Marine Life Science & Technology最新文献

{"title":"Deciphering microeukaryotic-bacterial co-occurrence networks in coastal aquaculture ponds.","authors":"Xiafei Zheng, Kui Xu, Jonathan Naoum, Yingli Lian, Bo Wu, Zhili He, Qingyun Yan","doi":"10.1007/s42995-022-00159-6","DOIUrl":"10.1007/s42995-022-00159-6","url":null,"abstract":"<p><p>Microeukaryotes and bacteria are key drivers of primary productivity and nutrient cycling in aquaculture ecosystems. Although their diversity and composition have been widely investigated in aquaculture systems, the co-occurrence bipartite network between microeukaryotes and bacteria remains poorly understood. This study used the bipartite network analysis of high-throughput sequencing datasets to detect the co-occurrence relationships between microeukaryotes and bacteria in water and sediment from coastal aquaculture ponds. Chlorophyta and fungi were dominant phyla in the microeukaryotic-bacterial bipartite networks in water and sediment, respectively. Chlorophyta also had overrepresented links with bacteria in water. Most microeukaryotes and bacteria were classified as generalists, and tended to have symmetric positive and negative links with bacteria in both water and sediment. However, some microeukaryotes with high density of links showed asymmetric links with bacteria in water. Modularity detection in the bipartite network indicated that four microeukaryotes and twelve uncultured bacteria might be potential keystone taxa among the module connections. Moreover, the microeukaryotic-bacterial bipartite network in sediment harbored significantly more nestedness than that in water. The loss of microeukaryotes and generalists will more likely lead to the collapse of positive co-occurrence relationships between microeukaryotes and bacteria in both water and sediment. This study unveils the topology, dominant taxa, keystone species, and robustness in the microeukaryotic-bacterial bipartite networks in coastal aquaculture ecosystems. These species herein can be applied for further management of ecological services, and such knowledge may also be very useful for the regulation of other eutrophic ecosystems.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s42995-022-00159-6.</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"5 1","pages":"44-55"},"PeriodicalIF":5.8,"publicationDate":"2023-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10077187/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9440242","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Early life history affects fish size mainly by indirectly regulating the growth during each stage: a case study in a demersal fish.","authors":"Rui Wu, Qinghuan Zhu, Satoshi Katayama, Yongjun Tian, Jianchao Li, Kunihiro Fujiwara, Yoji Narimatsu","doi":"10.1007/s42995-022-00145-y","DOIUrl":"10.1007/s42995-022-00145-y","url":null,"abstract":"<p><p>The complex life histories of demersal fishes are artificially separated into multiple stages along with changes in morphology and habitat. It is worth exploring whether the phenotypes expressed earlier and later during the life cycle are related or decoupled. The life stages of first year Pacific cod (<i>Gadus macrocephalus</i>) were tracked over different hatch years and regions to test whether the early life history had a long-lasting effect on subsequent growth. We further explored the contribution of growth in the early and subsequent life history stages to body size at the end of each stage. In addition to the accessory growth centre and the first annual ring, the other two checks on the otolith possibly related to settlement and entering deeper waters were identified in 75 Pacific cod individuals. The direct and indirect relationships among the life history stages was interpreted based on path analysis. The results showed that growth prior to the formation of the accessory growth centre had a significant effect on the absolute growth of the fish before and after settlement and migration to deep water. However, there was no or moderate evidence that early growth affected the body size at each stage, which was mainly regulated by growth during the stage. This study supports the lasting effect of early growth and clarifies that it affects size mainly by indirectly regulating staged growth. Quantifying the phenotype relationships and identifying the internal mechanisms form the basis for assessing population dynamics and understanding the processes behind the changes.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s42995-022-00145-y.