bluuebunny/crossref_metadata_2025 huggingface dataset:
Diverse Epigenetic Regulations of Macrophages in Atherosclerosis
Authors: Yang Hongmei , Sun Yue , Li Qingchao , Jin Fengyan , Dai Yun
Published: March 2022

Emerging research on epigenetics has resulted in many novel discoveries in atherosclerosis (AS), an inflammaging-associated disease characterized by chronic inflammation primarily driven by macrophages. The bulk of evidence has demonstrated the central role of epigenetic machinery in macrophage polarization to pro- (M1-like) or anti-inflammatory (M2-like) phenotype. An increasing number of epigenetic alterations and their modifiers involved in reprogramming macrophages by regulating DNA methylation or histone modifications (e.g., methylation, acetylation, and recently lactylation) have been identified. They may act to determine or skew the direction of macrophage polarization in AS lesions, thereby representing a promising target. Here we describe the current understanding of the epigenetic machinery involving macrophage polarization, to shed light on chronic inflammation-driving onset and progression of inflammaging-associated diseases, using AS as a prototypic example, and discuss the challenge for developing effective therapies targeting the epigenetic modifiers against these diseases, particularly highlighting a potential strategy based on epigenetically-governed repolarization from M1-like to M2-like phenotype.
Scientific Societies Fostering Inclusivity in the Life Sciences Through Engagement of Undergraduate Scientists
Authors: Primus Clara , Zimmerman Alexandra N. , Terovolas Avanthia K. , Block Kirsten F. , Brown Christopher G. , Burton Michael D. , Edwards Ashanti , Etson Candice M. , Flores Sonia C. , Fry Catherine , Guillory Ashley N. , Ingram Susan L. , McGee Richard , Neely-Fisher Deborah L. , Paxson Stephanie , Phelan Laura , Suggs Kirsta , Vega Leticia R. , Vuong Elizabeth , Lujan J. Luis , Ramirez-Alvarado Marina , Segarra Verónica A.
Published: March 2022

Scientific societies serve as communities of practice in which scientists develop many of the skills and connections required for the progression of their careers. For example, scientific societies offer their members opportunities to attend career development programs, gain experience in communicating science, and receive recognition for achievements within their discipline. Programming for undergraduate student members has recently been increasing, both in prevalence and in its range of offerings. The Alliance to Catalyze Change for Equity in STEM Success, ACCESS, a meta-organization seeking equity and inclusivity in life sciences fields, has examined programs and opportunities focused on undergraduates across its member scientific societies to identify common themes, promising practices and challenges. In this article, we share and discuss our findings.
Serum Bilirubin Level Is Increased in Metabolically Healthy Obesity
Authors: Fu Jing , Wang Qiu , Zhang Lin , Liu Jia , Wang Guang
Published: March 2022

Objectives

Bilirubin is a biochemical substance with metabolic benefits. The objective of this research was to elucidate the association between serum bilirubin levels and metabolic alterations in different obesity phenotypes.

Methods

In total, 1,042 drug-naive participants were included in the study. Of them, 541 were obese patients and 501 were age-matched and sex-matched healthy control subjects. The obese patients were divided into metabolically healthy obesity (MHO) group and metabolically unhealthy obesity (MUHO) group according to the levels of fasting plasma glucose (FBG), triglyceride (TG), high-density lipoprotein cholesterol (HDL-C) and blood pressure (BP). Clinical and biochemical parameters including total bilirubin (TBil), indirect bilirubin (IBil) and direct bilirubin (DBil) were measured. ANOVA or Kruskal-Wallis H test was used to test differences among the three groups. Pearson and Spearman correlations were used to analyze the relationships between two parameters. The relationships between bilirubin and other variables were analyzed using Multivariate regression analysis.

Results

MHO group had favorable blood pressure, glucose and lipids profiles, along with increased TBil and DBil, and decreased high-sensitivity C-reactive protein (hsCRP) and homeostasis model assessment of insulin resistance (HOMA-IR) levels when compared to MUHO group (P < 0.05 for all). TBil and DBil were negatively correlated with total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), fasting insulin (FINS), hsCRP and HOMA-IR, even after adjusted for age, gender and BMI (all P <0.01). Multivariate regression analysis demonstrated that HOMA-IR was independently correlated with TBil and DBIi levels (β = -0.400, P < 0.01).

Conclusion

MHO group harbors increased bilirubin level compared with MUHO group. HOMA-IR was independently correlated with TBil and DBIi levels.
Sporadic Medullary Thyroid Carcinoma: Towards a Precision Medicine
Authors: Matrone Antonio , Gambale Carla , Prete Alessandro , Elisei Rossella
Published: March 2022

Medullary thyroid carcinoma (MTC) is a neuroendocrine malignant tumor originating from parafollicular C-cells producing calcitonin. Most of cases (75%) are sporadic while the remaining (25%) are hereditary. In these latter cases medullary thyroid carcinoma can be associated (multiple endocrine neoplasia type IIA and IIB) or not (familial medullary thyroid carcinoma), with other endocrine diseases such as pheochromocytoma and/or hyperparathyroidism. RET gene point mutation is the main molecular alteration involved in MTC tumorigenesis, both in sporadic and in hereditary cases. Total thyroidectomy with prophylactic/therapeutic central compartment lymph nodes dissection is the initial treatment of choice. Further treatments are needed according to tumor burden and rate of progression. Surgical treatments and local therapies are advocated in the case of single or few local or distant metastasis and slow rate of progression. Conversely, systemic treatments should be initiated in cases with large metastatic and rapidly progressive disease. In this review, we discuss the details of systemic treatments in advanced and metastatic sporadic MTC, focusing on multikinase inhibitors, both those already used in clinical practice and under investigation, and on emerging treatments such as highly selective RET inhibitors and radionuclide therapy.
Improvement Pathway of Energy Transition: From the Perspective of Directed Technical Change
Authors: Hou Guisheng , Song Hongyu
Published: March 2022

