bluuebunny/crossref_metadata_2025 huggingface dataset:
Myomedin replicas of gp120 V3 loop glycan epitopes recognized by PGT121 and PGT126 antibodies as non-cognate antigens for stimulation of HIV-1 broadly neutralizing antibodies
Authors: Daniel Lišková Veronika , Kosztyu Petr , Kuchař Milan , Černý Jiří , Bharadwaj Shiv , Petroková Hana , Vroblová Eliška , Křupka Michal , Malý Michal , Zosinčuková Tereza , Šulc Josef , Rašková Kafková Leona , Raška Milan , Malý Petr
Published: December 2022

Introduction

Imprinting broadly neutralizing antibody (bNAb) paratopes by shape complementary protein mimotopes represents a potential alternative for developing vaccine immunogens. This approach, designated as a Non-Cognate Ligand Strategy (NCLS), has recently been used for the identification of protein variants mimicking CD4 binding region epitope or membrane proximal external region (MPER) epitope of HIV-1 envelope (Env) glycoprotein. However, the potential of small binding proteins to mimic viral glycan-containing epitopes has not yet been verified.

Methods

In this work, we employed a highly complex combinatorial Myomedin scaffold library to identify variants recognizing paratopes of super candidate bNAbs, PGT121 and PGT126, specific for HIV-1 V3 loop epitopes.

Results

In the collection of Myomedins called MLD variants targeted to PGT121, three candidates competed with gp120 for binding to this bNAb in ELISA, thus suggesting an overlapping binding site and epitope-mimicking potential. Myomedins targeted to PGT126 designated MLB also provided variants that competed with gp120. Immunization of mice with MLB or MLD binders resulted in the production of anti-gp120 and -Env serum antibodies. Mouse hyper-immune sera elicited with MLB036, MLB041, MLB049, and MLD108 moderately neutralized 8-to-10 of 22 tested HIV-1-pseudotyped viruses of A, B, and C clades in vitro.

Discussion

Our data demonstrate that Myomedin-derived variants can mimic particular V3 glycan epitopes of prominent anti-HIV-1 bNAbs, ascertain the potential of particular glycans controlling neutralizing sensitivity of individual HIV-1 pseudoviruses, and represent promising prophylactic candidates for HIV-1 vaccine development.
Dysregulation of the immune response in TGF-β signalopathies
Authors: Rodari Marco M. , Cerf-Bensussan Nadine , Parlato Marianna
Published: December 2022

The transforming growth factor-β (TGF-β) family of cytokines exerts pleiotropic functions during embryonic development, tissue homeostasis and repair as well as within the immune system. Single gene defects in individual component of this signaling machinery cause defined Mendelian diseases associated with aberrant activation of TGF-β signaling, ultimately leading to impaired development, immune responses or both. Gene defects that affect members of the TGF-β cytokine family result in more restricted phenotypes, while those affecting downstream components of the signaling machinery induce broader defects. These rare disorders, also known as TGF-β signalopathies, provide the unique opportunity to improve our understanding of the role and the relevance of the TGF-β signaling in the human immune system. Here, we summarize this elaborate signaling pathway, review the diverse clinical presentations and immunological phenotypes observed in these patients and discuss the phenotypic overlap between humans and mice genetically deficient for individual components of the TGF-β signaling cascade.
The ER Aminopeptidases, ERAP1 and ERAP2, synergize to self-modulate their respective activities
Authors: Martín-Esteban Adrian , Rodriguez Jesus Contreras , Peske David , Lopez de Castro Jose A. , Shastri Nilabh , Sadegh-Nasseri Scheherazade
Published: December 2022

Introduction

Critical steps in Major Histocompatibility Complex Class I (MHC-I) antigen presentation occur in the endoplasmic reticulum (ER). In general, peptides that enter the ER are longer than the optimal length for MHC-I binding. The final trimming of MHC-I epitopes is performed by two related aminopeptidases, ERAP1 and ERAP2 in humans that possess unique and complementary substrate trimming specificities. While ERAP1 efficiently trims peptides longer than 9 residues, ERAP2 preferentially trims peptides shorter than 9 residues.

Materials and Methods

Using a combination of biochemical and proteomic studies followed by biological verification.

Results

We demonstrate that the optimal ligands for either enzyme act as inhibitors of the other enzyme. Specifically, the presence of octamers reduced the trimming of long peptides by ERAP1, while peptides longer than nonomers inhibit ERAP2 activity.

Discussion

We propose a mechanism for how ERAP1 and ERAP2 synergize to modulate their respective activities and shape the MHC-I peptidome by generating optimal peptides for presentation.
Neoadjuvant chemoradiotherapy combined with immunotherapy for locally advanced rectal cancer: A new era for anal preservation
Authors: Wang Yaqi , Shen Lijun , Wan Juefeng , Zhang Hui , Wu Ruiyan , Wang Jingwen , Wang Yan , Xu Ye , Cai Sanjun , Zhang Zhen , Xia Fan
Published: December 2022

