scholarly journals Two New Dihydrosphingosine Analogs Against Mycobacterium tuberculosis Affect gltA1, lprQ, and rpsO Expression

2021 ◽  
Vol 12 ◽  
Author(s):  
Katia Peñuelas-Urquides ◽  
Mario Bermúdez de León ◽  
Beatriz Silva-Ramírez ◽  
Fabiola Castorena-Torres ◽  
Gloria María Molina-Salinas ◽  
...  
Keyword(s):  
Gene Expression ◽  
Mycobacterium Tuberculosis ◽  
Lipid Metabolism ◽  
Molecular Mechanisms ◽  
Rna Isolation ◽  
Multidrug Resistant ◽  
Mechanisms Of Action ◽  
Preclinical Studies ◽  
Gene Expression Alterations ◽  
Total Rna Isolation

The emergence of multidrug-resistant (MDR) Mycobacterium tuberculosis strains threaten the control of tuberculosis. New antitubercular dihydrosphingosine analogs, named UCIs, have been evaluated in preclinical studies but their cellular and molecular mechanisms of action against M. tuberculosis are still unknown. The aim of this study was to evaluate the effect of UCI exposure on gene expression of drug-sensitive H37Rv and MDR CIBIN:UMF:15:99 clones of M. tuberculosis which were isolated, phenotypically, and genetically characterized, cultured to log phase and treated with UCI compounds; followed by total RNA isolation, reverse transcription and hybridization assays on Affymetrix genomic microarrays. Data were validated with RT-qPCR assays. As results, UCI-05 and UCI-14 exposure increased gltA1 expression in drug-sensitive H37Rv clones. Furthermore, UCI-05 increased lprQ expression in MDR CIBIN:UMF:15:99 M. tuberculosis clones while UCI-14 reduced the expression of this gene in drug-sensitive H37Rv clones. In addition, UCI-05 reduced rpsO expression in drug-sensitive H37Rv clones. We found gene expression alterations that suggest these molecules may alter carbon and lipid metabolism as well as interfere in the protein-producing machinery in M. tuberculosis.

scholarly journals Insights into how environment shapes post-mortem RNA transcription in mouse brain

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Raphael Severino Bonadio ◽  
Larissa Barbosa Nunes ◽  
Patricia Natália S. Moretti ◽  
Juliana Forte Mazzeu ◽  
Stefano Cagnin ◽  
...  
Keyword(s):  
Lipid Metabolism ◽  
Mouse Brain ◽  
Molecular Mechanisms ◽  
Cell Communication ◽  
Rna Degradation ◽  
The Body ◽  
Biological Processes ◽  
Post Mortem ◽  
Gene Expression Alterations ◽  
Upregulated Genes

AbstractMost biological features that occur on the body after death were already deciphered by traditional medicine. However, the molecular mechanisms triggered in the cellular microenvironment are not fully comprehended yet. Previous studies reported gene expression alterations in the post-mortem condition, but little is known about how the environment could influence RNA degradation and transcriptional regulation. In this work, we analysed the transcriptome of mouse brain after death under three concealment simulations (air exposed, buried, and submerged). Our analyses identified 2,103 genes differentially expressed in all tested groups 48 h after death. Moreover, we identified 111 commonly upregulated and 497 commonly downregulated genes in mice from the concealment simulations. The gene functions shared by the individuals from the tested environments were associated with RNA homeostasis, inflammation, developmental processes, cell communication, cell proliferation, and lipid metabolism. Regarding the altered biological processes, we identified that the macroautophagy process was enriched in the upregulated genes and lipid metabolism was enriched in the downregulated genes. On the other hand, we also described a list of biomarkers associated with the submerged and buried groups, indicating that these environments can influence the post-mortem RNA abundance in its particular way.