</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"5 1","pages":"75-84"},"PeriodicalIF":5.7,"publicationDate":"2023-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10077272/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9752857","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of marine natural product Pretrichodermamide B as a STAT3 inhibitor for efficient anticancer therapy.","authors":"Rui Li, Yue Zhou, Xinxin Zhang, Lujia Yang, Jieyu Liu, Samantha M Wightman, Ling Lv, Zhiqing Liu, Chang-Yun Wang, Chenyang Zhao","doi":"10.1007/s42995-022-00162-x","DOIUrl":"10.1007/s42995-022-00162-x","url":null,"abstract":"<p><p>The Janus kinase (JAK)/signal transducer and activator of transcription 3 (STAT3) regulates the expression of various critical mediators of cancer and is considered as one of the central communication nodes in cell growth and survival. Marine natural products (MNP) represent great resources for discovery of bioactive lead compounds, especially anti-cancer agents. Through the medium-throughput screening of our in-house MNP library, Pretrichodermamide B, an epidithiodiketopiperazine, was identified as a JAK/STAT3 signaling inhibitor. Further studies identified that Pretrichodermamide B directly binds to STAT3, preventing phosphorylation and thus inhibiting JAK/STAT3 signaling. Moreover, it suppressed cancer cell growth, in vitro, at low micromolar concentrations and demonstrated efficacy in vivo by decreasing tumor growth in a xenograft mouse model. In addition, it was shown that Pretrichodermamide B was able to induce cell cycle arrest and promote cell apoptosis. This study demonstrated that Pretrichodermamide B is a novel STAT3 inhibitor, which should be considered for further exploration as a promising anti-cancer therapy.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s42995-022-00162-x.</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"5 1","pages":"94-101"},"PeriodicalIF":5.8,"publicationDate":"2023-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10077262/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9384075","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Improving the genome and proteome annotations of the marine model diatom <i>Thalassiosira pseudonana</i> using a proteogenomics strategy.","authors":"Xiao-Huang Chen,&nbsp;Ming-Kun Yang,&nbsp;Yuan-Yuan Li,&nbsp;Zhang-Xian Xie,&nbsp;Shu-Feng Zhang,&nbsp;Mats Töpel,&nbsp;Shady A Amin,&nbsp;Lin Lin,&nbsp;Feng Ge,&nbsp;Da-Zhi Wang","doi":"10.1007/s42995-022-00161-y","DOIUrl":"https://doi.org/10.1007/s42995-022-00161-y","url":null,"abstract":"<p><p>Diatoms are unicellular eukaryotic phytoplankton that account for approximately 20% of global carbon fixation and 40% of marine primary productivity; thus, they are essential for global carbon biogeochemical cycling and climate. The availability of ten diatom genome sequences has facilitated evolutionary, biological and ecological research over the past decade; however, a complimentary map of the diatom proteome with direct measurements of proteins and peptides is still lacking. Here, we present a proteome map of the model marine diatom <i>Thalassiosira pseudonana</i> using high-resolution mass spectrometry combined with a proteogenomic strategy. In-depth proteomic profiling of three different growth phases and three nutrient-deficient samples identified 9526 proteins, accounting for ~ 81% of the predicted protein-coding genes. Proteogenomic analysis identified 1235 novel genes, 975 revised genes, 104 splice variants and 234 single amino acid variants. Furthermore, our quantitative proteomic analysis experimentally demonstrated that a considerable number of novel genes were differentially translated under different nutrient conditions. These findings substantially improve the genome annotation of <i>T. pseudonana</i> and provide insights into new biological functions of diatoms. This relatively comprehensive diatom proteome catalog will complement available diatom genome and transcriptome data to advance biological and ecological research of marine diatoms.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s42995-022-00161-y.