keyword
https://read.qxmd.com/read/38542267/whole-genome-survey-analyses-of-five-goby-species-provide-insights-into-their-genetic-evolution-and-invasion-related-genes
#21
JOURNAL ARTICLE
Siyu Ma, Xiang Zhao, Na Song
As one of the most abundant groups in marine fish families, Gobiidae fish are important fishery resources in China, and some are also invasive species in certain regions worldwide. However, the phylogenetic relationships of Gobiidae fish remain ambiguous, and the study of their invasion-related genes is still scarce. This study used high-throughput sequencing technology to conduct a whole-genome survey of five Gobiidae fish species: Acanthogobius flavimanus , Acanthogobius stigmothonus , Favonigobius gymnauchen , Ctenotrypauchen microcephalus , and Tridentiger barbatus ...
March 14, 2024: International Journal of Molecular Sciences
https://read.qxmd.com/read/38541150/transcriptomic-profiling-of-pleural-effusions-differences-in-malignant-and-infectious-fluids
#22
JOURNAL ARTICLE
Lucía Zamora-Molina, Eduardo García-Pachón, Marta Amorós, Julia Gijón-Martínez, Judith Sánchez-Almendro, Carlos Baeza-Martínez, Luis Hernández-Blasco, Antonio Galiana
Background and Objectives : Different cellular and molecular processes are involved in the production of malignant and infectious pleural effusions. However, the underlying mechanisms responsible for these differences or their consequences remain incompletely understood. The objective of this study was to identify differences in gene expression in pleural exudates of malignant and infectious aetiology and establish the possible different biological processes involved in both situations. Materials and Methods : RNA transcriptomic analysis was performed on 46 pleural fluid samples obtained during diagnostic thoracocenteses from 46 patients...
March 1, 2024: Medicina
https://read.qxmd.com/read/38540904/differential-characteristics-of-the-metabolic-profiles-and-microbial-community-between-superior-and-normal-grades-of-nongxiangxing-daqu
#23
JOURNAL ARTICLE
Xiaoge Hou, Ming Hui, Xiaoman Gu, Xin Shi, Chenming Fan, Junfei Wang, Xuesi Li, Chunmei Pan, Ruifang Li
Nongxiangxing-daqu (NXDQ), as a saccharification and fermentation agent, directly affects the flavor and yield of fresh Nongxiangxing Baijiu (NXBJ). The difference in fermentation temperature owing to the artificial turning operation leads to the formation of superior (S) and normal (N) grades of NXDQ. Here, aiming to explore the discriminant characteristics of two grades of NXDQ, we studied the physicochemical properties, volatile compounds and microbial communities using HS-SPME-GC/MS and high-throughput sequencing technology...
March 17, 2024: Foods (Basel, Switzerland)
https://read.qxmd.com/read/38540035/comparative-analysis-of-how-the-fecal-microbiota-of-green-winged-saltator-saltator-similis-diverge-among-animals-living-in-captivity-and-in-wild-habitats
#24
JOURNAL ARTICLE
Larissa Caló Zitelli, Gabriela Merker Breyer, Mariana Costa Torres, Luiza de Campos Menetrier, Ana Paula Muterle Varela, Fabiana Quoos Mayer, Cláudio Estêvão Farias Cruz, Franciele Maboni Siqueira
The microbiota's alteration is an adaptive mechanism observed in wild animals facing high selection pressure, especially in captive environments. The objective of this study is to compare and predict the potential impact of habitat on the fecal bacterial community of Saltator similis , a songbird species that is a victim of illegal trafficking, living in two distinct habitats: wild and captivity. Nine wild and nine captive S. similis were sampled, and total bacterial DNA was obtained from the feces. Each DNA sample was employed to the amplification of the V4 region of the 16S rDNA following high -throughput sequencing...
March 19, 2024: Animals: An Open Access Journal From MDPI
https://read.qxmd.com/read/38539064/classifying-breast-cancer-subtypes-on-multi-omics-data-via-sparse-canonical-correlation-analysis-and-deep-learning
#25
JOURNAL ARTICLE
Yiran Huang, Pingfan Zeng, Cheng Zhong
BACKGROUND: Classifying breast cancer subtypes is crucial for clinical diagnosis and treatment. However, the early symptoms of breast cancer may not be apparent. Rapid advances in high-throughput sequencing technology have led to generating large number of multi-omics biological data. Leveraging and integrating the available multi-omics data can effectively enhance the accuracy of identifying breast cancer subtypes. However, few efforts focus on identifying the associations of different omics data to predict the breast cancer subtypes...