New Data on Robustness of Gene Expression Signatures in Leukemia: Comparison of Three Distinct Total RNA Preparation Procedures.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 4288-4288
Author(s):  
Marta Campo ◽  
Andrea Zangrando ◽  
Luca Trentin ◽  
Rui Li ◽  
Wei-min Liu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Data ◽  
Rna Isolation ◽  
Expression Data ◽  
Microarray Technology ◽  
Isolation Method ◽  
Acute Leukemias ◽  
Preparation Methods ◽  
Total Rna ◽  
Total Rna Isolation

Abstract Gene expression microarrays had been used to classify known tumor types and various hematological malignancies (Yeoh et al, Cancer Cell 2002; Kohlmann et al, Genes Chromosomes Cancer 2003), enforcing the objective that microarray analysis could be introduced soon in the routine classification of cancer (Haferlach et al, Blood 2005). However, there’re still doubts about gene expression experiments performance in clinical laboratory diagnosis. For instance, the quality of starting material is a major concern in microarray technology and there are no data on the variation in gene expression profiles ensuing from different RNA extraction procedures. Here, as part of the internal multicenter MILE Study program, we assess the impact of different RNA preparation methods on gene expression data, analyzing 27 patients representative of nine different subtypes of pediatric acute leukemias. We compared the three currently most used protocols to isolate RNA for routine diagnosis (PCR assays) and microarray experiments. They are named as method A: lysis of mononuclear leukemia cells, followed by lysate homogeniziation, followed by total RNA isolation; method B: TRIzol RNA isolation, and method C: TRIzol RNA isolation followed by total RNA purification step. The methods were analyzed in triplicates for each sample (24) and additional three samples were performed in technical replicates of three data sets for each preparation (HG-U133 Plus 2.0). Method A results in better total RNA quality as demonstrated by 3′/5′ GAPD ratios and by RNA degradation plots. High comparability of gene expression data is found between samples in the same leukemia subclasses and collected with different RNA preparation methods thus demonstrating that sample preparation procedures do not impair the overall signal distribution. Unsupervised analyses showed clustering of samples first by each patient’s replicate conditions, then by leukemia type, and finally by leukemia lineage. In fact, B-ALL samples are clustered together, separately from T-ALL and AML, demonstrating that clustering reflects biological differences between leukemias and that the RNA isolation method is a secondary effect. Also, supervised cluster analyses highlight that samples are grouped depending on intra-lineage features (i.e. chromosomal aberrations) thus confirming the clustering organizations as reported in recent gene expression profiling studies of acute leukemias. Our study shows that biological features of pediatric acute leukemia classes largely exceed the variations between different total RNA sample preparation protocols. However, technical replicates analyses reveal that gene expression data from method A have the lowest degree of variation, are more reproducible and more precise as compared to the other two methods. Furthermore, compared to methods B and C, method A produces more differentially expressed probe sets between distinct leukemia classes and is therefore considered the more robust RNA isolation procedure for gene expression experiments using high-density microarray technology. We therefore conclude that method A (initial homogenization of the leukemia cell lysate followed by total RNA isolation) combined with a standardized microarray analysis protocol is highly reproducible and contributes to robustness of gene expression data and that this procedure is most practical for a routine laboratory use.

Gene Expression Analysis on the Early Development of Pig Embryos Exposed to Malathion

2007 ◽  
Vol 26 (2) ◽  
pp. 143-149 ◽  
Author(s):  
Zayil Salazar ◽  
Yvonne Ducolomb ◽  
Miguel Betancourt ◽  
Edmundo Bonilla ◽  
Leticia Cortés ◽  
...  
Keyword(s):  
Gene Expression ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Hypothetical Protein ◽  
Cdna Libraries ◽  
Mhc I ◽  
Vitro Fertilization ◽  
Embryo Cells ◽  
Gene Expression Alterations

Malathion is a widely used pesticide and there is evidence that it could alter mammal’s germ and somatic cells, as well as cell lines. There are not enough studies showing how the nonacute malathion doses affect gene expression. This study analyzes gene expression alterations in pig morular embryos exposed in vitro , for 96 h, to several malathion concentrations after in vitro fertilization. cDNA libraries of isolated morular embryos were created and differential screenings performed to identify target genes. Seven clones were certainly identified. Genes related to mitochondrial metabolism as cytochrome c subunits I and III, nuclear genes such as major histocompatibility complex I (MHC I), and a hypothetical protein related with a splicing factor were the target of malathion’s deregulation effect. The widespread use of malathion as a pesticide should be regarded with reproductive implications and more detailed analysis would yield more about molecular mechanisms of malathion injury on embryo cells.

scholarly journals Flavanone metabolites decrease monocyte adhesion to TNF-α-activated endothelial cells by modulating expression of atherosclerosis-related genes

