bluuebunny/crossref_metadata_2025 huggingface dataset:
Visceral fat correlates with insulin secretion and sensitivity independent of BMI and subcutaneous fat in Chinese with type 2 diabetes
Authors: Huang Haishan , Zheng Xiaobin , Wen Xiaoming , Zhong Jingyi , Zhou Yanting , Xu Lingling
Published: February 2023

Aim

Clinical heterogeneity exists in overall obesity and abdominal obesity in terms of insulin secretion and sensitivity. Further, the impact of visceral fat (VF) on the first- and second-phase insulin secretion (FPIS and SPIS) is controversial. We aim to investigate insulin secretion and sensitivity in Chinese patients with T2DM according to different BMI and VF levels.

Methods

This study enrolled 300 participants. A dual bioelectrical impedance analyzer was used to assess the visceral and subcutaneous fat area (VFA and SFA). VF levels were categorized as normal or high, with the cutoff value of 100 cm2. FPIS and SPIS were evaluated by arginine stimulation test and standardized steamed bread meal tolerance test, respectively. β-cell function (HOMA2-β), insulin resistance (HOMA2-IR), and Gutt’s insulin sensitivity index (Gutt-ISI) were also calculated. Spearman’s correlation analysis and multivariate linear regression analysis were adopted for statistical analysis.

Results

Participants were categorized into four groups: normal weight-normal VF, normal weight-high VF, overweight/obese-normal VF and overweight/obese-high VF. Multivariate linear regression showed that both VFA and SFA were correlated with FPIS, HOMA2-IR and Gutt-ISI after controlling for gender and diabetes duration. After further adjustment for BMI and VFA, some associations of SFA with insulin secretion and sensitivity disappeared. After adjustment for gender, diabetes duration, BMI and SFA, VFA was positively correlated with FPIS, SPIS and HOMA2-IR. Subjects with overweight/obese-high VF were more likely to have higher FPIS, HOMA2-IR and lower Gutt-ISI (all p < 0.05).

Conclusion

VF affects both FPIS and SPIS, and worsens insulin sensitivity independent of BMI and subcutaneous fat in Chinese patients with T2DM.

Clinical trial registration

http://www.chictr.org.cn, identifier ChiCTR2200062884.
Regional sustainability: Pressures and responses of tourism economy and ecological environment in the Yangtze River basin, China
Authors: Zhu Kai , Zhou Quan , Cheng Yufeng , Zhang Youtian , Li Ting , Yan Xiaoyue , Alimov Atabek , Farmanov Erkin , Dávid Lóránt Dénes
Published: February 2023

The relationship between the tourism economy and the ecological environment is under pressure, and balancing this relationship is crucial for promoting regional sustainability. In this study, the Yangtze River basin, the first largest river in Asia and third largest in the world, was selected as the focus area. The spatial and temporal characteristics of tourism economic development and ecological environmental pressure from 2000 to 2019 were analyzed using the tourism economic development index, ecological environmental pressure index and dynamic change index, and the decoupling process of tourism and the economic system was studied dynamically using the decoupling analysis model. The results show that (1) spatially, the tourism economy in the Yangtze River basin exhibits a pattern of high development in the east and low development in the west, and high in the south and low in the north. Ecological environmental pressures varied greatly, with less pressure in the upstream provinces and more pressure in the middle and downstream provinces. (2) Temporally, the tourism economies of Qinghai and Tibet started with a lower but faster growth rate, while Hunan and Hubei have a higher starting point but limited change. The ecological environmental pressure changes do not show a clear spatial distribution pattern. (3) The decoupling relationship between tourism economy and ecological environment in the Yangtze River basin is moving toward a harmonious development. Achieving a harmonious balance between the two systems is crucial for maintaining ecological balance and regional sustainability.
Exploration of prognostic genes and risk signature in breast cancer patients based on RNA binding proteins associated with ferroptosis
Authors: Chen Xiang , Yang Changcheng , Wang Wei , He Xionghui , Sun Hening , Lyu Wenzhi , Zou Kejian , Fang Shuo , Dai Zhijun , Dong Huaying
Published: February 2023

Background: Breast cancer (BRCA) is a life-threatening malignancy in women with an unsatisfactory prognosis. The purpose of this study was to explore the prognostic biomarkers and a risk signature based on ferroptosis-related RNA-binding proteins (FR-RBPs).

Methods: FR-RBPs were identified using Spearman correlation analysis. Differentially expressed genes (DEGs) were identified by the “limma” R package. The univariate Cox and multivariate Cox analyses were executed to determine the prognostic genes. The risk signature was constructed and verified with the training set, testing set, and validation set. Mutation analysis, immune checkpoint expression analysis in high- and low-risk groups, and correlation between risk signature and chemotherapeutic agents were conducted using the “maftools” package, “ggplot2” package, and the CellMiner database respectively. The Human Protein Atlas (HPA) database was employed to confirm protein expression trends of prognostic genes in BRCA and normal tissues. The expression of prognostic genes in cell lines was verified by Real-time quantitative polymerase chain reaction (RT-qPCR). Kaplan-meier (KM) plotter database analysis was applied to predict the correlation between the expression levels of signature genes and survival statuses.

