scholarly journals Metatranscriptome Analysis for Insight into Whole-Ecosystem Gene Expression during Spontaneous Wheat and Spelt Sourdough Fermentations

2010 ◽  
Vol 77 (2) ◽  
pp. 618-626 ◽  
Author(s):  
Stefan Weckx ◽  
Joke Allemeersch ◽  
Roel Van der Meulen ◽  
Gino Vrancken ◽  
Geert Huys ◽  
...  
Keyword(s):  
Gene Expression ◽  
Metabolic Pathways ◽  
Fermented Foods ◽  
Gene Microarray ◽  
Organoleptic Properties ◽  
Redox Equilibrium ◽  
Flavor Compound ◽  
Approaches To Study ◽  
Microarray Analyses ◽  
Insight Into

ABSTRACTLactic acid bacteria (LAB) are of industrial importance in the production of fermented foods, including sourdough-derived products. Despite their limited metabolic capacity, LAB contribute considerably to important characteristics of fermented foods, such as extended shelf-life, microbial safety, improved texture, and enhanced organoleptic properties. Triggered by the considerable amount of LAB genomic information that became available during the last decade, transcriptome and, by extension, metatranscriptome studies have become one of the most appropriate research approaches to study whole-ecosystem gene expression in more detail. In this study, microarray analyses were performed using RNA sampled during four 10-day spontaneous sourdough fermentations carried out in the laboratory with an in-house-developed LAB functional gene microarray. For data analysis, a new algorithm was developed to calculate a net expression profile for each of the represented genes, allowing use of the microarray analysis beyond the species level. In addition, metabolite target analyses were performed on the sourdough samples to relate gene expression with metabolite production. The results revealed the activation of different key metabolic pathways, the ability to use carbohydrates other than glucose (e.g., starch and maltose), and the conversion of amino acids as a contribution to redox equilibrium and flavor compound generation in LAB during sourdough fermentation.

scholarly journals New Insight into Bacterial Interaction with the Matrix of Plant-Based Fermented Foods

Foods ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1603
Author(s):  
Klaudia Gustaw ◽  
Iwona Niedźwiedź ◽  
Kamila Rachwał ◽  
Magdalena Polak-Berecka
Keyword(s):  
Gene Loss ◽  
Bacterial Species ◽  
Evolutionary Process ◽  
Fermented Foods ◽  
Deep Insight ◽  
Chemical Profile ◽  
Organoleptic Properties ◽  
Bacterial Interaction ◽  
The Matrix ◽  
Insight Into

Microorganisms have been harnessed to process raw plants into fermented foods. The adaptation to a variety of plant environments has resulted in a nearly inseparable association between the bacterial species and the plant with a characteristic chemical profile. Lactic acid bacteria, which are known for their ability to adapt to nutrient-rich niches, have altered their genomes to dominate specific habitats through gene loss or gain. Molecular biology approaches provide a deep insight into the evolutionary process in many bacteria and their adaptation to colonize the plant matrix. Knowledge of the adaptive characteristics of microorganisms facilitates an efficient use thereof in fermentation to achieve desired final product properties. With their ability to acidify the environment and degrade plant compounds enzymatically, bacteria can modify the textural and organoleptic properties of the product and increase the bioavailability of plant matrix components. This article describes selected microorganisms and their competitive survival and adaptation in fermented fruit and vegetable environments. Beneficial changes in the plant matrix caused by microbial activity and their beneficial potential for human health are discussed as well.

scholarly journals Chitin-Induced Gene Expression in Secondary Metabolic Pathways of Streptomyces coelicolor A3(2) Grown in Soil

2012 ◽  
Vol 79 (2) ◽  
pp. 707-713 ◽  
Author(s):  
Behnam Nazari ◽  
Michihiko Kobayashi ◽  
Akihiro Saito ◽  
Azam Hassaninasab ◽  
Kiyotaka Miyashita ◽  
...  
Keyword(s):  
Gene Expression ◽  
Secondary Metabolism ◽  
Stress Responses ◽  
Metabolic Pathways ◽  
Streptomyces Coelicolor ◽  
Regulation Of Gene Expression ◽  
Content Type ◽  
Metabolic Genes ◽  
Expression Of Genes ◽  
Microarray Analyses

ABSTRACTMicroarray analyses revealed that the expression of genes for secondary metabolism together with that of primary metabolic genes was induced by chitin in autoclaved soil cultures ofStreptomyces coelicolorA3(2). The data also indicated that DasR was involved in the regulation of gene expression for chitin catabolism, secondary metabolism, and stress responses.

scholarly journals Stenotrophomonas maltophiliaDifferential Gene Expression in Synthetic Cystic Fibrosis Sputum Reveals Shared and Cystic Fibrosis Strain-Specific Responses to the Sputum Environment

2019 ◽  
Vol 201 (15) ◽  
Author(s):  
Graham G. Willsey ◽  
Korin Eckstrom ◽  
Annette E. LaBauve ◽  
Lauren A. Hinkel ◽  
Kristin Schutz ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cystic Fibrosis ◽  
Stress Responses ◽  
Metabolic Pathways ◽  
Stenotrophomonas Maltophilia ◽  
Acute Infection ◽  
Survival Strategies ◽  
Transcriptional Responses ◽  
Content Type ◽  
Insight Into

