bluuebunny/crossref_metadata_2025 huggingface dataset:
Gut transcriptome analysis of P450 genes and cytochrome P450 reductase in three moth species feeding on gymnosperms or angiosperms
Authors: Zhang Xiaoman , Shi Zhiyong , Yang Cai-qing , Li Jing , Liu Jingze , Zhang Ai-bing
Published: November 2022

Cytochrome P450 enzymes (P450s, CYPs) are a superfamily of heme–thiolate proteins involved in the metabolism of endogenous and exogenous substances in insects. In this study, the identification of putative P450 proteins was done and the elimination of the repeated sequences resulted in 57 proteins from Gastropacha populifolia, 63 proteins from Dendrolimus punctatus, and 53 proteins from Dendrolimus tabulaeformis. The putative P450 proteins were aligned together with seven other insect species based on five conserved domains. A total of ten co-orthologous groups were identified. Interestingly, one co-orthologous gene, CYP4g15 in CYP4 clan, was identified and its 3D structure analysis showed that the highly conserved sites of the predicted motifs were close to the active sites of P450. Furthermore, this study revealed that insect CYP4g15 and two bacteria cytochrome P450 were monophyletic. This suggests that insects CYP4g15 are not only functionally conserved but also an ancient gene originating from different bacteria species.
Unraveling global impacts of climate change on amphibians distributions: A life-history and biogeographic-based approach
Authors: Alves-Ferreira Gabriela , Talora Daniela C. , Solé Mirco , Cervantes-López Martín J. , Heming Neander M.
Published: November 2022

Climate change can affect species distribution patterns in three different ways: pushing them to disperse to new suitable areas, forcing them to adapt to novel climatic conditions, or driving them to extinction. However, the biological and geographical traits that lead to these different responses remain poorly explored. Here, we evaluated how ecological and biogeographic traits influence amphibians’ response to climate change. We performed a systematic review searching for studies that evaluated the effects of future climate change on amphibian’s distribution. Our research returned 31 articles that projected the distribution of 331 amphibians. Our results demonstrate that species inhabiting an elevation above 515 m will lose a significant portion of their climatically suitable area. We also found that as isothermality increases, the amount of area suitable in response to climate change also increases. Another important discovery was that as the size of the baseline area increases, the greater must be the loss of climatically suitable areas. On the other hand, species with very small areas tend to keep their current climatically suitable area in the future. Furthermore, our results indicate that species that inhabit dry habitats tend to expand their suitable area in response to climate change. This result can be explained by the environmental characteristics of these habitats, which tend to present extreme seasonal climates with well-defined periods of drought and rain. We also found that anurans that inhabit exclusively forests are projected to lose a greater portion of their suitable areas, when compared to species that inhabit both forest and open areas, wetlands, and dry and rupestrian environments. The biogeographical realm also influenced anuran’s range shifts, with Afrotropic and Nearctic species projected to expand their geographical ranges. The assessment of climate change effects on amphibian distribution has been the focus of a growing number of studies. Despite this, some regions and species remain underrepresented. Current literature evaluates about 4% of the 7,477 species of Anura and 8% of the 773 species of Caudata and some regions rich in amphibian species remain severely underrepresented, such as Madagascar. Thus, future studies should focus on regions and taxas that remain underrepresented.
Influence of topography, vegetation, weather, and climate on Big-cone Douglas-Fir fire refugia and high fire-induced mortality after two large mixed-severity wildfires
Authors: Parkinson Anne-Marie L. , D’Antonio Carla M. , Moritz Max A.
Published: November 2022

Big-cone Douglas-Fir (Pseudotsuga macrocarpa, hereafter BCDF) is an endemic, fire-adapted conifer found throughout the mountains of southern California. Because recent large high intensity wildfires have resulted in loss of BCDF, understanding how environmental factors, such as topography, fuels, climate, and weather, impact BCDF survivorship is important for informing restoration and conservation efforts. Here, we used randomForest (RF) and accumulated local effects (ALE) plots to examine how environmental variables contribute to the occurrence of both fire refugia and high fire-induced mortality of BCDF stands during two large wildfires. Additionally, we explored how the influence of these variables changed between the use of two different response variables: (1) visually-assessed mortality evaluated through estimation of canopy survival using Google Earth imagery and (2) RdNBR. This comparison allows us to evaluate the potential that RdNBR overestimates BCDF mortality because it is highly indicative of understory conditions post-fire, rather than direct changes to BCDF trees. We found that pre-fire fuel was one of the most influential variables contributing to both fire refugia and high mortality; sparse and oak dominant understories contributed to fire refugia, while chaparral contributed to high mortality. We also found that the role of certain variables was not consistent across the two fires. For example, areas of the landscape with hotter temperature and higher vapor pressure deficit (VPD) during the fire experienced high BCDF mortality in the Zaca Fire, but had the inverse effect in the Thomas Fire. Lastly, we found that our two metrics of response resulted in significantly different classification of BCDF stands: RdNBR resulted in more stands being classified as high intensity and fewer low severity/unburned areas, supporting our concern that it can overestimate high severity impact in some ecosystems. However, the two model types resulted in relatively similar explanatory environmental variable selections, although different rankings.
Understanding the genetics of peripartum depression: Research challenges, strategies, and opportunities
Authors: Lancaster Eva E. , Lapato Dana M. , Peterson Roseann E.
Published: November 2022