March 27, 2024: BMC Bioinformatics
https://read.qxmd.com/read/38537835/driving-mechanism-of-different-nutrient-conditions-on-microbial-mediated-nitrate-reduction-in-magnetite-present-river-infiltration-zone
#26
JOURNAL ARTICLE
Jia Niu, Yuyu Wan, Zhe Ma, Zhen Wang, Weihong Dong, Xiaosi Su, Xiaofang Shen, Yuanzheng Zhai
Significant research is focused on the ability of riparian zones to reduce groundwater nitrate contamination. Owing to the extremely high redox activity of nitrate, naturally existing electron donors, such as organic matter and iron minerals, are crucial in facilitating nitrate reduction in the riparian zone. Here, we examined the coexistence of magnetite, an iron mineral, and nitrate, a frequently observed coexisting system in sediments, to investigate nitrate reduction features at various C/N ratios and evaluate the response of microbial communities to these settings...
March 25, 2024: Science of the Total Environment
https://read.qxmd.com/read/38537823/identification-of-keystone-taxa-in-rhizosphere-microbial-communities-using-different-methods-and-their-effects-on-compounds-of-the-host-cinnamomum-migao
#27
JOURNAL ARTICLE
Qing-Wen Sun, Jing-Zhong Chen, Xiao-Feng Liao, Xiao-Long Huang, Ji-Ming Liu
Exploring keystone taxa affecting microbial community stability and host function is crucial for understanding ecosystem functions. However, identifying keystone taxa from humongous microbial communities remains challenging. We collected 344 rhizosphere and bulk soil samples from the endangered plant C. migao for 2 years consecutively. Used high-throughput sequencing 16S rDNA and ITS to obtain the composition of bacterial and fungal communities. We explored keystone taxa and the applicability and limitations of five methods (SPEC-OCCU, Zi-Pi, Subnetwork, Betweenness, and Module), as well as the impact of microbial community domain, time series, and rhizosphere boundary on the identification of keystone taxa in the communities...
March 25, 2024: Science of the Total Environment
https://read.qxmd.com/read/38537479/comparison-of-treatment-performance-and-microbial-community-evolution-of-typical-dye-wastewater-by-different-combined-processes
#28
JOURNAL ARTICLE
Zhihao Chen, Minquan Feng, Yibo Wang, Xiaohui Ling
The degradation of typical dye wastewater is a focus of research in the printing and dyeing industry. In this study, a combined micro-electrolysis and microbial treatment method was established to treat refractory dye wastewater, and the pivotal factors in the microbial treatment were optimized. In the series and coupled modes, the removal rates of chroma reached 98.75% and 92.50%, and the removal rates of chemical oxygen demand (COD) reached 96.17% and 82.29%, respectively. The high-throughput sequencing results showed that the microbial communities in the microbial system varied at different treatment stages...
March 26, 2024: Ecotoxicology and Environmental Safety
https://read.qxmd.com/read/38536604/oral-microbiota-and-porphyromonas-gingivalis-kgp-genotypes-altered-in-parkinson-s-disease-with-mild-cognitive-impairment
#29
JOURNAL ARTICLE
Dongcheng Li, Tengzhu Ren, Hao Li, Mingdi Huang, Jiaxin Chen, Qishan He, Wei Lv, Hailing Liu, Renshi Xu, Xiong Zhang
Cognitive impairment (CI) is a common complication of the non-motor symptoms in Parkinson's disease (PD), including PD with mild cognitive impairment (PD-MCI) and PD dementia. Recent studies reported the oral dysbiosis in PD and CI, respectively. Porphyromonas gingivalis (P. gingivalis), a pathogen of oral dysbiosis, plays an important role in PD, whose lysine-gingipain (Kgp) could lead to AD-type pathologies. No previous study investigated the composition of oral microbiota and role of P. gingivalis in PD-MCI...
March 27, 2024: Molecular Neurobiology
https://read.qxmd.com/read/38535376/effects-of-diet-on-the-gut-bacterial-community-of-aldrichina-grahami-diptera-calliphoridae-across-developmental-stages
#30
JOURNAL ARTICLE
Zhen Li, Chao Yue, Na Ma, Guanjie Yan
The blowfly, Aldrichina grahami (Diptera: Calliphoridae), is a well-known forensically important insect. Basic data related to A. grahami have been well documented; but despite the pivotal role of gut microbes in various facets of insect biology, little is known about its gut microbiome. To investigate the gut bacterial community of A. grahami and explore its stability, diet and developmental stage were selected as the two variables. Larvae were reared on bovine liver, swine manure, and chicken manure, and high-throughput sequencing of the 1st, 2nd, and 3rd instar larvae and the newly emerged adults was performed...