For locally advanced (T3-4/N+M0) rectal cancer (LARC), neoadjuvant chemoradiotherapy (nCRT) followed by total mesorectal excision (TME) is the standard treatment. It was demonstrated to decrease the local recurrence rate and increase the tumor response grade. However, the distant metastasis remains an unresolved issue. And the demand for anus preservation and better quality of life increases in recent years. Radiotherapy and immunotherapy can be supplement to each other and the combination of the two treatments has a good theoretical basis. Recently, multiple clinical trials are ongoing in terms of the combination of nCRT and immunotherapy in LARC. It was reported that these trials achieved promising short-term efficacy in both MSI-H and MSS rectal cancers, which could further improve the rate of clinical complete response (cCR) and pathological complete response (pCR), so that increase the possibility of ‘Watch and Wait (W&W)’ approach. However, the cCR and pCR is not always consistent, which occurs more frequent when nCRT is combined with immunotherapy. Thus, the efficacy evaluation after neoadjuvant therapy is an important issue for patient selection of W&W approach. Evaluating the cCR accurately needs the combination of multiple traditional examinations, new detective methods, such as PET-CT, ctDNA-MRD and various omics studies. And finding accurate biomarkers can help guide the risk stratification and treatment decisions. And large-scale clinical trials need to be performed in the future to demonstrate the surprising efficacy and to explore the long-term prognosis.
The single-cell landscape of cystic echinococcosis in different stages provided insights into endothelial and immune cell heterogeneity
Authors: Jiang Xiaofeng , Zhang Xiaofan , Jiang Nan , Sun Yeting , Li Teng , Zhang Jing , Shen Yujuan , Cao Jianping
Published: December 2022

Introduction

Hydatid cysts and angiogenesis are the key characteristics of cystic echinococcosis, with immune cells and endothelial cells mediating essential roles in disease progression. Recent single-cell analysis studies demonstrated immune cell infiltration after Echinococcus granulosus infection, highlighting the diagnostic and therapeutic potential of targeting certain cell types in the lesion microenvironment. However, more detailed immune mechanisms during different periods of E. granulosus infection were not elucidated.

Methods

Herein, we characterized immune and endothelial cells from the liver samples of mice in different stages by single-cell RNA sequencing.

Results

We profiled the transcriptomes of 45,199 cells from the liver samples of mice at 1, 3, and 6 months after infection (two replicates) and uninfected wild-type mice. The cells were categorized into 26 clusters with four distinct cell types: natural killer (NK)/T cells, B cells, myeloid cells, and endothelial cells. An SPP1+ macrophage subset with immunosuppressive and pro-angiogenic functions was identified in the late infection stage. Single-cell regulatory network inference and clustering (SCENIC) analysis suggested that Cebpe, Runx3, and Rora were the key regulators of the SPP1+ macrophages. Cell communication analysis revealed that the SPP1+ macrophages interacted with endothelial cells and had pro-angiogenic functions. There was an obvious communicative relationship between SPP1+ macrophages and endothelial cells via Vegfa–Vegfr1/Vegfr2, and SPP1+ macrophages interacted with other immune cells via specific ligand–receptor pairs, which might have contributed to their immunosuppressive function.

Discussion

Our comprehensive exploration of the cystic echinococcosis ecosystem and the first discovery of SPP1+ macrophages with infection period specificity provide deeper insights into angiogenesis and the immune evasion mechanisms associated with later stages of infection.
Comparison between Lactobacillus rhamnosus GG and LuxS-deficient strain in regulating gut barrier function and inflammation in early-weaned piglets
Authors: Deng Zhaoxi , Dai Jinyan , Wei Yusen , Ma Yanfei , Mao Yingying , Zhang Jinzhi , Hua Weidong , Wang Haifeng
Published: December 2022

Background

Early weaning-induced stress impairs the intestinal barrier function and adversely affects the health of piglet. Probiotics can be used to prevent and treat various intestinal diseases. Lactobacillus rhamnosus GG (LGG) has an LuxS/AI-2 quorum sensing (QS) system that senses environmental changes through chemical signaling molecules. The aim of the study was to explore whether luxS mutant affects the protective role of LGG in the gut barrier of weaned piglets by comparing the luxS mutant (ΔluxS) with its wild-type (WT).

Methods

Newborn piglets were orally administered with WT and ΔluxS at dosage of 109 CFU, respectively. Accordingly, newborn piglets in the Con group were orally administered with PBS. Piglets were weaned on day 21 and euthanized on day 24, three days following weaning.

Results

Supplementation of ΔluxS in advance significantly boosted the relative abundances of healthy microbes (including Catenibacterium, Eubacterium, Lachnospiraceae and Bifidobacterium). WT and ΔluxS maintain intestinal barrier function mainly by promoting intestinal villus to crypt ratio (VCR), occludin protein expression and mucus secretion (P<0.05). Furthermore, LGG reduces pro-inflammatory mediators by inhibiting TLR4 and MAPK signal transduction (P<0.05).

Conclusion

Both WT and ΔluxS were shown to resist weaning stress by enhancing the intestinal barrier function of piglets. It has to be said that the ability of ΔluxS to maintain intestinal tissue morphology and promote mucus secretion significantly decreased compared with that of WT.
Stepwise acquisition of unique epigenetic signatures during differentiation of tissue Treg cells
Authors: Braband Kathrin L. , Kaufmann Tamara , Floess Stefan , Zou Mangge , Huehn Jochen , Delacher Michael
Published: December 2022

Regulatory T cells in non-lymphoid tissues are not only critical for maintaining self-tolerance, but are also important for promoting organ homeostasis and tissue repair. It is proposed that the generation of tissue Treg cells is a stepwise, multi-site process, accompanied by extensive epigenome remodeling, finally leading to the acquisition of unique tissue-specific epigenetic signatures. This process is initiated in the thymus, where Treg cells acquire core phenotypic and functional properties, followed by a priming step in secondary lymphoid organs that permits Treg cells to exit the lymphoid organs and seed into non-lymphoid tissues. There, a final specialization process takes place in response to unique microenvironmental cues in the respective tissue. In this review, we will summarize recent findings on this multi-site tissue Treg cell differentiation and highlight the importance of epigenetic remodeling during these stepwise events.
Chickens, more than humans, focus the diversity of their immunoglobulin genes on the complementarity-determining region but utilise amino acids, indicative of a more cross-reactive antibody repertoire
Authors: Mallaby Jessica , Ng Joseph , Stewart Alex , Sinclair Emma , Dunn-Walters Deborah , Hershberg Uri
Published: December 2022