Peripartum depression (PD) is a common mood disorder associated with negative outcomes for mother and child. PD is an understudied disorder in psychiatric genetics, and progress characterizing its genetic architecture has been limited by a lack of disorder-specific research, heterogeneous and evolving phenotypic definitions, inadequate representation of global populations, low-powered studies, and insufficient data amenable to large meta-analyses. The increasing availability of large-scale, population-level efforts, like biobanks, have the potential to accelerate scientific discovery and translational research by leveraging clinical, molecular, and self-report data from hundreds of thousands of individuals. Although these efforts will not fully equip researchers to confront every challenge posed by systemic issues in data collection, such as the reliance on minimal phenotyping strategies, the field is in a position to learn from other successful psychiatric genetic investigations. This review summarizes the current state of PD genetics research and highlights research challenges, including the impact of phenotype depth, measurement, and definition on the replicability and interpretability of genomic research. Recommendations for advancing health equity and improving the collection, analysis, discussion, and reporting of measures for PD research are provided.
Benefit sharing in genomic and biobanking research in Uganda: Perceptions of researchers and research ethics committee members
Authors: Mwaka Erisa Sabakaki , Bagenda Godfrey , Sebatta Deborah Ekusai , Nabukenya Sylvia , Munabi Ian
Published: November 2022

Background:Genomic and biobanking research has increased in Africa over the past few years. This has raised pertinent ethical, legal, and societal concerns for stakeholders such as sample or data ownership, commercialization, and benefit sharing. There is limited awareness of the concept of benefit sharing by stakeholders in sub-Saharan Africa.

Objective:This study aimed to explore the perceptions of researchers and research ethics committee members on benefit sharing in international collaborative genomic and biobanking research.

Methods:Qualitative in-depth interviews were conducted with 15 researchers and 19 research ethics committee members. A thematic approach was used to interpret the results.

Results:Six themes emerged from the data and these included perceptions on the benefits of genomic and biobanking research; discussion of benefit sharing with participants during the informed consent process; legal implications of benefit sharing and the role of material transfer agreements; equity and fairness in sharing the benefits of genomic research; perceived barriers to fair benefit sharing; and recommendations for fostering fair and equitable benefit sharing in genomic and biobanking research. Most respondents clearly understood the various forms of benefits of genomic and biobanking research and opined that such benefits should be fairly and equitably shared with low and middle-income country researchers and their institutions, and research communities. The perceived barriers to the fair benefit sharing unfavorable include power disparities, weak research regulatory frameworks, and lack of scientific integrity.

Conclusion:Overall, respondents believed that the distribution of the advantages of genomic and biobanking research in North-South collaborative research was not equitable nor fair, and that the playing field was not leveled. Therefore, we advocate the following for fair and equitable benefit sharing: Building the capacities and empowering research scientists in developing nations; strengthening regulatory frameworks and extending the purview of the research ethics committee in the development and implementation of material transfer agreements; and meaningfully involving local research communities in benefit sharing negotiations.
Single cell sequencing revealed the mechanism of PD-1 resistance affected by the expression profile of peripheral blood immune cells in ESCC
Authors: Deng Ting , Wang Huiya , Yang Changliang , Zuo Mengsi , Ji Zhi , Bai Ming , Ning Tao , Liu Rui , Wang Junyi , Ge Shaohua , Zhang Le , Ba Yi , Zhang Haiyang
Published: November 2022

Background

Esophageal squamous carcinoma (ESCC) is a highly lethal malignancy with poor prognosis. The effect of transcriptome characteristics of patient immune microenvironment (TME) on the efficacy of immunosuppressive agents is still poorly understood.

Methods

Here we extracted and isolated immune cells from peripheral blood of patients with PD-1 monoclonal antibody sensitivity and resistance, and conducted deep single-cell RNA sequencing to describe the baseline landscape of the composition, lineage, and functional status of infiltrating immune cells in peripheral blood of patients with esophageal cancer.

Results

The transcriptome characteristics of immune cells were comprehensively analyzed, and the dynamic changes of cell percentage, heterogeneity of cell subtypes and interactions between cells were explained. Co-expression and pedigree tracking based on T-cell antigen receptors revealed a significant proportion of highly migratory intertissue-effector T cells. GO and KEGG enrichment pathway Analysis of CD8+ effect-T cells ESCC_S group and ESCC_D1,2 group, found that in the up-regulated enrichment pathway, ESCC_S group enriched more PD-L1 and PD-1 checkpoint pathways expressed in tumors (JUN/NFKBIA/FOS/KRAS/IFNG), which also exist in T cell receptor signaling pathways. MT2A, MT1X and MT1E were differentially expressed in ESCC patients with PD-1 monoclonal antibody resistance, which may be related to the resistance of PD-1 mMAB.

Conclusions

This study has an in-depth understanding of the influence of peripheral immune cell infiltration on the sensitivity of monoclonal antibody PD-1 in patients with esophageal cancer, which is helpful to promote the immunotherapy of patients with esophageal cancer.
Integrated machine learning approaches for flow cytometric quantification of myeloid-derived suppressor cells in acute sepsis
Authors: Bonavia Anthony S. , Samuelsen Abigail , Luthy Joshua , Halstead E. Scott
Published: November 2022