Results: Five prognostic genes (GSPT2, RNASE1, TIPARP, TSEN54, and SAMD4A) to construct an FR-RBPs-related risk signature were identified and the risk signature was validated by the International Cancer Genome Consortium (ICGC) cohort. Univariate and multivariate Cox regression analysis demonstrated the risk score was a robust independent prognostic factor in overall survival prediction. The Tumor Mutational Burden (TMB) analysis implied that the high- and low-risk groups responded differently to immunotherapy. Drug sensitivity analysis suggested that the risk signature may serve as a chemosensitivity predictor. The results of GSEA suggested that five prognostic genes might be related to DNA replication and the immune-related pathways. RT-qPCR results demonstrated that the expression trends of prognostic genes in cell lines were consistent with the results from public databases. KM plotter database analysis suggested that high expression levels of GSPT2, RNASE1, and SAMD4A contributed to poor prognoses.

Conclusion: In conclusion, this study identified the FR-RBPs-related prognostic genes and developed an FR-RBPs-related risk signature for the prognosis of BRCA, which will be of great significance in developing new therapeutic targets and prognostic molecular biomarkers for BRCA.
Genome-wide association study and identification of systemic comorbidities in development of age-related macular degeneration in a hospital-based cohort of Han Chinese
Authors: Shih Chien-Hung , Chuang Hao-Kai , Hsiao Tzu-Hung , Yang Yi-Ping , Gao Chong-En , Chiou Shih-Hwa , Hsu Chih-Chien , Hwang De-Kuang
Published: February 2023

Background: Age-related macular degeneration (AMD) is the main cause of severe vision loss in elderly populations of the developed world with limited therapeutic medications available. It is a multifactorial disease with a strong genetic susceptibility which exhibits the differential genetic landscapes among different ethnic groups.

Methods: To investigate the Han Chinese-specific genetic variants for AMD development and progression, we have presented a genome-wide association study (GWAS) on 339 AMD cases and 3,390 controls of a Han Chinese population recruited from the Taiwan Precision Medicine Initiative (TPMI).

Results: In this study, we have identified several single nucleotide polymorphisms (SNPs) significantly associated with AMD, including rs10490924, rs3750848, and rs3750846 in the ARMS2 gene, and rs3793917, rs11200638, and rs2284665 in the HTRA1 gene, in which rs10490924 was highly linked to the other variants based upon linkage disequilibrium analysis. Moreover, certain systemic comorbidities, including chronic respiratory diseases and cerebrovascular diseases, were also confirmed to be independently associated with AMD. Stratified analysis revealed that both non-exudative and exudative AMD were significantly correlated with these risk factors. We also found that homozygous alternate alleles of rs10490924 could lead to an increased risk of AMD incidence compared to homozygous references or heterozygous alleles in the cohorts of chronic respiratory disease, cerebrovascular disease, hypertension, and hyperlipidemia. Ultimately, we established the SNP models for AMD risk prediction and found that rs10490924 combined with the other AMD-associated SNPs identified from GWAS improved the prediction model performance.

Conclusion: These results suggest that genetic variants combined with the comorbidities could effectively identify any potential individuals at a high risk of AMD, thus allowing for both early prevention and treatment.
Identification of a cellular senescence-related-lncRNA (SRlncRNA) signature to predict the overall survival of glioma patients and the tumor immune microenvironment
Authors: Liu Qing , Bao Hongbo , Zhang Sibin , Song Tianjun , Li Chenlong , Sun Guiyin , Sun Xiaoyang , Fu Tianjiao , Wang Yujie , Liang Peng
Published: February 2023

Background: Gliomas are brain tumors that arise from glial cells, and they are the most common primary intracranial tumors with a poor prognosis. Cellular senescence plays a critical role in cancer, especially in glioma. In this study, we constructed a senescence-related lncRNA (SRlncRNA) signature to assess the prognosis of glioma.

Methods: The Cancer Genome Atlas was used to collect SRlncRNA transcriptome profiles and clinical data about glioma. Patients were randomized to training, testing, and whole cohorts. LASSO and Cox regression analyses were employed to construct the SRlncRNA signature, and Kaplan–Meier (K-M) analysis was performed to determine each cohort’s survival. Receiver operating characteristic (ROC) curves were applied to verify the accuracy of this signature. Gene set enrichment analysis was used to visualize functional enrichment (GSEA). The CIBERSORT algorithm, ESTIMATE and TIMER databases were utilized to evaluate the differences in the infiltration of 22 types of immune cells and their association with the signature. RT–qPCR and IHC were used to identify the consistency of the signature in tumor tissue.

Results: An SRlncRNA signature consisting of six long non-coding RNAs (lncRNAs) was constructed, and patients were divided into high-risk and low-risk groups by the median of their riskscore. The KM analysis showed that the high-risk group had worse overall survival, and the ROC curve confirmed that the riskscore had more accurate predictive power. A multivariate Cox analysis and its scatter plot with clinical characteristics confirmed the riskscore as an independent risk factor for overall survival. GSEA showed that the GO and KEGG pathways were mainly enriched in the immune response to tumor cells, p53 signaling pathway, mTOR signaling pathway, and Wnt signaling pathway. Further validation also yielded significant differences in the risk signature in terms of immune cell infiltration, which may be closely related to prognostic differences, and qRT–PCR and IHC confirmed the consistency of the expression differences in the major lncRNAs with those in the prediction model.

