bluuebunny/crossref_metadata_2025 huggingface dataset:
Arbovirus infection in Aedes aegypti from different departments of Colombia
Authors: Gómez Marcela , Martínez David , Hernández Carolina , Luna Nicolás , Patiño Luz Helena , Bohórquez Melo Ramiro , Suarez Luis Alejandro , Palma-Cuero Mónica , Murcia Luz Mila , González Páez Leonel , Estrada Bustos Leonardo , Medina Manuel Alfonso , Ariza Campo Katiuska , Padilla Holmer David , Zamora Flórez Alexander , De las Salas Jorge Luis , Muñoz Marina , Ramírez Juan David
Published: September 2022

The lack of precise and timely knowledge about the molecular epidemiology of arboviruses of public health importance, particularly in the vector, has limited the comprehensive control of arboviruses. In Colombia and the Americas, entomovirological studies are scarce. Therefore, this study aimed to describe the frequency of natural infection and/or co-infection by Dengue (DENV), Zika (ZIKV), and Chikungunya (CHIKV) inAedesspp. circulating in different departments of Colombia (Amazonas, Boyacá, Magdalena, and Vichada) and identifying vector species by barcoding.Aedesmosquitoes were collected in departments with reported prevalence or incidence of arbovirus cases during 2020–2021, located in different biogeographic zones of the country: Amazonas, Boyacá, Magdalena, and Vichada. The insects were processed individually for RNA extraction, cDNA synthesis, and subsequent detection of DENV (serotypes DENV1-4 by multiplex PCR), CHIKV, and ZIKV (qRT-PCR). The positive mosquitoes for arboviruses were sequenced (Sanger method) using the subunit I of the cytochrome oxidase (COI) gene for species-level identification. In total, 558Aedesmosquitoes were captured, 28.1% (n= 157) predominantly infected by DENV in all departments. The serotypes with the highest frequency of infection were DENV-1 and DENV-2 with 10.7% (n= 58) and 14.5% (n= 81), respectively. Coinfections between serotypes represented 3.9% (n= 22). CHIKV infection was detected in one individual (0.2%), and ZIKV infections were not detected. All infected samples were identified asA. aegypti(100%). From the COI dataset (593 bp), high levels of haplotype diversity (H = 0.948 ± 0.012) and moderate nucleotide diversity (π = 0.0225 ± 0.003) were identified, suggesting recent population expansions. Constructed phylogenetic analyses showed our COI sequences’ association with lineage I, which was reported widespread and related to a West African conspecific. We conclude that natural infection inA. aegyptiby arbovirus might reflect the country’s epidemiological behavior, with a higher incidence of serotypes DENV-1 and DENV-2, which may be associated with high seroprevalence and asymptomatic infections in humans. This study demonstrates the high susceptibility of this species to arbovirus infection and confirms thatA. aegyptiis the main vector in Colombia. The importance of including entomovirological surveillance strategy within public health systems to understand transmission dynamics and the potential risk to the population is highlighted herein.
Y-specific amh allele, amhy, is the master sex-determining gene in Japanese flounder Paralichthys olivaceus
Authors: Hattori Ricardo Shohei , Kumazawa Keiichiro , Nakamoto Masatoshi , Nakano Yuki , Yamaguchi Toshiya , Kitano Takeshi , Yamamoto Eiichi , Fuji Kanako , Sakamoto Takashi
Published: September 2022

Japanese flounder (Paralichthys olivaceus) is an important marine fish species of both fisheries and aquaculture in Northeast Asia. The commercial interest for all-female progenies due to several sex-related traits has prompted basic research on the mechanisms of sex determination in this species. By conducting a linkage analysis of the sex-determining locus, we initially identified 12 microsatellite markers linked to sex in 11 scaffolds, whose localization was restricted to a specific region of linkage group 9. Sequence analysis of this region identified 181 genes based on the UniProt database annotations. Among them, the amh gene was considered a potential candidate for sex determination because this gene is known to have taken over the role of sex determination in many teleosts. An in-depth sequence analysis of both the coding and non-coding regions of amh in XX and XY individuals detected nine SNPs linked with maleness. However, because these substitutions were synonymous, the upstream and downstream regions of amh were also investigated and a male-specific variant with deletions in the promoter region was detected. This truncated Y-specific amh variant was named amhy, and the amh shared by both sexes was named amhx. The association analysis using both females and males of the genotypic sex inferred by the presence/absence of amhy found complete association with phenotypic sex and genotype. Gene expression analysis in larvae derived from a single-pair progeny by quantitative real-time PCR detected amhy transcripts in the larval trunks between 20 and 100 days after hatching only in XY larvae. Localization of amhy by in situ hybridization was detected in presumptive Sertoli cells of XY gonads. Expression of amhx was almost undetectable in both XX and XY genotypes. Loss of Amh function by CRISPR-Cas9 induced male-to-female sex reversal, indicating that this gene was necessary for the masculinization of XY individuals. In conclusion, the complete linkage of amhy with males, its early expression in XY gonads before testicular differentiation, and the induction of sex reversal by loss-of-function mutation support the view that amhy is the sex-determining gene in this species.
Identifying the EMT-related signature to stratify prognosis and evaluate the tumor microenvironment in lung adenocarcinoma
Authors: Li Feng , Song Qing-Zhen , Zhang Yi-Fan , Wang Xing-Ru , Cao Li-Min , Li Nan , Zhao Ling-Xia , Zhang Sheng-Xiao , Zhuang Xiao-Fei
Published: September 2022

Background: Epithelial-mesenchymal transition (EMT) is a critical process in tumor invasion and metastasis. EMT has been shown to significantly influence the invasion, metastasis, and poor prognosis in lung adenocarcinoma (LUAD). This study aimed to develop a novel EMT-related prognostic model capable of predicting overall survival (OS) in patients with LUAD.

