bluuebunny/crossref_metadata_2025 huggingface dataset:
Chemical Compositions in Winter PM2.5 in Changzhou of the Yangtze River Delta Region, China: Characteristics and Atmospheric Responses Along With the Different Pollution Levels
Authors: Zhao Zhuzi , Sun Ning , Zhou Wenlin , Ma Shuaishuai , Li Xudong , Li Malong , Zhang Xian , Tang Shishi , Ye Zhaolian
Published: June 2022

Changzhou, a typical industrial city located in the center of the Yangtze River Delta (YRD) region, has experienced serious air pollution in winter. However, Changzhou still receives less attention compared with other big cities in YRD. In this study, a four-month PM2.5sampling campaign was conducted in Changzhou, China from 1 November 2019, to 1 February 2020. The period covers the entire wintertime and includes first week of the Level 1 response stage of the lockdown period due to the outbreak of COVID-19. The mean PM2.5concentrations were 67.9 ± 29.0 μg m−3, ranging from 17.4 to 157.4 μg m−3. Secondary inorganic ions were the most abundant species, accounting for 37 and 50% during the low and high PM2.5pollution periods, respectively. Nitrogen oxidation ratio (NOR) during the high PM concentration level period was twice the low PM concentration period whereas sulfur oxidation ratio (SOR) showed a less significant increase. This represents that nitrate formation is potentially the predominant factor controlling the occurrence of PM pollution. The analysis of NOR, SOR as functions of relative humidity (RH) and ozone (O3) concentrations suggest that the sulfate formation was mainly through aqueous-phase reaction, while nitrate formation was driven by both photochemistry and heterogeneous reaction. And, excess ammonium could promote the formation of nitrate during the high PM period, indicating that ammonia gas played a critical role in regulating nitrate. Furthermore, a special period-Chinese New Year overlapping first week of COVID-19 lockdown period, offered a precious window to study the impact of human activity pattern changes on air pollution variation. During the special period, the average PM2.5mean concentration was 60.4 μg m−3, which did not show in a low value as expected. The declines in nitrogen oxide (NOx) emissions led to rapid increases in O3and atmospheric oxidizing capacity, as well as sulfate formation. The chemical profiles and compositions obtained during different periods provide a scientific basis for establishing efficient atmospheric governance policies in the future.
Genomics and Geographic Diversity of Bacteriophages Associated With Endosymbionts in the Guts of Workers and Alates of Coptotermes Species (Blattodea: Rhinotermitidae)
Authors: Chen Junyan , Gissendanner Christopher R. , Tikhe Chinmay V. , Li Hou-Feng , Sun Qian , Husseneder Claudia
Published: June 2022

Subterranean termites depend nutritionally on their gut microbiota, which includes protozoa as well as taxonomically and functionally diverse bacteria. Our previous metavirome study revealed a high diversity and novel families of bacteriophages in the guts of Coptotermes formosanus workers from New Orleans, Louisiana, United States. Two assembled bacteriophage genomes (Phages TG-crAlp-04 and 06, family Podoviridae) existed in all colonies and showed similarity to a prophage (ProJPt-Bp1) previously sequenced from a bacterial endosymbiont (Candidatus Azobacteroides pseudotrichonymphae, CAP) of protozoa in the gut of a termite species of the genus Prorhinotermes from Taiwan. In this study the genomes of Phage TG-crAlp-04 and 06 were subjected to detailed functional annotation. Both phage genomes contained conserved genes for DNA packaging, head and tail morphogenesis, and phage replication. Approximately 30% of the amino acid sequences derived from genes in both genomes matched to those of ProJPt-Bp1 phage or other phages from the crAss-like phage group. No integrase was identified; the lack of a lysogeny module is a characteristic of crAss-like phages. Primers were designed to sequence conserved genes of the two phages and their putative host bacterium (CAP) to detect their presence in different termite species from native and introduced distribution ranges. Related strains of the host bacterium were found across different termite genera and geographic regions. Different termite species had separate CAP strains, but intraspecific geographical variation was low. These results together with the fact that CAP is an important intracellular symbiont of obligate cellulose-digesting protozoa, suggest that CAP is a core gut bacterium and co-evolved across several subterranean termite species. Variants of both crAss-like phages were detected in different Coptotermes species from the native and introduced range, but they did not differentiate by species or geographic region. Since similar phages were detected in different termite species, we propose the existence of a core virome associated with core bacterial endosymbionts of protozoa in the guts of subterranean termites. This work provides a strong basis for further study of the quadripartite relationship of termites, protozoa, bacteria, and bacteriophages.
Genome-Wide Selection Signatures and Human-Mediated Introgression Events in Bos taurus indicus-influenced Composite Beef Cattle
Authors: Vahedi Seyed Milad , Salek Ardestani Siavash , Pahlevan Afshari Kian , Ghoreishifar Seyed Mohammad , Moghaddaszadeh-Ahrabi Sima , Banabazi Mohammad Hossein , Brito‬‬ Luiz Fernando
Published: June 2022