Conclusion Our findings indicated that the SRlncRNA signature might be used as a predictive biomarker and that there is a link between it and immune infiltration. This discovery is consistent with the present categorization system and may open new avenues for research and personalized therapy.
Gene profiling reveals the role of inflammation, abnormal uterine muscle contraction and vascularity in recurrent implantation failure
Authors: Dong Xinyi , Zhou Mi , Li Xinyu , Huang Huijing , Sun Yun
Published: February 2023

Objective: Recurrent implantation failure (RIF) is now disturbing numerous infertile couples accepting assisted reproductive technology (ART). And the endometrial factors are crucial causes of recurrent implantation failure. However, its mechanism is still unclear. Thus, the aim of this study is to identify altered biologic processes in endometrium that may contribute to recurrent implantation failure.

Methods: We recruited two microarray datasets (GSE103465, GSE111974) from Gene Expression Omnibus database (GEO), which contain endometrium from RIF and normal women during implantation period. Using the online tools GEO2R and Venny, we identified Differentially Expressed Genes (DEGs) of selected datasets, and obtained common DEGs. Gene Ontology (GO) terms, Kyoto Encyclopedia of Genes and Genomes (KEGG) and BioCatar pathway enrichment were conducted with Enrichr platform, “ssgsea” and “ggplot2” package of RStudio. PPI networks and hub gene related TF-gene interaction and TF-miRNA co-regulation networks were built via online tools STRING and NetworkAnalyst. Immune infiltration analysis was performed by CIBERSORT platform. Recurrent implantation failure subgroup identification was achieved through “ConsensusClusterPlus,” “tsne,” “ssgsea”, and “ggpubr” package in RStudio. Diagnostic characteristic ROC curves were constructed via “pROC” and “ggplot2” package of RStudio. Enrichr platform was utilized to find drugs targeting hub genes.

Results: 26 common DEGs were confirmed. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes/BioCarta analysis determined common DEGs were mainly enriched in inflammation associated pathways including TNF, NF-κB, IL-4, IL-10, IL-6, and TGF-β signaling pathways. Five hub genes (PTGS2, VCAM1, EDNRB, ACTA2, and LIF) and related TF-gene and TF-miRNA interactions were identified. Immune infiltration analysis indicated the importance of macrophage M2 in recurrent implantation failure patients. Importantly, subgroup identification analysis highlighted that recurrent implantation failure patients can be divided into two subgroups with different phenotypes. Moreover, the ROC curves and drugs may provide new diagnostic and therapeutic thought for recurrent implantation failure.
The 4G/5G polymorphism of plasminogen activator inhibitor type 1 is a predictor of allergic cough
Authors: Tang Rui , Lyu Xiaohong , Li Hong , Sun Jinlyu
Published: February 2023

Background: It has been suggested that genetic factors may be substantially linked to allergy disorders. This study aims to investigate the relationship between the genetic susceptibility of Chinese patients with allergy disorders and the polymorphisms of plasminogen activator inhibitor 1 gene (PAI-1) rs1799762, cysteinyl leukotriene receptor 1 gene (CYSLTR1) rs320995, gasdermin B gene (GSDMB) rs7216389, glycoprotein IIIa gene (GPIIIa) rs5918, glycoprotein Ib alpha gene (GP1BA) rs6065, platelet endothelial aggregation receptor 1 gene (PEAR1) rs12041331, and tumor necrosis factor alpha gene (TNF-α) rs1800629.

Methods: From the Peking Union Medical College Hospital, this study enrolled 60 healthy participants and 286 participants with allergic diseases. TaqMan-minor groove binder (MGB) quantitative polymerase chain reaction (qPCR) was used to examine the gene polymorphisms in each group.

Results: The TaqMan-MGB qPCR results were completely consistent with the DNA sequencing results, according to other studies in this medical center (Kappa = 1, p < .001). Only the distribution of PAI-1 rs1799762 was different between patients with allergic cough and healthy people (χ2 = 7.48, p = .0238). With regard to cough patients, the 4G4G and 5G5G genotypes were more frequent (allergic cough vs. healthy individuals: 4G4G 57.9% vs. 26.7%; 5G5G 20.0% vs. 13.3%), but the 4G5G genotype was more frequent in healthy people (allergic cough vs. healthy individuals: 45.7% vs. 60.0%). The CYSLTR1 rs320995, GSDMB rs7216389, GPIIIa rs5918, GP1BA rs6065, PEAR1 rs12041331, and TNF-α rs1800629 polymorphisms, however, did not show any of such relationships.

Conclusion: The PAI-1 rs1799762 polymorphisms may be associated with the genetic susceptibility of Chinese allergic disease patients with cough performance.
Towards reproducible research in recurrent pregnancy loss immunology: Learning from cancer microenvironment deconvolution
Authors: Betti Martina , Vizza Enrico , Piccione Emilio , Pietropolli Adalgisa , Chiofalo Benito , Pallocca Matteo , Bruno Valentina
Published: February 2023

The most recent international guidelines regarding recurrent pregnancy loss (RPL) exclude most of the immunological tests recommended for RPL since they do not reach an evidence-based level. Comparisons for metanalysis and systematic reviews are limited by the ambiguity in terms of RPL definition, etiological and risk factors, diagnostic work-up, and treatments applied. Therefore, cohort heterogeneity, the inadequacy of numerosity, and the quality of data confirm a not standardized research quality in the RPL field, especially for immunological background, for which potential research application remains confined in a separate single biological layer. Innovative sequencing technologies and databases have proved to play a significant role in the exploration and validation of cancer research in the context of dataset quality and bioinformatics tools. In this article, we will investigate how bioinformatics tools born for large-scale cancer immunological research could revolutionize RPL immunological research but are limited by the nature of current RPL datasets.
Identification of tumor mutation burden-associated molecular and clinical features in cancer by analyzing multi-omics data
Authors: Li Mengyuan , Gao Xuejiao , Wang Xiaosheng
Published: February 2023

Background

Tumor mutation burden (TMB) has been recognized as a predictive biomarker for immunotherapy response in cancer. Systematic identification of molecular features correlated with TMB is significant, although such investigation remains insufficient.