Methods: A total of 283 LUAD patients from TCGA RNA-seq dataset were assigned to a training cohort for model building, and 310 LUAD patients from GEO RNA-seq dataset were assigned to a validation cohort. EMT genes were acquired from MsigDB database and then prognosis-related EMT genes were identified by univariate Cox regression. Lasso regression was then performed to determine the genes and the corresponding variables to construct a prognosis risk model from the training cohort. Furthermore, characteristics of the tumor microenvironment (TME), mutation status and chemotherapy responses were analyzed to assess the differences between the two risk groups based on the prognostic model. In addition, RT-qPCR was employed to validate the expression patterns of the 6 genes derived from the risk model.

Results: A six-gene EMT signature (PMEPA1, LOXL2, PLOD2, MMP14, SPOCK1 and DCN) was successfully constructed and validated. The signature assigned the LUAD patients into high-risk and low-risk groups. In comparison with the low-risk group, patients in the high-risk group had a significantly lower survival rate. ROC curves and calibration curves for the risk model demonstrated reliable stratification and predictive ability. The risk model was robustly correlated with multiple TME characteristics. Besides, the data showed that patients in the low-risk group had more immune activities, higher stemness scores and cytolytic activity scores and higher TMB. In addition, RT-qPCR results revealed that PMEPA1, LOXL2, PLOD2, MMP14, and SPOCK1 were notably upregulated in LUAD tissues, while DCN was downregulated.

Conclusion: Our study successfully developed a novel EMT-related signature to predict prognosis of LUAD patients and guide treatment strategies. The six genes derived from the prediction signature might play a potential role in antitumor immunity and serve as promising therapeutic targets in LUAD.
Aberrant expression of SPAG6 and NM23 predicts poor prognosis of human osteosarcoma
Authors: Bao Zhengqi , Zhu Ruizhi , Fan Huagang , Ye Yuchen , Li Tian , Chai Damin
Published: September 2022

Objective: To investigate the expression and clinical significance of sperm-associated antigen 6 and NM23 proteins in human osteosarcoma.

Methods: The specimens of conventional osteosarcoma with follow-up from 42 Chinese patients were analyzed in this study, and 12 cases of osteochondroma were considered controls. The expression of SPAG6 and NM23 was inspected using immunohistochemical staining, qRT-PCR, and Western blotting methods.

Results: The positive expression rate of SPAG6 protein (71.43%) in 42 cases of osteosarcoma tissue was significantly higher than that (33.33%) in 12 cases of osteochondroma tissues (p < 0.05), while the positive rate of NM23 protein (35.71%) in osteosarcoma tissue was lower than that (58.33%) in osteochondroma tissue (p < 0.05). The mRNA and protein levels of SPAG6 were significantly higher than those of the adjacent normal tissues, while the expression of NM23 was lower in osteosarcoma tissues than that in the controls (p < 0.05 for all). There was a positive relationship between the expression of SPAG6 and pathological grade, metastasis, and Enneking stage (p < 0.05 for all). The overall survival rate of osteosarcoma patients with SPAG6 positive expression was significantly lower than that with SPAG6 negative expression. The relationship between the expression of NM23 and pathological grade, metastasis, and Enneking stage was negative (p < 0.05 for all). The overall survival rate of the osteosarcoma patients with NM23 positive expression was higher than that of the patients with NM23 negative expression (p < 0.05).

Conclusion: Overexpression of SPAG6 and low expression of NM23 are negatively related to pathological grade, metastasis, and Enneking stage and prognosis of osteosarcoma patients. This suggested that SPAG6 and NM23 should be considered candidate prognostic biomarkers for patients with osteosarcoma.
Integrated bioinformatics analysis for novel miRNAs markers and ceRNA network in diabetic retinopathy
Authors: Li Jingru , Li Chaozhong , Zhao Yulan , Wu Xinyu , Yu Shuai , Sun Guihu , Ding Peng , Lu Si , Zhang Lijiao , Yang Ping , Peng Yunzhu , Fu Jingyun , Wang Luqiao
Published: September 2022

In order to seek a more outstanding diagnosis and treatment of diabetic retinopathy (DR), we predicted the miRNA biomarkers of DR and explored the pathological mechanism of DR through bioinformatics analysis.

Method: Based on public omics data and databases, we investigated ncRNA (non-coding RNA) functions based on the ceRNA hypothesis.

Result: Among differentially expressed miRNAs (DE-miRNAs), hsa-miR-1179, -4797-3p and -665 may be diagnosis biomarkers of DR. Functional enrichment analysis revealed differentially expressed mRNAs (DE-mRNAs) enriched in mitochondrial transport, cellular respiration and energy derivation. 18 tissue/organ-specific expressed genes, 10 hub genes and gene cluster modules were identified. The ceRNA networks lncRNA FBXL19-AS1/miR-378f/MRPL39 and lncRNA UBL7-AS1/miR-378f/MRPL39 might be potential RNA regulatory pathways in DR.

Conclusion: Differentially expressed hsa-miR-1179, -4797-3p and -665 can be used as powerful markers for DR diagnosis, and the ceRNA network: lncRNA FBXL19-AS1/UBL7-AS1-miR-378f-MRPL39 may represent an important regulatory role in DR progression.
Comprehensive analysis of SLC43A2 on the tumor immune microenvironment and prognosis of liver hepatocellular carcinoma
Authors: Liao Yan , Weng Junmei , Chen Lian , Hu Nan , Yuan Xun , Wang Jianhua , He Feng , Cai Yixin , Huang Qin , Wang Jianing , Huang Liu
Published: September 2022

Background: Tumor cells outcompete T cells for methionine via overexpressing SLC43A2, causing T cells exhaustion. We explored the influence of SLC43A2 on tumor immune microenvironment (TIME), immune-related genes (IRGs) and the prognosis of liver hepatocellular carcinoma (LIHC) patients.