Energy transition can effectively promote the green transformation of economic development. With capital, traditional fossil energy, clean energy generation, thermal power generation, and the GDP of the provinces, we built a stochastic production frontier model based on a translog production function, which measures the bias of directed technical changes and substitution elasticities of 30 provinces in mainland China from 2000 to 2017. The results show that the directed technical change in China is more biased to thermal power generation and deviated from clean energy generation. In addition, except for traditional fossil generation and thermal power generation with a complementary relationship, there is a substitution relationship between other energy factors. At the regional level, the production patterns of 9 provinces (Beijing, Fujian, Hainan, Tianjin, Chongqing, Gansu, Neimenggu, Ningxia, and Xinjiang) are conducive to the external electric transition, and nine provinces (Beijing, Fujian, Guangxi, Hainan, Hubei, Jilin, Jiangsu, Qinghai, and Zhejiang) are beneficial to the internal electric transition. We find that there is a large room for improvement in external and internal electric transitions in most provinces. We propose that the Chinese government should promote the reform of the market-oriented energy pricing mechanism according to different production modes in different regions. Furthermore, the results from the analysis of China show that it is also possible for other countries to treat their energy transition differently due to their characteristic production patterns.
Predation in Many Dimensions: Spatial Context Is Important for Meaningful Functional Response Experiments
Authors: Juliano Steven A. , Goughnour Jonah A. , Ower Geoffrey D.
Published: March 2022

For simplicity and to minimize variation, functional response experiments frequently use environments of simple physical structure and small size. Less attention is paid to similarity of the experimental environment to the natural environment where predation occurs. Assumptions about predator and prey use of space are often implied in the choice of experimental environment. We illustrate how these assumptions may affect conclusions with an experiment testing how arena size affects a functional response.Toxorhynchites rutiluspreyed upon larvalCulex restuansin containers differing in volume by 15x, but spanning a similar range of prey/liter. The most plausible Type II model included attack rates that were statistically indistinguishable, but in the larger volume, had handling time that was lower by > 30x compared to the smaller volume, suggesting a major change in predator behavior with container volume. When we altered our assumption that predation scales with prey/liter, assuming instead that aggregation causes predation to scale with prey/area of surface or bottom, the conclusions changed: neither attack rate nor handling time differed with container size. Thus, our assumption about how predator and prey used space altered the conclusions of the experiment. We then summarize recently published experiments showing that spatial context affects estimated functional responses. We suggest that functional response experiments would be improved by using larger experimental spaces that represent physical complexity of environments where predation occurs. Greater spatial extent and complexity are likely to cause aggregation of predation. Effects of more realistic spatial context are likely to yield more complete understanding of quantitative aspects of predation.
Frugivory and Seed Dispersal by Carnivorans
Authors: Draper John P. , Young Julie K. , Schupp Eugene W. , Beckman Noelle G. , Atwood Trisha B.
Published: March 2022

Seed dispersal is critical to the ecological performance of sexually reproducing plant species and the communities that they form. The Mammalian order Carnivora provide valuable and effective seed dispersal services but tend to be overlooked in much of the seed dispersal literature. Here we review the literature on the role of Carnivorans in seed dispersal, with a literature search in the Scopus reference database. Overall, we found that Carnivorans are prolific seed dispersers. Carnivorans’ diverse and plastic diets allow them to consume large volumes of over a hundred families of fruit and disperse large quantities of seeds across landscapes. Gut passage by these taxa generally has a neutral effect on seed viability. While the overall effect of Carnivorans on seed dispersal quality is complex, Carnivorans likely increase long-distance dispersal services that may aid the ability of some plant species to persist in the face of climate change.
Complete Chloroplast Genomes and Comparative Analyses of Three Ornamental Impatiens Species
Authors: Luo Chao , Huang Wulue , Yer Huseyin , Kamuda Troy , Li Xinyi , Li Yang , Rong Yuhong , Yan Bo , Wen Yonghui , Wang Qiong , Huang Meijuan , Huang Haiquan
Published: March 2022