March 7, 2024: Insects
https://read.qxmd.com/read/38535220/diversity-community-structure-and-antagonism-of-endophytic-fungi-from-asymptomatic-and-symptomatic-mongolian-pine-trees
#31
JOURNAL ARTICLE
Ninghong Ren, Lei Wang, Chongjuan You
Diplodia tip blight, caused by Diplodia sapinea (= Sphaeropsis sapinea ), are widely distributed in Honghuaerji, Inner Mongolia, China, causing severe damage on natural Mongolian pine ( Pinus sylvestris var. mongolica ). D. sapinea is an endophyte that becomes pathogenic under conditions of drought, hail damage, or temperature-associated stress. The role of the endophytic community inhabiting different pine tissues in the expression of disease is still unknown. In this study, the diversity and community structure of endophytic fungi among asymptomatic and symptomatic Mongolian pine were detected using culture-based isolation and high-throughput sequencing (HTS), and the potential antagonistic endophytes against D...
March 13, 2024: Journal of Fungi (Basel, Switzerland)
https://read.qxmd.com/read/38535204/community-structure-and-diversity-of-endophytic-fungi-in-cultivated-polygala-crotalarioides-at-two-different-growth-stages-based-on-culture-independent-and-culture-based-methods
#32
JOURNAL ARTICLE
Kaize Shen, Yu Xiong, Yanfang Liu, Xingwang Fan, Rui Zhu, Zumao Hu, Congying Li, Yan Hua
Polygala crotalarioides , a perennial herbaceous plant found in southwest China, has the potential to be used in the treatment of Alzheimer's disease. Endophytic fungi that reside within medicinal herbs play an important ecological role in their host plants and can serve as a valuable source for identifying active components. However, little is known about the diversity, and structure of endophytic fungi in P. crotalarioides . In this study, we investigated the community structure and diversity of endophytic fungi in the leaves, stems, and roots of P...
March 4, 2024: Journal of Fungi (Basel, Switzerland)
https://read.qxmd.com/read/38533455/toward-understanding-and-utilizing-crop-heterosis-in-the-age-of-biotechnology
#33
REVIEW
Wenwen Liu, Guangming He, Xing Wang Deng
Heterosis, a universal phenomenon in nature, mainly reflected in the superior productivity, quality, and fitness of F1 hybrids compared with their inbred parents, has been exploited in agriculture and greatly benefited human society in terms of food security. However, the flexible and efficient utilization of heterosis has remained a challenge in hybrid breeding systems because of the limitations of "three-line" and "two-line" methods. In the past two decades, rapidly developed biotechnologies have provided unprecedented conveniences for both understanding and utilizing heterosis...
February 16, 2024: IScience
https://read.qxmd.com/read/38533399/phyllosphere-bacterial-community-dynamics-in-response-to-bacterial-wildfire-disease-succession-and-interaction-patterns
#34
JOURNAL ARTICLE
Deyuan Peng, Zhenhua Wang, Jinyan Tian, Wei Wang, Shijie Guo, Xi Dai, Huaqun Yin, Liangzhi Li
Plants interact with complex microbial communities in which microorganisms play different roles in plant development and health. While certain microorganisms may cause disease, others promote nutrient uptake and resistance to stresses through a variety of mechanisms. Developing plant protection measures requires a deeper comprehension of the factors that influence multitrophic interactions and the organization of phyllospheric communities. High-throughput sequencing was used in this work to investigate the effects of climate variables and bacterial wildfire disease on the bacterial community's composition and assembly in the phyllosphere of tobacco ( Nicotiana tabacum L...
2024: Frontiers in Plant Science
https://read.qxmd.com/read/38532500/divergent-composition-and-transposon-silencing-activity-of-small-rnas-in-mammalian-oocytes
#35
JOURNAL ARTICLE
Li Hou, Wei Liu, Hongdao Zhang, Ronghong Li, Miao Liu, Huijuan Shi, Ligang Wu
BACKGROUND: Small RNAs are essential for germ cell development and fertilization. However, fundamental questions remain, such as the level of conservation in small RNA composition between species and whether small RNAs control transposable elements in mammalian oocytes. RESULTS: Here, we use high-throughput sequencing to profile small RNAs and poly(A)-bearing long RNAs in oocytes of 12 representative vertebrate species (including 11 mammals). The results show that miRNAs are generally expressed in the oocytes of each representative species (although at low levels), whereas endo-siRNAs are specific to mice...