Methods

We analyzed associations of somatic mutations, pathways, protein expression, microRNAs (miRNAs), long non-coding RNAs (lncRNAs), competing endogenous RNA (ceRNA) antitumor immune signatures, and clinical features with TMB in various cancers using multi-omics datasets from The Cancer Genome Atlas (TCGA) program and datasets for cancer cohorts receiving the immune checkpoint blockade therapy.

Results

Among the 32 TCGA cancer types, melanoma harbored the highest percentage of high-TMB (≥ 10/Mb) cancers (49.4%), followed by lung adenocarcinoma (36.9%) and lung squamous cell carcinoma (28.1%). Three hundred seventy-six genes had significant correlations of their mutations with increased TMB in various cancers, including 11 genes (ARID1A, ARID1B, BRIP1, NOTCH2, NOTCH4, EPHA5, ROS1, FAT1, SPEN, NSD1,and PTPRT) with the characteristic of their mutations associated with a favorable response to immunotherapy. Based on the mutation profiles in three genes (ROS1, SPEN, and PTPRT), we defined the TMB prognostic score that could predict cancer survival prognosis in the immunotherapy setting but not in the non-immunotherapy setting. It suggests that the TMB prognostic score’s ability to predict cancer prognosis is associated with the positive correlation between immunotherapy response and TMB. Nine cancer-associated pathways correlated positively with TMB in various cancers, including nucleotide excision repair, DNA replication, homologous recombination, base excision repair, mismatch repair, cell cycle, spliceosome, proteasome, and RNA degradation. In contrast, seven pathways correlated inversely with TMB in multiple cancers, including Wnt, Hedgehog, PI3K-AKT, MAPK, neurotrophin, axon guidance, and pathways in cancer. High-TMB cancers displayed higher levels of antitumor immune signatures and PD-L1 expression than low-TMB cancers in diverse cancers. The association between TMB and survival prognosis was positive in bladder, gastric, and endometrial cancers and negative in liver and head and neck cancers. TMB also showed significant associations with age, gender, height, weight, smoking, and race in certain cohorts.

Conclusions

The molecular and clinical features significantly associated with TMB could be valuable predictors for TMB and immunotherapy response and therefore have potential clinical values for cancer management.
Single-cell analysis reveals TLR-induced macrophage heterogeneity and quorum sensing dictate population wide anti-inflammatory feedback in response to LPS
Authors: Tiemeijer Bart M. , Heester Sebastiaan , Sturtewagen Ashley Y. W. , Smits Anthal I. P. M. , Tel Jurjen
Published: February 2023

The role of macrophages in controlling tissue inflammation is indispensable to ensure a context-appropriate response to pathogens whilst preventing excessive tissue damage. Their initial response is largely characterized by high production of tumor necrosis factor alpha (TNFα) which primes and attracts other immune cells, thereafter, followed by production of interleukin 10 (IL-10) which inhibits cell activation and steers towards resolving of inflammation. This delicate balance is understood at a population level but how it is initiated at a single-cell level remains elusive. Here, we utilize our previously developed droplet approach to probe single-cell macrophage activation in response to toll-like receptor 4 (TLR4) stimulation, and how single-cell heterogeneity and cellular communication affect macrophage-mediated inflammatory homeostasis. We show that only a fraction of macrophages can produce IL-10 in addition to TNFα upon LPS-induced activation, and that these cells are not phenotypically different from IL-10 non-producers nor exhibit a distinct transcriptional pathway. Finally, we demonstrate that the dynamics of TNFα and IL-10 are heavily controlled by macrophage density as evidenced by 3D hydrogel cultures suggesting a potential role for quorum sensing. These exploratory results emphasize the relevance of understanding the complex communication between macrophages and other immune cells and how these amount to population-wide responses.
Ecotourism in Marine Protected Areas as a tool to valuate natural capital and enhance good marine governance: A review
Authors: Casimiro Daniela , Ventura Maria Anunciação , Botelho Andrea Zita , Guerreiro José
Published: February 2023