Methods: The TCGA-LIHC dataset (n = 374) and the ICGC-LIRI-JP-LIHC (n = 231) datasets were used as training and validation cohort, respectively. IRGs were obtained from ImmPort. Statistical analyses were performed using R (V 4.0.5). Online databases such as GEPIA, GSCALite, the Kaplan–Meier plotter, KEGG, TIMER2, and CMap were used for differential expression, immune infiltration, functional enrichment, survival, and drug-induced gene perturbation analysis.

Results: SLC43A2 expression was higher in LIHC, correlated with worse survival, but could not predict prognosis of LIHC separately (AUC = 0.467). SLC43A2 positively correlated with immune exhaustion markers (all p < 0.001) and with increased infiltration of Tregs, macrophages and myeloid-derived suppressor cells (MDSC) (all p < 0.05). SLC43A2 may regulate 120 IRGs. A prognostic risk score model was developed using the TCGA-LIHC cohort and validated by the ICGC-LIRI-JP cohort. Arachidonic acid, SB-202190 and guanethidine were identified as possible immunomodulators pharmacologically targeting SLC43A2 in LIHC.

Conclusion: SLC43A2 may create suppressive tumor microenvironment and regulate related IRGs, thus affecting the prognosis of LIHC. Arachidonic acid, SB-202190, and guanethidine may be worthy of further study as immunomodulators on SLC43A2.
The potential role of integrin alpha 6 in human mesenchymal stem cells
Authors: Al-Obaide Mohammed , Ishmakej Albi , Brown Christina , Mazzella Matteo , Agosta Patrina , Perez-Cruet Mick , Chaudhry G. Rasul
Published: September 2022

Human mesenchymal stem cells (MSCs) are isolated from various adult and perinatal tissues. Although mesenchymal stem cells from multiple sources exhibit similar morphology and cell surface markers, they differ in their properties. In this study, we determined that the expression of integrin alpha 6 (ITGA6) and ITGA6 antisense RNA (ITGA6-AS1) correlates with the proliferation, cell size, and differentiation potential. The expression of ITGA6 was inversely correlated with ITGA6-AS1 in MSCs. The expression of ITGA6 was higher, but ITGA6-AS1 was lower in MSCs from cord placenta junction, cord tissue, and Wharton’s jelly. In contrast, ITGA6 expression was lower, while ITGA6-AS1 was higher in MSCs from the placenta. The bioinformatic analysis showed that ITGA6 genomic DNA transcribes ITGA6-AS1 from the reverse strand, overlapping ITGA6 exon-2. Additionally, we identify several putative promoters (P1-P10) of ITGA6. ITGA6-P10 is CG rich and contains CGI. EMBOSS Cpgplot software revealed a CGI length of 180 bp that extends from nucleotide 125 to 304 of the P10 sequence. We suggest that the post-transcriptional regulation of the ITGA6 in mesenchymal stem cells is controlled by the ITGA6-AS1, which could be a critical factor responsible for the heterogeneity in function and cell fate of human MSCs. These results may provide further impetus for investigations to unravel the mechanisms of ITGA6 regulation that could help maintain or improve the properties of mesenchymal stem cells.
Identification of the circRNA–miRNA–mRNA regulatory network in osteoarthritis using bioinformatics analysis
Authors: Xu Wen-Bin , Kotheeranurak Vit , Zhang Huang-Lin , Feng Jin-Yi , Liu Jing-Wei , Chen Chien-Min , Lin Guang-Xun , Rui Gang
Published: September 2022

Background: Osteoarthritis (OA) is a degenerative joint disease that seriously affects the quality of people. Unfortunately, the pathogenesis of OA has not been fully known. Therefore, this study aimed to construct a ceRNA regulatory network related to OA to explore the pathogenesis of OA.

Methods: Differentially expressed circRNAs (DEcircRNAs), microRNAs (DEmiRNAs), and mRNAs (DEmRNAs) were obtained from the Gene Expression Omnibus microarray data (GSE175959, GSE105027, and GSE169077). The miRNA response elements and target mRNAs were identified using bioinformatics approaches. Additionally, a circRNA–miRNA–mRNA network was established using Cytoscape version 3.8.0. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of mRNAs in the network were conducted to explore the possible mechanisms underlying OA development. Protein–protein interaction (PPI) analysis was performed to determine the hub genes. Based on the hub genes, a sub network was constructed using Cytoscape 3.8.0 version. Finally, connectivity map (CMap) and drug–gene interaction database (DGIdb) analyses were performed to identify the potential therapeutic targets for OA.

Results: Altogether, five DEcircRNAs, 89 DEmiRNAs, and 345 DEmRNAs were identified. Moreover, a circRNA–miRNA–mRNA network was established using three circRNAs, seven miRNAs, and 37 mRNAs. GO and KEGG analyses demonstrated that the mRNAs in the network could be related to the occurrence and development of OA. PPI analysis was performed and six key genes, namely serpin family H member 1 [SERPINH1], collagen type VIII alpha 2 chain [COL8A2], collagen type XV alpha 1 chain [COL15A1], collagen type VI alpha 3 chain [COL6A3], collagen type V alpha 1 chain [COL5A1], and collagen type XI alpha 1 chain [COL11A1], were identified. Furthermore, a circRNA–miRNA–hub gene subnetwork was established in accordance with two circRNAs (hsa_circ_0075320 and hsa_circ_0051428), two miRNAs (hsa-miR-6124 and hsa-miR-1207-5p), and six hub genes (COL11A1, SERPINH1, COL6A3, COL5A1, COL8A2, and COL15A1). Finally, three chemicals (noscapine, diazepam, and TG100-115) based on CMap analysis and two drugs (collagenase Clostridium histolyticum and ocriplasmin) based on DGIdb were discovered as potential treatment options for OA.