Genetic introgression from interbreeding hybridization of European Bos taurus taurus (EBT) and Indian Bos taurus indicus (IBI) cattle breeds have been widely used to combine the climatic resilience of the IBI cattle and the higher productivity of EBT when forming new composite beef cattle (CB) populations. The subsequent breeding strategies have shifted their initial genomic compositions. To uncover population structure, signatures of selection, and potential introgression events in CB populations, high-density genotypes [containing 492,954 single nucleotide polymorphisms (SNPs) after the quality control] of 486 individuals from 15 cattle breeds, including EBT, IBI, and CB populations, along with two Bos grunniens genotypes as outgroup were used in this study. Then, in-depth population genetics analyses were performed for three CB breeds of Beefmaster, Brangus, and Santa Gertrudis. Neighbor-joining, principal components, and admixture analyses confirmed the historical introgression of EBT and IBI haplotypes into CB breeds. The fdM statistics revealed that only 12.9% of CB populations’ genetic components are of IBI origin. The results of signatures of selection analysis indicated different patterns of selection signals in the three CB breeds with primary pressure on pathways involved in protein processing and stress response in Beefmaster, cell proliferation regulation and immune response in Brangus, and amino acids and glucose metabolisms in Santa Gertrudis. An average of >90% of genomic regions underlying selection signatures were of EBT origin in the studied CB populations. Investigating the CB breeds’ genome allows the estimation of EBT and IBI ancestral proportions and the locations within the genome where either taurine or indicine origin alleles are under selective pressure. Such findings highlight various opportunities to control the selection process more efficiently and explore complementarity at the genomic level in CB populations.
Genome-Wide Association Study and Genomic Prediction for Bacterial Wilt Resistance in Common Bean (Phaseolus vulgaris) Core Collection
Authors: Zia Bazgha , Shi Ainong , Olaoye Dotun , Xiong Haizheng , Ravelombola Waltram , Gepts Paul , Schwartz Howard F. , Brick Mark A. , Otto Kristen , Ogg Barry , Chen Senyu
Published: June 2022

Common bean (Phaseolus vulgaris) is one of the major legume crops cultivated worldwide. Bacterial wilt (BW) of common bean (Curtobacterium flaccumfaciens pv. flaccumfaciens), being a seed-borne disease, has been a challenge in common bean producing regions. A genome-wide association study (GWAS) was conducted to identify SNP markers associated with BW resistance in the USDA common bean core collection. A total of 168 accessions were evaluated for resistance against three different isolates of BW. Our study identified a total of 14 single nucleotide polymorphism (SNP) markers associated with the resistance to BW isolates 528, 557, and 597 using mixed linear models (MLMs) in BLINK, FarmCPU, GAPIT, and TASSEL 5. These SNPs were located on chromosomes Phaseolus vulgaris [Pv]02, Pv04, Pv08, and Pv09 for isolate 528; Pv07, Pv10, and Pv11 for isolate 557; and Pv04, Pv08, and Pv10 for isolate 597. The genomic prediction accuracy was assessed by utilizing seven GP models with 1) all the 4,568 SNPs and 2) the 14 SNP markers. The overall prediction accuracy (PA) ranged from 0.30 to 0.56 for resistance against the three BW isolates. A total of 14 candidate genes were discovered for BW resistance located on chromosomes Pv02, Pv04, Pv07, Pv08, and Pv09. This study revealed vital information for developing genetic resistance against the BW pathogen in common bean. Accordingly, the identified SNP markers and candidate genes can be utilized in common bean molecular breeding programs to develop novel resistant cultivars.
Identification and Validation of the Diagnostic Characteristic Genes of Ovarian Cancer by Bioinformatics and Machine Learning
Authors: Liu Jinya , Liu Leping , Antwi Paul Akwasi , Luo Yanwei , Liang Fang
Published: June 2022

Background: Ovarian cancer (OC) has a high mortality rate and poses a severe threat to women’s health. However, abnormal gene expression underlying the tumorigenesis of OC has not been fully understood. This study aims to identify diagnostic characteristic genes involved in OC by bioinformatics and machine learning.

Methods: We utilized five datasets retrieved from the Gene Expression Omnibus (GEO) database, The Cancer Genome Atlas (TCGA) database, and the Genotype-Tissue Expression (GTEx) Project database. GSE12470 and GSE18520 were combined as the training set, and GSE27651 was used as the validation set A. Also, we combined the TCGA database and GTEx database as validation set B. First, in the training set, differentially expressed genes (DEGs) between OC and non-ovarian cancer tissues (nOC) were identified. Next, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Disease Ontology (DO) enrichment analysis, and Gene Set Enrichment Analysis (GSEA) were performed for functional enrichment analysis of these DEGs. Then, two machine learning algorithms, Least Absolute Shrinkage and Selector Operation (LASSO) and Support Vector Machine-Recursive Feature Elimination (SVM-RFE), were used to get the diagnostic genes. Subsequently, the obtained diagnostic-related DEGs were validated in the validation sets. Then, we used the computational approach (CIBERSORT) to analyze the association between immune cell infiltration and DEGs. Finally, we analyzed the prognostic role of several genes on the KM-plotter website and used the human protein atlas (HPA) online database to analyze the expression of these genes at the protein level.

Results: 590 DEGs were identified, including 276 upregulated and 314 downregulated DEGs.The Enrichment analysis results indicated the DEGs were mainly involved in the nuclear division, cell cycle, and IL−17 signaling pathway. Besides, DEGs were also closely related to immune cell infiltration. Finally, we found that BUB1, FOLR1, and PSAT1 have prognostic roles and the protein-level expression of these six genes SFPR1, PSAT1, PDE8B, INAVA and TMEM139 in OC tissue and nOC tissue was consistent with our analysis.