Marine Protected Areas (MPAs) are essential to reach the UN Ocean’s Decade challenges and the Sustainable Development Goal 14 (life bellow water – conserve coastal and marine areas), and their crucial role for the health of the planet was highlighted in the United Nations Ocean Conference. However, often these MPA’s are no more than Paper Parks, with poor financial and human resources, thus lacking effectiveness. Moreover, they frequently trigger conflicts with local communities, by imposing restrictions to their activities with no alternative or compensations, causing serious governance inefficiencies. Thus, within the UN Oceans Decade, MPA’s must face simultaneously three of the challenges: Protect and restore ecosystems and biodiversity (Challenge 2); Develop a sustainable and equitable ocean economy (Challenge 4) and Change humanity’s relationship with the ocean (Challenge 10). To address those challenges, it becomes clear that management models of MPA’s had to find ways to value natural capital and, at the same time, involve local communities and stakeholders in the governance processes. The conservation of biodiversity has both direct and indirect economic benefits for many sectors of the economy, namely tourism, being ecotourism considered one of the segments particularly adequate to value natural capital. Ecotourism, defined as “environmentally responsible travel and visitation to relatively undisturbed natural areas”, to enjoy and appreciate nature, is often used to enhance the natural capital, while protecting and promoting protected areas. Several studies have been carried out about ecotourism in MPA’s all over the world, particularly in the 21stcentury. In this article, we analyzed several case studies focusing ecotourism in MPAs, to better understand the connection between the development of this industry, the development of sustainable blue economy, and the efforts for ocean conservation. From the analysis conducted, we conclude that ecotourism development and community participation are of paramount importance in achieving sustainable development in MPAs, although there is still room to new advances improving good marine governance.
Commercial sharks under scrutiny: Baseline genetic distinctiveness supports structured populations of small-spotted catsharks in the Mediterranean Sea
Authors: Melis Riccardo , Vacca Laura , Cariani Alessia , Carugati Laura , Cau Alessandro , Charilaou Charis , Di Crescenzo Simone , Ferrari Alice , Follesa Maria Cristina , Hemida Farid , Helyar Sarah , Lo Brutto Sabrina , Sion Letizia , Tinti Fausto , Cannas Rita
Published: February 2023

The present study, based on microsatellite markers, describes a population genetic analysis of the small-spotted catshark Scyliorhinus canicula (Linnaeus, 1758), representing one of the most abundant and commonly caught cartilaginous fishes in the Mediterranean Sea and adjacent areas. The analyses were performed to unravel the genetic features (variability, connectivity, sex-biased dispersal) of their relative geographic populations, both at the small (around the coast of Sardinia, Western Mediterranean Sea) and at a larger spatial scale (pan-Mediterranean level and between the Atlantic Ocean and the Mediterranean Sea). Individual clustering, multivariate and variance analyses rejected the hypothesis of genetic homogeneity, with significant genetic differences mainly within the Mediterranean between the Western and Eastern basins, as well as between the Mediterranean and the NE Atlantic Ocean. In detail, our results seem to confirm that the Strait of Gibraltar could not represent a complete barrier to the exchange of individuals of small-spotted catshark between the Atlantic Ocean and the Mediterranean Sea. In the latter area, a complex genetic structuring for S. canicula was found. Apart from differences among the Western, Eastern and Adriatic sites, within the Western basin the small-spotted catsharks around Sardinian waters are strongly differentiated from all others (both from the eastern Tyrrhenian Sea and southernmost part of the Algerian basin) and are demographically stable. Several possible mechanisms, both biological and abiotic (e.g., migratory behavior, waterfronts, and oceanographic discontinuities), are discussed here to explain their peculiar characteristics. Overall, the genetic data presented, both at the local and regional level, could represent a baseline information, useful for the temporal monitoring of populations, and to assess the effects of present or future fishing/management/conservation measures.
Hydrocarbons occurrence and transcriptomic response of oyster Crassostrea virginica from lagoons of the Southern Gulf of Mexico
Authors: López-Landavery Edgar A. , Galindo-Sánchez Clara E. , López-Galindo Laura L. , Ramírez-Álvarez Nancy , Saavedra-Flores Anaid , Amador-Cano Gerardo , Ventura-López Claudia , San Martín-Del Ángel Pablo , Hernández-Herrera Rosa I.
Published: February 2023

The Gulf of Mexico is an important crude oil reserve worldwide, and the oyster Crassostrea virginica is an excellent candidate to study the oil spill impacts on marine invertebrates. In this work, the concentrations of polycyclic aromatic hydrocarbons (PAHs) and aliphatic hydrocarbons (AHs) from eight productive oyster areas in the Gulf of Mexico were measured on sediment, water, and tissues from C. virginica. In water, the highest AHs concentration was detected in Tamiahua (0.50 ng/mL), while for PAHs, the highest concentration was > 0.10 ng/mL in Tampamachoco. In sediment, Tamiahua and Tampamachoco lagoons had the highest AHs concentrations with values near 2.5 μg/g dry weight. Considering the PAHs, Tamiahua, Carmen, and Tampamachoco lagoons registered the highest levels, with values > 60 ng/g dry weight. In tissues from C. virginica, La Pesca, Cármen and Mecoacán presented the highest PAHs concentrations with values between 0.20 and 0.25 μg/g dry weight. Furthermore, from the molecular analysis of genes related with different phases of the xenobiotic detoxification process such as hypoxia inducible factor (hif-1a), cytochrome P450 10 (cyp10), flavin mono-oxygenase (fmo), glutathione S-transferase (gstΩ1), multidrug resistant protein (mdrd1), catalase (cat), among others, the differences between lagoons were significant (P< 0.05) and generally with Las Enramadas showing the highest expression levels. From genes evaluated in this study, hif-1a, cyp10, fmo, mdrd1 and cat presented the highest expression differentials between lagoons. The above allowed us to validate the utility of molecular markers in the assessment of the hydrocarbons effect on oyster under the conditions from the Southern Gulf of Mexico.
Response of bacterial communities (Marivita, Marinobacter, and Oceanicaulis) in the phycosphere to the growth of Phaeodactylum tricornutum in different inorganic nitrogen sources
Authors: Wei Xiaoxue , Shi Feng , Chen Zixi , Feng Jianfeng , Zhu Lin
Published: February 2023

Introduction

In marine ecosystems, microbial communities are important drivers of material circulation and energy flow. The complex interactions between phytoplankton and bacterial communities constitute one of the most crucial ecological relationships in the marine environment. Inorganic nitrogen can affect the type of relationship between algae and bacteria. However, the quantitative relationship between the bacterial communities, inorganic nitrogen, and phytoplankton remains unclear.