2013 ◽  
Vol 110 (4) ◽  
pp. 587-598 ◽  
Author(s):  
Audrey Chanet ◽  
Dragan Milenkovic ◽  
Sylvain Claude ◽  
Jeanette A. M. Maier ◽  
Muhammad Kamran Khan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Endothelial Cells ◽  
Vascular Function ◽  
Molecular Mechanisms ◽  
Umbilical Vein ◽  
Inhibitory Effect ◽  
Mechanisms Of Action ◽  
Monocyte Adhesion ◽  
Tnf Α ◽  
The Impact

Flavanones are found specifically and abundantly in citrus fruits. Their beneficial effect on vascular function is well documented. However, little is known about their cellular and molecular mechanisms of action in vascular cells. The goal of the present study was to identify the impact of flavanone metabolites on endothelial cells and decipher the underlying molecular mechanisms of action. We investigated the impact of naringenin and hesperetin metabolites at 0·5, 2 and 10 μm on monocyte adhesion to TNF-α-activated human umbilical vein endothelial cells (HUVEC) and on gene expression. Except hesperetin-7-glucuronide and naringenin-7-glucuronide (N7G), when present at 2 μm, flavanone metabolites (hesperetin-3′-sulphate, hesperetin-3′-glucuronide and naringenin-4′-glucuronide (N4′G)) significantly attenuated monocyte adhesion to TNF-α-activated HUVEC. Exposure of both monocytes and HUVEC to N4′G and N7G at 2 μm resulted in a higher inhibitory effect on monocyte adhesion. Gene expression analysis, using TaqMan Low-Density Array, revealed that flavanone metabolites modulated the expression of genes involved in atherogenesis, such as those involved in inflammation, cell adhesion and cytoskeletal organisation. In conclusion, physiologically relevant concentrations of flavanone metabolites reduce monocyte adhesion to TNF-α-stimulated endothelial cells by affecting the expression of related genes. This provides a potential explanation for the vasculoprotective effects of flavanones.

scholarly journals Relationship between insulin sensitivity and gene expression in human skeletal muscle

2020 ◽  
Author(s):  
Hemang Parikh ◽  
Targ Elgzyri ◽  
Amra Alibegovic ◽  
Natalie Hiscock ◽  
Ola Ekström ◽  
...  
Keyword(s):  
Gene Expression ◽  
Skeletal Muscle ◽  
Lipid Metabolism ◽  
Insulin Sensitivity ◽  
Human Skeletal Muscle ◽  
Molecular Mechanisms ◽  
Mammalian Target Of Rapamycin ◽  
Independent Study ◽  
Nutrient Sensing ◽  
Muscle Gene Expression

Abstract BackgroundInsulin resistance in skeletal muscle is a key feature of the pre-diabetic state, hypertension, dyslipidemia, cardiovascular diseases, and also predicts type 2 diabetes. However, the underlying molecular mechanisms are still poorly understood. MethodsTo explore these mechanisms, we related global skeletal muscle gene expression profiling of 38 non-diabetic men to physiological measures of insulin sensitivity. Results We identified 70 genes positively and 110 genes inversely correlated with insulin sensitivity in human skeletal muscle, identifying autophagy-related genes as positively correlated with insulin sensitivity. Replication in an independent study of 9 non-diabetic men resulted in 10 overlapping genes that strongly correlated with insulin sensitivity, including CPT1B and SIRT2 , involved in lipid metabolism, and FBXW5 that regulates mammalian target-of-rapamycin (mTOR) and autophagy. The expression of CPT1B , SIRT2 and FBXW5 was also positively correlated with the expression of key genes promoting the phenotype of an insulin sensitive myocyte e.g. PPARGC1A . ConclusionsThese data suggest that activation of genes involved in lipid metabolism, e.g. CPT1B and SIRT2 , and genes regulating autophagy and mTOR signaling, e.g. FBXW5 , are associated with increased insulin sensitivity in human skeletal muscle, reflecting a highly flexible nutrient sensing.

scholarly journals Endometrial gene expression in high- and low-fertility heifers in the late luteal phase of the estrous cycle and a comparison with midluteal gene expression

2016 ◽  
Vol 48 (4) ◽  
pp. 306-319 ◽  
Author(s):  
Aideen P. Killeen ◽  
Michael G. Diskin ◽  
Dermot G. Morris ◽  
David A. Kenny ◽  
Sinéad M. Waters
Keyword(s):  
Gene Expression ◽  
Lipid Metabolism ◽  
Estrous Cycle ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Molecular Transport ◽  
Early Embryo ◽  
Endometrial Tissue ◽  
Cellular Growth ◽  
Low Fertility