Conclusions: We screened nine diagnostic characteristic genes of OC, including SFRP1, PSAT1, BUB1B, FOLR1, ABCB1, PDE8B, INAVA, BUB1, TMEM139. Combining these genes may be useful for OC diagnosis and evaluating immune cell infiltration.
CILP, a Putative Gene Associated With Immune Infiltration in Breast Cancer Brain Metastases
Authors: Sun Xiaolin , Yang Ning , Zhou Xingguo , Dai Honghai , Li Qiang , Feng Alei , Xu Gongwen , Liu Yingchao , Xu Linzong , Zhang Zhanyu , Yang Zhe , Li Xiaomei
Published: June 2022

Breast cancer (BC) is the second leading cause of brain metastases (BM), with high morbidity and mortality. The aim of our study was to explore the effect of the cartilage intermediate layer protein (CILP) on breast cancer brain metastases (BCBM). Using a weighted gene coexpression network analysis (WGCNA) in GSE100534 and GSE125989 datasets, we found that the yellow module was closely related to the occurrence of BCBM, and CILP was a hub gene in the yellow module. Low CILP expression was associated with a poor prognosis, and it was an independent prognostic factor for stage III–IV BC determined using Cox regression analysis. A nomogram model including CILP expression was established to predict the 5-, 7-, and 10-year overall survival (OS) probabilities of stage III–IV BC patients. We found that CILP mRNA expression was downregulated in BCBM through GSE100534, GSE125989, and GSE43837 datasets. In addition, we found that CILP mRNA expression was negatively correlated with vascular endothelial growth factor A (VEGFA), which is involved in regulating the development of BM. UALCAN analysis showed that CILP expression was downregulated in HER2-positive (HER2+) and triple-negative breast cancer (TNBC), which are more prone to BM. The vitro experiments demonstrated that CILP significantly inhibited BC cell proliferation and metastasis. Western blot (WB) results further showed that the mesenchymal protein marker vimentin was significantly downregulated following CILP overexpression, suggesting that CILP could participate in migration through epithelial–mesenchymal transition (EMT). A comparison of CILP expression using immunohistochemistry in BC and BCBM showed that CILP was significantly downregulated in BCBM. In addition, gene set variation analysis (GSVA) revealed that CILP was associated with the T-cell receptor signaling pathway in BCBM and BC, indicating that CILP may be involved in BCBM through immune effects. BCBM showed lower immune infiltration than BC. Moreover, CILP expression was positively correlated with HLA-II, T helper cells (CD4+ T cells), and Type II IFN Response in BCBM. Collectively, our study indicates that CILP is associated with immune infiltration and may be a putative gene involved in BCBM. CILP offers new insights into the pathogenesis of BCBM, which will facilitate the development of novel targets for BCBM patients.
Selective Sphingosine 1-Phosphate Receptor 1 Modulation Augments Thrombolysis of Low-Dose Tissue Plasminogen Activator Following Cerebrovascular Thrombosis
Authors: Li Han-Dong , Li Ran , Kong Ying , Zhang Wenyan , Qi Caiyun , Wang Dan , Hao Hongying , Liu Qiang
Published: June 2022

Background

Results from our recent study demonstrate that sphingosine-1-phosphate receptor 1 (S1PR1) modulation improves microvascular hemodynamics after cerebrovascular thrombosis. This study was to determine the microvascular hemodynamic effects of a sub-thrombolytic dose of tPA combined with a selective S1PR1 modulator ozanimod in a mouse model of cerebrovascular thrombosis.

Methods

Microvascular circulation in mice was monitored in vivo by two-photon microscopy. Thrombosis was induced in cortical arterioles by laser irradiation. Arteriolar flow velocity was measured by line-scanning following plasma-labeling with fluorescein-dextran.

Results

Laser‐induced thrombosis led to a persistent reduction of flow velocity in cortical arterioles. Sub-thrombolytic dose of tPA along with vehicle control did not improve the flow velocity in cortical arterioles following thrombosis. In contrast, a sub-thrombolytic dose of tPA along with ozanimod dramatically restored flow velocity in cortical arterioles following thrombosis. Ozanimod did not affect coagulation and bleeding time. Notably, ozanimod reduced thrombus volume without altering microvascular lumen diameter. In addition, ozanimod reduced leukocyte components within the thrombus.

Conclusions

These findings demonstrate that the thrombolytic effect of a sub-thrombolytic dose of tPA is markedly enhanced by S1PR1 modulation, implying that S1PR1 modulation may improve the therapeutic benefit of low-dose tPA in patients with acute ischemic stroke.
Distinct Roles of Classical and Lectin Pathways of Complement in Preeclamptic Placentae
Authors: Belmonte Beatrice , Mangogna Alessandro , Gulino Alessandro , Cancila Valeria , Morello Gaia , Agostinis Chiara , Bulla Roberta , Ricci Giuseppe , Fraggetta Filippo , Botto Marina , Garred Peter , Tedesco Francesco
Published: June 2022

