint development of HAB early warning systems in different regions along the European Atlantic Area. Advancement of the existing HAB forecasting systems requires development of forecasting tools, improvements in data flow and processing, but also additional data inputs to assess the distribution of HAB species, especially in areas away from national monitoring stations, usually located near aquaculture sites. In this contribution, we review different novel technologies for acquiring HAB data and report on the experience gained in several novel local data collection exercises performed during the project. Demonstrations include the deployment of autonomous imaging flow cytometry (IFC) sensors near two aquaculture areas: a mooring in the Daoulas estuary in the Bay of Brest and pumping from a bay in the Shetland Islands to an inland IFC; and several drone deployments, both of Unmanned Aerial Vehicles (UAV) and of Autonomous Surface vehicles (ASVs). Additionally, we have reviewed sampling approaches potentially relevant for HAB early warning including protocols for opportunistic water sampling by coastguard agencies. Experiences in the determination of marine biotoxins in non-traditional vectors and how they could complement standard routine HAB monitoring are also considered.
Seasonal Trophic Dynamics of Sinking Particles in the Ulleung Basin of the East Sea (Japan Sea): An Approach Employing Nitrogen Isotopes of Amino Acids
Authors: Choi Hyuntae , Hwang Jeomshik , Ryu Yeongjin , Kim Guebuem , Shin Kyung-Hoon
Published: April 2022

To identify the sources of organic matter, we examined nitrogen isotopes of the amino acids of sinking particles collected from July 2017 to March 2018 at 1000 and 2250 m in the Ulleung Basin, the southwestern part of the East Sea (Japan Sea). Compared to the 1000 m samples, sinking particles at 2250 m were found to contain more resuspended sediment and underwent more microbial degradation. The signature of microbial degradation was significant in winter-early spring than in late summer-autumn. The source amino acids of sinking particles showed a substantial decline in the isotopic ratio during winter at both depths, suggesting changes in the nitrogen source for primary production. The average trophic positions (TPs) of sinking particles were larger at 1000 m (2.3 ± 0.3) than at 2250 m (1.9 ± 0.2), indicating that organic matter was mainly derived from fecal pellet and other organic debris from heterotrophs. In winter, the average TPs of sinking particles at 1000 m decreased below 2.0, which probably reflects the minimum zooplankton grazing in the euphotic layer. Sinking particles near the seafloor (2250 m) showed lower TP values than those at 1000 m, demonstrating that sinking particles at 2250 m are affected by lateral transport, particularly during winter. Our results show that the nitrogen isotope ratios of amino acids in sinking particles reflect the seasonal dynamics of both nitrogen sources and trophic structure in the water column.
Mitogenomes Provide Insights Into the Evolution of Thoracotremata (Brachyura: Eubrachyura)
Authors: Sun Shao’e , Jiang Wei , Yuan Ziming , Sha Zhongli
Published: April 2022

Thoracotremata is a group of Brachyura, with 1,248 extant species. To date, parts of the thoracotreme phylogeny are not yet resolved and require further investigation. In this study, 12 new mitogenomes from the four thoracotreme superfamilies were sequenced. They contain a standard set of 37 genes, and vary in size from 15,422 (Hapalocarcinus marsupialis Stimpson, 1858 sensu lato) to 16,490 bp [Arcotheres sinensis (Shen, 1932)]. Combined with 58 thoracotreme mitochondrial genomes (mitogenomes) from GenBank, we described the evolution of gene rearrangement and the internal phylogenetic relationships of Thoracotremata, and evaluated the phylogenetic position of Cryptochiroidea and Pinnotheroidea. Nine distinct patterns of mitochondrial gene order (MGO) among thoracotreme mitogenomes are identified, with four MGOs newly found in Thoracotremata. All other gene orders are the result of transformational pathways originating from brachyuran gene order (BraGO). The different gene orders have variable levels of gene rearrangements, which involve both tRNAs and protein-coding genes. No link between variable gene arrangements (breakpoint distances) and nucleotide substitution rates (branch lengths) is found in thoracotreme crabs. The symbiotic groups, the cryptochiroid and pinnotheroid crabs, display variable MGOs (CryGO, Pin1GO, and Pin2GO), providing evidence for possible correlations of rearranged MGOs to the adaptations to specialized lifestyles. In our phylogenetic analyses, Cryptochiridae (Cryptochiroidea) show close relationship with an Ocypodoidea lineage (Camptandriidae/Xenophthalmidae/Dotillidae). Pinnotheridae (Pinnotheroidea) form the basal monophyletic clade.
A 4D-Printed Structure With Reversible Deformation for the Soft Crawling Robot
Authors: Duan Guifang , Liu Han , Liu Zhenyu , Tan Jianrong
Published: April 2022