The mechanisms of B-cell diversification differ greatly between aves and mammals, but both produce B cells and antibodies capable of supporting an effective immune response. To see how differences in the generation of diversity might affect overall repertoire diversity, we have compared the diversity characteristics of immunoglobulin genes from domestic chickens to those from humans. Both use V(D)J gene rearrangement and somatic hypermutation, but only chickens use somatic gene conversion. A range of diversity analysis tools were used to investigate multiple aspects of amino acid diversity at both the germline and repertoire levels. The effect of differing amino acid usages on antibody characteristics was assessed. At both the germline and repertoire levels, chickens exhibited lower amino acid diversity in comparison to the human immunoglobulin genes, especially outside of the complementarity-determining region (CDR). Chickens were also found to possess much larger and more hydrophilic CDR3s with a higher predicted protein binding potential, suggesting that the antigen-binding site in chicken antibodies is more flexible and more polyreactive than that seen in human antibodies.
Plasma cell subtypes analyzed using artificial intelligence algorithm for predicting biochemical recurrence, immune escape potential, and immunotherapy response of prostate cancer
Authors: Xie Xiao , Dou Chun-Xia , Luo Ming-Rui , Zhang Ke , Liu Yang , Zhou Jia-Wei , Huang Zhi-Peng , Xue Kang-Yi , Liang Hao-Yu , Ouyang Ao-Rong , Ma Sheng-Xiao , Yang Jian-Kun , Zhou Qi-Zhao , Guo Wen-Bing , Liu Cun-Dong , Zhao Shan-Chao , Chen Ming-Kun
Published: December 2022

Background

Plasma cells as an important component of immune microenvironment plays a crucial role in immune escape and are closely related to immune therapy response. However, its role for prostate cancer is rarely understood. In this study, we intend to investigate the value of a new plasma cell molecular subtype for predicting the biochemical recurrence, immune escape and immunotherapy response in prostate cancer.

Methods

Gene expression and clinicopathological data were collected from 481 prostate cancer patients in the Cancer Genome Atlas. Then, the immune characteristics of the patients were analyzed based on plasma cell infiltration fractions. The unsupervised clustering based machine learning algorithm was used to identify the molecular subtypes of the plasma cell. And the characteristic genes of plasma cell subtypes were screened out by three types of machine learning models to establish an artificial neural network for predicting plasma cell subtypes. Finally, the prediction artificial neural network of plasma cell infiltration subtypes was validated in an independent cohort of 449 prostate cancer patients from the Gene Expression Omnibus.

Results

The plasma cell fraction in prostate cancer was significantly decreased in tumors with high T stage, high Gleason score and lymph node metastasis. In addition, low plasma cell fraction patients had a higher risk of biochemical recurrence. Based on the differential genes of plasma cells, plasma cell infiltration status of PCa patients were divided into two independent molecular subtypes(subtype 1 and subtype 2). Subtype 1 tends to be immunosuppressive plasma cells infiltrating to the PCa region, with a higher likelihood of biochemical recurrence, more active immune microenvironment, and stronger immune escape potential, leading to a poor response to immunotherapy. Subsequently, 10 characteristic genes of plasma cell subtype were screened out by three machine learning algorithms. Finally, an artificial neural network was constructed by those 10 genes to predict the plasma cell subtype of new patients. This artificial neural network was validated in an independent validation set, and the similar results were gained.

Conclusions

Plasma cell infiltration subtypes could provide a potent prognostic predictor for prostate cancer and be an option for potential responders to prostate cancer immunotherapy.
The BLM helicase is a new therapeutic target in multiple myeloma involved in replication stress survival and drug resistance
Authors: Ovejero Sara , Viziteu Elena , Dutrieux Laure , Devin Julie , Lin Yea-Lih , Alaterre Elina , Jourdan Michel , Basbous Jihane , Requirand Guilhem , Robert Nicolas , de Boussac Hugues , Seckinger Anja , Hose Dirk , Vincent Laure , Herbaux Charles , Constantinou Angelos , Pasero Philippe , Moreaux Jérôme
Published: December 2022

Multiple myeloma (MM) is a hematologic cancer characterized by accumulation of malignant plasma cells in the bone marrow. To date, no definitive cure exists for MM and resistance to current treatments is one of the major challenges of this disease. The DNA helicase BLM, whose depletion or mutation causes the cancer-prone Bloom’s syndrome (BS), is a central factor of DNA damage repair by homologous recombination (HR) and genomic stability maintenance. Using independent cohorts of MM patients, we identified that high expression of BLM is associated with a poor outcome with a significant enrichment in replication stress signature. We provide evidence that chemical inhibition of BLM by the small molecule ML216 in HMCLs (human myeloma cell lines) leads to cell cycle arrest and increases apoptosis, likely by accumulation of DNA damage. BLM inhibition synergizes with the alkylating agent melphalan to efficiently inhibit growth and promote cell death in HMCLs. Moreover, ML216 treatment re-sensitizes melphalan-resistant cell lines to this conventional therapeutic agent. Altogether, these data suggest that inhibition of BLM in combination with DNA damaging agents could be of therapeutic interest in the treatment of MM, especially in those patients with high BLM expression and/or resistance to melphalan.
Both N- and C-terminal domains of galectin-9 are capable of inducing HIV reactivation despite mediating differential immunomodulatory functionalities
Authors: Shete Ashwini , Bhat Mahalakshmi , Sawant Jyoti , Deshpande Supriya
Published: December 2022