Impatiens L., the largest genus in the family Balsaminaceae with approximately 1,000 species, is a controversial genus. Due to the conflict of morphological features and insufficient genomic resources, the studies of systematic evolution and understanding of taxonomic identification are considered to be very limited. Hence, we have sequenced the complete chloroplast genomes of three ornamental species (Impatiens balsamina, I. hawkeri, and I. walleriana), and compared them with previously published wild species data. We performed a detailed comparison of a highly similar basic structure, size, GC content, gene number, order, and functional array among them. Similarly, most divergent genes were detected from previous work in the literature. The mutational regions containing highly variable nucleotide hotspots were identified and may be used as potential markers for species identification and taxonomy. Furthermore, using whole chloroplast genome data to analysis the phylogenetic relationship of the Balsaminaceae species, we found that they were all part of a single clade. The three phenotypically different ornamental species were clustered together, suggesting that they were very likely to be closely related. We achieved and characterized the plastid genome structure, identified the divergence hotspots, and determined the phylogenetic and taxonomic positions of the three cultivated species in the Impatiens genus. The results may show that the chloroplast genome can be used to solve phylogenetic problems in or between the Impatiens genus and also provide genomic resources for the study of the Balsaminaceae family’s systematics and evolution.
Comparative Analysis on Proteomics Profiles of Intracellular and Extracellular M.tb and BCG From Infected Human Macrophages
Authors: Liu Han , Su Li , Zhu Tingting , Zhu Xiaojie , Zhu Yifan , Peng Yonchong , Zhang Kailun , Wang Longwei , Hu Changmin , Chen Huanchun , Chen Yingyu , Guo Aizhen
Published: March 2022

Tuberculosis is the second cause in infectious diseases leading to human death. Understanding the virulence mechanism is inevitable if the disease needs to be fully cured. Therefore, this study aimed to reveal this mechanism by comparing proteomic profiles of intracellular and extracellular virulent strainM.tband bacille Calmette–Guérin (BCG) from infected THP-1cells. First,M.tband BCG infected THP-1 at MOI 10:1. Twelve hours postinfection, intracellular bacteria ofM.tband BCG were collected, whereas the two bacilli cultured in 7H9 broth media were used as the control. Then four groups of bacilli were subjected to proteomic analysis, and differential proteomic profiles betweenM.tband BCG were comparatively analyzed with bioinformatics tools. As a result, we identified a total of 1,557 proteins. Further, they were divided into four groups for comparison ofM.tbversus BCG under 7H9 culture (shorten as out),M.tbin (intracellular) versusM.tbout, BCG in versus BCG out andM.tbin versus BCG in. BetweenM.tbin versus BCG in, a total of 211 differentially expressed proteins were found. Eight proteins like ESAT-6 distributed in six RDs and some known proteins related to virulence. Besides, five uncharacterized proteins were differentially expressed. Further analysis revealed enriched pathways were associated with glyoxylate and dicarboxylate metabolism pathways. InM.tbout versus BCG out, a total of 144 differential proteins were identified and mainly involved in metabolism pathways. Then, 121 differential proteins in the group ofM.tbin versusM.tbout were enriched in ribosome and oxidative phosphorylation related to adaptation to the host environment. The group of BCG in versus BCG out shared the same trend of different pathways to theM.tbin versusM.tbout. Finally, 42 proteins were identified to be up-regulated only in intracellularM.tbincluding eight RD proteins, whereas 22 up-regulated uniquely in intracellular BCG. Besides, only two proteins (Pks13 and Rv1405c) were commonly up-regulated in intracellularM.tband BCG. Further, some unknown proteins were uniquely up-regulated in the intracellularM.tband BCG. These findings provide valuable data for further exploration of molecular mechanism forM.tbvirulence and BCG immune response.
An Efficient Signature Based on Necroptosis-Related Genes for Prognosis of Patients With Pancreatic Cancer
Authors: Shi Heng , Peng Qin , Zhou Xianling , He Yushan , Sun Shengyun
Published: March 2022

Pancreatic cancer (PCa) is a highly lethal and aggressive disease, characterized by high mortality rates. Although necroptosis plays a vital role in tumor progression, cancer metastasis, prognosis of cancer patients, necroptosis-related gene (NRG) sets have rarely been analyzed in PCa. Therefore, definition of novel necroptosis-related prognostic markers for PCa patients is urgently needed. Here, we screened 159 NRGs and identified 132 differentially expressed NRGs in The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) cohorts. Next, we employed univariate and multivariate Cox proportional regression models to establish a prognostic-related NRG signature comprising five NRGs that could stratify patients into high-risk and low-risk groups. Results from survival analysis showed that patients in the high-risk had dramatically shorter overall survival (OS) rates compared with their low-risk counterparts. Results from univariate and multivariate Cox regression analysis further confirmed the independent prognostic value of the established necroptosis-related signature, and the area under receiver (AUC) of the operating curve (ROC) for 1-, 3-, 5-years was 0.72, 0.74, and 0.75, respectively. Finally, we validated the signature efficacy using an independent cohort from the Gene Expression Omnibus (GEO) database. The ROC curve confirmed the predictive capacity of the five-gene signature. Furthermore, we validated expression of the signature proteins using the Human Protein Atlas (HPA) database. In conclusion, we successfully constructed a novel necroptosis-related signature for prognosis of patients with pancreatic cancer.
Single Cell Transcriptome Sequencing of Zebrafish Testis Revealed Novel Spermatogenesis Marker Genes and Stronger Leydig-Germ Cell Paracrine Interactions
Authors: Qian Peipei , Kang Jiahui , Liu Dong , Xie Gangcai
Published: March 2022