Highly heterogeneous cell populations require multiple flow cytometric markers for appropriate phenotypic characterization. This exponentially increases the complexity of 2D scatter plot analyses and exacerbates human errors due to variations in manual gating of flow data. We describe a semi-automated workflow, based entirely on the Flowjo Graphical User Interface (GUI), that involves the stepwise integration of several, newly available machine learning tools for the analysis of myeloid-derived suppressor cells (MDSCs) in septic and non-septic critical illness. Supervised clustering of flow cytometric data showed correlation with, but significantly different numbers of, MDSCs as compared with the cell numbers obtained by manual gating. Neither quantification method predicted 30-day clinical outcomes in a cohort of 16 critically ill and septic patients and 5 critically ill and non-septic patients. Machine learning identified a significant decrease in the proportion of PMN-MDSC in critically ill and septic patients as compared with healthy controls. There was no difference between the proportion of these MDSCs in septic and non-septic critical illness.
Hemocyte response to treatment of susceptible and resistant Asian corn borer (Ostrinia furnacalis) larvae with Cry1F toxin from Bacillus thuringiensis
Authors: Prabu Sivaprasath , Jing Dapeng , Jurat-Fuentes Juan Luis , Wang Zhenying , He Kanglai
Published: November 2022

Midgut receptors have been recognized as the major mechanism of resistance to Cry proteins in lepidopteran larvae, while there is a dearth of data on the role of hemocyte’s response to Cry intoxication and resistance development. We aimed at investigating the role of circulating hemocytes in the intoxication of Cry1F toxin in larvae from susceptible (ACB-BtS) and resistant (ACB-FR) strains of the Asian corn borer (ACB), Ostrinia furnacalis. Transcriptome and proteome profiling identified genes and proteins involved in immune-related (tetraspanin and C-type lectins) and detoxification pathways as significantly up-regulated in the hemocytes of Cry1F treated ACB-FR. High-throughput in vitro assays revealed the binding affinity of Cry1F with the tetraspanin and C-type lectin family proteins. We found significant activation of MAPKinase (ERK 1/2, p38α, and JNK 1/2) in the hemocytes of Cry1F treated ACB-FR. In testing plausible crosstalk between a tetraspanin (CD63) and downstream MAPK signaling, we knocked down CD63 expression by RNAi and detected an alteration in JNK 1/2 level but a significant increase in susceptibility of ACB-FR larvae to Cry1F toxin. Information from this study advances a change in knowledge on the cellular immune response to Cry intoxication and its potential role in resistance in a lepidopteran pest.
The associations of maternal and children’s gut microbiota with the development of atopic dermatitis for children aged 2 years
Authors: Fan Xiaoxiao , Zang Tianzi , Dai Jiamiao , Wu Ni , Hope Chloe , Bai Jinbing , Liu Yanqun
Published: November 2022

Background

It is critical to investigate the underlying pathophysiological mechanisms in the development of atopic dermatitis. The microbiota hypothesis suggested that the development of allergic diseases may be attributed to the gut microbiota of mother-offspring pairs. The purpose of this study was to investigate the relationship among maternal-offspring gut microbiota and the subsequent development of atopic dermatitis in infants and toddlers at 2 years old.

Methods

A total of 36 maternal-offspring pairs were enrolled and followed up to 2 years postpartum in central China. Demographic information and stool samples were collected perinatally from pregnant mothers and again postpartum from their respective offspring at the following time intervals: time of birth, 6 months, 1 year and 2 years. Stool samples were sequenced with the 16S Illumina MiSeq platform. Logistic regression analysis was used to explore the differences in gut microbiota between the atopic dermatitis group and control group.

Results

Our results showed that mothers of infants and toddlers with atopic dermatitis had higher abundance of Candidatus_Stoquefichus and Pseudomonas in pregnancy and that infants and toddlers with atopic dermatitis had higher abundance of Eubacterium_xylanophilum_group at birth, Ruminococcus_gauvreauii_group at 1 year and UCG-002 at 2 years, and lower abundance of Gemella and Veillonella at 2 years. Additionally, the results demonstrated a lower abundance of Prevotella in mothers of infants and toddlers with atopic dermatitis compared to mothers of the control group, although no statistical difference was found in the subsequent analysis.

Conclusion

The results of this study support that gut microbiota status among mother-offspring pairs appears to be associated with the pathophysiological development of pediatric atopic dermatitis.
Orofacial clefts lead to increased pro-inflammatory cytokine levels on neonatal oral mucosa
Authors: Seidel Corinna L. , Percivalle Elena , Tschaftari Marco , Weider Matthias , Strobel Karin , Willershausen Ines , Unertl Christoph , Schmetzer Helga M. , Weber Manuel , Schneider Michael , Frey Benjamin , Gaipl Udo S. , Beckmann Matthias W. , Gölz Lina
Published: November 2022

Orofacial clefts (OFC) are frequent congenital malformations characterized by insufficient separation of oral and nasal cavities and require presurgical infant orthopedics and surgical interventions within the first year of life. Wound healing disorders and higher prevalence of gingivitis and plaque levels are well-known challenges in treatment of children with OFC. However, oral inflammatory mediators were not investigated after birth using non-invasive sampling methods so far. In order to investigate the impact of OFC on oral cytokine levels, we collected tongue smear samples from 15 neonates with OFC and 17 control neonates at two time points (T), T0 at first consultation after birth, and T1, 4 to 5 weeks later. The samples were analyzed using multiplex immunoassay. Overall, we found significantly increased cytokine levels (TNF, IL-1β/-2/-6/-8/-10) in tongue smear samples from neonates with OFC compared to controls, especially at T0. The increase was even more pronounced in neonates with a higher cleft severity. Further, we detected a significant positive correlation between cleft severity score and distinct pro-inflammatory mediators (GM-CSF, IL-1β, IL-6, IL-8) at T0. Further, we found that breast-milk (bottle) feeding was associated with lower levels of pro-inflammatory cytokines (IL-6/-8) in neonates with OFC compared to formula-fed neonates. Our study demonstrated that neonates with OFC, especially with high cleft severity, are characterized by markedly increased inflammatory mediators in tongue smear samples within the first weeks of life potentially presenting a risk for oral inflammatory diseases. Therefore, an inflammatory monitoring of neonates with (severe) OFC and the encouragement of mother to breast-milk (bottle) feed might be advisable after birth and/or prior to cleft surgery.
Cell-based therapy in prophylaxis and treatment of chronic graft-versus-host disease
Authors: Doglio Matteo , Crossland Rachel E. , Alho Ana C. , Penack Olaf , Dickinson Anne M. , Stary Georg , Lacerda João F. , Eissner Günther , Inngjerdingen Marit
Published: November 2022