</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"5 1","pages":"102-115"},"PeriodicalIF":5.7,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10077189/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9384070","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High cholesterol intake remodels cholesterol turnover and energy homeostasis in Nile tilapia (<i>Oreochromis niloticus</i>).","authors":"Rui-Xin Li,&nbsp;Ling-Yun Chen,&nbsp;Samwel M Limbu,&nbsp;Yu-Cheng Qian,&nbsp;Wen-Hao Zhou,&nbsp;Li-Qiao Chen,&nbsp;Yuan Luo,&nbsp;Fang Qiao,&nbsp;Mei-Ling Zhang,&nbsp;Zhen-Yu Du","doi":"10.1007/s42995-022-00158-7","DOIUrl":"https://doi.org/10.1007/s42995-022-00158-7","url":null,"abstract":"<p><p>The roles of dietary cholesterol in fish physiology are currently contradictory. The issue reflects the limited studies on the metabolic consequences of cholesterol intake in fish. The present study investigated the metabolic responses to high cholesterol intake in Nile tilapia (<i>Oreochromis niloticus</i>), which were fed with four cholesterol-contained diets (0.8, 1.6, 2.4 and 3.2%) and a control diet for eight weeks. All fish-fed cholesterol diets showed increased body weight, but accumulated cholesterol (the peak level was in the 1.6% cholesterol group). Then, we selected 1.6% cholesterol and control diets for further analysis. The high cholesterol diet impaired liver function and reduced mitochondria number in fish. Furthermore, high cholesterol intake triggered protective adaptation via (1) inhibiting endogenous cholesterol synthesis, (2) elevating the expression of genes related to cholesterol esterification and efflux, and (3) promoting chenodeoxycholic acid synthesis and efflux. Accordingly, high cholesterol intake reshaped the fish gut microbiome by increasing the abundance of <i>Lactobacillus</i> spp. and <i>Mycobacterium</i> spp., both of which are involved in cholesterol and/or bile acids catabolism. Moreover, high cholesterol intake inhibited lipid catabolic activities through mitochondrial β-oxidation, and lysosome-mediated lipophagy, and depressed insulin signaling sensitivity. Protein catabolism was elevated as a compulsory response to maintain energy homeostasis. Therefore, although high cholesterol intake promoted growth, it led to metabolic disorders in fish. For the first time, this study provides evidence for the systemic metabolic response to high cholesterol intake in fish. This knowledge contributes to an understanding of the metabolic syndromes caused by high cholesterol intake or deposition in fish.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s42995-022-00158-7.</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"5 1","pages":"56-74"},"PeriodicalIF":5.7,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10077235/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9384073","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Light history modulates growth and photosynthetic responses of a diatom to ocean acidification and UV radiation.","authors":"Wei Li,&nbsp;Tifeng Wang,&nbsp;Douglas A Campbell,&nbsp;Kunshan Gao","doi":"10.1007/s42995-022-00138-x","DOIUrl":"https://doi.org/10.1007/s42995-022-00138-x","url":null,"abstract":"<p><p>To examine the synergetic effects of ocean acidification (OA) and light intensity on the photosynthetic performance of marine diatoms, the marine centric diatom <i>Thalassiosira weissflogii</i> was cultured under ambient low CO₂ (LC, 390 μatm) and elevated high CO₂ (HC, 1000 μatm) levels under low-light (LL, 60 μmol m^-2 s^-1) or high-light (HL, 220 μmol m^-2 s^-1) conditions for over 20 generations. HL stimulated the growth rate by 128 and 99% but decreased cell size by 9 and 7% under LC and HC conditions, respectively. However, HC did not change the growth rate under LL but decreased it by 9% under HL. LL combined with HC decreased both maximum quantum yield (<i>F</i> _V/<i>F</i> _M) and effective quantum yield (<i>Φ</i> _PSII), measured under either low or high actinic light. When exposed to UV radiation (UVR), LL-grown cells were more prone to UVA exposure, with higher UVA and UVR inducing inhibition of <i>Φ</i> _PSII compared with HL-grown cells. Light use efficiency (<i>α</i>) and maximum relative electron transport rate (rETR_max) were inhibited more in the HC-grown cells when UVR (UVA and UVB) was present, particularly under LL. Our results indicate that the growth light history influences the cell growth and photosynthetic responses to OA and UVR.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s42995-022-00138-x.