Reversible deformations of the 4D-printed structures are attractive and promising for various application fields. In this study, the principle of reversible deformations for the bilayer structure consisting of SMP and elastic material is illustrated. By exploring the influence of printing parameters on deformation and resistance, a low-cost reversible bilayer structure with rational resistance distribution is designed to realize reversible deformation. Subsequently, the bilayer structure is employed to design a soft crawling robot with asymmetrical variable friction coefficient feet. By revealing the principle of locomotion by force analysis and deformation process analysis, a wave-like strategy is proposed to actuate the robot. Experiments verify the effectiveness of the designed structures.
The Protective Effects of Inulin-Type Fructans Against High-Fat/Sucrose Diet-Induced Gestational Diabetes Mice in Association With Gut Microbiota Regulation
Authors: Miao Miao , Wang Qing , Wang Xinyan , Fan Chong , Luan Ting , Yan Lina , Zhang Yue , Zeng Xin , Dai Yongmei , Li Ping
Published: April 2022

Background

Inulin-type fructans (ITF) have been used as prebiotics to alleviate glucose and lipid metabolism disorders. However, few studies evaluated the microbial mechanism of ITF in improving maternal metabolic status during pregnancy.

Methods

C57BL/6J mice were fed a high-fat/sucrose diet (HFD) for 4 weeks before and throughout pregnancy to induce a model of gestational diabetes mellitus (GDM). Body weight, glycolipid metabolic parameters, and fecal short-chain fatty acids (SCFAs) were assessed in the experimental process. The effects of ITF on the fecal microbiota were analyzed by 16S rRNA gene amplicon sequencing.

Results

Pregnant HFD-fed mice displayed significant insulin resistance and dyslipidemia. ITF (3.33 g/kg/day) treatment improved glucose and lipid metabolism disorder parameters in HFD-induced GDM mice and alleviated fat accumulation and glucose intolerance. The alpha diversity of the gut microbial community was increased in ITF mice, while the beta diversity returned to the level of normal chow diet (NCD) mice. Interestingly, Verrucomicrobia, Bifidobacterium, and Akkermansia were obviously enriched, while Dubosiella was obviously lessened after inulin treatment. Further analysis indicated that Dubosiella was positively correlated with markers of glycolipid metabolism disorders, whereas the ITF-supplemented diet partially reversed the changes.

Conclusion

Our results suggest that the ITF treatment may alleviate glucose and lipid metabolism disorders with the mediation of gut microbiota.
Liposomal Dexamethasone Reduces A/H1N1 Influenza-Associated Morbidity in Mice
Authors: Kwon Jung Won , Quan Hailian , Song Juha , Chung Hyewon , Jung Daun , Hong Jung Joo , Na Yi Rang , Seok Seung Hyeok
Published: April 2022

Re-emerging viral threats have continued to challenge the medical and public health systems. It has become clear that a significant number of severe viral infection cases are due to an overreaction of the immune system, which leads to hyperinflammation. In this study, we aimed to demonstrate the therapeutic efficacy of the dexamethasone nanomedicine in controlling the symptoms of influenza virus infection. We found that the A/Wisconsin/WSLH34939/2009 (H1N1) infection induced severe pneumonia in mice with a death rate of 80%, accompanied by significant epithelial cell damage, infiltration of immune cells, and accumulation of pro-inflammatory cytokines in the airway space. Moreover, the intranasal delivery of liposomal dexamethasone during disease progression reduced the death rate by 20%. It also significantly reduced the protein level of tumor necrosis factor-alpha (TNFα), interleukin-1β (IL-1β), IL-6, and the C-X-C motif chemokine ligand 2 (CXCL2) as well as the number of infiltrated immune cells in the bronchoalveolar lavage fluids as compared to the control and free dexamethasone. The liposomal dexamethasone was mainly distributed into the monocyte/macrophages as a major cell population for inducing the cytokine storm in the lungs. Taken together, the intranasal delivery of liposomal dexamethasone may serve as a novel promising therapeutic strategy for the treatment of influenza A-induced pneumonia.
Iodate Reduction by Shewanella oneidensis Requires Genes Encoding an Extracellular Dimethylsulfoxide Reductase
Authors: Shin Hyun-Dong , Toporek Yael , Mok Jung Kee , Maekawa Ruri , Lee Brady D. , Howard M. Hope , DiChristina Thomas J.
Published: April 2022