Conclusion: This study presents novel perspectives on the pathogenesis and treatment of OA based on circRNA-related competitive endogenous RNA regulatory networks.
Splicing factor SRSF1 is essential for CD8 T cell function and host antigen-specific viral immunity
Authors: Juarez Ignacio , Su Shi , Herbert Zachary T. , Teijaro John R. , Moulton Vaishali R.
Published: September 2022

Cytotoxic CD8 T cells are crucial for the host antigen-specific immune response to viral pathogens. Here we report the identification of an essential role for the serine/arginine-rich splicing factor (SRSF) 1 in CD8 T cell homeostasis and function. Specifically, SRSF1 is necessary for the maintenance of normal CD8 T lymphocyte numbers in the lymphoid compartment, and for the proliferative capacity and cytotoxic function of CD8 T cells. Furthermore, SRSF1 is required for antigen-specific IFN-γ cytokine responses in a viral infection challenge in mice. Transcriptomics analyses of Srsf1-deficient T cells reveal that SRSF1 controls proliferation, MAP kinase signaling and IFN signaling pathways. Mechanistically, SRSF1 controls the expression and activity of the Mnk2/p38-MAPK axis at the molecular level. Our findings reveal previously unrecognized roles for SRSF1 in the physiology and function of cytotoxic CD8 T lymphocytes and a potential molecular mechanism in viral immunopathogenesis.
Immune landscape and risk prediction based on pyroptosis-related molecular subtypes in triple-negative breast cancer
Authors: Luo Lixi , Wei Qun , Xu Chenpu , Dong Minjun , Zhao Wenhe
Published: September 2022

The survival outcome of triple-negative breast cancer (TNBC) remains poor, with difficulties still existing in prognosis assessment and patient stratification. Pyroptosis, a newly discovered form of programmed cell death, is involved in cancer pathogenesis and progression. The role of pyroptosis in the tumor microenvironment (TME) of TNBC has not been fully elucidated. In this study, we disclosed global alterations in 58 pyroptosis-related genes at somatic mutation and transcriptional levels in TNBC samples collected from The Cancer Genome Atlas and Gene Expression Omnibus databases. Based on the expression patterns of genes related to pyroptosis, we identified two molecular subtypes that harbored different TME characteristics and survival outcomes. Then, based on differentially expressed genes between two subtypes, we established a 12-gene score with robust efficacy in predicting short- and long-term overall survival of TNBC. Patients at low risk exhibited a significantly better prognosis, more antitumor immune cell infiltration, and higher expression of immune checkpoints including PD-1, PD-L1, CTLA-4, and LAG3. The comprehensive analysis of the immune landscape in TNBC indicated that alterations in pyroptosis-related genes were closely related to the formation of the immune microenvironment and the intensity of the anticancer response. The 12-gene score provided new information on the risk stratification and immunotherapy strategy for highly heterogeneous patients with TNBC.
Crosstalk between epithelium, myeloid and innate lymphoid cells during gut homeostasis and disease
Authors: Ghilas Sonia , O’Keefe Ryan , Mielke Lisa Anna , Raghu Dinesh , Buchert Michael , Ernst Matthias
Published: September 2022

The gut epithelium not only provides a physical barrier to separate a noxious outside from a sterile inside but also allows for highly regulated interactions between bacteria and their products, and components of the immune system. Homeostatic maintenance of an intact epithelial barrier is paramount to health, requiring an intricately regulated and highly adaptive response of various cells of the immune system. Prolonged homeostatic imbalance can result in chronic inflammation, tumorigenesis and inefficient antitumor immune control. Here we provide an update on the role of innate lymphoid cells, macrophages and dendritic cells, which collectively play a critical role in epithelial barrier maintenance and provide an important linkage between the classical innate and adaptive arm of the immune system. These interactions modify the capacity of the gut epithelium to undergo continuous renewal, safeguard against tumor formation and provide feedback to the gut microbiome, which acts as a seminal contributor to cellular homeostasis of the gut.
Targeting 4-1BB for tumor immunotherapy from bench to bedside
Authors: Wang Ya-Tao , Ji Wei-Dong , Jiao Hong-Mei , Lu Ang , Chen Kun-Feng , Liu Qi-Bing
Published: September 2022

Immune dysfunction has been proposed as a factor that may contribute to disease progression. Emerging evidence suggests that immunotherapy aims to abolish cancer progression by modulating the balance of the tumor microenvironment. 4-1BB (also known as CD137 and TNFRS9), a member of tumor necrosis factor receptor superfamily, has been validated as an extremely attractive and promising target for immunotherapy due to the upregulated expression in the tumor environment and its involvement in tumor progression. More importantly, 4-1BB-based immunotherapy approaches have manifested powerful antitumor effects in clinical trials targeting 4-1BB alone or in combination with other immune checkpoints. In this review, we will summarize the structure and expression of 4-1BB and its ligand, discuss the role of 4-1BB in the microenvironment and tumor progression, and update the development of drugs targeting 4-1BB. The purpose of the review is to furnish a comprehensive overview of the potential of 4-1BB as an immunotherapeutic target and to discuss recent advances and prospects for 4-1BB in cancer therapy.
Prospects of animal models and their application in studies on adaptive immunity to SARS-CoV-2
Authors: Wei Xiaohui , Rong Na , Liu Jiangning
Published: September 2022