Hematopoietic allogeneic stem cell transplantation (allo-SCT) is a curative option for patients with hematological malignancies. However, due to disparities in major and minor histocompatibility antigens between donor and recipient, severe inflammatory complications can occur, among which chronic graft-versus-host disease (cGVHD) can be life-threatening. A classical therapeutic approach to the prevention and treatment of cGVHD has been broad immunosuppression, but more recently adjuvant immunotherapies have been tested. This review summarizes and discusses immunomodulatory approaches with T cells, including chimeric antigen receptor (CAR) and regulatory T cells, with natural killer (NK) cells and innate lymphoid cells (ILCs), and finally with mesenchymal stromal cells (MSC) and extracellular vesicles thereof. Clinical studies and pre-clinical research results are presented likewise.
Human lymphoid tissue sampling for vaccinology
Authors: Kwiatkowska Karolina M. , Mkindi Catherine G. , Nielsen Carolyn M.
Published: November 2022

Long-lived plasma cells (LLPCs) – largely resident in the bone marrow – secrete antibody over months and years, thus maintaining serum antibody concentrations relevant for vaccine-mediated immunity. Little is known regarding factors that can modulate the induction of human LLPC responses in draining lymph node germinal centres, or those that maintain LLPCs in bone marrow niches following vaccination. Here, we review human and non-human primate vaccination studies which incorporate draining lymph node and/or bone marrow aspirate sampling. We emphasise the key contributions these samples can make to improve our understanding of LLPC immunology and guide rational vaccine development. Specifically, we highlight findings related to the impact of vaccine dosing regimens, adjuvant/vaccine platform selection, duration of germinal centre reactions in draining lymph nodes and relevance for timing of tissue sampling, and heterogeneity in bone marrow plasma cell populations. Much of this work has come from recent studies with SARS-CoV-2 vaccine candidates or, with respect to the non-human primate work, HIV vaccine development.
Systematic pan-cancer analysis identifies RALA as a tumor targeting immune therapeutic and prognostic marker
Authors: Jin Haoer , Qin Sha , He Jiang , Xiao Juxiong , Li Qingling , Mao Yitao , Zhao Luqing
Published: November 2022

Introduction

RALA is a member of the small GTPase Ras superfamily and has been shown to play a role in promoting cell proliferation and migration in most tumors, and increase the resistance of anticancer drugs such as imatinib and cisplatin. Although many literatures have studied the cancer-promoting mechanism of RALA, there is a lack of relevant pan-cancer analysis.

Methods

This study systematically analyzed the differential expression and mutation of RALA in pan-cancer, including different tissues and cancer cell lines, and studied the prognosis and immune infiltration associated with RALA in various cancers. Next, based on the genes co-expressed with RALA in pan-cancer, we selected 241 genes with high correlation for enrichment analysis. In terms of pan-cancer, we also analyzed the protein-protein interaction pathway of RALA and the application of small molecule drug Guanosine-5'-Diphosphate. We screened hepatocellular cancer (HCC) to further study RALA.

Results

The results indicated that RALA was highly expressed in most cancers. RALA was significantly correlated with the infiltration of B cells and macrophages, as well as the expression of immune checkpoint molecules such as CD274, CTLA4, HAVCR2 and LAG3, suggesting that RALA can be used as a kind of new pan-cancer immune marker. The main functions of 241 genes are mitosis and protein localization to nucleosome, which are related to cell cycle. For HCC, the results displayed that RALA was positively correlated with common intracellular signaling pathways such as angiogenesis and apoptosis.

Discussion

In summary, RALA was closely related to the clinical prognosis and immune infiltration of various tumors, and RALA was expected to become a broad-spectrum molecular immune therapeutic target and prognostic marker for pan-cancer.
Neutrophil extracellular traps and complications of liver transplantation
Authors: Liu Yanyao , Yan Ping , Bin Yue , Qin Xiaoyan , Wu Zhongjun
Published: November 2022

Many end-stage liver disease etiologies are attributed to robust inflammatory cell recruitment. Neutrophils play an important role in inflammatory infiltration and neutrophil phagocytosis, oxidative burst, and degranulation. It has also been suggested that neutrophils may release neutrophil extracellular traps (NETs) to kill pathogens. It has been proven that neutrophil infiltration within the liver contributes to an inflammatory microenvironment and immune cell activation. Growing evidence implies that NETs are involved in the progression of numerous complications of liver transplantation, including ischemia-reperfusion injury, acute rejection, thrombosis, and hepatocellular carcinoma recurrence. NETs are discussed in this comprehensive review, focusing on their effects on liver transplantation complications. Furthermore, we discuss NETs as potential targets for liver transplantation therapy.
Identification of immune infiltration and cuproptosis-related subgroups in Crohn’s disease
Authors: Yuan Yifan , Fu Mingyue , Li Na , Ye Mei
Published: November 2022

Background

Crohn’s disease (CD) is a type of heterogeneous, dysfunctional immune-mediated intestinal chronic and recurrent inflammation caused by a variety of etiologies. Cuproptosis is a newly discovered form of programmed cell death that seems to contribute to the advancement of a variety of illnesses. Consequently, the major purpose of our research was to examine the role of cuproptosis-related genes in CD.