Microbial iodate (IO3–) reduction is a major component of the iodine biogeochemical reaction network in anaerobic marine basins and radioactive iodine-contaminated subsurface environments. Alternative iodine remediation technologies include microbial reduction of IO3– to iodide (I–) and microbial methylation of I– to volatile gases. The metal reduction pathway is required for anaerobic IO3– respiration by the gammaproteobacterium Shewanella oneidensis. However, the terminal IO3– reductase and additional enzymes involved in the S. oneidensis IO3– electron transport chain have not yet been identified. In this study, gene deletion mutants deficient in four extracellular electron conduits (EECs; ΔmtrA, ΔmtrA-ΔmtrDEF, ΔmtrA-ΔdmsEF, ΔmtrA-ΔSO4360) and DMSO reductase (ΔdmsB) of S. oneidensis were constructed and examined for anaerobic IO3– reduction activity with either 20 mM lactate or formate as an electron donor. IO3– reduction rate experiments were conducted under anaerobic conditions in defined minimal medium amended with 250 μM IO3– as anaerobic electron acceptor. Only the ΔmtrA mutant displayed a severe deficiency in IO3– reduction activity with lactate as the electron donor, which suggested that the EEC-associated decaheme cytochrome was required for lactate-dependent IO3– reduction. The ΔmtrA-ΔdmsEF triple mutant displayed a severe deficiency in IO3– reduction activity with formate as the electron donor, whereas ΔmtrA-ΔmtrDEF and ΔmtrA-ΔSO4360 retained moderate IO3– reduction activity, which suggested that the EEC-associated dimethylsulfoxide (DMSO) reductase membrane-spanning protein DmsE, but not MtrA, was required for formate-dependent IO3– reduction. Furthermore, gene deletion mutant ΔdmsB (deficient in the extracellular terminal DMSO reductase protein DmsB) and wild-type cells grown with tungsten replacing molybdenum (a required co-factor for DmsA catalytic activity) in defined growth medium were unable to reduce IO3– with either lactate or formate as the electron donor, which indicated that the DmsAB complex functions as an extracellular IO3– terminal reductase for both electron donors. Results of this study provide complementary genetic and phenotypic evidence that the extracellular DMSO reductase complex DmsAB of S. oneidensis displays broad substrate specificity and reduces IO3– as an alternate terminal electron acceptor.
A Novel Efficient L-Lysine Exporter Identified by Functional Metagenomics
Authors: Malla Sailesh , van der Helm Eric , Darbani Behrooz , Wieschalka Stefan , Förster Jochen , Borodina Irina , Sommer Morten Otto Alexander
Published: April 2022

Lack of active export system often limits the industrial bio-based production processes accumulating the intracellular product and hence complexing the purification steps. L-lysine, an essential amino acid, is produced biologically in quantities exceeding two million tons per year; yet, L-lysine production is challenged by efficient export system at high titers during fermentation. To address this issue, new exporter candidates for efficient efflux of L-lysine are needed. Using metagenomic functional selection, we identified 58 genes encoded on 28 unique metagenomic fragments from cow gut microbiome library that improved L-lysine tolerance. These genes include a novel L-lysine transporter, belonging to a previously uncharacterized EamA superfamily, which is further in vivo characterized as L-lysine exporter using Xenopus oocyte expression system as well as Escherichia coli host. This novel exporter improved L-lysine tolerance in E. coli by 40% and enhanced yield, titer, and the specific production of L-lysine in an industrial Corynebacterium glutamicum strain by 7.8%, 9.5%, and 12%, respectively. Our approach allows the sequence-independent discovery of novel exporters and can be deployed to increase titers and productivity of toxicity-limited bioprocesses.
Assessment of the Transmission Dynamics of Clostridioides difficile in a Farm Environment Reveals the Presence of a New Toxigenic Strain Connected to Swine Production
Authors: Alves Frederico , Nunes Alexandra , Castro Rita , Sequeira António , Moreira Olga , Matias Rui , Rodrigues João Carlos , Silveira Leonor , Gomes João Paulo , Oleastro Mónica
Published: April 2022