Methods

Under laboratory conditions, we altered the forms (nitrate and ammonium) and amounts of nitrogen sources to study the dynamics of bacterial biomass, diversity, and community structure in the phycosphere of the marine model species Phaeodactylum tricornutum. The bacterial community structure during P. tricornutum growth was analyzed using Illumina HiSeq sequencing of 16S rDNA amplicons.

Results

The results indicated that inorganic nitrogen concentration was the main factor promoting P. tricornutum biomass growth. The change in the algal biomass would significantly increase the phycosphere bacterial biomass. The bacterial biomass in the algal-bacteria co-culture system was 1.5 ~ 5 times that of the conditional control groups without microalgae under the same culture conditions. The variation of P. tricornutum biomass also affected the bacterial communities in the phycosphere. When P. tricornutum was in the exponential phase (96 ~ 192 h), the bacterial community structure differed between the high- and low-concentration groups. The difference in the bacterial communities over time in the high-concentration groups was more prominent than in the low-concentration groups. Under high-concentration groups (HA and HN), the relative abundance of Marivita and Marinobacter, engaged in the transformation of aquatic inorganic nitrogen, gradually decreased with time. However, the relative abundance of Oceanicaulis, closely related to algal growth, gradually increased with time.

Discussion

The above phenomena might be related to the change in P. tricornutum biomass. Our results explain when and how the phycosphere bacterial communities responded to algal biomass variations. The study provides a foundation for the quantitative relationship among nutrients, microalgae, and bacteria in this system.
Effects of habitat usage on hypoxia avoidance behavior and exposure in reef-dependent marine coastal species
Authors: Yu Haolin , Fang Guangjie , Rose Kenneth A. , Lin Jiazheng , Feng Jie , Wang Haiyan , Cao Qingxian , Tang Yanli , Zhang Tao
Published: February 2023

Reef habitat in coastal ecosystems is increasingly being augmented with artificial reefs (ARs) and is simultaneously experiencing increasing hypoxia due to eutrophication and climate change. Relatively little is known about the effects of hypoxia on organisms that use complex habitat arrangements and how the presence of highly preferred AR habitat can affect the exposure of organisms to low dissolved oxygen (DO). We performed two laboratory experiments that used video recording of behavioral movement to explore 1) habitat usage and staying duration of individuals continuously exposed to 3, 5, and 7 mg/L dissolved oxygen (DO) in a complex of multiple preferred and avoided habitat types, and 2) the impact of ARs on exposure to different DO concentrations under a series of two-way replicated choice experiments with or without AR placement on the low-oxygen side. Six common reef-dependent species found in the northeastern sea areas of China were used (i.e., rockfish Sebastes schlegelii and Hexagrammos otakii, filefish Thamnaconus modestus, flatfish Pseudopleuronectes yokohamae, sea cucumber Stichopus japonicus, and crab Charybdis japonica). Results showed that lower DO levels decreased the usage of preferred habitats of the sea cucumber and the habitat-generalist filefish but increased the habitat affinity to preferred habitat types for the two habitat-specific rockfishes. Low DO had no effect on the crab’s habitat usage. In the choice experiment, all three fish species avoided 1 mg/L, and the rockfish S. schlegelii continued to avoid the lower DO when given choices involving pairs of 3, 5, and 7 mg/L, while H. otakii and the flatfish showed less avoidance. The availability of ARs affected exposure to low DO for the habitat-preferring rockfishes but was not significant for the flatfish. This study provides information for assessing the ecological effects and potential for adaptation through behavioral movement for key reef-dependent species under the increasing overlap of ARs and hypoxia anticipated in the future.
Ship-to-ship maritime wireless channel modeling under various sea state conditions based on REL model
Authors: Li Fang , Shui Yishui , Liang Jiayao , Yang Kun , Yu Junyi
Published: February 2023

The propagation of electromagnetic waves on land and sea is significantly different. Although the Los scenario is significant in marine wireless communication, the marine wireless channel exists an obvious two-ray phenomenon due to the strong reflection path reflected through the sea surface. By modeling the measured data of marine wireless channels, this paper calculates the radio propagation characteristics of the Pearl River estuary. In addition, the wave fluctuations and high humidity environment will also impact the properties of the marine wireless channel. Therefore, sea surface morphology models under multiple wind speeds are built. To estimate the path loss in the same area under different conditions, the Monte Carlo method is employed to quantify the results. The simulation results show that the electric wave propagation gradually degenerated from the round earth loss (REL) model to the free space model with increasing wind speed. Moreover, the distribution of the shadow fading varies with distance. The findings provide references for the network planning of marine communication.
First insights into an exceptionally deep blue hole in the Western Caribbean: The Taam ja’ Blue Hole
Authors: Alcérreca-Huerta Juan C. , Álvarez-Legorreta Teresa , Carrillo Laura , Flórez-Franco Laura M. , Reyes-Mendoza Oscar F. , Sánchez-Sánchez Joan A.
Published: February 2023