Methods

We obtained two CD datasets from the gene expression omnibus (GEO) database, and immune cell infiltration was created to investigate immune cell dysregulation in CD. Based on differentially expressed genes (DEGs) and the cuproptosis gene set, differentially expressed genes of cuproptosis (CuDEGs) were found. Then, candidate hub cuproptosis-associated genes were found using machine learning methods. Subsequently, using 437 CD samples, we explored two distinct subclusters based on hub cuproptosis-related genes. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, Gene set variation analysis (GSVA) and immune infiltration analysis studies were also used to assess the distinct roles of the subclusters.

Results

Overall, 25 CuDEGs were identified, including ABCB6, BACE1, FDX1, GLS, LIAS, MT1M, PDHA1, etc. And most CuDEGs were expressed at lower levels in CD samples and were negatively related to immune cell infiltration. Through the machine learning algorithms, a seven gene cuproptosis-signature was identified and two cuproptosis-related subclusters were defined. Cluster-specific differentially expressed genes were found only in one cluster, and functional analysis revealed that they were involved in several immune response processes. And the results of GSVA showed positive significant enrichment in immune-related pathways in cluster A, while positive significant enrichment in metabolic pathways in cluster B. In addition, an immune infiltration study indicated substantial variation in immunity across different groups. Immunological scores were higher and immune infiltration was more prevalent in Cluster A.

Conclusion

According to the current research, the cuproptosis phenomenon occurs in CD and is correlated with immune cell infiltration and metabolic activity. This information indicates that cuproptosis may promote CD progression by inducing immunological response and metabolic dysfunction. This research has opened new avenues for investigating the causes of CD and developing potential therapeutic targets for the disease.
Low fish meal diet supplemented with probiotics ameliorates intestinal barrier and immunological function of Macrobrachium rosenbergii via the targeted modulation of gut microbes and derived secondary metabolites
Authors: Zheng Xiaochuan , Liu Bo , Wang Ning , Yang Jie , Zhou Qunlan , Sun Cunxin , Zhao Yongfeng
Published: November 2022

The unsuitable substitution ratio of fish meal by plant protein will reshape the intestinal microbial composition and intestine immunity. However, previous studies were mostly limited to investigating how different feed or probiotics characterized the microbial composition but ignored the biological interactions between bacteria and host physiology through secondary metabolites. Therefore, this study integrates the apparent indicators monitoring, 16S rDNA sequencing, and metabonomics to systematically investigate the effects of cottonseed protein concentrate (CPC) substitution of fish meal and Bacillus coagulans intervention on gut microbes, secondary metabolites, and intestinal immunity of Macrobrachium rosenbergii. Prawns were fed with three diets for 70 days: HF diets contained 25% fish meal, CPC in LF diets were replaced with 10% fish meal, and LF diets supplemented with 2 × 108 CFU/g diet B. coagulans were designated as BC diets. Results showed that CPC substitution induced a significant decrease in digestive enzyme activities (trypsin and lipase) and gut barrier protein PT-1 expression and a significant increase in γ-GT enzyme activity and inflammatory-related factors (Relish and Toll) expression. B. coagulans treatment mitigated the negative changes of the above indicators. Meanwhile, it significantly improved the expression levels of the barrier factor PT-1, the reparative cytokine IL-22, and Cu/Zn-SOD. CPC substitution resulted in a remarkable downregulated abundance of Firmicutes phyla, Flavobacterium spp., and Bacillus spp. B. coagulans treatment induced the callback of Firmicutes abundance and improved the relative abundance of Sphingomonas, Bacillus, and Ralstonia. Functional prediction indicated that CPC substitution resulted in elevated potential pathogenicity of microbial flora, and B. coagulans reduces the pathogenesis risk. Pearson’s correlation analysis established a significant positive correlation between differential genera (Sphingomonas, Bacillus, and Ralstonia) and secondary metabolites (including sphingosine, dehydrophytosphingosine, amino acid metabolites, etc.). Meanwhile, the latter were significantly associated with intestinal immunoregulation-related genes (Cu/Zn-SOD, IL-22, PT-1, Toll, and Relish). This study indicated that B. coagulans could mediate specific gut microbes and the combined action of multiple functional secondary metabolites to affect intestinal barrier function, digestion, and inflammation. Our study revealed the decisive role of gut microbes and derived secondary metabolites in the model of dietary composition-induced intestinal injury and probiotic treatment from a new perspective.
Novel T-cell signature based on cell pair algorithm predicts survival and immunotherapy response for patients with bladder urothelial carcinoma
Authors: Yan Xin , Zhang Xiao , Wu Hua-Hui , Wu Shao-Jie , Tang Xiao-Yu , Liu Tong-Zu , Li Sheng
Published: November 2022

Background

T-cell–T-cell interactions play important roles in the regulation of T-cells’ cytotoxic function, further impacting the anti-tumor efficacy of immunotherapy. There is a lack of comprehensive studies of T-cell types in bladder urothelial carcinoma (BLCA) and T-cell-related signatures for predicting prognosis and monitoring immunotherapy efficacy.

