Jaime García-Mena

Genome-wide association study of type 2 diabetes in a sample from Mexico City and a meta-analysis of a Mexican-American sample from Starr County, Texas

Aims/hypothesisWe report a genome-wide association study of type 2 diabetes in an admixed sample from Mexico City and describe the results of a meta-analysis of this study and another genome-wide scan in a Mexican-American sample from Starr County, TX, USA. The top signals observed in this meta-analysis were followed up in the Diabetes Genetics Replication and Meta-analysis Consortium (DIAGRAM) and DIAGRAM+ datasets.MethodsWe analysed 967 cases and 343 normoglycaemic controls. The samples were genotyped with the Affymetrix Genome-wide Human SNP array 5.0. Associations of genotyped and imputed markers with type 2 diabetes were tested using a missing data likelihood score test. A fixed-effects meta-analysis including 1,804 cases and 780 normoglycaemic controls was carried out by weighting the effect estimates by their inverse variances.ResultsIn the meta-analysis of the two Hispanic studies, markers showing suggestive associations (p < 10−5) were identified in two known diabetes genes, HNF1A and KCNQ1, as well as in several additional regions. Meta-analysis of the two Hispanic studies and the recent DIAGRAM+ dataset identified genome-wide significant signals (p < 5 × 10−8) within or near the genes HNF1A and CDKN2A/CDKN2B, as well as suggestive associations in three additional regions, IGF2BP2, KCNQ1 and the previously unreported C14orf70.Conclusions/interpretationWe observed numerous regions with suggestive associations with type 2 diabetes. Some of these signals correspond to regions described in previous studies. However, many of these regions could not be replicated in the DIAGRAM datasets. It is critical to carry out additional studies in Hispanic and American Indian populations, which have a high prevalence of type 2 diabetes.

Candidate gene association study conditioning on individual ancestry in patients with type 2 diabetes and metabolic syndrome from Mexico City

Type 2 diabetes (T2D) is influenced by diverse environmental and genetic risk factors. Metabolic syndrome (MS) increases the risk of cardiovascular disease and diabetes. We analysed 14 cases of polymorphisms located in 10 candidate loci, in a sample of patients with T2D and controls from Mexico City.

A novel mutation in the KH domain of polynucleotide phosphorylase affects autoregulation and mRNA decay in Escherichia coli.

Polynucleotide phosphorylase (PNPase) is a key 3′–5′ exonuclease for mRNA decay in bacteria. Here, we report the isolation of a novel mutant of Escherichia coli PNPase that affects autogenous control and mRNA decay. We show that the inactivation of PNPase by a transposon insertion increases the half‐life of galactokinase mRNA encoded by a plasmid. When the bacteriophage lambda int gene retroregulator (sib/tI ) is placed between pgal and galK, it severely diminishes galactokinase expression because of transcription termination. The expression of galK from this construct is increased by a single base mutation, sib1, which causes a partial readthrough of transcription at tI. We have used this plasmid system with sib1 to select E. coli mutants that depress galK expression. Genetic and molecular analysis of one such mutant revealed that it contains a mutation in the pnp gene, which encodes the PNPase catalytic subunit α. The mutation responsible (pnp‐71 ) has substituted a highly conserved glycine residue in the KH domain of PNPase with aspartate. We show that this G‐570D substitution causes a higher accumulation of the α‐subunit as a result of defective autoregulation, thereby increasing the PNPase activity in the cell. The purified mutant α‐subunit shows the same electrophoretic mobility in denaturing gels as the wild‐type subunit, as expected. However, the mutant protein present in crude extracts displays an altered electrophoretic mobility in non‐denaturing gels that is indicative of a novel enzyme complex. We present a model for how the pnp‐71 mutation might affect autoregulation and mRNA decay based on the postulated role of the KH domain in RNA–protein and protein–protein interactions.