Embryonic mortality is a major constraint to improving reproductive efficiency and profitability in livestock enterprises. We previously reported differential expression of genes with identified roles in cellular growth and proliferation, lipid metabolism, endometrial remodeling, inflammation, angiogenesis, and metabolic exchange in endometrial tissue on day 7 of the estrous cycle (D7), between heifers ranked as either high (HF) or low (LF) for fertility. The aim of the current study was to further elucidate the underlying molecular mechanisms contributing to early embryo loss by examining differential endometrial gene expression in HF or LF heifers at a later stage of the estrous cycle; day 14 (D14). A second objective was to compare these expression profiles with those from midluteal HF and LF endometrium. Using the same animal model as employed in the previous study, we slaughtered HF and LF animals on D14, harvested endometrial tissue, and carried out global gene expression analysis using the Affymetrix Bovine GeneChip. Microarray analysis detected 430 differentially expressed genes (DEG) between HF and LF animals. Ingenuity Pathway Analysis revealed enrichment for a host of biological pathways including lipid metabolism, molecular transport, immune response, cell morphology and development, and cell growth and proliferation. Important DEG included ALB, BMPR2, CCL28, COL4A3/4, FADS1, ITGA6, LDLR, PLCB3, PPARG, PTGS2, and SLC27A4. Furthermore, DEG expressed on both D7 and D14 included: PCCB, SLC25A24, DAP, and COL4A4. This study highlights some of the pathways and mechanisms underpinning late luteal bovine endometrial physiology and endometrial-related conception rate variance.

scholarly journals The Study of Cerebrospinal Fluid microRNAs in Spinal Cord Injury and Neurodegenerative Diseases: Methodological Problems and Possible Solutions

2021 ◽  
Vol 23 (1) ◽  
pp. 114
Author(s):  
Irina Baichurina ◽  
Victor Valiullin ◽  
Victoria James ◽  
Albert Rizvanov ◽  
Yana Mukhamedshina
Keyword(s):  
Gene Expression ◽  
Spinal Cord ◽  
Spinal Cord Injury ◽  
Cerebrospinal Fluid ◽  
Neurodegenerative Diseases ◽  
Neurological Disorders ◽  
Molecular Mechanisms ◽  
Current Knowledge ◽  
Rna Isolation ◽  
Cord Injury

Despite extensive research on neurological disorders, unanswered questions remain regarding the molecular mechanisms underpinning the course of these diseases, and the search continues for effective biomarkers for early diagnosis, prognosis, or therapeutic intervention. These questions are especially acute in the study of spinal cord injury (SCI) and neurodegenerative diseases. It is believed that the changes in gene expression associated with processes triggered by neurological disorders are the result of post-transcriptional gene regulation. microRNAs (miRNAs) are key regulators of post-transcriptional gene expression and, as such, are often looked to in the search for effective biomarkers. We propose that cerebrospinal fluid (CSF) is potentially a source of biomarkers since it is in direct contact with the central nervous system and therefore may contain biomarkers indicating neurodegeneration or damage to the brain and spinal cord. However, since the abundance of miRNAs in CSF is low, their isolation and detection is technically difficult. In this review, we evaluate the findings of recent studies of CSF miRNAs as biomarkers of spinal cord injury (SCI) and neurodegenerative diseases. We also summarize the current knowledge concerning the methods of studying miRNA in CSF, including RNA isolation and normalization of the data, highlighting the caveats of these approaches and possible solutions.

scholarly journals Transcriptomics and methylomics study on the effect of iodine-containing drug FS-1 on Escherichia coli ATCC BAA-196

2020 ◽  
Author(s):  
Ilya S. Korotetskiy ◽  
Ardak B. Jumagaziyeva ◽  
Sergey V. Shilov ◽  
Tatyana V. Kuznetsova ◽  
Auyes N. Myrzabayeva ◽  
...  
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Antibiotic Therapy ◽  
Nutrient Uptake ◽  
Anaerobic Respiration ◽  
Mechanisms Of Action ◽  
Antibiotic Resistant ◽  
E Coli ◽  
Gene Expression Alterations ◽  
Increased Susceptibility