March 26, 2024: Genome Biology
https://read.qxmd.com/read/38531647/chemical-manipulation-of-m-1-a-mediates-its-detection-in-human-trna
#36
JOURNAL ARTICLE
Kinga Pajdzik, Ruitu Lyu, Xiaoyang Dou, Chang Ye, Li-Sheng Zhang, Qing Dai, Chuan He
N 1 -methyl adenosine (m1 A) is a wide-spread RNA modification present in tRNA, rRNA and mRNA. m1 A modification sites in tRNAs are evolutionary conserved and its formation on tRNA is catalyzed by methyltransferase TRMT61A and TRMT6 complex. m1 A promotes translation initiation and elongation. Due to its positive charge under physiological conditions, m1 A can notably modulate RNA structure. It also blocks Watson-Crick-Franklin base pairing and causes mutation and truncation during reverse transcription. Several misincorporation-based high throughput sequencing methods have been developed to sequence m1 A...
March 26, 2024: RNA
https://read.qxmd.com/read/38530822/soil-fungal-communities-varied-across-aspects-of-restored-grassland-in-former-mining-areas-of-the-qinghai-tibet-plateau
#37
JOURNAL ARTICLE
Xiaoqing Li, Qiang Li, Yinzhu Duan, Haiqun Sun, Hui Chu, Shunbin Jia, Hongjie Chen, Wenxi Tang
To determine whether different aspects lead to a heterogeneous distribution of soil fungi, we investigated artificially established alpine grasslands in the Muli mining area in the Qinghai-Tibet Plateau. Employing high-throughput sequencing techniques, we analyzed the composition, diversity, and function of soil fungal communities across various aspects (flat, East-facing, South-facing, West-facing, North-facing). We also examined their relationships with environmental factors. Soil fungal communities of restored alpine grasslands differed significantly across aspects in terms of the dominant phyla, classes and species level...
2024: PloS One
https://read.qxmd.com/read/38529528/juveniles-young-adults-and-infants-with-hepatitis-b-virus-infection-a-genomic-study
#38
JOURNAL ARTICLE
Hanwen Zhang, Meina Li, Huijuan Liu, Yi Dong, Weijie Li, Pan Zhao
Integration of hepatitis B virus (HBV) DNA into the human genome is recognized as an oncogenic factor and a barrier to hepatitis B cure. In the study, biopsy liver tissues were collected from adolescents and young adults with acute HBV infection younger than or equal to 35 years of age and from HBV-infected infant patients younger than or equal to 6 months of age. A high-throughput sequencing method was used to detect HBV DNA integration. Totally, 12 adolescents, young adults, and 6 infants were included. Among the 12 patients with acute HBV infection, immunohistochemical staining of intrahepatic hepatitis B surface antigen for all displayed negative results, and no HBV DNA integrants in the hepatocyte DNA were confirmed...
March 2024: Journal of Medical Virology
https://read.qxmd.com/read/38529176/unraveling-the-shift-in-bacterial-communities-profile-grown-in-sediments-co-contaminated-with-chlorolignin-waste-of-pulp-paper-mill-by-metagenomics-approach
#39
JOURNAL ARTICLE
Vineet Kumar, Fuad Ameen, Pradeep Verma
Pulp-paper mills (PPMs) are known for consistently generating a wide variety of pollutants, that are often unidentified and highly resistant to environmental degradation. The current study aims to investigate the changes in the indigenous bacterial communities profile grown in the sediment co-contaminated with organic and inorganic pollutants discharged from the PPMs. The two sediment samples, designated PPS-1 and PPS-2, were collected from two different sites. Physico-chemical characterization of PPS-1 and PPS-2 revealed the presence of heavy metals (mg kg-1 ) like Cu (0...
2024: Frontiers in Microbiology
https://read.qxmd.com/read/38528494/pituitary-transcriptome-profile-from-laying-period-to-incubation-period-of-changshun-green-shell-laying-hens
#40
JOURNAL ARTICLE
Zhi Chen, Di Wen, Yan Zhang, Jiaying Chen, Fengqian Pan, Wen Zhang, Shuangshuang Zhou, Fen Wang, Ren Mu
BACKGROUND: Incubation behaviour, an instinct for natural breeding in poultry, is strictly controlled by the central nervous system and multiple neuroendocrine hormones and neurotransmitters, and is closely associated with the cessation of egg laying. Therefore, it is essential for the commercial poultry industry to clarify the molecular regulation mechanism of incubation behaviour. Here, we used high-throughput sequencing technology to examine the pituitary transcriptome of Changshun green-shell laying hen, a local breed from Guizhou province, China, with strong broodiness, in two reproductive stages, including egg-laying phase (LP) and incubation phase (BP)...
March 25, 2024: BMC Genomics
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