</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"5 1","pages":"116-125"},"PeriodicalIF":5.7,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10077217/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9384068","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Trait-based approach revealed the seasonal variation of mesozooplankton functional groups in the South Yellow Sea.","authors":"Zhishuang Zhang,&nbsp;Hongju Chen,&nbsp;Yixuan Li,&nbsp;Ruping Ge,&nbsp;Guangxing Liu,&nbsp;Shaukat Ali,&nbsp;Yunyun Zhuang","doi":"10.1007/s42995-022-00156-9","DOIUrl":"https://doi.org/10.1007/s42995-022-00156-9","url":null,"abstract":"<p><p>Functional traits determine the fitness of organisms and mirror their ecological functions. Although trait-based approaches provide ecological insights, it is underexploited for marine zooplankton, particularly with respect to seasonal variation. Here, based on four major functional traits, including body length, feeding type, trophic group, and reproduction mode, we quantified the seasonal variations of mesozooplankton functional groups in the South Yellow Sea (SYS) in the spring, summer, and autumn of 2018. Strong seasonal dynamics were identified for all traits but patterns varied among traits. Small zooplankton (47.7-88.6%), omnivores-herbivores (81.3-97.6%), and free spawners (54.8-92.5%) dominated in three seasons, while ambush feeders and current feeders dominated in spring (45.7%), and autumn (73.4%), respectively. Cluster analysis of the functional traits showed that the mesozooplankton in the SYS can be classified into eight functional groups. The biogeographic and seasonal variations of functional groups can be partially explained by environmental drivers. Group 1, represented by omnivores-herbivores, was the most dominant functional group, the abundance of which peaked in spring and was positively correlated with chlorophyll <i>a</i> concentration, indicating its close association with phytoplankton dynamics. The contribution of giant, active ambush carnivores, passive ambush carnivore jellyfish, current omnivores-detritivores, and parthenogenetic cladocerans increased with sea surface temperature. The proportion of giant, active ambush carnivores and active ambush omnivore-carnivore copepods decreased with salinity in autumn. This study presents a new perspective for understanding the dynamics of zooplankton and paves the way for further research on the functional diversity of zooplankton in the SYS.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s42995-022-00156-9.</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"5 1","pages":"126-140"},"PeriodicalIF":5.7,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10077163/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9384071","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic diversity and ecological distribution of marine <i>Pseudoalteromonas</i> phages.","authors":"Kaiyang Zheng,&nbsp;Yue Dong,&nbsp;Yantao Liang,&nbsp;Yundan Liu,&nbsp;Xinran Zhang,&nbsp;Wenjing Zhang,&nbsp;Ziyue Wang,&nbsp;Hongbing Shao,&nbsp;Yeong Yik Sung,&nbsp;Wen Jye Mok,&nbsp;Li Lian Wong,&nbsp;Andrew McMinn,&nbsp;Min Wang","doi":"10.1007/s42995-022-00160-z","DOIUrl":"10.1007/s42995-022-00160-z","url":null,"abstract":"<p><p><i>Pseudoalteromonas</i>, with a ubiquitous distribution, is one of the most abundant marine bacterial genera. It is especially abundant in the deep sea and polar seas, where it has been found to have a broad metabolic capacity and unique co-existence strategies with other organisms. However, only a few <i>Pseudoalteromonas</i> phages have so far been isolated and investigated and their genomic diversity and distribution patterns are still unclear. Here, the genomes, taxonomic features and distribution patterns of <i>Pseudoalteromonas</i> phages are systematically analyzed, based on the microbial and viral genomes and metagenome datasets. A total of 143 complete or nearly complete <i>Pseudoalteromonas</i>-associated phage genomes (PSAPGs) were identified, including 34 <i>Pseudoalteromonas</i> phage isolates, 24 proviruses, and 85 <i>Pseudoalteromonas</i>-associated uncultured viral genomes (UViGs); these were assigned to 47 viral clusters at the genus level. Many integrated proviruses (<i>n</i> = 24) and filamentous phages were detected (<i>n</i> = 32), suggesting the prevalence of viral lysogenic life cycle in <i>Pseudoalteromonas</i>. PSAPGs encoded 66 types of 249 potential auxiliary metabolic genes (AMGs) relating to peptidases and nucleotide metabolism. They may also participate in marine biogeochemical cycles through the manipulation of the metabolism of their hosts, especially in the phosphorus and sulfur cycles. Siphoviral and filamentous PSAPGs were the predominant viral lineages found in polar areas, while some myoviral and siphoviral PSAPGs encoding transposase were more abundant in the deep sea. This study has expanded our understanding of the taxonomy, phylogenetic and ecological scope of marine <i>Pseudoalteromonas</i> phages and deepens our knowledge of viral impacts on <i>Pseudoalteromonas</i>. It will provide a baseline for the study of interactions between phages and <i>Pseudoalteromonas</i> in the ocean.