ABSTRACTStenotrophomonas maltophiliais a Gram-negative opportunistic pathogen that can infect the lungs of people with cystic fibrosis (CF). The highly viscous mucus in the CF lung, expectorated as sputum, serves as the primary nutrient source for microbes colonizing this site and induces virulence-associated phenotypes and gene expression in several CF pathogens. Here, we characterized the transcriptional responses of threeS. maltophiliastrains during exposure to synthetic CF sputum medium (SCFM2) to gain insight into how this organism interacts with the host in the CF lung. These efforts led to the identification of 881 transcripts differentially expressed by all three strains, many of which reflect the metabolic pathways used byS. maltophiliain sputum, as well as altered stress responses. The latter correlated with increased resistance to peroxide exposure after pregrowth in SCFM2 for two of the strains. We also compared the SCFM2 transcriptomes of twoS. maltophiliaCF isolates to that of the acute infection strain,S. maltophiliaK279a, allowing us to identify CF isolate-specific signatures in differential gene expression. The expression of genes from the accessory genomes was also differentially altered in response to SCFM2. Finally, a number of biofilm-associated genes were differentially induced in SCFM2, particularly in K279a, which corresponded to increased aggregation and biofilm formation in this strain relative to both CF strains. Collectively, this work details the response ofS. maltophiliato an environment that mimics important aspects of the CF lung, identifying potential survival strategies and metabolic pathways used byS. maltophiliaduring infections.IMPORTANCEStenotrophomonas maltophiliais an important infecting bacterium in the airways of people with cystic fibrosis (CF). However, compared to the other CF pathogens,S. maltophiliahas been relatively understudied. The significance of our research is to provide insight into the global transcriptomic changes ofS. maltophiliain response to a medium that was designed to mimic important aspects of the CF lung. This study elucidates the overall metabolic changes that occur whenS. maltophiliaencounters the CF lung and generates a road map of candidate genes to test usingin vitroandin vivomodels of CF.

scholarly journals Mass spectrometry based metabolomics approach on the elucidation of volatile metabolites formation in fermented foods: A mini review

2021 ◽  
Author(s):  
Min Kyung Park ◽  
Young-Suk Kim
Keyword(s):  
Mass Spectrometry ◽  
Amino Acids ◽  
Metabolic Pathways ◽  
Metabolic Changes ◽  
Fermented Foods ◽  
Organoleptic Properties ◽  
Efficient Tool ◽  
Microbial Enzymes ◽  
Volatile Metabolites ◽  
Quantitative Analyses

AbstractMetabolomics can be applied for comparative and quantitative analyses of the metabolic changes induced by microorganisms during fermentation. In particular, mass spectrometry (MS) is a powerful tool for metabolomics that is widely used for elucidating biomarkers and patterns of metabolic changes. Fermentation involves the production of volatile metabolites via diverse and complex metabolic pathways by the activities of microbial enzymes. These metabolites can greatly affect the organoleptic properties of fermented foods. This review provides an overview of the MS-based metabolomics techniques applied in studies of fermented foods, and the major metabolic pathways and metabolites (e.g., sugars, amino acids, and fatty acids) derived from their metabolism. In addition, we suggest an efficient tool for understanding the metabolic patterns and for identifying novel markers in fermented foods.

Gene expression and neovascularization: analysis of mouse retinae by gene microarray

2006 ◽  
Vol 1 (S 1) ◽  
Author(s):  
J Lin ◽  
S Zeller ◽  
J Huber ◽  
N Dietrich ◽  
Y Feng ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Microarray

Nanoparticle-plasma Membrane Interactions: Thermodynamics, Toxicity and Cellular Response

2020 ◽  
Vol 27 (20) ◽  
pp. 3330-3345
Author(s):  
Ana G. Rodríguez-Hernández ◽  
Rafael Vazquez-Duhalt ◽  
Alejandro Huerta-Saquero
Keyword(s):  
Gene Expression ◽  
Immune Responses ◽  
Cellular Response ◽  
Cellular Level ◽  
Membrane Interactions ◽  
Daily Lives ◽  
Cellular Physiology ◽  
Associated Proteins ◽  
First Contact ◽  
Insight Into

Nanomaterials have become part of our daily lives, particularly nanoparticles contained in food, water, cosmetics, additives and textiles. Nanoparticles interact with organisms at the cellular level. The cell membrane is the first protective barrier against the potential toxic effect of nanoparticles. This first contact, including the interaction between the cell membranes -and associated proteins- and the nanoparticles is critically reviewed here. Nanoparticles, depending on their toxicity, can cause cellular physiology alterations, such as a disruption in cell signaling or changes in gene expression and they can trigger immune responses and even apoptosis. Additionally, the fundamental thermodynamics behind the nanoparticle-membrane and nanoparticle-proteins-membrane interactions are discussed. The analysis is intended to increase our insight into the mechanisms involved in these interactions. Finally, consequences are reviewed and discussed.