Spermatogenesis in testis is an important process for sexual reproduction, and worldwide about 10–15 percent of couples suffer from infertility. It is of importance to study spermatogenesis at single cell level in both of human and model organisms. Currently, single-cell RNA sequencing technologies (scRNA-seq) had been extensively applied to the study of cellular components and its gene regulations in the testes of different species, including human, monkey, mouse, and fly, but not in zebrafish. Zebrafish was a widely used model organism in biology and had been extensively used for the study of spermatogenesis in the previous studies. Therefore, it is also important to profile the transcriptome of zebrafish testis at single cell level. In this study, the transcriptomes of 14, 315 single cells from adult male zebrafish testes were profiled by scRNA-seq, and 10 cell populations were revealed, including Leydig cell, Sertoli cell, spermatogonia cell (SPG), spermatocyte, and spermatids. Notably, thousands of cell-type specific novel marker genes were identified, including sumo3b for SPG, krt18a.1 for Sertoli cells, larp1b and edrf1 for spermatids, which were also validated by RNA in situ hybridization experiments. Interestingly, through Ligand-Receptor (LR) analyses, zebrafish Leydig cells demonstrated stronger paracrine influence on germ cells than Sertoli cells. Overall, this study could be an important resource for the study of spermatogenesis in zebrafish and might also facilitate the study of the genes associated with human infertility through using zebrafish as a model organism.
Leveraging Optimized Transcriptomic and Personalized Stem Cell Technologies to Better Understand Syncytialization Defects in Preeclampsia
Authors: Choi Sehee , Khan Teka , Roberts R. Michael , Schust Danny J.
Published: March 2022

Understanding the process of human placentation is important to the development of strategies for treatment of pregnancy complications. Several animal and in vitro human model systems for the general study human placentation have been used. The field has expanded rapidly over the past decades to include stem cell-derived approaches that mimic preclinical placental development, and these stem cell-based models have allowed us to better address the physiology and pathophysiology of normal and compromised trophoblast (TB) sublineage development. The application of transcriptomic approaches to these models has uncovered limitations that arise when studying the distinctive characteristics of the large and fragile multinucleated syncytiotrophoblast (STB), which plays a key role in fetal-maternal communication during pregnancy. The extension of these technologies to induced pluripotent stem cells (iPSCs) is just now being reported and will allow, for the first time, a reproducible and robust approach to the study of the developmental underpinnings of late-manifesting diseases such as preeclampsia (PE) and intrauterine growth retardation in a manner that is patient- and disease-specific. Here, we will first focus on the application of various RNA-seq technologies to TB, prior limitations in fully accessing the STB transcriptome, and recent leveraging of single nuclei RNA sequencing (snRNA-seq) technology to improve our understanding of the STB transcriptome. Next, we will discuss new stem-cell derived models that allow for disease- and patient-specific study of pregnancy disorders, with a focus on the study of STB developmental abnormalities in PE that combine snRNA-seq approaches and these new in vitro models.
Emerging Strategies in TCR-Engineered T Cells
Authors: Wei Fang , Cheng Xiao-Xia , Xue John Zhao , Xue Shao-An
Published: March 2022

Immunotherapy of cancer has made tremendous progress in recent years, as demonstrated by the remarkable clinical responses obtained from adoptive cell transfer (ACT) of patient-derived tumor infiltrating lymphocytes, chimeric antigen receptor (CAR)-modified T cells (CAR-T) and T cell receptor (TCR)-engineered T cells (TCR-T). TCR-T uses specific TCRS optimized for tumor engagement and can recognize epitopes derived from both cell-surface and intracellular targets, including tumor-associated antigens, cancer germline antigens, viral oncoproteins, and tumor-specific neoantigens (neoAgs) that are largely sequestered in the cytoplasm and nucleus of tumor cells. Moreover, as TCRS are naturally developed for sensitive antigen detection, they are able to recognize epitopes at far lower concentrations than required for CAR-T activation. Therefore, TCR-T holds great promise for the treatment of human cancers. In this focused review, we summarize basic, translational, and clinical insights into the challenges and opportunities of TCR-T. We review emerging strategies used in current ACT, point out limitations, and propose possible solutions. We highlight the importance of targeting tumor-specific neoAgs and outline a strategy of combining neoAg vaccines, checkpoint blockade therapy, and adoptive transfer of neoAg-specific TCR-T to produce a truly tumor-specific therapy, which is able to penetrate into solid tumors and resist the immunosuppressive tumor microenvironment. We believe such a combination approach should lead to a significant improvement in cancer immunotherapies, especially for solid tumors, and may provide a general strategy for the eradication of multiple cancers.
Schisandrin B Induced ROS-Mediated Autophagy and Th1/Th2 Imbalance via Selenoproteins in Hepa1-6 Cells
Authors: Tan Siran , Zheng Zhi , Liu Tianqi , Yao Xiaoyun , Yu Miao , Ji Yubin
Published: March 2022