Methods

More than 3,400 BLCA patients were collected and used in the present study. The ssGSEA algorithm was applied to calculate the infiltration level of 19 T-cell types. A cell pair algorithm was applied to construct a T-cell-related prognostic index (TCRPI). Survival analysis was performed to measure the survival difference across TCRPI-risk groups. Spearman’s correlation analysis was used for relevance assessment. The Wilcox test was used to measure the expression level difference.

Results

Nineteen T-cell types were collected; 171 T-cell pairs (TCPs) were established, of which 26 were picked out by the least absolute shrinkage and selection operator (LASSO) analysis. Based on these TCPs, the TCRPI was constructed and validated to play crucial roles in survival stratification and the dynamic monitoring of immunotherapy effects. We also explored several candidate drugs targeting TCRPI. A composite TCRPI and clinical prognostic index (CTCPI) was then constructed, which achieved a more accurate estimation of BLCA’s survival and was therefore a better choice for prognosis prediction in BLCA.

Conclusions

All in all, we constructed and validated TCRPI based on cell pair algorithms in this study, which might put forward some new insights to increase the survival estimation and clinical response to immune therapy for individual BLCA patients and contribute to the personalized precision immunotherapy strategy of BLCA.
Mapping the Changjiang Diluted Water in the East China Sea during summer over a 10-year period using GOCI satellite sensor data
Authors: Son Young Baek , Choi Jong-Kuk
Published: November 2022

The Changjiang River loads freshwater into the East China Sea (ECS) and the Yellow Sea (YS). A low-salinity plume known as Changjiang Diluted Water (CDW) is formed by mixing with saline ambient waters; it disperses toward Jeju Island and the East/Japan Sea due to the dominant southerly wind and tide during summer. To map the offshore surface CDW in the ECS, a proxy was developed using surface water beam attenuation (c) and salinity from 18 annual summer cruises matched with synchronous Geostationary Ocean Color Imager (GOCI) satellite data. We followed a two-step empirical approach. First, a relationship between in situ salinity and c was obtained from hydrographic cruises (1998, 2003–2018, and 2021). Second, in situ c was matched with GOCI remote-sensing reflectance (Rrs) band ratios of all available blue-to-green wavelengths (2011–2018). Finally, satellite-derived surface salinity was determined directly by combining the two empirical relationships, providing a robust estimate over a range of salinities (22–34 psu). Our algorithm was then compared and validated with five previous satellite-derived salinity algorithms based on colored dissolved organic matter and particle concentrations. In the first step, surface salinity was matched and well correlated with c using an 18-year full conductivity–temperature–depth (CTD) dataset (N = 1,345, R2 = 0.93). In the second step, c was synchronously matched and well correlated with GOCI Rrs band ratios using an 8-year summer CTD dataset (N = 391, R2 = 0.93). The satellite-derived surface salinity based on the GOCI was compared with five other approaches and validated using an 8-year summer CTD dataset (2011–2018, N = 707, RMSE = 0.43, bias = 0.053, mean ratio = 1.002). We mapped satellite-derived surface salinity using monthly GOCI images during the summer from 2011 to 2020. The spatial patterns of the CDW were connected to the Changjiang River mouth and extended to the east–northeast during summer. Saline water was confined to the warm current and the upper slope in the eastern part of the study area. Anomalous dispersion of the CDW occurred in August 2016, 2017, and 2020, and limited dispersion occurred in August 2014 and 2019.
Oxygen scavenging activity of smart colophony microcapsules containing nitrite corrosion inhibitors for steel reinforced concrete
Authors: Ress Jacob , Martin Ulises , Bastidas David M.
Published: November 2022

In this study, the electrochemical performance of microcapsules (MCs) containing NaNO2corrosion inhibitors for steel reinforcements was studied in 0.6 M chloride contaminated simulated concrete pore solutions (SCPS) with varying pH for a period of 28 days. The corrosion inhibition was studied by potentiodynamic polarization and electrochemical impedance spectroscopy (EIS). The polarization results for the MC samples showed improved corrosion resistance, with anicorrof 2.54 ×10–6A/cm2after 28 days exposure in SCPS. Oxygen scavenging activity from the MCs was observed by reduced cathodic kinetics, displaying decreased cathodic exchange current densities of 2.66 ×10−8A/cm2, thus imparting cathodic inhibition in conjunction with anodic corrosion inhibitors. The microcapsules additionally displayed improvement over free NaNO2inhibitors after sufficient release time. The decrease in cathodic and anodic kinetics, along with the improved corrosion resistance, show a dual synergistic corrosion inhibition of the NaNO2loaded colophony MC.
Overview on performance degradation behavior of 20Cr25NiNb steel for gas cooled reactor cladding during service
Authors: Shu Ming , Sun Yongduo , Zhou Qin , Xiao Jun , Ma Zhaodandan , Liu Xiao
Published: November 2022