Analysis of the contribution of FTO , NPC1, ENPP1, NEGR1, GNPDA2 and MC4R genes to obesity in Mexican children

BackgroundRecent genome wide association studies (GWAS) and previous positional linkage studies have identified more than 50 single nucleotide polymorphisms (SNPs) associated with obesity, mostly in Europeans. We aimed to assess the contribution of some of these SNPs to obesity risk and to the variation of related metabolic traits, in Mexican children.MethodsThe association of six European obesity-related SNPs in or near FTO, NPC1, ENPP1, NEGR1, GNPDA2 and MC4R genes with risk of obesity was tested in 1,463 school-aged Mexican children (Ncases = 514; Ncontrols = 949). We also assessed effects of these SNPs on the variation of body mass index (BMI), fasting serum insulin levels, fasting plasma glucose levels, total cholesterol and triglyceride levels, in a subset of 1,171 nonobese Mexican children.ResultsWe found a significant effect of GNPDA2 rs10938397 on risk of obesity (odds ratio [OR] = 1.30; P = 1.34 × 10-3). Furthermore, we found nominal associations between obesity risk or BMI variation and the following SNPs: ENPP1 rs7754561, MC4R rs17782313 and NEGR1 rs2815752. Importantly, the at-risk alleles of both MC4R rs17782313 and NPC1 rs1805081 showed significant effect on increased fasting glucose levels (β = 0.36 mmol/L; P = 1.47 × 10-3) and decreased fasting serum insulin levels (β = −0.10 μU/mL; P = 1.21 × 10-3), respectively.ConclusionOur present results suggest that some obesity-associated SNPs previously reported in Europeans also associate with risk of obesity, or metabolic quantitative traits, in Mexican children. Importantly, we found new associations between MC4R and fasting glucose levels, and between NPC1 and fasting insulin levels.

Recognition of the 70S ribosome and polysome by the RNA degradosome in Escherichia coli

The RNA degradosome is a multi-enzyme assembly that contributes to key processes of RNA metabolism, and it engages numerous partners in serving its varied functional roles. Small domains within the assembly recognize collectively a diverse range of macromolecules, including the core protein components, the cytoplasmic lipid membrane, mRNAs, non-coding regulatory RNAs and precursors of structured RNAs. We present evidence that the degradosome can form a stable complex with the 70S ribosome and polysomes, and we demonstrate the proximity in vivo of ribosomal proteins and the scaffold of the degradosome, RNase E. The principal interactions are mapped to two, independent, RNA-binding domains from RNase E. RhlB, the RNA helicase component of the degradosome, also contributes to ribosome binding, and this is favoured through an activating interaction with RNase E. The catalytic activity of RNase E for processing 9S RNA (the ribosomal 5S RNA precursor) is repressed in the presence of the ribosome, whereas there is little affect on the cleavage of single-stranded substrates mediated by non-coding RNA, suggestings that the enzyme retains capacity to cleave unstructured substrates when associated with the ribosome. We propose that polysomes may act as antennae that enhance the rates of capture of the limited number of degradosomes, so that they become recruited to sites of active translation to act on mRNAs as they become exposed or tagged for degradation.

A Replication Study of the IRS1, CAPN10, TCF7L2, and PPARG Gene Polymorphisms Associated with Type 2 Diabetes in Two Different Populations of Mexico

Type 2 diabetes (T2D) is a chronic degenerative disease that involves the participation of several genetic and environmental factors. The objective of the study was to determine the association of the IRS1 (rs1801278), CAPN10 (rs3792267), TCF7L2 (rs7903146 and rs12255372), and PPARG (rs1801282) gene polymorphisms with T2D, in two different Mexican populations. We conducted a case‐control replication study in the state of Guerrero and in Mexico City, with 400 subjects from Guerrero and 1065 from Mexico City. Data were analyzed by logistic regression, adjusting by ancestry, age, gender, and BMI, to determine the association with T2D. Heterozygosity for the Gly972Arg variant of the IRS1 gene showed the strongest association for T2D in both analyzed samples (OR = 2.43, 95% CI 1.12–5.26 and 2.64, 95% CI 1.37–5.10, respectively). In addition, an association of two SNPs of the TCF7L2 gene with T2D was observed in both cities: rs7903146, (for Guerrero OR = 1.98 CI95% 1.02–3.89 and for Mexico OR = 1.94 CI95% 1.31–2.88) and rs12255372 (OR = 1.79 CI95% 1.08–2.97, OR = 1.78 CI95% 1.17–2.71 respectively). We suggest that our results provide strong evidence that variation in the IRS1 and TCF7L2 genes confers susceptibility to T2D in our studied populations.