Schisandrin B (Sch B) is well-known for its antitumor effect; however, its underlying mechanism remains confusing. Our study aimed to investigate the role of selenoproteins in Sch B-induced autophagy and Th1/Th2 imbalance in Hepa1-6 cells. Hepa1-6 cells were chosen to explore the antitumor mechanism and were treated with 0, 25, 50, and 100 μM of Sch B for 24 h, respectively. We detected the inhibition rate of proliferation, transmission electron microscopy (TEM), monodansylcadaverine (MDC) staining, reactive oxygen species (ROS) level and oxidative stress-related indicators, autophagy-related genes, related Th1/Th2 cytokines, and selenoprotein mRNA expression. Moreover, the heat map, principal component analysis (PCA), and correlation analysis were used for further bioinformatics analysis. The results revealed that Sch B exhibited well-inhibited effects on Hepa1-6 cells. Subsequently, under Sch B treatment, typical autophagy characteristics were increasingly apparent, and the level of punctate MDC staining enhanced and regulated the autophagy-related genes. Overall, Sch B induced autophagy in Hepa1-6 cells. In addition, Sch B-promoted ROS accumulation eventually triggered autophagy initiation. Results of Th1 and Th2 cytokine mRNA expression indicated that Th1/Th2 immune imbalance was observed by Sch B treatment in Hepa1-6 cells. Intriguingly, Sch B downregulated the majority of selenoprotein expression. Also, the heat map results observed significant variation of autophagy-related genes, related Th1/Th2 cytokines, and selenoprotein expression in response to Sch B treatment. PCA outcome suggested the key role of Txnrd1, Txnrd3, Selp, GPX2, Dio3, and Selr with its potential interactions in ROS-mediated autophagy and Th1/Th2 imbalance of Hepa1-6 cells. In conclusion, Sch B induced ROS-mediated autophagy and Th1/Th2 imbalance in Hepa1-6 cells. More importantly, the majority of selenoproteins were intimately involved in the process of autophagy and Th1/Th2 imbalance, Txnrd3, Selp, GPX2, Dio3, and Selr had considerable impacts on the process.
Translational Control of COVID-19 and Its Therapeutic Implication
Authors: Zhang Dejiu , Zhu Lei , Wang Yin , Li Peifeng , Gao Yanyan
Published: March 2022

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of COVID-19, which has broken out worldwide for more than two years. However, due to limited treatment, new cases of infection are still rising. Therefore, there is an urgent need to understand the basic molecular biology of SARS-CoV-2 to control this virus. SARS-CoV-2 replication and spread depend on the recruitment of host ribosomes to translate viral messenger RNA (mRNA). To ensure the translation of their own mRNAs, the SARS-CoV-2 has developed multiple strategies to globally inhibit the translation of host mRNAs and block the cellular innate immune response. This review provides a comprehensive picture of recent advancements in our understanding of the molecular basis and complexity of SARS-CoV-2 protein translation. Specifically, we summarize how this viral infection inhibits host mRNA translation to better utilize translation elements for translation of its own mRNA. Finally, we discuss the potential of translational components as targets for therapeutic interventions.
Cathelicidin-3 Associated With Serum Extracellular Vesicles Enables Early Diagnosis of a Transmissible Cancer
Authors: Espejo Camila , Wilson Richard , Pye Ruth J. , Ratcliffe Julian C. , Ruiz-Aravena Manuel , Willms Eduard , Wolfe Barrett W. , Hamede Rodrigo , Hill Andrew F. , Jones Menna E. , Woods Gregory M. , Lyons A. Bruce
Published: March 2022

The identification of practical early diagnostic biomarkers is a cornerstone of improved prevention and treatment of cancers. Such a case is devil facial tumor disease (DFTD), a highly lethal transmissible cancer afflicting virtually an entire species, the Tasmanian devil (Sarcophilus harrisii). Despite a latent period that can exceed one year, to date DFTD diagnosis requires visual identification of tumor lesions. To enable earlier diagnosis, which is essential for the implementation of effective conservation strategies, we analyzed the extracellular vesicle (EV) proteome of 87 Tasmanian devil serum samples using data-independent acquisition mass spectrometry approaches. The antimicrobial peptide cathelicidin-3 (CATH3), released by innate immune cells, was enriched in serum EV samples of both devils with clinical DFTD (87.9% sensitivity and 94.1% specificity) and devils with latent infection (i.e., collected while overtly healthy, but 3-6 months before subsequent DFTD diagnosis; 93.8% sensitivity and 94.1% specificity). Although high expression of antimicrobial peptides has been mostly related to inflammatory diseases, our results suggest that they can be also used as accurate cancer biomarkers, suggesting a mechanistic role in tumorous processes. This EV-based approach to biomarker discovery is directly applicable to improving understanding and diagnosis of a broad range of diseases in other species, and these findings directly enhance the capacity of conservation strategies to ensure the viability of the imperiled Tasmanian devil population.
Increased HBV Coinfection and Decreased IFN-γ-Producing HBV-Specific CD8+ T Cell Numbers During HIV Disease Progression
Authors: Zhu Zhiqiang , Qin Yuanyuan , Liang Qi , Xia Wei , Zhang Tong , Wang Wen , Zhang Mengmeng , Jiang Taiyi , Wu Hao , Tian Ye
Published: March 2022

Objective

To investigate the characteristics and mechanism of the dynamics of HBV infection with the progression of HIV disease and to explore the different responses of T lymphocytes to HBV in HIV patients in different stages of disease.

Methods

We compared the rates and characteristics of HBV coinfection between 372 early HIV-infected and 306 chronically HIV-infected men who have sex with men (MSM) in the Beijing Youan Hospital from October 2006 to November 2014. We further analysed IFN-γ-producing HBV-specific CD8+ T cells in 15 early HIV-infected individuals and 20 chronic HIV-infected individuals with HBV coinfection.

Results

Twenty-three HBsAg-positive cases were detected among the 372 early HIV-infected patients of this cohort, and the coinfection rate was 6.18%, while 35 HBsAg-positive cases were detected among the 306 chronically HIV-infected patients, with a coinfection rate of 11.44%. The coinfection rate of the chronically HIV-infected patients was significantly higher than that of the early-infected patients (p=0.0005). The median CD4+ T cell count in the early HIV infection patients was 445 cells/μL (196-1,030 cells/μL), which was higher than that in the chronic HIV infection patients [358 cells/μL (17-783 cells/μL)] (p<0.001). The proportion of IFN-γ-producing CD8+ T cells in early HIV-infected patients was significantly higher than that in chronically HIV-infected patients.