The adaptive immune response induced by SARS-CoV-2 plays a key role in the antiviral process and can protect the body from the threat of infection for a certain period of time. However, owing to the limitations of clinical studies, the antiviral mechanisms, protective thresholds, and persistence of the immune memory of adaptive immune responses remain unclear. This review summarizes existing research models for SARS-CoV-2 and elaborates on the advantages of animal models in simulating the clinical symptoms of COVID-19 in humans. In addition, we systematically summarize the research progress on the SARS-CoV-2 adaptive immune response and the remaining key issues, as well as the application and prospects of animal models in this field. This paper provides direction for in-depth analysis of the anti-SARS-CoV-2 mechanism of the adaptive immune response and lays the foundation for the development and application of vaccines and drugs.
Regulation of CIRP by genetic factors of SP1 related to cold sensitivity
Authors: Kim Soo Yeon , Ban Hyo-Jeong , Lee Siwoo , Jin Hee-Jeong
Published: September 2022

Cold-inducible RNA-binding-protein (CIRP) is a cold shock protein that plays a protective role in genotoxic stress response. CIRP modulates inflammation in human diseases, inhibits cell proliferation, and protects cells from genotoxic damage during cellular stress. The mild cold responsive element and specificity protein 1 (SP1) play a role in Cirp expression at low temperatures. Although previous studies have provided insights into the immune functions of SP1 or CIRP, the mechanisms by which CIRP and SP1 me diate inflammatory responses remain largely unknown. Therefore, in the current study, we examined whether Cirp expression is affected by genetic factors related to temperature sensitivity as well as under low temperature. We performed a genome-wide association study on cold sensitivity in 2,000 participants. Fifty-six genome-wide significant trait-locus pairs were identified (p<1×10-5, false discovery rate < 0.05). Among these variants, rs1117050 and rs11170510 had a strong linkage disequilibrium (r2 > 0.8) relationship and expression quantitative trait locus-associated signals with the nearest Sp1 gene. We confirmed that the minor alleles of rs11170510 and rs58123204 were associated with increased Sp1 expression. Additionally, Sp1 overexpression led to CIRP translocation from the nucleus to the cytoplasm. CIRP protein levels increased in serum samples that had minor alleles of rs11170510 and rs58123204. Levels of various pro-inflammatory cytokines were also significantly increased in human peripheral blood mononuclear cells with minor alleles of rs11170510 and rs58123204. These results suggest that genetic factors related to cold sensitivity regulate CIRP expression and function and provide valuable insights into prediction of potential diseases through analysis of inherent genetic factors in humans.
Metabolic reserves of diapausing western cherry fruit fly (Diptera: Tephritidae) pupae in relation to chill duration and post-chill rearing conditions
Authors: Neven Lisa G. , Yee Wee L.
Published: September 2022

How different macronutrients are utilized at various stages of pupal diapause and the effects of winter length on nutrient reserves remain poorly studied for most insects. Western cherry fruit fly, Rhagoletis indifferens (Diptera: Tephritidae), is a specialist on cherries in higher latitudes or elevations in western North America that exhibits a obligate pupal diapause requiring chilling before adult development can occur. We determined the relationship between metabolic reserves and diapause status in R. indifferens pupae, testing the hypotheses that lipids are the primary reserves utilized during diapause and that long periods of warmth deplete these reserves more than periods of cold. Effects of 0- to 20-week durations at 3°C and subsequent exposure to 23°C and 16:8 L:D (warm rearing conditions) for 0 to 7 weeks on lipid, protein, soluble carbohydrates, and glycogen reserves of R. indifferens pupae were determined. During diapause, lipid reserves were the primary source of energy utilized by R. indifferens, while protein and soluble carbohydrates levels were stable throughout diapause and thus less utilized. At post-diapause, glycogen levels fluctuated the most, indicating that lipid reserves were utilized to produce glycogen to support metabolism for adult fly development. Unchilled pupae did not deplete lipid reserves, unlike chilled pupae, likely because unchilled pupae remained in diapause. Rhagoletis indifferens may have evolved a nutrient utilization strategy typical of rigid diapausing insects in higher latitude environments.
A decade of coral biobanking science in Australia - transitioning into applied reef restoration
Authors: Hobbs Rebecca J. , O'Brien Justine K. , Bay Line K. , Severati Andrea , Spindler Rebecca , Henley E. Michael , Quigley Kate M. , Randall Carly J. , van Oppen Madeleine J. H. , Carter Virginia , Zuchowicz Nikolas , Hagedorn Mary , Daly Jonathan
Published: September 2022

Active restoration or intervention programs will be required in the future to support the resilience and adaptation of coral reef ecosystems in the face of climate change. Selective propagation of corals ex situ can help conserve keystone species and the ecosystems they underpin; cross-disciplinary research and communication between science and industry are essential to this success. Zoos and aquaria have a long history of managing ex situ breed-for-release programs and have led the establishment of wildlife biobanks (collections of cryopreserved living cells) along with the development of associated reproductive technologies for their application to wildlife conservation. Taronga Conservation Society Australia’s CryoDiversity Bank includes cryopreserved coral sperm from the Great Barrier Reef, which represents the largest repository from any reef system around the globe. This paper presents results from an inventory review of the current collection. The review highlighted the skew toward five Acropora species and the necessity to increase the taxonomic diversity of the collection. It also highlighted the need to increase geographic representation, even for the most well represented species. The inventory data will inform Taronga’s future research focus and sampling strategy to maximize genetic variation and biodiversity within the biobank and provide a test case for other practitioners implementing biobanking strategies for coral conservation around the world. Through co-investment and collaboration with research partners over the next decade, Taronga will prioritize and resource critical applied research and expand biobanking efforts to assist interventions for reef recovery and restoration.
Emergency responses to acrylonitrile maritime spills from the perspective of marine ecological protection
Authors: Wang Xiaotong , Meng Fanping
Published: September 2022