The recent increase in community-acquired Clostridioides difficile infections discloses the shift in this bacterium epidemiology. This study aimed at establishing a transmission network involving One Health components, as well as assessing the zoonotic potential and genomic features of dominant clones. Samples were collected from different compartments of animal, human and environmental origin, from an animal production unit. C. difficile isolates were characterized for toxigenic profile by multiplex-PCR, while genetic diversity was evaluated by PCR-ribotyping and whole genome-based analysis. The overall C. difficile prevalence was 37.2% (70/188), and included samples from environmental (58.3%, 35/60) and animal (31.5%, 35/111) compartments; human samples (n = 17) taken from healthy workers were negative. A predominant clone from RT033 was found in almost 90% of the positive samples, including samples from all compartments connected to the pig production unit, with core-genome single nucleotide variant (SNV)-based Analysis supporting a clonal transmission between them (mean distance of 0.1 ± 0.1 core-SNVs). The isolates from this clone (herein designated PT RT033) were positive for all C. difficile toxin genes (tcdA, tcdB, cdtA/cdtB). The phyloGenetic positioning of this clone was clearly distinct from the classical RT033 cluster, suggesting a different evolutionary route. This new clone shares genomic features with several RTs from the clade 5 Sequence Type (ST) 11, including a complete pathogenicity locus (PaLoc) that is more similar to the one found in toxigenic strains and contrasting to the less virulent classical RT033 (tcdA-, tcdB-, cdtA + /cdtB +). The presence of a tcdA gene truncated into two ORFs, not previously described, requires further evaluation concerning toxin functionality. We hypothesize that the unique combination of genetic elements found in the PT RT033 clone may contribute to host tropism and environmental dissemination and maintenance. This study constitutes the first report of a toxigenic RT033 clone and adds to the overall knowledge on Clade 5 sequence type 11, considered the C. difficile evolutionary lineage with the highest zoonotic potential. The presence of this clone in all compartments associated with the pig production unit suggests a transmission chain involving these animals and contributes to unveil the role played by animal and environmental reservoirs in this pathogen epidemiology.
Colletotrichum Spp. Diversity Between Leaf Anthracnose and Crown Rot From the Same Strawberry Plant
Authors: Hu Shuodan , Zhang Yanting , Yu Hong , Zhou Jiayan , Hu Meihua , Liu Aichun , Wu Jianyan , Wang Hancheng , Zhang Chuanqing
Published: April 2022

Leaf anthracnose (LA) and anthracnose crown rot (ACR) represent serious fungal diseases that pose significant threats to strawberry production. To characterize the pathogen diversity associated with above diseases, 100 strawberry plants, including varieties of “Hongjia,” “Zhangji,” and “Tianxianzui,” were sampled from Jiande and Zhoushan, the primary plantation regions of Zhejiang province, China. A total of 309 Colletotrichum isolates were isolated from crown (150 isolates) and leaves (159 isolates) of affected samples. Among these, 100 isolates obtained from the plants showing both LA and CR symptoms were selected randomly for further characterization. Based on the morphological observations combined with phylogenetic analysis of multiple genes (ACT, ITS, CAL, GAPDH, and CHS), all the 100 tested isolates were identified as C. gloeosporioides species complex, including 91 isolates of C. siamense, 8 isolates of C. fructicola causing both LA and ACR, and one isolate of C. aenigma causing ACR. The phenotypic characteristics of these isolated species were investigated using the BIOLOG phenotype MicroArray (PM) and a total of 950 different metabolic phenotype were tested, showing the characteristics among these isolates and providing the theoretical basis for pathogenic biochemistry and metabolism. The pathogenicity tests showed that even the same Colletotrichum species isolated from different diseased tissues (leaves or crowns) had significantly different pathogenicity toward strawberry leaves and crown. C. siamense isolated from diseased leaves (CSLA) was more aggressive than C. siamense isolated from rotted crown (CSCR) during the infection on “Zhangji” leaves. Additionally, C. fructicola isolated from affected leaf (CFLA) caused more severe symptoms on the leaves of four strawberry varieties compared to C. fructicola isolated from diseased crown (CFCR). For crown rot, the pathogenicity of CSCR was higher than that of CSLA.
Alterations and Correlations of Gut Microbiota and Fecal Metabolome Characteristics in Experimental Periodontitis Rats
Authors: Wu Lan , Han Jie , Nie Jia-Yan , Deng Tong , Li Cheng , Fang Cheng , Xie Wen-Zhong , Wang Shuang-Ying , Zeng Xian-Tao
Published: April 2022

Objectives

Periodontitis affects the progression of many diseases, while its detailed mechanism remains unclear. This study hopes to provide new ideas for exploring its mechanism by analyzing the gut microbiota and fecal metabolic characteristics of experimental periodontitis rats.

Methods

A total of 10 rats were randomly divided into ligature-induced experimental periodontitis (EP) group and healthy control group. After 4 weeks of the experiment, the feces of all rats were collected for sequencing through 16S ribosomal DNA (rDNA) sequencing technology and liquid chromatography–mass spectrometry (LC–MS).