Conclusion

The coinfection rate of HBV in HIV patients increases with HIV disease progression, which might be related to the decreased IFN-γ-producing HBV-specific CD8+ T cell numbers. The closely monitored HBV serum markers from the early stage of HIV infection are warranted.
Leishmania Major Centrin Gene-Deleted Parasites Generate Skin Resident Memory T-Cell Immune Response Analogous to Leishmanization
Authors: Ismail Nevien , Karmakar Subir , Bhattacharya Parna , Sepahpour Telly , Takeda Kazuyo , Hamano Shinjiro , Matlashewski Greg , Satoskar Abhay R. , Gannavaram Sreenivas , Dey Ranadhir , Nakhasi Hira L.
Published: March 2022

Leishmaniasis is a vector-borne parasitic disease transmitted through the bite of a sand fly with no available vaccine for humans. Recently, we have developed a live attenuated Leishmania major centrin gene-deleted parasite strain (LmCen-/-) that induced protection against homologous and heterologous challenges. We demonstrated that the protection is mediated by IFN (Interferon) γ-secreting CD4+ T-effector cells and multifunctional T cells, which is analogous to leishmanization. In addition, in a leishmanization model, skin tissue-resident memory T (TRM) cells were also shown to be crucial for host protection. In this study, we evaluated the generation and function of skin TRM cells following immunization with LmCen-/- parasites and compared those with leishmanization. We show that immunization with LmCen-/- generated skin CD4+ TRM cells and is supported by the induction of cytokines and chemokines essential for their production and survival similar to leishmanization. Following challenge with wild-type L. major, TRM cells specific to L. major were rapidly recruited and proliferated at the site of infection in the immunized mice. Furthermore, upon challenge, CD4+ TRM cells induce higher levels of IFNγ and Granzyme B in the immunized and leishmanized mice than in non-immunized mice. Taken together, our studies demonstrate that the genetically modified live attenuated LmCen-/- vaccine generates functional CD4+ skin TRM cells, similar to leishmanization, that may play a crucial role in host protection along with effector T cells as shown in our previous study.
Differential Expression of miRNAs in Trichloroethene-Mediated Inflammatory/Autoimmune Response and Its Modulation by Sulforaphane: Delineating the Role of miRNA-21 and miRNA-690
Authors: Banerjee Nivedita , Wang Hui , Wang Gangduo , Boor Paul J. , Khan M. Firoze
Published: March 2022

Trichloroethene (TCE), an occupational and ubiquitous environmental contaminant, is associated with the induction of autoimmune diseases (ADs). Although oxidative stress plays a major role in TCE-mediated autoimmunity, the underlying molecular mechanisms still need to be delineated. Altered non-coding RNAs, including the expression of microRNAs (miRNAs), can influence target genes, especially related to apoptosis and inflammation, and contribute to ADs. Therefore, the objective of this study was to delineate the contribution of miRNAs in TCE-mediated inflammatory and autoimmune response. To achieve this, we treated female MRL+/+ mice with TCE (10 mmol/kg in corn oil, i.p., every fourth day) with/without antioxidant sulforaphane (SFN; 8 mg/kg in corn oil, i.p., every other day) for 6 weeks. With the use of miRNA microarray, 293 miRNAs were analyzed, which included 35 miRNAs that were relevant to inflammation and ADs. Among those 35 miRNAs, 8 were modulated by TCE and/or TCE+SFN exposure. TCE treatment led to increased expression of 3 miRNAs and also decreased expression of 3 miRNAs. Interestingly, among the 35 differentially expressed miRNAs, antioxidant SFN modulated the expression of 6 miRNAs. Based on the microarray findings, we subsequently focused on two miRNAs (miRNA-21 and miRNA-690), which are known to be involved in inflammation and autoimmune response. The increases in miRNA-21 and miR-690 (observed using miRNA microarray) were further validated by RT-PCR, and the TCE-mediated increases in miR-21 and miR-690 were ameliorated by SFN treatment. Modulating miR-21 and miR-690 by respective inhibitors or mimics suppressed the expression of NF-κB (p65) and IL-12 in RAW 264.7 cells. Our findings suggest a contributory role of miR-21 and miR-690 in TCE-mediated and its metabolite dichloroacetyl chloride (DCAC)-mediated inflammation and autoimmune response and support that antioxidant SFN could be a potential therapeutic candidate for inflammatory responses and ADs.
Effects of Immobilized Antimicrobial Peptides on Growth Performance, Serum Biochemical Index, Inflammatory Factors, Intestinal Morphology, and Microbial Community in Weaning Pigs
Authors: Liu Nian , Ma Xiaokang , Jiang Xianren
Published: March 2022