The increases in chemical shipping volumes increase the risk of hazardous noxious substances (HNSs) spills at sea. As one of the most frequently transported HNSs, acrylonitrile (ACN) spill incidents occur from time to time. The spilled ACN will have a wide range of short-term and long-term impacts on the marine environment. To reasonably standardise and optimise the emergency response countermeasures for ACN spill and maintain marine ecological health, the marine ecological hazards and physico-chemical behaviours of ACN were summarised. Based on this, the emergency response countermeasures for ACN spill at sea were studied and summarised in five aspects: spill source control, rapid prediction, emergency monitoring, numerical simulation and impact assessment, and elimination of ACN. This review forms a set of systematic emergency response countermeasures for deployment in ACN maritime spill incidents.
Effect of Sasobit warm mix on micro properties of asphalt with different degrees of regeneration
Authors: Tong Bin , Song Xuyan , Shen Junan , Jiang Ting , Chen Jiafan , Niu Junfeng
Published: September 2022

In this work, an aged asphalt was mixed with a new modified asphalt based on styrene–butadiene–styrene (SBS) in different proportions, and the warm mixing agent was added to simulate the asphalt fusion behaviour in the warm mixed recycled asphalt with different aged asphalt fertilizer (reclaimed asphalt pavement, RAP) content. Low field nuclear magnetic resonance (LF-NMR), atomic force microscopy (AFM), and Fourier transform infrared spectroscopy (FTIR) were used as analytical techniques to study the role of the warm mixing agent in terms of molecular bond energy, apparent morphology, and functional groups. It was found that the softening point and penetration of asphalt are reduced, and the ductility is increased, during the regeneration process. Sasobit warm mix agent can reduce the penetration and ductility of asphalt and improve the softening point. Its viscosity reduction effect is mainly achieved by adsorbing saturated components and decreasing the bond energy between 1H and other molecules; Sasobit warm mix agent can improve the aging state of mixed asphalt. On the AFM two-dimensional adhesion diagram, the number of bee-shaped structures and the single area is reduced; in the new and old mixed asphalt, the greater the proportion of new asphalt, the more evident the effect of Sasobit warm mix agent is.
Comparison of high-intensity focused ultrasound ablation and uterine artery embolization in the management of cervical pregnancy
Authors: Li Waixing , Gan Xiaoli , Kashyap Nidhi , Zou Lingxiao , Zhang Aiqian , Xu Dabao
Published: September 2022

Background

Cervical pregnancy (CP) is an uncommon type of ectopic pregnancy with a rising risk to life. Currently, there is no universal protocol for the safe and effective management of CP. This study aimed to investigate the clinical efficacy of high-intensity focused ultrasound ablation (HIFU) vs. uterine artery embolization (UAE) in the management of CP to develop a standard for the treatment of CP.

Methods

From January 2015 to October 2021, 36 patients with CP were diagnosed, treated, and followed up at the Department of Gynecology of Third Xiangya Hospital of Central South University. A total of 11 patients were treated with HIFU followed by suction curettage under hysteroscopic guidance, and 25 patients were treated with UAE followed by suction curettage under hysteroscopic guidance. Medical records and pregnancy outcomes were retrospectively analyzed.

Results

Compared to the UAE group, the HIFU group had a shorter interval time (1.5 ± 0.21 days vs. 2.6 ± 0.26 days), shorter duration of hospitalization (5.5 ± 0.31 days vs. 6.6 ± 0.21 days), shorter recovery time of menstruation (30.6 ± 7.09 days vs. 36.9 ± 5.54 days), fewer adverse reactions (0/11 vs. 9/25), and fewer postoperative complications (1/11 vs. 8/25). There were no significant differences in age, gravidity, parity, abortion, gestational age, cardiac pulsation, admission symptoms, hemoglobin level, largest diameter of the sac/mass, serum human chorionic gonadotropin (hCG) level at admission, hospitalization expenses, hospitalization days, blood loss during curettage, degree of hCG decline, residue after curettage, fertility requirement, and pregnancy outcomes.

Conclusion

Both HIFU and UAE are safe and effective in the treatment of patients with CP. Compared to UAE, HIFU treatment for CP is a safer and more effective therapeutic schedule owing to the advantages of being more minimally invasive, shorter interval time, shorter hospitalization days and recovery time of menstruation, fewer adverse reactions, and fewer postoperative complications.
Hospital admissions and mortality for acute exacerbations of COPD during the COVID-19 pandemic: A nationwide study in France
Authors: Poucineau Jonas , Delory Tristan , Lapidus Nathanaël , Hejblum Gilles , Chouaïd Christos , Le Cœur Sophie , Khlat Myriam
Published: September 2022

Background

A global reduction in hospital admissions for acute exacerbations of chronic obstructive pulmonary disease (AECOPD) was observed during the first months of the COVID-19 pandemic. Large-scale studies covering the entire pandemic period are lacking. We investigated hospitalizations for AECOPD and the associated in-hospital mortality at the national level in France during the first 2 years of the pandemic.

Methods

We used the French National Hospital Database to analyse the time trends in (1) monthly incidences of hospitalizations for AECOPD, considering intensive care unit (ICU) admission and COVID-19 diagnoses, and (2) the related in-hospital mortality, from January 2016 to November 2021. Pandemic years were compared with the pre-pandemic years using Poisson regressions.