Background

The shock-and-kill strategy for HIV cure requires the reactivation of latent HIV followed by the killing of the reactivated cellular reservoir. Galectin-9, an immunomodulatory protein, is shown to induce HIV reactivation as well as contribute to non-AIDS- and AIDS-defining events. The protein is prone to cleavage by inflammatory proteases at its linker region separating the N- and C-terminal carbohydrate-binding domains (N- and C-CRDs) which differ in their binding specificities. It is important to study the activity of its cleaved as well as uncleaved forms in mediating HIV reactivation and immunomodulation in order to understand their role in HIV pathogenesis and their further utilization for the shock-and-kill strategy.

Methodology

The PBMCs of HIV patients on virally suppressive ART (n = 11) were stimulated using 350 nM of the full-length protein and N- and C-CRDs of Gal-9. HIV reactivation was determined by analyzing gag RNA copies using qPCR using isolated CD4 cells and intracellular P24 staining of PBMCs by flow cytometry. Cytokine responses induced by the full-length protein and N- and C-CRDs of Gal-9 were also assessed by flow cytometry, Luminex, and gene expression assays. Changes in T helper cell gene expression pattern after the stimulation were also determined by real-time PCR array.

Results

Both N- and C-CRDs of galectin-9 induced HIV reactivation in addition to the full-length galectin-9 protein. The two domains elicited higher cytokine responses than the full-length protein, possibly capable of mediating higher perturbations in the immune system if used for HIV reactivation. N-CRD was found to induce the development of Treg cells, whereas C-CRD inhibited the induction of Treg cells. Despite this, both domains elicited IL-10 secretory response although targeting different CD4 cell phenotypes.

Conclusion

N- and C-CRDs were found to induce HIV reactivation similar to that of the full-length protein, indicating their possible usefulness in the shock-and-kill strategy. The study indicated an anti-inflammatory role of N-CRD versus the proinflammatory properties of C-CRD of galectin-9 in HIV infection.
Decidual macrophages in recurrent spontaneous abortion
Authors: Zhao Qiu-Yan , Li Qing-Hui , Fu Yao-Yao , Ren Chun-E , Jiang Ai-Fang , Meng Yu-Han
Published: December 2022

Recurrent spontaneous abortion (RSA) is defined as two or more pregnancy loss, affecting the happiness index of fertility couples. The mechanisms involved in the occurrence of RSA are not clear to date. The primary problem for the maternal immune system is how to establish and maintain the immune tolerance to the semi-allogeneic fetuses. During the pregnancy, decidual macrophages mainly play an important role in the immunologic dialogue. The purpose of this study is to explore decidual macrophages, and to understand whether there is a connection between these cells and RSA by analyzing their phenotypes and functions. Pubmed, Web of Science and Embase were searched. The eligibility criterion for this review was evaluating the literature about the pregnancy and macrophages. Any disagreement between the authors was resolved upon discussion and if required by the judgment of the corresponding author. We summarized the latest views on the phenotype, function and dysfunction of decidual macrophages to illuminate its relationship with RSA.
GLP-1 receptor agonist as a modulator of innate immunity
Authors: Chen Jun , Mei Aihua , Wei Yingying , Li Chunlei , Qian Hang , Min Xinwen , Yang Handong , Dong Lingli , Rao Xiaoquan , Zhong Jixin
Published: December 2022

Glucagon-like peptide-1 (GLP-1) is a 30-amino acid hormone secreted by L cells in the distal ileum, colon, and pancreatic α cells, which participates in blood sugar regulation by promoting insulin release, reducing glucagon levels, delaying gastric emptying, increasing satiety, and reducing appetite. GLP-1 specifically binds to the glucagon-like peptide-1 receptor (GLP-1R) in the body, directly stimulating the secretion of insulin by pancreatic β-cells, promoting proliferation and differentiation, and inhibiting cell apoptosis, thereby exerting a glycemic lowering effect. The glycemic regulating effect of GLP-1 and its analogues has been well studied in human and murine models in the circumstance of many diseases. Recent studies found that GLP-1 is able to modulate innate immune response in a number of inflammatory diseases. In the present review, we summarize the research progression of GLP-1 and its analogues in immunomodulation and related signal pathways.
On the dissolution of sponge silica: Assessing variability and biogeochemical implications
Authors: Maldonado Manuel , López-Acosta María , Abalde Samuel , Martos Isabel , Ehrlich Hermann , Leynaert Aude
Published: December 2022