Pre-eclampsia is a pregnancy complication characterized by defective vascular remodeling in maternal decidua responsible for reduced blood flow leading to functional and structural alterations in the placenta. We have investigated the contribution of the complement system to decidual vascular changes and showed that trophoblasts surrounding unremodeled vessels prevalent in preeclamptic decidua fail to express C1q that are clearly detected in cells around remodeled vessels predominant in control placenta. The critical role of C1q is supported by the finding that decidual trophoblasts of femaleC1qa-/-pregnant mice mated toC1qa+/+male mice surrounding remodeled vessels express C1q of paternal origin. UnlikeC1qa-/-pregnant mice, heterozygousC1qa+/-and wild type pregnant mice share a high percentage of remodeled vessels. C1q was also found in decidual vessels and stroma of normal placentae and the staining was stronger in preeclamptic placentae. Failure to detect placental deposition of C1r and C1s associated with C1q rules out complement activation through the classical pathway. Conversely, the intense staining of decidual endothelial cells and villous trophoblast for ficolin-3, MASP-1 and MASP-2 supports the activation of the lectin pathway that proceeds with the cleavage of C4 and C3 and the assembly of the terminal complex. These data extend to humans our previous findings of complement activation through the lectin pathway in an animal model of pre-eclampsia and provide evidence for an important contribution of C1q in decidual vascular remodeling.
NK Cells, Monocytes and Macrophages in HIV-1 Control: Impact of Innate Immune Responses
Authors: Mensching Leonore , Hoelzemer Angelique
Published: June 2022

Rapid and synchronized responses of innate immune cells are an integral part of managing viral spread in acute virus infections. In human immunodeficiency virus type 1 (HIV-1) infection, increased immune control has been associated with the expression of certain natural killer (NK) cell receptors. Further, immune activation of monocytes/macrophages and the presence of specific cytokines was linked to low levels of HIV-1 replication. In addition to the intrinsic antiviral capabilities of NK cells and monocytes/macrophages, interaction between these cell types has been shown to substantially enhance NK cell function in the context of viral infections. This review discusses the involvement of NK cells and monocytes/macrophages in the effective control of HIV-1 and highlights aspects of innate immune crosstalk in viral infections that may be of relevance to HIV-1 infection.
Heterogeneous SARS-CoV-2-Neutralizing Activities After Infection and Vaccination
Authors: Graninger Marianne , Camp Jeremy V. , Aberle Stephan W. , Traugott Marianna T. , Hoepler Wolfgang , Puchhammer-Stöckl Elisabeth , Weseslindtner Lukas , Zoufaly Alexander , Aberle Judith H. , Stiasny Karin
Published: June 2022

Background

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) with different resistance levels to existing immunity have recently emerged. Antibodies that recognize the SARS-CoV-2 spike (S) protein and exhibit neutralizing activities are considered the best correlate of protection and an understanding of humoral immunity is crucial for controlling the pandemic. We thus analyzed such antibodies in individuals recovered from infection in 2020 as well as vaccinees after two doses of an mRNA vaccine.

Methods

Neutralizing antibody responses against three SARS-CoV-2 variants (D614G, VOCs Beta and Delta) were determined in serum samples from 54 infected individuals (24 non-hospitalized, 30 hospitalized) and 34 vaccinees shortly after symptom onset or second vaccination, respectively, as well as six months later. In addition, the effect of the S sequence of the infecting strain on neutralization was studied.

Results

Non-hospitalized patients had the lowest neutralization titers against all variants, while those of hospitalized patients equaled or exceeded those of vaccinees. Neutralizing activity was lower against the two VOCs and declined significantly in all cohorts after six months. This decrease was more pronounced in hospitalized and vaccinated individuals than in non-hospitalized patients. Of note, the specific neutralizing activity (NT titer/ELISA value ratio) was higher in the infected cohorts than in vaccinees and did not differ between non-hospitalized and hospitalized patients. Patients infected with viral strains carrying mutations in the N-terminal domain of the spike protein were impaired in Beta VOC neutralization.

Conclusions

Specific neutralizing activities were higher in infected than in vaccinated individuals, and no difference in the quality of these antibodies was observed between hospitalized and non-hospitalized patients, despite significantly lower titers in the latter group. Additionally, antibody responses of infected individuals showed greater heterogeneity than those of vaccinees, which was associated with mutations in the spike protein of the infecting strain. Overall, our findings yielded novel insights into SARS-CoV-2-specific neutralizing antibodies, evolving differently after virus infection and COVID-19 vaccination, which is an important issue to consider in ongoing vaccine strategy improvements.
Novel Immune-Based treatments for Diffuse Large B-Cell Lymphoma: The Post-CAR T Cell Era
Authors: Atallah-Yunes Suheil Albert , Robertson Michael J. , Davé Utpal P. , Ghione Paola , Perna Fabiana
Published: June 2022

Prognosis for patients with refractory/relapsed (R/R) diffuse large B-cell lymphoma (DLBCL) is poor. Immune-based therapeutic treatments such as CD19 Chimeric Antigen Receptor (CAR) T cell therapies have dramatically changed the treatment landscape for R/R DLBCL leading to durable remissions in ~ 50% of patients. However, there remains an unmet need for developing novel therapies to improve clinical outcomes of patients not responding or relapsing after CAR T cell therapies. Lack of suitable immunotherapeutic targets and disease heterogeneity represent the foremost challenges in this emerging field. In this review, we discuss the recently approved and emerging novel immunotherapies for patients with R/R DLBCL in the post-CAR T era and the cell surface targets currently used.
Autophagy Hijacking in PBMC From COVID-19 Patients Results in Lymphopenia
Authors: Barbati Cristiana , Celia Alessandra Ida , Colasanti Tania , Vomero Marta , Speziali Mariangela , Putro Erisa , Buoncuore Giorgia , Savino Flavia , Colafrancesco Serena , Ucci Federica Maria , Ciancarella Claudia , Balbinot Eugenia , Scarpa Susanna , Natalucci Francesco , Pellegrino Greta , Ceccarelli Fulvia , Spinelli Francesca Romana , Mastroianni Claudio Maria , Conti Fabrizio , Alessandri Cristiano
Published: June 2022

