Results 91 to 100 of about 253,664 (304)

Using short-read 16S rRNA sequencing of multiple variable regions to generate high-quality results to a species level

Frontiers in Bioinformatics
IntroductionShort-read amplicon sequencing studies have typically focused on 1-2 variable regions of the 16S rRNA gene. Species-level resolution is limited in these studies, as each variable region enables the characterisation of a different subsection ...
Amy S. Graham, Amy S. Graham, Fadheela Patel, Francesca Little, Andre van der Kouwe, Andre van der Kouwe, Mamadou Kaba, Martha J. Holmes, Martha J. Holmes, Martha J. Holmes, Martha J. Holmes   +10 more
doaj   +1 more source

Species identification and profiling of complex microbial communities using shotgun Illumina sequencing of 16S rRNA amplicon sequences.

PLoS ONE, 2013
The high throughput and cost-effectiveness afforded by short-read sequencing technologies, in principle, enable researchers to perform 16S rRNA profiling of complex microbial communities at unprecedented depth and resolution. Existing Illumina sequencing
Swee Hoe Ong, Vinutha Uppoor Kukkillaya, Andreas Wilm, Christophe Lay, Eliza Xin Pei Ho, Louie Low, Martin Lloyd Hibberd, Niranjan Nagarajan   +7 more
doaj   +1 more source

A comprehensive evaluation of the sl1p pipeline for 16S rRNA gene sequencing analysis

Microbiome, 2017
Advances in next-generation sequencing technologies have allowed for detailed, molecular-based studies of microbial communities such as the human gut, soil, and ocean waters.
F. Whelan, M. Surette
semanticscholar   +1 more source

A Peripheral Mechanism of Depression: Disturbed Intestinal Epithelial Per2 Gene Expression Causes Depressive Behaviors in Mice with Circadian Rhythm Disruption via Gut Barrier Damage and Microbiota Dysbiosis

Advanced Science, EarlyView.
Circardian rhythm disorder (CRD) causes abnormal expression of intestinal Period 2 (Per2) gene, which compromising intestinal barrier integrity and altering the gut microenvironment. Microbiota dysbiosis and aberrant metabolites production drive central inflammation, impair neurogenesis, and promote functional deficits, ultimately facilitating the ...
Huiliang Zhang, Xuan Qin, Haiyue Song, Jieru Zhou, Hui Wei, Lun Zhang, Yi Liu, Zhuoqun Wang, Yiren Zhang, Yiwen Lai, Jiayu Yang, Wenting Hu, Zhongshan Chen, Ji Zeng, Yu Jin, Xiaochuan Wang, Rong Liu   +16 more
wiley   +1 more source

Calhm6 Governs Macrophage Polarization Through Chp1‐Camk4‐Creb1 Axis and Ectosomal Delivery in Inflammatory Responses

Advanced Science, EarlyView.
Calhm6 drives M2 macrophage polarization via the Chp1‐Camk4‐Creb1 axis, suppressing inflammation through calcium‐dependent ectosomal delivery. Calhm6 deficiency enhances M1 responses, boosting bactericidal activity but exacerbating tissue damage. LPS/IFNγ upregulate Calhm6 via Irf1, while IL‐4/Stat6 inhibits it, balancing immune outcomes.
Yanlong Xin, Xiaofan Xiong, Yan Zhang, Siyu Zhang, Shuting Zhang, Yu Yang, Yingxue Liang, Lulu Zang, Xi Chen, Wenjuan Li, Issam Halalmeh, Rui Zhou, Zongfang Li, Haowen Liu, Jing Geng   +14 more
wiley   +1 more source

Snord15b Maintains Stemness of Intestinal Stem Cells via Enhancement of Alternative Splicing of Btrc Short Isoform for Suppression of β‐Catenin Ubiquitination

Advanced Science, EarlyView.
In intestinal stem cells (ISCs), Snord15b associates with Ilf2 to recruit splicing factors for alternative splicing of Btrc mRNA, leading to the generation of short Btrc. This short Btrc fails to form a functional E3 ubiquitin ligase complex for β‐catenin ubiquitination and degradation.
Yuwei Xu, Peikang Zhang, Zhen Xiong, Yufei Lan, Hui Guo, Runyuan Wu, Cunzhen Li, Hongzhe Fan, Ying Du, Xiaoxiao Zhu, Dongdong Fan, Zhonglong Wang, Yong Tian, Zusen Fan   +13 more
wiley   +1 more source

Benchmarking a targeted 16S ribosomal RNA gene enrichment approach to reconstruct ancient microbial communities [PDF]

PeerJ
The taxonomic characterization of ancient microbiomes is a key step in the rapidly growing field of paleomicrobiology. While PCR amplification of the 16S ribosomal RNA (rRNA) gene is a widely used technique in modern microbiota studies, this method has ...
Raphael Eisenhofer, Sterling Wright, Laura Weyrich   +2 more
doaj   +2 more sources

Restoring Histone Acetylation Accelerates Diabetic Wound Repair by Improving the Spatiotemporal Dynamics of Macrophages

Advanced Science, EarlyView.
Butyrate—via epigenetic modulation of the histone core—rebalance dysregulated macrophage function and promotes wound healing under persisting hostile conditions of diabetic mice. Additionally, butyrate harmonizes macrophage interactions with keratinocytes and fibroblasts as well as breaks the vicious cycle of inflammation in chronic wounds by restoring
Karmveer Singh, Albert Kallon Koroma, Rajeev Kumar Pandey, Yongfang Wang, Jinnan Cheng, Philipp Haas, Mahyar Aghapour, Linda Krug, Adelheid Hainzl, Meinhard Wlaschek, Pallab Maity, Karin Scharffetter‐Kochanek   +11 more
wiley   +1 more source

Development and Validation of a Reference Data Set for Assigning Staphylococcus Species Based on Next-Generation Sequencing of the 16S-23S rRNA Region

Frontiers in Cellular and Infection Microbiology, 2019
Many members of the Staphylococcus genus are clinically relevant opportunistic pathogens that warrant accurate and rapid identification for targeted therapy.
Maja Kosecka-Strojek, Maja Kosecka-Strojek, Artur J. Sabat, Viktoria Akkerboom, Karsten Becker, Evert van Zanten, Guido Wisselink, Jacek Miedzobrodzki, Anna M. D. (Mirjam) Kooistra-Smid, Anna M. D. (Mirjam) Kooistra-Smid, Alexander W. Friedrich   +10 more
doaj   +1 more source

MicroPheno: predicting environments and host phenotypes from 16S rRNA gene sequencing using a k-mer based representation of shallow sub-samples

bioRxiv, 2018
Motivation Microbial communities play important roles in the function and maintenance of various biosystems, ranging from the human body to the environment.
Ehsaneddin Asgari, Kiavash Garakani, A. Mchardy, M. R. Mofrad   +3 more
semanticscholar   +1 more source