The dissolution of the biogenic silica that constitutes the skeletons of silicifying organisms is an important mechanism for regenerating dissolved silicon in the ocean. The silica skeletons deposited to the seafloor after the organisms die keep dissolving until becoming definitively buried. The low dissolution rate of sponge skeletons compared to that of diatom skeletons favors their burial and makes sponges (Phylum Porifera) to function as important silicon sinks in the oceans. However, it remains poorly understood whether the large variety of siliceous skeletons existing in the Porifera involves similar variability in their dissolution rates, which would affect the general conceptualization of these organisms as silicon sinks. Herein we investigated kinetics of silica dissolution for major types of skeletons in the three siliceous lineages of Porifera, following standardized digestion conditions in 1% sodium carbonate with orbital agitation at 85°C. The results are compared with those of a previous study conducted under identical conditions, which considered diatom silica, sponge silica, and lithogenic silica. Unexpectedly, the silica of homoscleromorph sponges dissolved only a bit slower than that of freshly cultured diatoms and as fast as diatom earth. However, the rest of sponge skeletons were far more resistant, although with some differences: the isolated spicules of hexactinellid sponges dissolved slightly faster than when forming frameworks of fused spicules, being hexactinellid frameworks as resistant to dissolution as the silica of demosponges, irrespective of occurring in the form of isolated spicules or frameworks. The experiments also indicated that the complexation of sponge silica with aluminum and with chitin does not increase its resistance to dissolution. Because the rapidly-dissolving homoscleromorph sponges represent less than 1% of extant sponges, the sponge skeletons are still conceptualized as important silicon sinks due to their comparative resistance to dissolution. Yet, the turnover of silica into dissolved silicon will always be faster in environments dominated by hexactinellids with isolated spicules than in environments dominated by other hexactinellids and/or demosponges. We discuss whether the time required for a given silica type to completely dissolve in 1% sodium carbonate could be a predictor of its preservation ratio in marine sediments.
Rolling Deck to Repository: Supporting the marine science community with data management services from academic research expeditions
Authors: Carbotte Suzanne M. , O’Hara Suzanne , Stocks Karen , Clark P. Dru , Stolp Laura , Smith Shawn R. , Briggs Kristen , Hudak Rebecca , Miller Emily , Olson Chris J. , Shane Neville , Uribe Rafael , Arko Robert , Chandler Cynthia L. , Ferrini Vicki , Miller Stephen P. , Doyle Alice , Holik James
Published: December 2022

Direct observations of the oceans acquired on oceanographic research ships operated across the international community support fundamental research into the many disciplines of ocean science and provide essential information for monitoring the health of the oceans. A comprehensive knowledge base is needed to support the responsible stewardship of the oceans with easy access to all data acquired globally. In the United States, the multidisciplinary shipboard sensor data routinely acquired each year on the fleet of coastal, regional and global ranging vessels supporting academic marine research are managed by the Rolling Deck to Repository (R2R, rvdata.us) program. With over a decade of operations, the R2R program has developed a robust routinized system to transform diverse data contributions from different marine data providers into a standardized and comprehensive collection of global-ranging observations of marine atmosphere, ocean, seafloor and subseafloor properties that is openly available to the international research community. In this article we describe the elements and framework of the R2R program and the services provided. To manage all expeditions conducted annually, a fleet-wide approach has been developed using data distributions submitted from marine operators with a data management workflow designed to maximize automation of data curation. Other design goals are to improve the completeness and consistency of the data and metadata archived, to support data citability, provenance tracking and interoperable data access aligned with FAIR (findable, accessible, interoperable, reusable) recommendations, and to facilitate delivery of data from the fleet for global data syntheses. Findings from a collection-level review of changes in data acquisition practices and quality over the past decade are presented. Lessons learned from R2R operations are also discussed including the benefits of designing data curation around the routine practices of data providers, approaches for ensuring preservation of a more complete data collection with a high level of FAIRness, and the opportunities for homogenization of datasets from the fleet so that they can support the broadest re-use of data across a diverse user community.
Three new species and two new records of Echinothuriidae (Echinodermata: Echinothurioida) from seamounts in the Northwest Pacific Ocean: Diversity, phylogeny and biogeography of deep-sea echinothuriids
Authors: Zheng Wanrui , Sun Shao’e , Sha Zhongli , Xiao Ning
Published: December 2022

The soft sea urchins Echinothuriidae Thomson, 1872, constitute the most commonly encountered sea urchins in the bathyal environment. The echinothuriids are common and frequently abundant in the Indo-Pacific, but the species diversity is still not completely known yet. Our examination of echinoid specimens collected from seven seamounts in the Northwest Pacific Ocean revealed three new species and two new records. The three new species are described as Araeosoma cucullatum sp. nov., Araeosoma polyporum sp. nov., and Hygrosoma involucrum sp. nov. The two new records included two species from the genus Araeosoma. They are distinguished from each other and from congeners by the following characteristics: coloring, ambulacrum, interambulacrum, apical system, spines, and pedicellariae. The identities of the five species are well supported by genetic distance and phylogenetic analyses based on the mitochondrial cytochrome oxidase subunit I (COI) and 16S rRNA genes. Based on the distribution data, we explored the distribution patterns of Araeosoma, Calveriosoma, Hapalosoma, Sperosoma, Tromikosoma, and Hygrosoma, the six echinothuriid genera occurring in deep sea, and delineated 10 isolated deep-sea biogeographic provinces all over the world. The Western Pacific harbors higher species diversity of deep-sea echinothuriids than other sea areas worldwide, indicating that the Western Pacific may play an important part in the dispersal and speciation of deep-sea echinothuriids.
Distribution and controlling factors of microplastics in surface sediments of typical deep-sea geomorphological units in the northern South China Sea
Authors: Zhang Xiaodong , Liu Zhifei , Zhao Yulong , Ma Pengfei , Colin Christophe , Lin Andrew Tien-Shun
Published: December 2022