Autophagy is a homeostatic process responsible for the self-digestion of intracellular components and antimicrobial defense by inducing the degradation of pathogens into autophagolysosomes. Recent findings suggest an involvement of this process in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. However, the role of autophagy in the immunological mechanisms of coronavirus disease 2019 (COVID-19) pathogenesis remains largely unexplored. This study reveals the presence of autophagy defects in peripheral immune cells from COVID-19 patients. The impairment of the autophagy process resulted in a higher percentage of lymphocytes undergoing apoptosis in COVID-19 patients. Moreover, the inverse correlation between autophagy markers levels and peripheral lymphocyte counts in COVID-19 patients confirms how a defect in autophagy might contribute to lymphopenia, causing a reduction in the activation of viral defense. These results provided intriguing data that could help in understanding the cellular underlying mechanisms in COVID-19 infection, especially in severe forms.
The Potential Value of m6A RNA Methylation in the Development of Cancers Focus on Malignant Glioma
Authors: Chen Fan , Xie Xuan , Chao Min , Cao Haiyan , Wang Liang
Published: June 2022

N6-methyladenosine (m6A) RNA methylation is an epigenetic modification that has emerged in the last few years and has received increasing attention as the most abundant internal RNA modification in eukaryotic cells. m6A modifications affect multiple aspects of RNA metabolism, and m6A methylation has been shown to play a critical role in the progression of multiple cancers through a variety of mechanisms. This review summarizes the mechanisms by which m6A RNA methylation induced peripheral cancer cell progression and its potential role in the infiltration of immune cell of the glioblastoma microenvironment and novel immunotherapy. Assessing the pattern of m6A modification in glioblastoma will contribute to improving our understanding of microenvironmental infiltration and novel immunotherapies, and help in developing immunotherapeutic strategies.
Amphipod Isotope Composition, Condition and Reproduction in Contrasting Sediments: A Reciprocal Transfer Experiment
Authors: Garrison Julie A. , Karlson Agnes M. L. , Nascimento Francisco J. A.
Published: June 2022

Eutrophication is a process that results in excessive phytoplankton blooms, which sink to the sediment and enrich the organic matter (OM). This alters the available resources to benthic organisms and may have consequences for feeding ecology and reproduction strategies of marine populations. While effects of eutrophication on biodiversity are well documented, the more subtle effects of OM on population dynamics and diet plasticity are understudied. We performed a reciprocal transfer experiment with the benthic bioindicator amphipod Monoporeia affinis from two stations in the Baltic Sea with differing sediment OM (low and high) creating four treatments (low control, low transferred, high transferred, and high control). We investigated sediment OM effects on: i) the dietary niche and organism body condition of two different life stages of M. affinis utilizing bulk stable isotopes δ13C and δ15N, and C:N ratio; and ii) M. affinis fecundity and embryo viability. There was no initial significant differences between the females from different stations in terms of δ13C, δ15N, C:N, fecundity or viable embryos. However, we found that moving females from high OM to low OM (where the low OM sediment has higher δ15N and lower δ13C) significantly depleted their 13C values, while amphipods in low OM sediment had always significantly enriched 15N regardless of female origin indicating feeding on the new sediment. Although end-of-experiment females had lower C:N than initial females, individuals in low OM sediment presented significantly higher C:N (indicating higher body condition) than those in high OM sediment. Conversely to adult amphipods, no effects of OM were seen for juveniles δ13C or δ15N, but their individual biomass was larger in high OM sediment treatments and high OM transferred to low OM sediment. Our results indicate that the low range of sediment OM tested here altered female amphipod δ13C, δ15N and C:N ratios, with those in low OM treatments having a better body condition, but those in high OM treatments had a greater reproductive success in terms of offspring biomass. Our findings suggest a tradeoff between female condition and reproduction and indicates that even relatively small levels of sediment organic enrichment will impact female condition. Our study provides valuable information useful to interpret the effects of OM on amphipod populations used as bioindicators for anthropogenic impacts.
The Characteristics and Expression Profile of Peptidoglycan Recognition Protein 2 in the Accessory Nidamental Gland of the Bigfin Reef Squid During Bacterial Colonization
Authors: Li Hau-Wen , Kuo Wei-Lun , Chen Chi , Tseng Yung-Che , Chang Ching-Fong , Wu Guan-Chung
Published: June 2022