Coastal karst formations may remain unexplored by the global marine scientific research community. Knowledge provided by fishermen coupled with scientific research on karstic formations prompted us to explore the geomorphometric and physicochemical features of a submerged blue hole in the large tropical estuary of Chetumal Bay in the southeastern coast of the Yucatán Peninsula, Mexico. Differently from the well-known literature on cenotes in the Yucatán Peninsula, no references are made to blue holes in the region. Sampling and surveying of the blue hole were conducted in September 2021 by scuba, echosounders, CTD profilers, and the collection of water samples. This study revealed a previously unknown maximum water depth for the Taam ja’ Blue Hole, as it is now named, of 274.4 meters below sea level (mbsl), making it the second deepest known blue hole in the world. The Taam ja’ Blue Hole has a nearly circular shape at its surface, encompassing an area of ~13,690 m2. The sides of the blue hole are steep, with slopes >80° that form a large conic structure covered by biofilms, sediments, limestone, and gypsum ledges. The blue hole mouth locates at ~4.5-5.0 mbsl, at which water properties change significantly with temperature and salinity gradients of 4.9°C/m and 9.8 PSU/m, respectively. Hydrographic profiles show a stratified water column inside the blue hole consisting of a hypoxic layer (5-20 mbsl), a chemocline (50-80 mbsl), and an anoxic layer (>110 mbsl). Evaluation of anions and cations indicated that the water inside corresponds mainly to that of diluted seawater.
Experimental assessment and semi empirical estimation of frost accretion—A case study on a spine-finned inverted-V tube array evaporator
Authors: Carvajal-Mariscal I. , De León-Ruiz J. E. , Belman-Flores J. M. , Martínez-Espinosa E. , José-Pineda O.
Published: February 2023

Present work focuses on frost accretion in a spine-finned inverted-V tube array evaporator. An experimental evaluation was performed using a standard issue, vertical top-mount, 18 cubic feet, 0.5 m3, refrigerator. Evaporator temperature distribution, inner airflow velocity, and relative humidity were measured to account for convective phenomena influencing frost distribution. Frost formation and accretion on the surface of the evaporator were visualized using thermal and microscopic imagery. The images were processed using a machine vision algorithm to measure frost thickness. Complementarily, frost density and vapor mass transfer were computed using available correlations. An estimation function was derived from the compiled data using a semi empirical approach, i.e., direct measurements and thermophysical substance properties. The resulting mathematical expression estimated the frost accretion rate within an error expectancy, RMSE, of 0.1479 and displayed a goodness-of-fit, R-Squared, of 0.9029. Based on these results, semi empirical estimation, is proposed as a viable approach to construct adequate limits for new predictions, vis-à-vis evaporator performance, ultimately reducing appliance energy consumption via implementing more effective control strategies regarding internal defrosting.
Metabolic and inflammatory linkage of the chicken cecal microbiome to growth performance
Authors: Wang Liqi , Zhang Fuping , Li Hui , Yang Shenglin , Chen Xiang , Long Shuihua , Yang Shenghong , Yang Yongxian , Wang Zhong
Published: February 2023

Introduction

Chinese indigenous chicken breeds are widely used as food in China but their slow growth rate and long farming cycle has limited their industrial production.

Methods

In the current study we examined whether the market weights of native chicken breeds were related to specific cecal bacteria, serum metabolites and inflammatory cytokines. We examined cecal bacterial taxa using 16S rDNA analysis along with untargeted serum metabolites and serum inflammatory cytokines.

Results

We found that the cecal microbiota could explain 10.1% of the individual differences in chicken weights and identified key cecal bacterial genera that influenced this phenotype. The presence of Sphaerochaeta spp. improved growth performance via bovinic acid metabolism. In contrast, Synergistes and norank_f_Desulfovibrionaceae had a negative effect on growth by inducing expression of the inflammatory cytokine IL-6.

Discussion

We were able to link specific bacterial genera with growth promotion in chickens and this study will allow further development of their use as probiotics in these animals.
Impact of particle flux on the vertical distribution and diversity of size-fractionated prokaryotic communities in two East Antarctic polynyas
Authors: Puigcorbé Viena , Ruiz-González Clara , Masqué Pere , Gasol Josep M.
Published: February 2023

Antarctic polynyas are highly productive open water areas surrounded by ice where extensive phytoplankton blooms occur, but little is known about how these surface blooms influence carbon fluxes and prokaryotic communities from deeper waters. By sequencing the 16S rRNA gene, we explored the vertical connectivity of the prokaryotic assemblages associated with particles of three different sizes in two polynyas with different surface productivity, and we linked it to the magnitude of the particle export fluxes measured using thorium-234 (234Th) as particle tracer. Between the sunlit and the mesopelagic layers (700 m depth), we observed compositional changes in the prokaryotic communities associated with the three size-fractions, which were mostly dominated by Flavobacteriia, Alphaproteobacteria, and Gammaproteobacteria. Interestingly, the vertical differences between bacterial communities attached to the largest particles decreased with increasing 234Th export fluxes, indicating a more intense downward transport of surface prokaryotes in the most productive polynya. This was accompanied by a higher proportion of surface prokaryotic taxa detected in deep particle-attached microbial communities in the station with the highest 234Th export flux. Our results support recent studies evidencing links between surface productivity and deep prokaryotic communities and provide the first evidence of sinking particles acting as vectors of microbial diversity to depth in Antarctic polynyas, highlighting the direct influence of particle export in shaping the prokaryotic communities of mesopelagic waters.
Schistosoma mansoni coactivator associated arginine methyltransferase 1 (SmCARM1) effect on parasite reproduction
Authors: Coelho Fernanda Sales , Gava Sandra Grossi , Andrade Luiza Freire , Geraldo Juliana Assis , Tavares Naiara Clemente , Lunkes Felipe Miguel Nery , Neves Renata Heisler , Machado-Silva José Roberto , Pierce Raymond J. , Oliveira Guilherme , Mourão Marina Moraes
Published: February 2023