Marine microplastics are widely distributed in deep-sea sedimentary environments and are altering sediment compositions and ecological conditions on the seafloor. However, the relation between the distribution of microplastics in deep-sea sediments and the sedimentary dynamic conditions is poorly understood. In this study, we collected surface sediments from some typical geomorphological units (sand dune, sediment drift, and submarine canyon channel/levee) in the northern South China Sea to study composition and distribution of the deep-sea microplastics and their controlling factors. The results show that the microplastic abundance in surface sediments ranges from 19 to 347 p·kg–1, and the identified microplastics consist of 10 types, including dominant polycarbonate (29%), polyethylene (27%), polyester fiber (16%), polyvinyl chloride (13%), and polypropylene (7%), and minor polyethylene terephthalate resin, acrylonitrile-butadiene-styrene, epoxy resin, hydrocarbon resin, and acrylic. The source analysis shows that the deep-sea microplastics may be influenced by riverine inputs from Taiwan and South China. In addition, the microplastic spatial distribution shows that the sand dune and canyon channel contain the highest abundances (136–347 p·kg–1) and more types (4–6 types) of microplastics, which are dominated by relatively high-density polycarbonate or polyvinyl chloride. The canyon levee contains the lowest abundances (19–132 p·kg–1) and less types (1–3 types) of microplastics, which are dominated by relatively low-density polyester fiber or polyethylene. Nevertheless, the microplastic composition of the sediment drift is between those of the canyon channel and the canyon levee. The abundance and polymer type (density) of microplastics all increase with the increased mean grain size of detrital sediments, which represents the progressively enhanced intensity of sedimentary dynamic conditions. We therefore infer that the sedimentary dynamic conditions control the composition and distribution of microplastics in the deep-sea sediments. This study highlights that some deep-sea environments with stronger sedimentary dynamic conditions may accumulate more microplastics, which is of great significance for evaluating the storage and ecological damage of deep-sea microplastics.
Environmental variables affecting Sargassum distribution in the East China Sea and the Yellow Sea
Authors: Shin Jisun , Choi Jang-Geun , Kim So-Hyun , Khim Boo-Keun , Jo Young-Heon
Published: December 2022

Floating Sargassum horneri has flowed into Jeju Island and the coast of the Korean Peninsula every year between February and May since 2015, causing considerable damage to aqua-farming sites and navigation. This study aimed to address the relationship between Sargassum distribution in the Yellow Sea (YS) and the East China Sea (ECS) and environmental variables for determining Sargassum distribution toward the Korean Peninsula. From feature importance ranking, we found that sea surface temperature (SST) is the most influential environmental variable in Sargassum distribution. From variables such as sea surface height (SSH), eastward seawater velocity (uo), and northward seawater velocity (vo), it was observed that Sargassum patches were not distributed in the southeast below 29 °N. Subsequently, we employed bagged tress models to evaluate the specific sensitivity of each environmental variable to Sargassum distribution. This model showed the best quantitative and qualitative performance when trained with physical and geographical variables. When estimating expanded areas of Sargassum distribution over time with the change in SST, a sider distribution range of Sargassum patches than usual and an early inflow into the Korean Peninsula were observed when the SST increased from the original. In addition, we found that the tolerable and favorable SST for Sargassum was 12–20 and 18°C, respectively. These results will enhance the understanding of the relationship between environmental variables and Sargassum distribution and provide valuable data for establishing a pre-disaster system for Sargassum blooms flowing toward the Korean Peninsula.
A socio-ecological assessment of land-based contamination and pollution: The Magdalena delta, Colombia
Authors: Gallo-Vélez David , Restrepo Juan Camilo , Newton Alice
Published: December 2022

River mouth systems, such as estuaries and deltas are important earth system transitional zones linking the land and coastal marine systems. They funnel anthropogenic contaminants and pollutants from the activities in the river catchment into the marine environment. The present study is focused on the Magdalena River-mouth at Bocas de Ceniza where land-based contamination and pollution are important issues. These were subsequently analysed using an expanded DPSIR framework (Drivers Pressures, State, Impacts Responses). Based on export coefficients and secondary information, the loads of BOD, TSS, Nutrients and solid waste from different sources were identified and compared to prioritize their management within the study area. Findings suggest that contaminants generated in the study area may be insignificant compared to the inputs from the Magdalena River, but they can have a significant impact on the state of local ecosystems. Of all the sources analysed, agriculture and livestock are theoretically the largest contributors of nitrogen (i.e., 14.84 t d-1 and 48.99 t d-1) and phosphorus (i.e., 5.90 t d-1 and 19.46 t d-1) in the basin ‘Direct to the Caribbean’ and ‘Cienaga de Mallorquín’ (that altogether are identified as DtC+) and the ‘Western bank of the lower Magdalena’ (DtM-LM), respectively. In the case of BOD, domestic and industrial wastewaters contribute about 5.10 t d-1 and 98.43 t d-1 in the same basins. Contributions of faecal coliforms were more than 4 orders of magnitude higher in untreated wastewater, being 4.86 x1016 NMP d-1 and 1.78 x1016 NMP d-1 in the lower Magdalena and Caribbean catchments, respectively. Inadequately managed waste and plastic represent a serious problem for the Caribbean Basin. Solid waste generated within the study area and coming from the Magdalena basin and the Caribbean Sea, reaches the coast and deteriorates its visual quality, affects mangrove ecosystems, and generates impacts on coastal populations. By basin, the DtM-LM is where the greatest pollutant loads are generated. However, in terms of impact on human well-being, it is the DtC+ that bears the brunt where pressures are translated in impacts such as increased maintenance and cleaning cost of beaches, reduction or loss of tourism revenue, adverse health effects to vulnerable groups, reduce protection against natural hazards, increased living costs and loss of cultural values.
Severity of frailty using modified Thai frailty index, social factors, and prediction of mortality among community-dwelling older adults in a middle-income country
Authors: Morkphrom Ekkaphop , Srinonprasert Varalak , Sura-amonrattana Unchana , Siriussawakul Arunotai , Sainimnuan Supawadee , Preedachitkun Rinrada , Aekplakorn Wichai
Published: December 2022

Background

Frailty has been increasingly recognized as a public health problem for aging populations with significant social impact, particularly in low- and middle-income countries. We aimed to develop a modified version of the Thai Frailty Index (TFI) and explore the association between different frailty statuses, socioeconomic factors, and mortality in community-dwelling older people from a middle-income country.