Some cephalopods carry microorganisms in two specialized organs, the light organ and the accessory nidamental gland (ANG). For the light organ, comprehensive mechanisms have been described for winnowing (bacterial selection) and maintenance of the symbiotic luminescent bacterium Vibrio fischeri (V. fischeri). However, the mechanisms controlling bacterial selection and maintenance during bacterial colonization of the ANG are open biological issues with physiological significance. Our recent study on bigfin reef squid (Sepioteuthis lessoniana) already showed that the ANG bacterial community shifts gradually and exhibits decreased diversity throughout maturation. This study further describes a potential role of an innate immunity-involved molecule, peptidoglycan recognition proteins (PGRPs), in the ANG of bigfin reef squid during bacterial transmission and colonization. First, we found that four homologs of the PGRP family are expressed in the ANG of bigfin reef squid (slPGRP2-5), but only slPgrp2 transcript levels are highly correlated with ANG development and bacterial colonization. Besides, slPgrp2 transcripts are mainly expressed in the epithelial cells of certain secondary tubules of ANG, and the expression levels are varied in the epithelial cells of other secondary tubules. This data reveals that slPgrp2 transcripts may associate with the composition of bacterial consortium and its secretary factors. Moreover, recombinant slPGRP2 had a negative effect of Escherichia coli (E.coli) which inhibited bacterial growth in culture. Therefore, our data suggest slPgrp2 expression in the epithelial cells of secondary tubules in the ANG may have an essential role in the winnowing and maintenance of holobiont homeostasis in bigfin reef squid.
Assessing Important Conservation Areas for Colonial Species From Individual Tracking Data: An Evaluation of the Effects of Colony Structure and Temporal Heterogeneity in Movement Patterns
Authors: Morinay Jennifer , De Pascalis Federico , Catoni Carlo , Benvenuti Andrea , Imperio Simona , Rubolini Diego , Cecere Jacopo G.
Published: June 2022

Sensitivity of marine ecosystems to human disturbance leads to an increasing need to devise effective conservation initiatives. One key conservation leverage tool is the establishment of marine protected areas, which can be derived by inspecting where marine sentinel species forage in their most sensitive life cycle phase (reproduction). Depending on their biological and legislative framework, important conservation areas (hereafter, ICAs) can correspond to Important Bird and biodiversity Areas, Key Biodiversity Areas, Marine Protected Areas, etc. Statistical methods allow for standardized assessment of ICAs based on GPS tracking data. However, several biological processes should be accounted for to provide reliable ICAs. In colonial seabirds and sea mammals, individuals breeding in different parts of a colony often spatially segregate while foraging at sea. Besides, environmental conditions may affect the location of foraging areas across years. To what extent relying on data collected in only one part of a colony or in a single breeding season may affect the location and size of ICAs remains unexplored. Here we aimed at 1) highlighting intra-colony and inter-annual heterogeneity of exploited marine areas during reproduction in a colonial seabird, the Scopoli’s shearwaters Calonectris diomedea; and 2) providing guidelines on how to methodologically best account for such spatio-temporal heterogeneity when deriving ICAs. We relied on 397 foraging trips performed by 73 individuals breeding in two distinct areas within the same colony (hereafter, sub-colonies) over 3 years. We showed that areas exploited by shearwaters breeding in two nearby sub-colonies were clearly segregated and differed between years. Relying on only one sub-colony or a single breeding season led to drastically smaller ICAs, biased either east- or west-ward depending on the sub-colony considered. We proposed to account for such heterogeneity by merging the different ICAs obtained for each sub-colony and year, instead of pooling tracking data and deriving a single ICA. Our method led to much larger ICAs, which were less affected by differences in sample sizes across sub-colonies or years, than when ignoring the spatio-temporal heterogeneity. Recently developed standardized statistical procedures and a careful consideration of population spatial structure and temporal heterogeneity will foster robust conservation actions for colonial marine species.
Spatio-Temporal Distribution of Juvenile Oceanic Whitetip Shark Incidental Catch in the Western Indian Ocean
Authors: Lopetegui-Eguren Leire , Poos Jan Jaap , Arrizabalaga Haritz , Guirhem Gency L. , Murua Hilario , Lezama-Ochoa Nerea , Griffiths Shane P. , Gondra Jon Ruiz , Sabarros Philippe S. , Báez José Carlos , Juan-Jordá Maria José
Published: June 2022

Oceanic whitetip shark (Carcharhinus longimanus) is an important top predator in pelagic ecosystems currently classified as globally Critically Endangered by the International Union for the Conservation of Nature. This species is incidentally caught by fisheries targeting highly migratory tunas and billfishes throughout the Indian Ocean. Understanding the temporal, spatial and environmental factors influencing the capture of this species is essential to reduce incidental catches. In this study, we used generalized additive models to analyze the spatio-temporal distributions of the juvenile oceanic whitetip shark catches and the environmental conditions in the western Indian Ocean using observer data from 2010 to 2020 of the European Union and associated flags purse seine fishery. We found sea surface temperature and nitrate concentration to be the most important environmental variables predicting the probability of catching an oceanic whitetip shark. A higher probability of capture was predicted in areas where sea surface temperature was below 24°C and with low nitrate concentrations close to zero and intermediate values (1.5-2.5 mmol.m-3). We also found a higher probability of capture in sets on fish aggregating devices than in sets on free schools of tuna. The Kenya and Somalia basin was identified to have higher probabilities of capture during the summer monsoon (June to September) when upwelling of deep cold waters occurs. We provide the first prediction maps of capture probabilities and insights into the environmental preferences of oceanic whitetip shark in the western Indian Ocean. However, the causal mechanisms behind these insights should be explored in future studies before they can be used to design spatial management and conservation strategies, such as time-area closures, for bycatch avoidance.
Uncertainty and Consistency Assessment in Multiple Microplastic Observation Datasets in the Baltic Sea
Authors: She Jun , Buhhalko Natalja , Lind Kati , Mishra Arun , Kikas Villu , Costa Elisa , Gambardella Chiara , Montarsolo Alessio , Faimali Marco , Garaventa Francesca , Lips Inga
Published: June 2022