Results

The database included 565,890 hospitalizations for AECOPD during the study period. The median age at admission was 74 years (interquartile range 65–83), and 37% of the stays concerned women. We found: (1) a dramatic and sustainable decline in hospitalizations for AECOPD over the pandemic period (from 8,899 to 6,032 monthly admissions, relative risk (RR) 0.65, 95% confidence interval (CI) 0.65–0.66), and (2) a concomitant increase in in-hospital mortality for AECOPD stays (from 6.2 to 7.6% per month, RR 1.24, 95% CI 1.21–1.27). The proportion of stays yielding ICU admission was similar in the pre-pandemic and pandemic years, 21.5 and 21.3%, respectively. In-hospital mortality increased to a greater extent for stays without ICU admission (RR 1.39, 95% CI 1.35–1.43) than for those with ICU admission (RR 1.09, 95% CI 1.05–1.13). Since January 2020, only 1.5% of stays were associated with a diagnosis of COVID-19, and their mortality rate was nearly three-times higher than those without COVID-19 (RR 2.66, 95% CI 2.41–2.93).

Conclusion

The decline in admissions for AECOPD during the pandemic could be attributed to a decrease in the incidence of exacerbations for COPD patients and/or to a possible shift from hospital to community care. The rise in in-hospital mortality is partially explained by COVID-19, and could be related to restricted access to ICUs for some patients and/or to greater proportions of severe cases among the patients hospitalized during the pandemic.
Catalyzing urea hydrolysis using two-step microbial-induced carbonate precipitation for copper immobilization: Perspective of pH regulation
Authors: Xue Zhong-Fei , Cheng Wen-Chieh , Wang Lin , Xie Yi-Xin
Published: September 2022

Microbial induced carbonate precipitation (MICP) has recently applied to immobilize heavy metals toward preventing their threats to public health and sustainable development of surrounding environments. However, for copper metallurgy activities higher copper ion concentrations cause the ureolytic bacteria to lose their activity, leading to some difficulty in forming carbonate precipitation for copper immobilization (referred to also as “biomineralization”). A series test tube experiments were conducted in the present work to investigate the effects of bacterial inoculation and pH conditions on the copper immobilization efficiency. The numerical simulations mainly aimed to compare with the experimental results to verify its applicability. The copper immobilization efficiency was attained through azurite precipitation under pH in a 4–6 range, while due to Cu2+ migration and diffusion, it reduced to zero under pH below 4. In case pH fell within a 7–9 range, the immobilization efficiency was attained via malachite precipitation. The copper-ammonia complexes formation reduced the immobilization efficiency to zero. The reductions were attributed either to the low degree of urea hydrolysis or to inappropriate pH conditions. The findings shed light on the necessity of securing the urease activity and modifying pH conditions using the two-step biomineralization approach while applying the MICP technology to remedy copper-rich water bodies.
Bacterial biomarkers capable of identifying recurrence or metastasis carry disease severity information for lung cancer
Authors: Yuan Xuelian , Wang Zhina , Li Changjun , Lv Kebo , Tian Geng , Tang Min , Ji Lei , Yang Jialiang
Published: September 2022

Background

Local recurrence and distant metastasis are the main causes of death in patients with lung cancer. Multiple studies have described the recurrence or metastasis of lung cancer at the genetic level. However, association between the microbiome of lung cancer tissue and recurrence or metastasis remains to be discovered. Here, we aimed to identify the bacterial biomarkers capable of distinguishing patients with lung cancer from recurrence or metastasis, and how it related to the severity of patients with lung cancer.

Methods

We applied microbiome pipeline to bacterial communities of 134 non-recurrence and non-metastasis (non-RM) and 174 recurrence or metastasis (RM) samples downloaded from The Cancer Genome Atlas (TCGA). Co-occurrence network was built to explore the bacterial interactions in lung cancer tissue of RM and non-RM. Finally, the Kaplan–Meier survival analysis was used to evaluate the association between bacterial biomarkers and patient survival.

Results

Compared with non-RM, the bacterial community of RM had lower richness and higher Bray–Curtis dissimilarity index. Interestingly, the co-occurrence network of non-RM was more complex than RM. The top 500 genera in relative abundance obtained an area under the curve (AUC) of 0.72 when discriminating between RM and non-RM. There were significant differences in the relative abundances of Acidovorax, Clostridioides, Succinimonas, and Shewanella, and so on between RM and non-RM. These biomarkers played a role in predicting the survival of lung cancer patients and were significantly associated with lung cancer stage.

Conclusion

This study provides the first evidence for the prediction of lung cancer recurrence or metastasis by bacteria in lung cancer tissue. Our results highlights that bacterial biomarkers that distinguish RM and non-RM are also associated with patient survival and disease severity.
Metabarcoding of mycetangia from the Dendroctonus frontalis species complex (Curculionidae: Scolytinae) reveals diverse and functionally redundant fungal assemblages
Authors: Vazquez-Ortiz Karina , Pineda-Mendoza Rosa María , González-Escobedo Román , Davis Thomas S. , Salazar Kevin F. , Rivera-Orduña Flor N. , Zúñiga Gerardo
Published: September 2022

