scholarly journals Characterization of genes differentially expressed within macrophages by virulent and attenuated Mycobacterium tuberculosis identifies candidate genes involved in intracellular growth

Microbiology ◽  
2008 ◽  
Vol 154 (8) ◽  
pp. 2291-2303 ◽  
Author(s):  
Alice H. Li ◽  
Wan L. Lam ◽  
Richard W. Stokes
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Candidate Genes ◽  
Differentially Expressed ◽  
Intracellular Growth

scholarly journals Characterization of Large Deletion Mutants of Mycobacterium tuberculosis Selected for Isoniazid Resistance

2020 ◽  
Vol 64 (9) ◽  
Author(s):  
Catherine Vilchèze ◽  
Rajagopalan Saranathan ◽  
Brian Weinrick ◽  
William R. Jacobs
Keyword(s):  
Oxidative Stress ◽  
Mycobacterium Tuberculosis ◽  
Large Deletion ◽  
Growth Defect ◽  
Intracellular Growth ◽  
Isoniazid Resistance ◽  
Content Type ◽  
Genomic Deletions

ABSTRACT Large genomic deletions (LGDs) (6 to 63 kbp) were observed in isoniazid-resistant Mycobacterium tuberculosis mutants derived from four M. tuberculosis strains. These LGDs had no growth defect in vitro but could be defective in intracellular growth and showed various sensitivities toward oxidative stress despite lacking katG. The LGD regions comprise 74 genes, mostly of unknown function, that may be important for M. tuberculosis intracellular growth and protection against oxidative stress.

scholarly journals Integration of multi-omics approaches for functional characterization of muscle related selective sweep genes in Nanchukmacdon

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Devender Arora ◽  
Krishnamoorthy Srikanth ◽  
Jongin Lee ◽  
Daehwan Lee ◽  
Nayoung Park ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Bisulfite Sequencing ◽  
Selective Sweep ◽  
Functional Characterization ◽  
Differentially Expressed ◽  
Published Data ◽  
Whole Genome ◽  
Whole Genome Bisulfite Sequencing ◽  
Genome Bisulfite Sequencing

AbstractPig as a food source serves daily dietary demand to a wide population around the world. Preference of meat depends on various factors with muscle play the central role. In this regards, selective breeding abled us to develop “Nanchukmacdon” a pig breeds with an enhanced variety of meat and high fertility rate. To identify genomic regions under selection we performed whole-genome resequencing, transcriptome, and whole-genome bisulfite sequencing from Nanchukmacdon muscles samples and used published data for three other breeds such as Landrace, Duroc, Jeju native pig and analyzed the functional characterization of candidate genes. In this study, we present a comprehensive approach to identify candidate genes by using multi-omics approaches. We performed two different methods XP-EHH, XP-CLR to identify traces of artificial selection for traits of economic importance. Moreover, RNAseq analysis was done to identify differentially expressed genes in the crossed breed population. Several genes (UGT8, ZGRF1, NDUFA10, EBF3, ELN, UBE2L6, NCALD, MELK, SERP2, GDPD5, and FHL2) were identified as selective sweep and differentially expressed in muscles related pathways. Furthermore, nucleotide diversity analysis revealed low genetic diversity in Nanchukmacdon for identified genes in comparison to related breeds and whole-genome bisulfite sequencing data shows the critical role of DNA methylation pattern in identified genes that leads to enhanced variety of meat. This work demonstrates a way to identify the molecular signature and lays a foundation for future genomic enabled pig breeding.

scholarly journals Role of Premycofactocin Synthase in Growth, Microaerophilic Adaptation, and Metabolism of Mycobacterium tuberculosis

mBio ◽  
2021 ◽  
Author(s):  
Gopinath Krishnamoorthy ◽  
Peggy Kaiser ◽  
Patricia Constant ◽  
Ulrike Abu Abed ◽  
Monika Schmid ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Mycobacterial Species ◽  
Intracellular Growth ◽  
Critical Research ◽  
Content Type ◽  
Research Priority ◽  
Functional Relevance ◽  
Almost All

Characterization of proteins with unknown functions is a critical research priority as the intracellular growth and metabolic state of Mycobacterium tuberculosis , the causative agent of tuberculosis, remain poorly understood. Mycofactocin is a peptide-derived redox cofactor present in almost all mycobacterial species; however, its functional relevance in M. tuberculosis pathogenesis and host survival has never been studied experimentally.

scholarly journals Genome-Wide Identification and Characterization of Long Noncoding RNAs Involved in Chinese Wheat Mosaic Virus Infection of Nicotiana benthamiana

Biology ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 232
Author(s):  
Weiran Zheng ◽  
Haichao Hu ◽  
Qisen Lu ◽  
Peng Jin ◽  
Linna Cai ◽  
...  
Keyword(s):  
Virus Infection ◽  
Mosaic Virus ◽  
Nicotiana Benthamiana ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Differentially Expressed ◽  
Genome Wide ◽  
Chinese Wheat

Recent studies have shown that a large number of long noncoding RNAs (lncRNAs) can regulate various biological processes in animals and plants. Although lncRNAs have been identified in many plants, they have not been reported in the model plant Nicotiana benthamiana. Particularly, the role of lncRNAs in plant virus infection remains unknown. In this study, we identified lncRNAs in N. benthamiana response to Chinese wheat mosaic virus (CWMV) infection by RNA sequencing. A total of 1175 lncRNAs, including 65 differentially expressed lncRNAs, were identified during CWMV infection. We then analyzed the functions of some of these differentially expressed lncRNAs. Interestingly, one differentially expressed lncRNA, XLOC_006393, was found to participate in CWMV infection as a precursor to microRNAs in N. benthamiana. These results suggest that lncRNAs play an important role in the regulatory network of N. benthamiana in response to CWMV infection.

scholarly journals Transcriptome-(phospho)proteome characterization of brain of a germline model of cytoplasmic-predominant Pten expression with autism-like phenotypes

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Stetson Thacker ◽  
Charis Eng
Keyword(s):  
Autism Spectrum ◽  
Pten Expression ◽  
Differentially Expressed ◽  
Risk Genes ◽  
Animal Modeling ◽  
Network Analyses ◽  
Phosphorylated Proteins ◽  
Mass Spectrometry Technology ◽  
Neurological Processes

AbstractPTEN has a strong Mendelian association with autism spectrum disorder (ASD), representing a special case in autism’s complex genetic architecture. Animal modeling for constitutional Pten mutation creates an opportunity to study how disruption of Pten affects neurobiology and glean potential insight into ASD pathogenesis. Subsequently, we comprehensively characterized the neural (phospho)proteome of Ptenm3m4/m3m4 mice, which exhibits cytoplasmic-predominant Pten expression, by applying mass spectrometry technology to their brains at two-weeks- (P14) and six-weeks-of-age (P40). The differentially expressed/phosphorylated proteins were subjected to gene enrichment, pathway, and network analyses to assess the affected biology. We identified numerous differentially expressed/phosphorylated proteins, finding greater dysregulation at P40 consistent with prior transcriptomic data. The affected pathways were largely related to PTEN function or neurological processes, while scant direct overlap was found across datasets. Network analysis pointed to ASD risk genes like Pten and Psd-95 as major regulatory hubs, suggesting they likely contribute to initiation or maintenance of cellular and perhaps organismal phenotypes related to ASD.

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