In this paper, the performance degradation behavior of fuel cladding material 20Cr25NiNb for the British Advanced Gas Reactor (AGR) is reviewed in detail, which is a strong guideline for the material selection of supercritical carbon dioxide cooled reactors. The degradation behavior during in-core service mainly includes high-temperature creep, thermal aging and mechanical property degradation caused by neutron irradiation (fission gas products, helium embrittlement and irradiation sensitization) and CO2 (oxidation and carburizing). Long-term service in AGR leads to coarsening of the second phase and precipitation of harmful phases such as σ, leading to performance degradation of the cladding. A point that should require special attention is that intergranular stress corrosion cracking (IGSCC) and intergranular attack (IGA) problems occur during wet storage of spent fuel.
Fatality rate, risk factors, and functional decline in peritoneal dialysis patients with coronavirus disease 2019: A nationwide cohort study
Authors: Chuengsaman Piyatida , Boongird Sarinya , Dandecha Phongsak , Hemachudha Thiravat , Nopsopon Tanawin , Kanjanabuch Talerngsak , Sritippayawan Suchai , Kantachuvesiri Surasak
Published: November 2022

Background

The fatality rates and factors associated with death from coronavirus disease 2019 (COVID-19) in hemodialysis patients have been extensively investigated. However, data on peritoneal dialysis (PD) patients remain scarce.

Materials and methods

In this nationwide cohort study, we assessed the 28-day COVID-19-related fatality rate in PD patients between August 2021 and July 2022 using data from the InCov19-PD registry. Predictors associated with death were evaluated using a multivariable Cox regression model. Changes in functional status before and during COVID-19 were also examined.

Results

A total of 1,487 eligible participants were evaluated. During the study period, 196 participants died within 28 days after COVID-19 diagnosis (case fatality rate: 13%). In a multivariable Cox regression model, an increased risk of death within 28 days after COVID-19 diagnosis among PD patients was independently associated with functional impairment during COVID-19 [adjusted hazard ratio (HR) 2.46, 95% confidence interval (CI) 1.59–3.81], SARS-CoV-2 infection with the Delta variant (HR 2.23, 95% CI 1.55–3.21), and the need for respiratory support (HR 7.13, 95% CI 3.74–13.57) (p < 0.01 for all). Conversely, the number of COVID-19 vaccines administered (HR 0.69, 95% CI 0.55–0.87; p = 0.001) and receiving corticosteroid therapy during COVID-19 (HR 0.72, 95% CI 0.54–0.97; p = 0.03) were associated with a decreased risk of death within 28 days after COVID-19 diagnosis. The number of functionally independent PD patients dropped from 94% at baseline to 63% during COVID-19 (p < 0.01).

Conclusions

The COVID-19-related 28-day fatality rate was high among PD patients. The predictors of COVID-19-related death in PD patients were similar to those in hemodialysis patients. During COVID-19, PD patients commonly experienced functional deterioration.
Serum myo-inositol and valine improve metabolomic-based estimated glomerular filtration rate among kidney transplant recipients
Authors: Meeusen Jeffrey W. , Stämmler Frank , Dasari Surendra , Schiffer Eric , Lieske John C.
Published: November 2022

Background

Close monitoring of glomerular filtration rate (GFR) is essential for the management of patients post kidney transplantation. Measured GFR (mGFR), the gold standard, is not readily accessible in most centers. Furthermore, the performance of new estimated GFR (eGFR) equations based upon creatinine and/or cystatin C have not been validated in kidney transplant patients. Here we evaluate a recently published eGFR equation using cystatin C, creatinine, myo-inositol and valine as measured by nuclear magnetic resonance (eGFRNMR).

Methods

Residual sera was obtained from a cohort of patients with clinically ordered iothalamate renal clearance mGFR (n = 602). Kidney transplant recipients accounted for 220 (37%) of participants.

Results

Compared to mGFR, there was no significant bias for eGFRcr or eGFRNMR, while eGFRcr-cys significantly underestimated mGFR. P30 values were similar for all eGFR. P15 was significantly higher for eGFRNMR compared to eGFRcr, while the P15 for eGFRcr-cys only improved among patients without a kidney transplant. Agreement with mGFR CKD stages of <15, 30, 45, 60, and 90 ml/min/1.73 m2 was identical for eGFRcr and eGFRcr-cys (61.8%, both cases) while eGFRNMR was significantly higher (66.4%) among patients with a kidney transplant.

Conclusion

The 2021 CKD-EPI eGFRcr and eGFRcr-cys have similar bias, P15, and agreement while eGFRNMR more closely matched mGFR with the strongest improvement among kidney transplant recipients.
Symbiotic microbiota and odor ensure mating in time for giant pandas
Authors: Ma Rui , Zheng Weichao , Guo Junliang , Hou Rong , Huang He , Xue Fei , Zhou Yanshan , Wu Wei , Huang Chong , Gu Jiang , Feng Feifei , Yu Xiang , Liu Jiabin , Li Zusheng , Zhang Long , Lan Guanwei , Chen Chao , Bi Wenlei , Dai Qiang , Owens Jacob R. , Yang Hong , Gu Xiaodong , Yan Qi-gui , Qi Dunwu
Published: November 2022

To achieve reproduction, male solitary mammals need to locate females using chemical communication with high levels of precision. In the case of giant pandas, the total estrus period of females was usually 15 days each year, however, successful mating activity is finished within 3 days from respective home range. The mating pattern of giant pandas, where multiple males compete for each female requires females employ efficient systems to communicate their estrus phases. To verifying whether the scent secretions of giant pandas changes by gender and estrus progression, the microbiota and compounds in 29 anogenital gland samples from 14 individuals during estrus were analyzed by 16S rRNA sequencing and GC-MS. We show that the microbiota communities covary by gender with 4 particular compounds of scent secretions. Among 597 genera, 34 were identified as biomarkers that could be used to distinguish between different estrus phases. By bacterial-compounds co-analysis, 3 fatty ester acids and squalene compounds covaried with the development of estrus in the bacterial communities of female giant pandas. This study helps clarify how a large, solitary mammal expresses accurate information to improve the likelihood of successful reproduction by changing the composition of microbiota and odor compounds of anogenital glands during estrus.
The role of SIRT1 in the process of Toxoplasma gondii infection of RAW 264.7 macrophages
Authors: Dong Kai , Jiang Ziyang , Zhang Jianhui , Qin Hanxiao , Chen Jianping , Chen Qiwei
Published: November 2022