This paper aims to quantify data uncertainties in marine microplastic measurements, including spatiotemporal sampling error and sample volume estimation error, identify impacts of varying mesh sizes, sampling and analysis methods, and evaluate consistency in multiple microplastic observation datasets. Twenty-seven datasets on surface marine microplastics with particle size >100 µm in the Baltic Sea are compiled. Results show that the trawl datasets have a spatiotemporal sampling error of 25% for microlitter concentration, 36% for microplastic fiber concentrations and 40-56% for microplastic particle concentration. By taking surface currents and wave-induced Stokes drift into account, the sample volume of the trawl measurements is corrected, leading to a mean microplastic concentration correction of 12%. The differences of microplastic concentration between datasets with varying mesh sizes from 100 – 500 µm are not statistically significant. Analysis methods, however, can lead to significant differences in microplastic datasets. The dataset consistency is further examined among the three dataset categories using trawl, pump and bulk sampling techniques. It is found that an individual dataset is often self-consistent. Most of the datasets within one monitoring category are more consistent than those from different categories. More than 70% of the datasets within individual categories are consistent, which have mean microplastic concentration significantly smaller than the rest of the datasets. Significant inconsistencies are identified between different data categories. Six out of eight highest relative standard deviations are found in the pump and bulk datasets. The median value of the mean microplastic concentration from the 10 pump datasets is about 4.5 times as much as that of the 14 trawl datasets, both for fiber and non-fiber particles. Significant differences are also identified on microplastic fiber fraction in different dataset categories. Two thirds of the 13 bulk and pump datasets have a microplastic fiber fraction >85% while the 14 trawl datasets show much lower microplastic fiber fractions between 45-70%. In addition, the particle collection efficiency, potential leakage of particles with irregular shapes, clogging, the false zero samples and related lower limit of the detectable microplastic concentration for given sampling methods and water environment, are also discussed.
Substantial Biogeochemical and Biomolecular Processing of Dissolved Organic Matter in an Anticyclonic Eddy in the Northern South China Sea Down to Bathypelagic Depths
Authors: Zhang Miao , Li Siyu , Hertkorn Norbert , Harir Mourad , Xu Dongfeng , Schmitt-Kopplin Philippe , Wu Ying
Published: June 2022

Solid-phase extracted dissolved organic matter (SPE-DOM) was isolated from two depth profiles at the core and at the edge of an anticyclonic eddy (ACE) in the northern South China Sea. Non-target nuclear magnetic resonance (NMR) spectroscopy and Fourier transform ion cyclotron mass spectrometry (FTICR/MS) of SPE-DOM revealed a higher uniformity of DOM molecules within the ACE than at the edge of the ACE. Small-scale upwelling of external nutrients may have contributed to higher productivity and production of fresher DOM, with higher proportions of CHNO and CHNOS compounds and low molecular weight species at the edge of the eddy. Common SPE-DOM molecules of supposedly biological origin such as carbohydrates and olefins were most abundant in the chlorophyll maximum layer in both stations. An unusual suite of ~10 abundant and ~35 less abundant tert-butyl benzene derivatives with potential to act as endocrine disruptors within a marine food chain and ~two dozen ketones of putative bacterial origin was recognized at meso- and bathypelagic depths in single-digit micromolar concentrations, with a distinct maximum at 1000 m depth at the edge of ACE. Downwelling might bring temporary large volumes of productive marine waters into deep waters, with micromolar concentration of abundant, microbial food web-specific metabolites (e.g. 2,4-di-tert-butylphenol et al.). In our study, these eventually added up to one quarter of common background biogeochemical marine organic matter even at bathypelagic depths and beneath and are significant food and energy sources for marine biota. Mesoscale chemical heterogeneity of marine water columns might extend to larger depths than currently anticipated and may create activity hotspots influencing biota, processing of DOM, and cycling of nutrients and trace elements.
Electroporation-Based CRISPR/Cas9 Mosaic Mutagenesis of β-Tubulin in the Cultured Oyster
Authors: Chan Jiulin , Zhang Wei , Xu Yue , Xue Yu , Zhang Linlin
Published: June 2022

Genome editing using clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 is enabling genetics improvement of productive traits in aquaculture. Previous studies have proven CRISPR/Cas9 to be feasible in oyster, one of the most cultured shellfish species. Here, we applied electroporation-based CRISPR/Cas9 knockout of β-tubulin and built a highly efficient genome editing system in Crassostrea gigas angulate. We identified the β-tubulin gene in the oyster genome and showed its spatiotemporal expression patterns by analyzing RNA-seq data and larval in situ hybridization. We further designed multiple highly specific guide RNAs (sgRNAs) for its coding sequences. Long fragment deletions were detected in the mutants by agarose gel electrophoresis screening and further verified by Sanger sequencing. In addition, the expression patterns of Cgβ-tubulin in the trochophore peritroch and intestinal cilia cells were altered in the mutants. Scanning electron microscopy represented shortened and almost complete depleted cilia at the positions of peritroch and the posterior cilium ring in Cgβ-tubulin mosaic knockout trochophores. Moreover, the larval swimming behavior in the mutants was detected to be significantly decreased by motility assay. These results demonstrate that β-tubulin is sufficient to mediate cilia development and swimming behavior in oyster larvae. By applying Cgβ-tubulin as a marker gene, our study established CRISPR/Cas9-mediated mosaic mutagenesis technology based on electroporation, providing an efficient tool for gene function validation in the oyster. Moreover, our research also set up an example that can be used in genetic engineering breeding and productive traits improvement in oysters and other aquaculture species.
Spatial Patterns of Microplastics in Surface Seawater, Sediment, and Sand Along Qingdao Coastal Environment
Authors: Luo Yadan , Sun Cuizhu , Li Chenguang , Liu Yifan , Zhao Shasha , Li Yuanyuan , Kong Fanna , Zheng Hao , Luo Xianxiang , Chen Lingyun , Li Fengmin
Published: June 2022