Dendroctonus-bark beetles are associated with microbes that can detoxify terpenes, degrade complex molecules, supplement and recycle nutrients, fix nitrogen, produce semiochemicals, and regulate ecological interactions between microbes. Females of someDendroctonusspecies harbor microbes in specialized organs called mycetangia; yet little is known about the microbial diversity contained in these structures. Here, we use metabarcoding to characterize mycetangial fungi from beetle species in theDendroctonus frontaliscomplex, and analyze variation in biodiversity of microbial assemblages between beetle species. Overall fungal diversity was represented by 4 phyla, 13 classes, 25 orders, 39 families, and 48 genera, including 33 filamentous fungi, and 15 yeasts. The most abundant genera wereEntomocorticium,Candida,Ophiostoma-Sporothrix,Ogataea,Nakazawaea,Yamadazyma,Ceratocystiopsis,Grosmannia-Leptographium,Absidia, andCyberlindnera. Analysis of α-diversity indicated that fungal assemblages ofD.viteishowed the highest richness and diversity, whereas those associated withD.brevicomisandD.barberihad the lowest richness and diversity, respectively. Analysis of β-diversity showed clear differentiation in the assemblages associated withD.adjunctus,D.barberi, andD.brevicomis, but not between closely related species, includingD.frontalisandD.mesoamericanusandD.mexicanusandD.vitei. A core mycobiome was not statistically identified; however, the genusCeratocystiopsiswas shared among seven beetle species. Interpretation of a tanglegram suggests evolutionary congruence between fungal assemblages and species of theD.frontaliscomplex. The presence of different amplicon sequence variants (ASVs) of the same genus in assemblages from species of theD.frontaliscomplex outlines the complexity of molecular networks, with the most complex assemblages identified fromD.vitei,D.mesoamericanus,D.adjunctus, andD.frontalis. Analysis of functional variation of fungal assemblages indicated multiple trophic groupings, symbiotroph/saprotroph guilds represented with the highest frequency (∼31% of identified genera). These findings improve our knowledge about the diversity of mycetangial communities in species of theD.frontaliscomplex and suggest that minimal apparently specific assemblages are maintained and regulated within mycetangia.
Diversity, antibacterial activity and chemical analyses of gut-associated fungi isolated from the Crocothemis servilia
Authors: Cui Pu , Liu Lijun , Huang Zhongdi , Shi Shuping , Kong Kun , Zhang Yinglao
Published: September 2022

Insect-associated fungi are a potentially rich source of novel natural products with antibacterial activity. Here, we investigated the community composition and phylogenetic diversity of gut-associated fungi of the dragonfly (Crocothemis Servilia) using a combination of culture-dependent and culture-independent methods. A total of 42 fungal isolates were obtained from the guts of the dragonfly, which belonged to four classes and thirteen different genera. Amplicon sequencing analyses revealed that the fungal communities were more diverse, and a total of 136 genera were identified and dominated by the genera Wojnowiciella and Phoma. The antibacterial bioassay showed that five fungal crude extracts of representative isolates have shown antibacterial activities. Among them, the extract of Phoma sp. QTH17 showed the best antibacterial activities against Escherichia coli, Micrococcus tetragenus, and Staphylococcus aureus with the disc diameter of inhibition zone diameter (IZD) of 6.50, 10.80, and 8.70 mm, respectively. Chemical analysis of Phoma sp. QTH17 led to the discovery of five known compounds, including ergosterol (1), 3-Chlorogentisyl alcohol (2), epoxydon (3), epoxydon 6-methylsalicylate ester (4) and mannitol (5). Among them, the compound 3 exhibited potent antibacterial activities against E. coli, M. tetragenus, and S. aureus with the IZD of 7.00, 14.00, and 12.50 mm, respectively, which were slightly weaker than those of the positive gentamicin sulfate with the IZD of 11.13, 18.30, and 12.13 mm, respectively. In conclusion, our results confirmed that the diversity of gut-associated fungi of C. Servilia could be expected to explore the resource of new species and antibacterial substances.
Enhanced mass transfer of pulsed vacuum pressure pickling and changes in quality of sour bamboo shoots
Authors: Dai Jian-Wu , Zhang Qing , Li Ming , Li Lian-Jie , Xu Li-Jia , Liu Yao-Wen , Yin Peng-Fei , Liu Shu-Xiang , Zhao Yong-Peng , Gou Kai-Yun , Li Ying-Lu , Qin Wen
Published: September 2022

Sour bamboo shoot is a traditional Chinese fermented vegetable food. The traditional pickling method of sour bamboo shoots has the disadvantages of being time-consuming, inhomogeneous, and difficult to control. Pulsed vacuum pressure pickling (PVPP) technology uses pulsed vacuum pressure to enhance the pickling efficiency significantly. To demonstrate the effects of salt content and PVPP technical parameters on the fermentation of bamboo shoots, the sample salinity, pH value, color, crunchiness and chewiness, nitrite content, and lactic acid bacteria content during the pickling process were investigated. The salt content inside the bamboo shoots gradually increased to the equilibrium point during the pickling process. The pickling efficiency of bamboo shoots under PVPP technology increased by 34.1% compared to the traditional control groups. Meanwhile, the uniform salt distribution under PVPP technology also obtained better performance in comparison with the traditional groups. The pH value declined slowly from 5.96 to 3.70 with the extension of pickling time and sour flavor accumulated progressively. No significant differences were found in the color values (L*, a*, and b*) and the crunchiness of the bamboo shoot under different salt solution concentrations, vacuum pressure, and pulsation frequency ratio conditions. Colony-forming unit of lactic acid bacteria (CFU of LAB) decreased, to begin with, and then increased until the 6th day, followed by a declining trend in volatility. The nitrate content of bamboo shoots samples under PVPP treatments did not exceed the safety standard (<20 mg/kg) during the whole fermentation process, which proves the safety of PVPP technology. In conclusion, PVPP technology can safely replace the traditional method with better quality performance. The optimal PVPP processing conditions (vacuum pressure 60 kPa, 10 min vacuum pressure time vs. 4 min atmospheric pressure time, salt solution concentration 6%) have been recommended for pickling bamboo shoots with high product quality.