Methods

The data from participants aged ≥60 years in the Fourth Thai National Health Examination Survey were used to construct the 30-item TFI. Cutoff points were created based on stratum-specific likelihood ratio. TFI ≤ 0.10 was categorized as fit, 0.10–0.25 as pre-frail, 0.25–0.45 as mildly frail, and >0.45 as severely frail. The association of frailty status with mortality was examined using Cox proportional hazard models.

Findings

Among 8,195 older adults with a mean age of 69.2 years, 1,284 died during the 7-year follow-up. The prevalence of frailty was 16.6%. The adjusted hazard ratio (aHR) for mortality in pre-frail was 1.76 (95% CI = 1.50–2.07), mildly frail 2.79 (95% CI = 2.33–3.35), and severely frail 6.34 (95% CI = 4.60–8.73). Having a caretaker in the same household alleviated mortality risk for severely frail participants with an aHR of 2.93 (95% CI = 1.92–4.46) compared with an aHR of 6.89 (95% CI = 3.87–12.26) among those living without a caretaker.

Interpretation

The severity of frailty classified by the modified TFI can predict long-term mortality risk for community-dwelling older adults. Identification of severely frail older people to provide appropriate care might alleviate mortality risk. Our findings can inform policymakers to appropriately allocate services in a resource-limited setting.
Effects of letrozole co-treatment on the cumulative live-birth rate among normal responders in gonadotropin-releasing hormone antagonist cycles
Authors: Zhang Shuyi , Gao Fumei , Fu Min , Shen Huan , Wang Yanbin , Han Hongjing
Published: December 2022

Studies have shown that letrozole cotreatment can improve clinical outcomes in high and poor responders in GnRH-antagonist protocol. However, whether letrozole is also beneficial to normal responders is not known. To investigate the clinical value of letrozole cotreatment during ovarian stimulation in vitro fertilization for normal ovarian reserve patients who were treated with the GnRH antagonist protocol, we conducted a retrospective study that based data from 1 January to 31 December 2017 for all IVF–ICSI GnRH-antagonist protocols. A total of 252 women who aged <40 years, FSH <10 IU/L on day 3 and antral follicle counting (AFC) >6 were included in the analysis (96 in the letrozole group and 156 in the no-letrozole group). The cumulative live-birth rate was calculated as the first live birth achieved after all cycles having an embryo transfer (cycles using fresh embryos and frozen–thawed embryos) among both groups. The initial gonadotropin (Gn) dosage and total Gn dosage were significantly lower and the number of days of Gn treatment was significantly fewer in the letrozole group than the non-letrozole group (p < 0.05). There were also significant between-group differences in luteinizing hormone, estradiol, and progesterone concentrations; and the number of metaphase II oocytes on the day of human chorionic gonadotropin treatment (p < 0.05). There was a significant difference in the implantation rate between the two groups that the letrozole group higher than the non-letrozole group (39.79 vs. 27.96%, p = 0.006), but there was no significant difference in the cumulative live-birth rate. The combination of letrozole with a GnRH antagonist may have no effect on the clinical pregnancy rate or cumulative live-birth rate in patients with a normal ovarian reserve. However, letrozole may increase the rate of embryo implantation and may reduce the requirement for exogenous gonadotrophins and, consequently, the cost of an IVF treatment cycle. In addition, the decreased estradiol level in the ovarian simulation by letrozole supports letrozole can be a safe solution for fertility preservation in estrogen-related cancer patients.
Aaqueous exposure to silver nanoparticles synthesized by abalone viscera hydrolysates promotes the growth, immunity and gut health of zebrafish (Danio rerio)
Authors: Ni Jing , Yang Zhuan , Zhang Yue , Ma Ying , Xiong Hejian , Jian Wenjie
Published: December 2022

Silver nanoparticles (AgNPs) have the potential to be used in aquaculture, but their influence on the growth and health of aquatic organisms has not been extensively investigated. In this study, the abalone viscera hydrolysates decorated AgNPs (AVH-AgNPs) were dispersed into aquaculture water at different concentrations (0, 6, 9, and 18 μg/l) to evaluate the biological effects on zebrafish (Danio rerio). The results showed that the AVH-AgNPs treatments of 6 and 9 μg/l promoted the growth and did not cause obvious damage to the gills, intestines, and livers of zebrafish. All the treatments induced catalase (CAT) and superoxide dismutase (SOD) activities and increased glutathione (GSH) content in the livers and upregulated the expression of immune related genes. The effects of 9 and 18 μg/l AVH-AgNPs treatments were more obvious. After AVH-AgNPs treatment, the abundances of some potential pathogens, such as species Plesimonas shigelloides and Pseudomonas alcaligenes and genus Flavobacterium decreased significantly. In contrast, the abundance of some beneficial bacteria that can degrade pollutants and toxins (e.g., Rhodococcus erythropolis) increased significantly. Thus, the application of low concentrations (6 ~ 18 μg/l) of AVH-AgNPs in aquaculture water is relatively safe and has a positive effect on zebrafish farming.
Prevotella genus and its related NOD-like receptor signaling pathway in young males with stage III periodontitis
Authors: Zhao Yaqiong , Ye Qin , Feng Yao , Chen Yun , Tan Li , Ouyang Zeyue , Zhao Jie , Hu Jing , Chen Ningxin , Su Xiaolin , Dusenge Marie Aimee , Feng Yunzhi , Guo Yue
Published: December 2022

Background

As periodontitis progresses, the oral microbiota community changes dynamically. In this study, we evaluated the dominant bacteria and their roles in the potential pathway in young males with stage III periodontitis.