scholarly journals Gene Expression and Carcass Traits Are Different between Different Quality Grade Groups in Red-Faced Hereford Steers

Animals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1910
Author(s):  
Bailey Engle ◽  
Molly Masters ◽  
Jane Ann Boles ◽  
Jennifer Thomson
Keyword(s):  
Gene Expression ◽  
Transcriptome Profiling ◽  
Fat Deposition ◽  
Lower Shear ◽  
The Us ◽  
Quality Grade ◽  
Longissimus Lumborum ◽  
Muscle Biochemistry ◽  
Marbling Deposition ◽  
Insight Into

Fat deposition is important to carcass value and some palatability characteristics. Carcasses with higher USDA quality grades produce more value for producers and processors in the US system and are more likely to have greater eating satisfaction. Using genomics to identify genes impacting marbling deposition provides insight into muscle biochemistry that may lead to ways to better predict fat deposition, especially marbling and thus quality grade. Hereford steers (16) were managed the same from birth through harvest after 270 days on feed. Samples were obtained for tenderness and transcriptome profiling. As expected, steaks from Choice carcasses had a lower shear force value than steaks from Select carcasses; however, steaks from Standard carcasses were not different from steaks from Choice carcasses. A significant number of differentially expressed (DE) genes was observed in the longissimus lumborum between Choice and Standard carcass RNA pools (1257 genes, p < 0.05), but not many DE genes were observed between Choice and Select RNA pools. Exploratory analysis of global muscle tissue transcriptome from Standard and Choice carcasses provided insight into muscle biochemistry, specifically the upregulation of extracellular matrix development and focal adhesion pathways and the downregulation of RNA processing and metabolism in Choice versus Standard. Additional research is needed to explore the function and timing of gene expression changes.

scholarly journals Interplay between cofactors and transcription factors in hematopoiesis and hematological malignancies

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Zi Wang ◽  
Pan Wang ◽  
Yanan Li ◽  
Hongling Peng ◽  
Yu Zhu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Hematological Malignancies ◽  
Current Knowledge ◽  
Regulation Of Gene Expression ◽  
Hematologic Disorders ◽  
Cell Lineages ◽  
Stage Of Development ◽  
Transcription Complexes ◽  
Insight Into

AbstractHematopoiesis requires finely tuned regulation of gene expression at each stage of development. The regulation of gene transcription involves not only individual transcription factors (TFs) but also transcription complexes (TCs) composed of transcription factor(s) and multisubunit cofactors. In their normal compositions, TCs orchestrate lineage-specific patterns of gene expression and ensure the production of the correct proportions of individual cell lineages during hematopoiesis. The integration of posttranslational and conformational modifications in the chromatin landscape, nucleosomes, histones and interacting components via the cofactor–TF interplay is critical to optimal TF activity. Mutations or translocations of cofactor genes are expected to alter cofactor–TF interactions, which may be causative for the pathogenesis of various hematologic disorders. Blocking TF oncogenic activity in hematologic disorders through targeting cofactors in aberrant complexes has been an exciting therapeutic strategy. In this review, we summarize the current knowledge regarding the models and functions of cofactor–TF interplay in physiological hematopoiesis and highlight their implications in the etiology of hematological malignancies. This review presents a deep insight into the physiological and pathological implications of transcription machinery in the blood system.

scholarly journals Effects of diethylcarbamazine and ivermectin treatment onBrugia malayigene expression in infected gerbils (Meriones unguiculatus)

2019 ◽  
Vol 5 ◽  
Author(s):  
Mary J. Maclean ◽  
W. Walter Lorenz ◽  
Michael T. Dzimianski ◽  
Christopher Anna ◽  
Andrew R. Moorhead ◽  
...  
Keyword(s):  
Gene Expression ◽  
Drug Action ◽  
Meriones Unguiculatus ◽  
Current Control ◽  
Direct Result ◽  
Ivermectin Treatment ◽  
Treatment Groups ◽  
Parasite Survival ◽  
Insight Into

AbstractLymphatic filariasis (LF) threatens nearly 20% of the world's population and has handicapped one-third of the 120 million people currently infected. Current control and elimination programs for LF rely on mass drug administration of albendazole plus diethylcarbamazine (DEC) or ivermectin. Only the mechanism of action of albendazole is well understood. To gain a better insight into antifilarial drug actionin vivo, we treated gerbils harbouring patentBrugia malayiinfections with 6 mg kg−1DEC, 0.15 mg kg−1ivermectin or 1 mg kg−1albendazole. Treatments had no effect on the numbers of worms present in the peritoneal cavity of treated animals, so effects on gene expression were a direct result of the drug and not complicated by dying parasites. Adults and microfilariae were collected 1 and 7 days post-treatment and RNA isolated for transcriptomic analysis. The experiment was repeated three times. Ivermectin treatment produced the most differentially expressed genes (DEGs), 113. DEC treatment yielded 61 DEGs. Albendazole treatment resulted in little change in gene expression, with only 6 genes affected. In total, nearly 200 DEGs were identified with little overlap between treatment groups, suggesting that these drugs may interfere in different ways with processes important for parasite survival, development, and reproduction.

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