AbstractBackgroundRecent studies showed promising results on application of iodine-containing nanomicelles, FS-1, against antibiotic resistant pathogens. The effect was studied on Escherichia coli ATCC BAA-196.Materials & methodsRNA sequencing for transcriptomics and the complete genome sequencing by SMRT PacBio RS II technology followed by genome assembly and methylomics study were performed.Results & conclusionsFS-1 treated E. coli showed an increased susceptibility to antibiotics ampicillin and gentamicin. The analysis of differential gene regulation showed that possible targets of iodine-containing particles are cell membrane fatty acids and proteins, particularly cytochromes, that leads to oxidative, osmotic and acidic stresses. Cultivation with FS-1 caused gene expression alterations towards anaerobic respiration, increased anabolism and inhibition of many nutrient uptake systems. Identification of methylated nucleotides showed an altered pattern in the FS-1 treated culture. Possible role of transcriptional and epigenetic modifications in the observed increase in susceptibility to gentamicin and ampicillin were discussed.Lay abstractNew approaches of combatting drug resistance infections are in demand as the development of new antibiotics is in a deep crisis. This study was set out to investigate molecular mechanisms of action of new iodine-containing nano-micelle drug FS-1, which potentially may improve the antibiotic therapy of drug resistant infections. Iodine is one of the oldest antimicrobials and until now there were no reports on development of resistance to iodine. Recent studies showed promising results on application of iodine-containing nano-micelles against antibiotic resistant pathogens as a supplement to antibiotic therapy. The mechanisms of action, however, remain unclear. The collection strain Escherichia coli ATCC BAA-196 showing an extended spectrum of resistance to beta-lactam and aminoglycoside antibiotics was used in this study as a model organism. Antibiotic resistance patterns, whole genomes and total RNA sequences of the FS-1 treated (FS) and negative control (NC) variants of E. coli BAA-196 were obtained and analyzed. FS culture showed an increased susceptibility to antibiotics associated with profound gene expression alterations switching the bacterial metabolism to anaerobic respiration, increased anabolism, osmotic stress response and inhibition of many nutrient uptake systems. Nucleotide methylation pattern were identified in FS and NC cultures. While the numbers of methylated sites in both genomes remained similar, some peculiar alterations were observed in their distribution along chromosomal and plasmid sequences.

scholarly journals Relationship between insulin sensitivity and gene expression in human skeletal muscle

2020 ◽  
Author(s):  
Hemang Parikh ◽  
Targ Elgzyri ◽  
Amra Alibegovic ◽  
Natalie Hiscock ◽  
Ola Ekström ◽  
...  
Keyword(s):  
Gene Expression ◽  
Insulin Resistance ◽  
Skeletal Muscle ◽  
Lipid Metabolism ◽  
Insulin Sensitivity ◽  
Human Skeletal Muscle ◽  
Molecular Mechanisms ◽  
Independent Study ◽  
Nutrient Sensing ◽  
Model Assessment

Abstract Background: Insulin resistance in skeletal muscle is a key feature of the pre-diabetic state, hypertension, dyslipidemia, cardiovascular diseases and also predicts type 2 diabetes. However, the underlying molecular mechanisms are still poorly understood. Methods: To explore these mechanisms, we related global skeletal muscle gene expression profiling of 38 non-diabetic men to a surrogate measure of insulin sensitivity, i.e. homeostatic model assessment of insulin resistance (HOMA-IR). Results: We identified 70 genes positively and 110 genes inversely correlated with insulin sensitivity in human skeletal muscle, identifying autophagy-related genes as positively correlated with insulin sensitivity. Replication in an independent study of 9 non-diabetic men resulted in 10 overlapping genes that strongly correlated with insulin sensitivity, including SIRT2, involved in lipid metabolism, and FBXW5 that regulates mammalian target-of-rapamycin (mTOR) and autophagy. The expressions of SIRT2 and FBXW5 were also positively correlated with the expression of key genes promoting the phenotype of an insulin sensitive myocyte e.g. PPARGC1A. Conclusions: These data suggest that activation of genes involved in lipid metabolism, e.g. SIRT2, and genes regulating autophagy and mTOR signaling, e.g. FBXW5, are associated with increased insulin sensitivity in human skeletal muscle, reflecting a highly flexible nutrient sensing.

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