Methods

16S rRNA sequencing was performed to evaluate variations in the composition of oral bacteria between males with stage I and III periodontitis and identify the dominant bacteria of each group. Function prediction was obtained based on 16S rRNA sequencing data. The inhibitor of the predominant pathway for stage III periodontitis was used to investigate the role of the dominant bacteria in periodontitis in vivo and in vitro.

Results

Chao1 index, Observed Species and Phylogenetic Diversity (PD) whole tree values were significantly higher in the stage III periodontitis group. β-diversity suggested that samples could be divided according to the stages of periodontitis. The dominant bacteria in stage III periodontitis were Prevotella, Prevotella_7, and Dialister, whereas that in stage I periodontitis was Cardiobacterium. KEGG analysis predicted that variations in the oral microbiome may be related to the NOD-like receptor signaling pathway. The inhibitor of this pathway, NOD-IN-1, decreased P. intermedia -induced Tnf-α mRNA expression and increased P. intermedia -induced Il-6 mRNA expression, consistent with the ELISA results. Immunohistochemistry confirmed the down-regulation of TNF-α and IL-6 expressions by NOD-IN-1 in P. intermedia–induced periodontitis.

Conclusion

The composition of the oral bacteria in young males varied according to the stage of periodontitis. The species richness of oral microtia was greater in young males with stage III periodontitis than those with stage I periodontitis. Prevotella was the dominant bacteria in young males with stage III periodontitis, and inhibition of the NOD-like receptor signaling pathway can decrease the periodontal inflammation induced by P. intermedia.
Detection of FeChPV in a cat shelter outbreak of upper respiratory tract disease in China
Authors: Hao Xiangqi , Li Yanchao , Chen Bo , Wang Hanhong , Wang Xinrui , Xiao Xiangyu , Zhou Pei , Li Shoujun
Published: December 2022

Feline parvovirus often causes a fatal infectious disease and has a serious impact on domestic cats and wild felines. Feline chaphamaparvovirus (FeChPV) is a novel type of feline parvovirus that has been successively identified in Canada, Italy, and Turkey. The prevalence and pathogenicity of FeChPV in other regions is still unknown. In this study, we recorded the detection of FeChPV in a cat shelter in China. A high prevalence (81.08%, 30/37) of FeChPV was detected in cats with symptoms of upper respiratory tract disease (URTD) in this cat shelter. Multiple pathogen testing indicated high coinfection rates of 80% (24/30) with other common viruses in FeChPV-positive cats. Analyses of the necropsy and histopathological findings revealed severe lymphadenitis, encephalitis, and viral DNA in several tissues (including brain) of the deceased cat. Finally, we obtained nearly full-length genomes of four strains with 98.4%~98.6% homology with previously reported genomes. Notably, VP1 proteins showed seven unique amino acid mutations, while NS1 proteins carried eight mutations. In the evolutionary tree based on VP1 and NS1, the sequences clustered in a large branch with Italian and Canadian FeChPV strains. Given the possible association of FeChPV with URTD, further studies are necessary to evaluate the pathogenicity and epidemiological characteristics of this novel feline pathogen.
Endophytic bacterium Pseudomonas protegens suppresses mycelial growth of Botryosphaeria dothidea and decreases its pathogenicity to postharvest fruits
Authors: Huang Yonghong , Liu Junping , Li Jinghui , Shan Xiaoying , Duan Yanxin
Published: December 2022

Apple (Malus domestica Borkh.), one of the most economically important fruits widely consumed worldwide, has been suffering from apple ring rot caused by Botryosphaeria dothidea, which dramatically affects its quality and yield. In the present study, we demonstrated that Pseudomonas protegens, isolated from Chinese leek (Allium tuberosum), significantly suppressed the mycelial growth and propagation of B. dothidea, respectively, further displayed a considerably inhibitory effect on the apple ring rot of postharvest fruits. In addition, P. protegens significantly improved the total soluble solid/titrable acidity (TSS/TA) ratio and soluble sugar/titrable acidity (SS/TA) ratio and drastically maintained the fruit firmness. Further analysis manifested that P. protegens substantially induced the defense-related genes such as MdGLU, MdPAL, MdPOD, MdCAL, and transcription factors related to the resistance to B. dothidea, including MdWRKY15, MdPUB29, MdMyb73, and MdERF11 in apple fruits. Meanwhile, P. protegens considerably restrained the expressions of the pathogenicity-related genes in B. dothidea, including the BdCYP450, BdADH, BdGHY, BdATS, Bdα/β-HY, and BdSTR. By inference, P. protegens inhibited the apple ring rot on postharvest fruits by activating the defense system of apple fruit and repressing the pathogenic factor of B. dothidea. The study provided a theoretical basis and a potential alternative to manage the apple ring rot on postharvest fruits.