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s42995-022-00160-z.</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"5 2","pages":"271-285"},"PeriodicalIF":5.7,"publicationDate":"2023-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10232697/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9584952","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Targeted isolation of antitubercular cycloheptapeptides and an unusual pyrroloindoline-containing new analog, asperpyrroindotide A, using LC-MS/MS-based molecular networking.","authors":"Yi-Qian Han, Qun Zhang, Wei-Feng Xu, Yang Hai, Rong Chao, Cui-Fang Wang, Xue-Mei Hou, Mei-Yan Wei, Yu-Cheng Gu, Chang-Yun Wang, Chang-Lun Shao","doi":"10.1007/s42995-022-00157-8","DOIUrl":"10.1007/s42995-022-00157-8","url":null,"abstract":"<p><p>Further insights on the secondary metabolites of a soft coral-derived fungus <i>Aspergillus versicolor</i> under the guidance of MS/MS-based molecular networking led to the isolation of seven known cycloheptapeptides, namely, asperversiamides A-C (<b>1</b>-<b>3</b>) and asperheptatides A-D (<b>4</b>-<b>7</b>) and an unusual pyrroloindoline-containing new cycloheptapeptide, asperpyrroindotide A (<b>8</b>). The structure of <b>8</b> was elucidated by comprehensive spectroscopic data analysis, and its absolute configuration was determined by advanced Marfey's method. The semisynthetic transformation of <b>1</b> into <b>8</b> was successfully achieved and the reaction conditions were optimized. Additionally, a series of new derivatives (<b>10</b>-<b>19</b>) of asperversiamide A (<b>1</b>) was semi-synthesized and their anti-tubercular activities were evaluated against <i>Mycobacterium tuberculosis</i> H37Ra. The preliminary structure-activity relationships revealed that the serine hydroxy groups and the tryptophan residue are important to the activity.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s42995-022-00157-8.</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"5 1","pages":"85-93"},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9854410/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9082139","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An expectation-maximization algorithm for estimating proportions of deletions among bacterial populations with application to study antibiotic resistance gene transfer in <i>Enterococcus faecalis</i>.","authors":"Yu Zhang, Cong Zhang, Wenwen Huo, Xinlei Wang, Michael Zhang, Kelli Palmer, Min Chen","doi":"10.1007/s42995-022-00144-z","DOIUrl":"10.1007/s42995-022-00144-z","url":null,"abstract":"<p><p>The emergence of antibiotic resistance in bacteria limits the availability of antibiotic choices for treatment and infection control, thereby representing a major threat to human health. The de novo mutation of bacterial genomes is an essential mechanism by which bacteria acquire antibiotic resistance. Previously, deletion mutations within bacterial immune systems, ranging from dozens to thousands of base pairs (bps) in length, have been associated with the spread of antibiotic resistance. Most current methods for evaluating genomic structural variations (SVs) have concentrated on detecting them, rather than estimating the proportions of populations that carry distinct SVs. A better understanding of the distribution of mutations and subpopulations dynamics in bacterial populations is needed to appreciate antibiotic resistance evolution and movement of resistance genes through populations. Here, we propose a statistical model to estimate the proportions of genomic deletions in a mixed population based on Expectation-Maximization (EM) algorithms and next-generation sequencing (NGS) data. The method integrates both insert size and split-read mapping information to iteratively update estimated distributions. The proposed method was evaluated with three simulations that demonstrated the production of accurate estimations. The proposed method was then applied to investigate the horizontal transfers of antibiotic resistance genes in concert with changes in the CRISPR-Cas system of <i>E. faecalis</i>.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s42995-022-00144-z.</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"5 1","pages":"28-43"},"PeriodicalIF":5.7,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9888353/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9392243","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}