This experiment was conducted to investigate the effects of immobilized antimicrobial peptides on growth performance, serum biochemical index, inflammatory factors, intestinal morphology, and microbial community of weaning piglets. A total of 21 weaning piglets [Duroc × (Landrace × Yorkshire)] with initial body weight (7.64 ± 0.65 kg) were randomly allocated to one of three treatments with seven replicates (one pig per replicate) per treatment according to sex and weight in randomized complete block design. Pigs in the three treatments were fed corn–soybean meal-based diet (CON), corn–soybean meal based diet + flavomycin (25 mg/kg) + quinone (50 mg/kg) (AB), and corn–soybean meal based diet + 1,000 mg/kg immobilized antimicrobial peptides (IAMPs), respectively. The experiment lasted for 28 days, including early stage (0–14 days) and late stage (15–28 days). The results showed the following: (1) compared with the CON group, the average daily gain in the whole experimental time (p < 0.05) was significantly increased, and the diarrhea rate of weaning piglets was decreased (p < 0.01) in the IAMPs group; (2) compared with the CON group, the concentrations of serum IgM and superoxide dismutase (SOD) in the IAMPs group were significantly higher than the CON and AB groups (p < 0.01); (3) compared with CON group, the concentrations of serum interleukin (IL)-10 and transforming growth factor (TGF-β) were significantly increased (p < 0.05), and the concentration of IL-12 was significantly decreased (p < 0.05) in the IAMPs group; (4) compared with CON group, the concentrations of serum endotoxin and D-lactate of piglets were significantly reduced (p < 0.05), and the relative expression of ZO-1 and occludin in the jejunum of piglets were significantly increased (p < 0.05) in the IAMPs group; (5) compared with the CON group, the villus height of the duodenum and jejunum of weaning piglets in IAMPs and AB groups was significantly increased (p < 0.05); and (6) compared with CON group, the relative abundance of Escherichia–Shigella in the colon and cecal digesta was decreased. In summary, the addition of 1,000 mg/kg immobilized antimicrobial peptides in the diet effectively relieved weaning stress by showing improved growth performance, antioxidant and immune capacity, intestinal morphology, and microorganisms.
Risk and Reward in Foraging Migrations of North Pacific Albacore Determined From Estimates of Energy Intake and Movement Costs
Authors: Muhling Barbara A. , Snyder Stephanie , Hazen Elliott L. , Whitlock Rebecca E. , Dewar Heidi , Park Jong-Yeon , Stock Charles A. , Block Barbara A.
Published: March 2022

North Pacific albacore (Thunnus alalunga) is a commercially important tuna species known to undertake extensive migratory movements between nearshore waters of the California Current and offshore environments in the central Pacific. However, these migration behaviors are highly variable, with some individuals traveling thousands of kilometers within a season, and others largely resident in the southern California Current throughout the year. In this study, we use data from 33 archival-tagged albacore (released between 2003 and 2011) to examine the movements, physiology and ecology of tuna following different migratory pathways. We used direct measurements of body temperature and ambient water temperature from internal archival tags to estimate energy intake via the Heat Increment of Feeding (HIF), the increased internal heat production associated with digestion of a meal. Our results indicate that HIF was variable in space and time, but it was highest for individuals foraging in the offshore North Pacific Transition Zone and southern California Current during spring and summer, and lowest in the Transition Zone in fall. None of the migratory strategies examined appeared to confer consistently higher energetic benefits than the others. Fish remaining resident in the southern California Current year-round incurred lower migration costs, and could access favorable foraging conditions off Baja California in spring and summer. In contrast, fish which undertook longer migrations had much higher energetic costs during periods of faster transit times, but were able to reach highly productive foraging areas in the central and western Pacific. HIF was generally higher in larger fish, and when ambient temperatures were cooler, but was not strongly correlated with other environmental covariates. Our analyses offer new avenues for studying the physiology of wild tuna populations, and can complement diet and isotopic studies to further understanding of fish ecology.
Comparative Food Web Analysis of Two Peruvian Bay Systems Along a Latitudinal Gradient: Resource Use and the Environmental Envelope
Authors: Del Solar Alonso , Romagnoni Giovanni , Kluger Lotta C. , Céspedes Carlos M. Salazar , Wolff Matthias
Published: March 2022

The coast of Peru lies within the tropics under the influence of the cold, nutrient-rich waters of the Humboldt Current and the interannual onslaught of the El Niño phenomenon. The Peruvian upwelling system is exceptionally productive and is comprised of subsystems at different scales along the coast. We aimed to understand the differences between two shallow coastal systems along a latitudinal gradient: Sechura Bay in the north (at the convergence of Humboldt and tropical waters) and Independencia Bay in the central-south (under typical upwelling conditions). We compared their biodiversity, trophic dynamics, community energetics, resource use and underlying abiotic conditions. Our analysis revealed that over the past two decades, Sechura has shown a warming trend, while Independencia has maintained its cold water conditions. Chlorophyll concentrations have risen significantly in both systems, higher values in Sechura suggesting there is an increase in local pressures that could lead to eutrophication. Trophic models of the La Niña 07/08 period revealed that both systems are bottom-up driven with high biomass and production at the lower trophic levels, though top-down controls were also shown, particularly in Sechura. While primary productivity was similar in both systems, differences were found in the structure and size of energy flows. More cycling and higher transfer efficiency were found in Independencia, where phytoplankton-based food chains played the main role in the overall dynamic. In contrast, the detritus food chain appears to be more relevant for energy flow in Sechura. Differences in biota and flow structure relate to the systems’ environmental conditions, i.e., more diverse warm-water species in the north and mostly cold water adapted species (mainly invertebrate filter-feeders and their predators) in the central-south. Catches in both systems were dominated by the diving fisheries and comprised mostly scallops (bottom-cultured), snails and fish in Sechura, and mussels, clams, crabs and fish in Independencia. Overall, system indicators suggest that Sechura is a comparatively less developed system. Independencia shall likely maintain its general highly productive system features, whereas Sechura will continue to be more frequently disturbed by El Niño and ongoing human-driven activities, reducing its overall stability and functionality. In the context of climate change, acknowledging these differences is essential for future adaptive management regimes.
Temperature Affects Antagonism Among Coral-Associated Bacteria
Authors: Guo Anjie , Li Jie , Wang Lin , Ju Huimin , Li Qiqi , Ren Lijuan , Zhang Si
Published: March 2022