Coastal environments, ecologically fragile zones, are subjected to great human pressures, particularly, xenobiotic pollutants such as microplastics (MPs) and trace metals. Yet, the impact of anthropogenic intervention on the spatial patterns of MPs in different coastal environmental compartments of Qingdao, a city located in the west Yellow Sea, is still unclear. Therefore, the spatial distribution, characteristics, and diversity of MPs (≥ 50 µm) in seawater, sediment, and sand samples collected from 10 zones intervened by different anthropogenic activities in Qingdao coastal environment were investigated. The abundance of MPs was 93.1 ± 63.5 items/m3 in seawater, which was 4577 ± 2902 items/kg in sediments and 3602 ± 1708 items/kg in the beach sands. A spatial analysis indicated that the distribution characteristics of MPs, including abundance, color, and type, greatly varied among the zones with different extent of human activities. The highest abundance of MPs in the seawater was detected in the abandoned aquafarm, followed by harbors, beaches, estuary, sewage discharge areas, operational aquafarm, and rural areas, whereas the highest MP abundance in the sediments followed the order of harbor, sewage discharge, estuary, abandoned aquafarm, beaches, rural area, and operational aquafarm. The highest MP abundance in the scenic and recreational beach sands was, respectively, in the intertidal and supratidal zone. The transparent chlorinated polyethylene fragments with the relatively small size of 50–100 μm were the dominant MPs in the coastal environment. The higher physicochemical characteristic diversity in terms of size, color, shape, and type of MPs in the aquafarms, harbors, and recreational beach than those of the other zones, illustrated the higher complexity and diversity of MP pollution sources in these zones. These results jointly indicated that aquaculture, navigation, and tourism mainly determined MP spatial distribution patterns in the coastal environment of Qingdao. These results also extend the understanding of the inventory and fate of MPs in coastal environment, thus providing important data to establish effective strategies for abating MP pollution in marine ecosystems.
Rational Synthesis of Freestanding NaxV2O5-rGO Paper as the Stable Cathode for Sodium Ion Batteries
Authors: Wang Qi , Li Xin , Xu Junmin , Yuan Yueyue , Li Xinyue , Wang Xinchang
Published: June 2022

Flexible NaxV2O5/rGO papers were successfully prepared via hydrothermal method followed by vacuum filtration as a high-performance cathode for SIBs. The as-prepared NaxV2O5/rGO combined flexibility and high conductivity that can buffer stress and facilitate the fast transportation of electrons during the charge-discharge process. As a result, the as-prepared NaxV2O5-rGO paper can exhibit a reversible Na-ion storage capacity of ∼197 mA h g−1 at 100 mA g−1 and a good cycling performance with 81% capacity retention for 400 cycles at a high current density of 500 mA g−1, showing great potential in flexible energy storage devices.
Effect of High Myopia and Cataract Surgery on the Correlation Between Diabetic Retinopathy and Chronic Kidney Disease
Authors: Kong Huiqian , Zang Siwen , Hu Yijun , Lin Zhanjie , Liu Baoyi , Zeng Xiaomin , Xiao Yu , Du Zijing , Guanrong Wu , Ren Yun , Fang Ying , Xiaohong Yang , Yu Honghua
Published: June 2022

Purpose

To investigate the effect of high myopia and cataract surgery on the grading of diabetic retinopathy (DR) and their roles in the correlation between DR and chronic kidney disease (CKD).

Methods

A total of 1,063 eyes of 1,063 diabetic patients were enrolled. We conducted binary and multiple multivariate regressions to analyze the ocular and systemic risk factors of DR. Based on the presence of myopia and history of cataract surgery, we divided the cases into four subgroups, namely those with high myopia, with the history of cataract surgery, with both conditions, and with neither, then determined the correlation between the stages of DR and CKD in each subgroup.

Results

In the binary analysis, high myopia was identified as the protective factor for DR odds ratio (OR): 0.312 [95% confidence interval (CI): 0.195–0.500, p < 0.001], whereas cataract surgery was one of the independent risk factors for DR [OR: 2.818 (95% CI: 1.507–5.273), p = 0.001]. With increased stages of DR, high myopia played an increasingly protective role [mild non-proliferative DR (NPDR), OR = 0.461, p = 0.004; moderate NPDR OR = 0.217, p = 0.003; severe NPDR, OR = 0.221, p = 0.008; proliferative DR (PDR), OR = 0.125, p = 0.001], whereas cataract surgery became a stronger risk factor, especially in PDR (mild NPDR, OR = 1.595, p = 0.259; moderate NPDR, OR = 3.955, p = 0.005; severe NPDR, OR = 6.836, p < 0.001; PDR, OR = 9.756, p < 0.001). The correlation between the stages of DR and CKD in the group with neither high myopia nor cataract surgery history was the highest among all subgroups.

Conclusion

High myopia was a protective factor, whereas cataract surgery is a risk factor for DR, and both factors showed stronger effects throughout the (natural disease) grading of DR. The stages of DR and CKD showed a higher correlation after adjustment of the ocular confounding factors.