Toxoplasma gondii is an opportunistic pathogenic protozoan that can infect almost all kinds of warm-blooded animals, including humans. T. gondii can evade the host's immune response, a process known as immune evasion. Our main objective was to evaluate the role played by Sirtuin1 (SIRT1) [one of the sirtuins (SIRTs) that are a family of nicotinamide adenine dinucleotide (NAD)-dependent histone deacetylases (HDACs)] in the T. gondii infection of RAW264.7 macrophages. In this study, we evaluated and observed alterations in the activity, expression, and localization of SIRT1 and assessed its involvement in the CD154/IFN-γ (CD40 ligand/interferon gamma) killing pathway and in autophagy during T. gondii infection. The inhibition of SIRT1 in host cells effectively reduced the number of intracellular tachyzoites, and the mechanism behind this effect might be the upregulation of IRGM1 [murine ortholog of IRGM (immunity-related GTPase family M)] and the initiation of autophagy. To the best of our knowledge, our study is the first to prove that T. gondii infection upregulates SIRT1 in RAW264.7 cells and that the inhibition of SIRT1 reduces the number of intracellular tachyzoites. Moreover, the upregulation of IRGM1 and the activation of autophagy may contribute to the intracellular inhibition of T. gondii caused by SIRT1 inhibition.
Diarrhea in suckling lambs is associated with changes in gut microbiota, serum immunological and biochemical parameters in an intensive production system
Authors: Zhong Tao , Wang Yaxuan , Wang Xinlu , Freitas-de-Melo Aline , Li Hua , Zhan Siyuan , Wang Linjie , Cao Jiaxue , Dai Dinghui , Guo Jiazhong , Li Li , Zhang Hongping , Liu Jinwang , Niu Lili
Published: November 2022

The incidence of diarrhea in lambs is frequent in large-scale sheep farms, which greatly impacts the growth and health of lambs. The aim of this study was to assess the changes in serum biochemical and immunological parameters and gut microbiome composition in suckling lambs suffering from diarrhea or not, reared on an intensive commercial farm. We found a reduced diversity of intestinal bacteria in suckling lambs suffering from diarrhea. Firmicutes and Bacteroidetes were the dominant flora in both groups of lambs, while the Bacteroidetes decreased in diarrheic lambs, no changes were reported in Firmicutes. Compared with healthy lambs, the proportion of aerobic bacteria, facultative anaerobic bacteria, and stress tolerant bacteria increased in lambs suffering from diarrhea, while that of anaerobic bacteria and potentially pathogenic bacteria decreased slightly. In addition, the contents of total cholesterol, immunoglobulins (Ig) G, and IgM in the serum of lambs suffering from diarrhea were lower than those of healthy lambs. This study explored the association between diarrhea occurrence, intestinal microbial community structure, and metabolic and immunological status in Hu lambs.
Human and mouse angiogenins: Emerging insights and potential opportunities
Authors: Sultana Mst. Farzana , Abo Hirohito , Kawashima Hiroto
Published: November 2022

Angiogenin, a well-known angiogenic factor, is crucial to the angiogenesis in gastrointestinal tumors. Human angiogenin has only one gene, whereas the murine angiogenin family has extended to incorporate six genes. Evolutionary studies have suggested functional variations among murine angiogenin paralogs, even though the three-dimensional structures of angiogenin proteins are remarkably similar. In addition to angiogenesis, the ubiquitous pattern of angiogenin expression suggests a variety of functions, such as tumorigenesis, neuroprotective, antimicrobial activity, and innate immunity. Here, we comprehensively reviewed studies on the structures and functions of human and mouse angiogenins. Understanding the structure and function of angiogenins from a broader perspective could facilitate future research related to development of novel therapeutics on its biological processes, especially in gastrointestinal cancers.
Biosynthesis of coelulatin for the methylation of anthraquinone featuring HemN-like radical S-adenosyl-L-methionine enzyme
Authors: Nie Lishuang , Wei Tianyi , Cao Mingming , Lyu Yunbin , Wang Shaochen , Feng Zhiyang
Published: November 2022

Bacterial aromatic polyketides are usually biosynthesized by the type II polyketide synthase (PKS-II) system. Advances in deoxyribonucleic acid (DNA) sequencing, informatics, and biotechnologies have broadened opportunities for the discovery of aromatic polyketides. Meanwhile, metagenomics is a biotechnology that has been considered as a promising approach for the discovery of novel natural products from uncultured bacteria. Here, we cloned a type II polyketide biosynthetic gene cluster (BGC) from the soil metagenome, and the heterologous expression of this gene cluster in Streptomyces coelicolor M1146 resulted in the production of three anthraquinones, two of which (coelulatins 2 and 3) had special hydroxymethyl and methyloxymethyl modifications at C2 of the polyketide scaffold. Gene deletion and in vitro biochemical characterization indicated that the HemN-like radical S-adenosyl-L-methionine (SAM) enzyme CoeI exhibits methylation and is involved in C2 modification.