Results

16S rDNA sequencing results showed that the β-diversity of gut microbiota was significantly different between the EP and control group, and the levels of dominant genera were different. Compared with the control group, Ruminococcus, Escherichia, and Roseburia were significantly enriched in EP, and Coprococcus, Turicibacter, Lachnospira were significantly decreased. Correlation analysis showed that Roseburia exhibited the highest correlation within the genus. Of 3,488 qualitative metabolites, 164 metabolites were upregulated and 362 metabolites were downregulated in EP. Enrichment analysis showed that periodontitis significantly changed 45 positive/negative ion metabolic pathways. Five KEGG pathways, protein digestion and absorption, tyrosine metabolism, glycolysis/gluconeogenesis, niacin and nicotinamide metabolism, and oxidative phosphorylation, are enriched in both the microbiome and metabolome. Correlation analysis showed that the genera with significant differences in periodontitis were usually significantly correlated with more metabolites, such as Roseburia, Lachnospira, Escherichia, Turicibacter, and Ruminococcus. The genera with the same changing trend tended to have a similar correlation with some certain metabolites. In addition, vitamin D2 and protoporphyrin IX have the most significant correlations with microorganisms.

Conclusion

Our study reveals that periodontitis alters gut microbiota and fecal metabolites. The correlation analysis of microbiota and metabolome provides a deeper understanding of periodontitis, and also provides a direction for the study of periodontitis affecting other diseases.
Dynamic Metabolic Response to (p)ppGpp Accumulation in Pseudomonas putida
Authors: Vogeleer Philippe , Létisse Fabien
Published: April 2022

The stringent response is a ubiquitous bacterial reaction triggered by nutrient deprivation and mediated by the intracellular concentrations of ppGpp and pppGpp. These alarmones, jointly referred to as (p)ppGpp, control gene transcription, mRNA translation and protein activity to adjust the metabolism and growth rate to environmental changes. While the ability of (p)ppGpp to mediate cell growth slowdown and metabolism adaptation has been demonstrated in Escherichia coli, it’s role in Pseudomonas putida remains unclear. The aims of this study were therefore to determine which forms of (p)ppGpp are synthetized in response to severe growth inhibition in P. putida, and to decipher the mechanisms of (p)ppGpp-mediated metabolic regulation in this bacterium. We exposed exponentially growing cells of P. putida to serine hydroxamate (SHX), a serine analog known to trigger the stringent response, and tracked the dynamics of intra- and extracellular metabolites using untargeted quantitative MS and NMR-based metabolomics, respectively. We found that SHX promotes ppGpp and pppGpp accumulation few minutes after exposure and arrests bacterial growth. Meanwhile, central carbon metabolites increase in concentration while purine pathway intermediates drop sharply. Importantly, in a ΔrelA mutant and a ppGpp0 strain in which (p)ppGpp synthesis genes were deleted, SHX exposure inhibited cell growth but led to an accumulation of purine pathway metabolites instead of a decrease, suggesting that as observed in other bacteria, (p)ppGpp downregulates the purine pathway in P. putida. Extracellular accumulations of pyruvate and acetate were observed as a specific metabolic consequence of the stringent response. Overall, our results show that (p)ppGpp rapidly remodels the central carbon metabolism and the de novo purine biosynthesis pathway in P. putida. These data represent a hypothesis-generating resource for future studies on the stringent response.
Inactivation of Salmonella typhimurium SL1344 by Chlorogenic Acid and the Impairment of Cellular Integrity
Authors: Yang Liang , Zhang Chunlin , Su Zijing , Zhao Liang , Wu Jiaxin , Sun Xiaoying , Zhang Xiujuan , Hu Xiaoqing
Published: April 2022

Chlorogenic acid (CGA) is an antibacterial agent that can be isolated from Eucommia ulmoides Oliver, a Chinese medicinal and edible plant food. The inhibitory effect of CGA on bacterial growth and stiffness of the outer membrane (OM) had been reported, while more evidence were required to elucidate its impairment of cell wall. In this study, the morphological and physiochemical changes of Salmonella cells under CGA treatment were investigated. Firstly, the minimum inhibitory concentration (MIC) of CGA against Salmonella was assayed. Later, the permeability of OM and activity of the proteins released were measured and observed to reveal the alteration of OM characteristic and cellular morphology. Finally, reactive oxygen species and cell membrane fluidity were analyzed, respectively, to elucidate how CGA damaged cell surface. The results showed that MIC of CGA against Salmonella was 6.25 mg/L. Under sub-lethal doses of CGA, the OM permeability and the release of soluble proteins were enhanced evidently, and Salmonella cells showed more deformed and shrunken, confirming the impairment of cellular integrity under CGA. Finally, the possible cause of cell surface damage was investigated. the fluidity of the membrane was increased upon CGA treatment, which may the possible cause of OM by CGA.