Introduction

The human blood fluke parasite Schistosoma mansoni relies on diverse mechanisms to adapt to its diverse environments and hosts. Epigenetic mechanisms play a central role in gene expression regulation, culminating in such adaptations. Protein arginine methyltransferases (PRMTs) promote posttranslational modifications, modulating the function of histones and non-histone targets. The coactivator-associated arginine methyltransferase 1 (CARM1/PRMT4) is one of the S. mansoni proteins with the PRMT core domain.

Methods

We carried out in silico analyses to verify the expression of SmPRMTs in public datasets from different infection stages, single-sex versus mixed-worms, and cell types. The SmCARM1 function was evaluated by RNA interference. Gene expression levels were assessed, and phenotypic alterations were analyzed in vitro, in vivo, and ex vivo.

Results

The scRNAseq data showed that SmPRMTs expression is not enriched in any cell cluster in adult worms or schistosomula, except for Smcarm1 expression which is enriched in clusters of ambiguous cells and Smprmt1 in NDF+ neurons and stem/germinal cells from schistosomula. Smprmt1 is also enriched in S1 and late female germ cells from adult worms. After dsRNA exposure in vitro, we observed a Smcarm1 knockdown in schistosomula and adult worms, 83 and 69%, respectively. Smcarm1-knockdown resulted in reduced oviposition and no significant changes in the schistosomula or adult worm phenotypes. In vivo analysis after murine infection with Smcarm1 knocked-down schistosomula, showed no significant change in the number of worms recovered from mice, however, a significant reduction in the number of eggs recovered was detected. The ex vivo worms presented a significant decrease in the ovary area with a lower degree of cell differentiation, vitelline glands cell disorganization, and a decrease in the testicular lobe area. The worm tegument presented a lower number of tubercles, and the ventral sucker of the parasites presented a damaged tegument and points of detachment from the parasite body.

Discussion

This work brings the first functional characterization of SmCARM1 shedding light on its roles in S. mansoni biology and its potential as a drug target. Additional studies are necessary to investigate whether the reported effects of Smcarm1 knockdown are a consequence of the SmCARM1-mediated methylation of histone tails involved in DNA packaging or other non-histone proteins.
Exopolysaccharide-producing Lacticaseibacillus paracasei strains isolated from kefir as starter for functional dairy products
Authors: Bengoa Ana Agustina , Dueñas María Teresa , Prieto Alicia , Garrote Graciela L. , Abraham Analía G.
Published: February 2023

Exopolysaccharides (EPS) produced by lactic acid bacteria are molecules of great interest for the dairy food industry. Lacticaseibacillus paracasei CIDCA 8339, CIDCA 83123, and CIDCA 83124 are potentially probiotic strains isolated from kefir grains whose EPS-production on MRS broth is dependent on incubation temperature. The aim of the present work is to evaluate the effect of fermentation temperature on the characteristics of EPS produced in milk by L. paracasei strains and the consequent impact on the rheological properties of the fermented products. Additionally, the protective effect of these EPS against Salmonella infection was evaluated in vitro. Acid gels with each strain were obtained by milk fermentation at 20°C, 30°C, and 37°C evidencing for all the strains a reduction in growth and acidification rate at lower temperature. Lacticaseibacillus paracasei CIDCA 83123 showed low fermentation rate at all temperatures requiring between 3 and 8 days to obtain acids gels, whereas CIDCA 8339 and 83124 needed between 24 and 48 h even when the temperature was 20°C. Fermentation temperature led to changes in crude EPS characteristics of the three strains, observing an increase in the relative amount of the high molecular weight fraction when the fermentation temperature diminished. Additionally, EPS83124 and EPS83123 presented modifications in monosaccharide composition, with a reduction of rhamnose and an increase of amino-sugars as temperature rise. These changes in the structure of EPS83124 resulted in an increase of the apparent viscosity of milks fermented at 20°C (223 mPa.s) and 30°C (217 mPa.s) with respect to acid gels obtained at 37°C (167 mPa.s). In order to deepen the knowledge on EPS characteristics, monosaccharide composition of low and high molecular weight EPS fractions were evaluated. Finally, it was evidenced that the preincubation of intestinal epithelial cells Caco-2/TC-7 with EPS8339 and EPS83124 partially inhibit the association and invasion of Salmonella. In light of these results, it can be concluded that the selection of the EPS-producing strain along with the appropriate fermentation conditions could be an interesting strategy to improve the technological properties of these L. paracasei fermented milks with potential protective effects against intestinal pathogens.