Reef-building corals are invertebrate animals that associate with diverse microorganisms, including Symbiodiniaceae, bacteria, fungi, and archaea. This symbiotic consortium, called the holobiont, is a dynamic system and rapidly responds to environmental temperatures. At present, the effects of temperature on bacteria-bacteria interactions in the coral-associated bacterial community are not clear. Antagonism is considered one of the potential structuring forces in coral microbial communities. Here, we examined the antagonistic interactions among 32 coral-associated bacteria and the physiological and biochemical characteristics of these isolates at different temperatures. The results showed that the antagonism breadth (i.e. the total number of antagonistic interactions) increased but antagonism intensity (i.e. the size of the inhibition zone) decreased at 32°C. The antagonistic interaction network was nested and sender-determined both at 25°C and 32°C, suggesting that the competition networks of coral-associated bacteria were more influenced by the antagonist strains than sensitive strains. Furthermore, we found that the elevated temperature increased the complexity of the antagonistic network. By evaluating the correlations between antagonism and the phylogenetic and phenotypic distances, we demonstrated that the antagonism probability correlated with the phylogenetic distance rather than phenotypic distance. Moreover, the antagonist strains have a wider metabolic niche space, i.e., grew on more carbon sources, than the antagonized strains at 25°C, while there was no difference at 32°C, suggesting the trade-off between antagonism and resource exploitation shifted in the antagonistic interactions under the higher temperature. These findings will be helpful for understanding the bacterial interactions in coral holobionts and the assembly of bacterial community in altered environments, especially under heat stress.
Suspension-Feeding Benthic Species’ Physiological and Microbiome Response to Salmon Farming and Associated Environmental Changes
Authors: Laroche Olivier , Meier Sonnich , Mjøs Svein A. , Keeley Nigel
Published: March 2022

Caged salmon farming is increasingly undertaken in water bodies with strong hydrodynamics where hard and mixed substrate habitats are more prevalent. Yet, these structurally complex and heterogeneous habitats support diverse benthic communities including several cnidarians and sponges that remain poorly characterized. This study used a combination of respirometry measurements, gas chromatography and 16S rRNA metabarcoding to define the respiration rate, stable carbon (δ13C) and nitrogen isotopes (δ15N), fatty acid (FA) and microbial profiles, and assess the impact of salmon farming on four important epibenthic suspension-feeders along the western Norwegian coast: the sponges Craniella and Weberella, the soft coral Duva florida and the anemone Hormathia digitata. Our results showed striking differences in fatty acid profiles and host microbiome communities in terms of identity, functional capabilities and genetic properties across the suspension-feeders. We found evidence of increased mortality rate in specimens located near fish farm activities and of a species-specific effect on respiration rate, with D. florida showing increased activity under the farm. Effects of fish farming on the suspension feeders were also species-specific and particularly evidenced by functional microbial turnover and by alteration of overall FA profiles in the soft coral and sea anemone. In particular, D. florida showed reduced level of FAs close to the farm (0-350 m), with significant difference in composition along a distance gradient. Only H. digitata showed evidence of incorporation of organic material from the fish farm waste via fatty acids trophic markers (FATM) and stable isotope analysis. Overall, our study demonstrates that suspension feeders have taxon-specific sensitivity towards the effect of salmon farming, and identified several potential molecular indicators that could be used as surrogate of impact gradient upon further research and validation. It also provides a wealth of ecological and physiological information on some of the most common sessile epibenthic organisms within Arctic and sub-Arctic regions, enabling us to better understand their response and evaluate their resilience to environmental changes.
Two Flavors of Intraseasonal Variability and Their Dynamics in the North Equatorial Current/Undercurrent Region
Authors: Wang Zhenxiao , Zhang Linlin , Hui Yuchao , Wang Fan , Hu Dunxin
Published: March 2022

Significant surface-intensified and subsurface-intensified intraseasonal variability (ISV) of the North Equatorial Current/Undercurrent with different periods are detected to coexist with mooring ADCP measurements at 13°N, 130°E. The ISV of the currents in the upper 200 m has a relatively shorter period of 45 days, while the period of the subsurface-intensified ISV between 400 and 800 m is around 85 days. By combining with sea surface height measurements from satellite altimeters and outputs from an eddy-resolving ocean general circulation model, the origin and dynamic mechanism of the two flavors of ISV are investigated. Eddy trajectory tracking and energy analysis indicate that both the surface-intensified and subsurface-intensified ISV are related to locally generated meso-scale eddies near the mooring sites. Stability analysis suggests the surface-intensified ISV is related to the baroclinic instability induced by the vertical velocity shear of the North Equatorial Current. While the generation of the subsurface-intensified ISV is more complex and is partly related to the enhanced barotropic instability induced by the intensified horizontal shear of the subsurface zonal background flow.