Resveratrol induces downregulation of Dna repair genes in Mcf-7 human breast cancer cells

To gain insights into the antitumor mechanisms of resveratrol (RES), we carried out a DNA microarray analysis in the breast cancer cell line MCF-7 to study the global gene expression profile induced by RES treatment. The mRNA expression level of 19 734 well-characterized human genes from MCF-7 cells was determined using Affymetrix microarrays under two different RES treatments: 150 &mgr;mol/l (IC50) and 250 &mgr;mol/l during 48 h. A total of 1211 genes were found to have altered mRNA expression levels of two-fold or more in the 150 &mgr;mol/l RES-treated group (518 upregulated and 693 downregulated genes). However, 2412 genes were found to have altered expression levels of two-fold or more in the 250 &mgr;mol/l RES-treated group (651 genes upregulated and 1761 downregulated). Under both conditions of RES treatment, several genes of mismatch repair, DNA replication, homologous recombination (HR), and cell cycle were strongly inhibited. Consistently, we found decreased protein levels of the MRN complex (MRE11-NBS1-RAD50), an important complex of the HR DNA repair pathway. The ability to inhibit the expression of DNA repair genes by RES could help to overcome drug resistance commonly shown by transformed cells and to provide a solid basis for carrying out clinical trials with RES, alone or in combination with other agents, to enhance treatment efficacy, reduce toxicity, and overcome chemoresistance. Remarkably, after RES treatment, we found a decrease in NBS1 and MRE11 protein levels, two major proteins involved in HR, which suggests that RES could be used to sensitize cancer cells to cell death in combination with anticancer drugs.

Association of polymorphisms within the transforming growth factor-β1 gene with diabetic nephropathy and serum cholesterol and triglyceride concentrations.

Aim:  The TGF‐β gene participates in the development of chronic kidney disease. We investigated whether the 869 T > C, 915 G > C and −800 G > A polymorphisms of TGF‐β1 are associated with diabetic nephropathy (DN).

OIL‐REMOVAL ENHANCEMENT IN MEDIA WITH KERATINOUS OR CHITINOUS WASTES BY HYDROCARBON‐DEGRADING BACTERIA ISOLATED FROM OIL‐POLLUTED SOILS

Abstract The aim of this work was to isolate oil‐degrading bacteria that use chitin or keratin as carbon sources from oil contaminated soils; and additionally to study if oil removal by these bacteria is enhanced when a chitinous or a keratinous waste is added to the culture media. To isolate the above‐mentioned bacteria, 12 soil samples were collected close to an oil‐well. Such soils showed unsuitable nutrients content, but their counts of heterotrophic bacteria ranged within 105–108 CFU g−1 soil, of which 0.1–77% corresponded to oil hydrocarbon‐degrading ones. By sampling on plates, 109 oil‐degrading bacterial isolates were obtained. Their keratinase and chitinase activities were then screened by plate assays and spectrophotometric methods, resulting in 13 isolates that were used to integrate two mixed cultures, one keratinolytic and the other chitinolytic. These mixed cultures were grown in media with oil, or oil supplemented with chicken‐feathers or shrimp wastes. The oil‐hydrocarbon removal was measured by gas chromatography. Results showed that keratinolytic bacteria were better enzyme producers than the chitinolytic ones, and that oil removal in the presence of chicken‐feathers was 3.8 times greater than with shrimp wastes, and almost twice, in comparison with oil‐only added cultures. Identification of microorganisms from the mixed cultures by 16S rDNA, indicated the presence of seven different bacterial genera; Stenotrophomonas, Pseudomonas, Brevibacillus, Bacillus, Micrococcus, Lysobacter and Nocardiodes. These findings suggest that the isolated microorganisms and the chicken‐feather wastes could be applied to the cleaning of oil‐contaminated environments, whether in soil or water.

Association of β1 and β3 adrenergic receptors gene polymorphisms with insulin resistance and high lipid profiles related to type 2 diabetes and metabolic syndrome

BACKGROUND Among the diverse genes associated to type 2 diabetes (T2D), the β-adrenergic receptors are an excellent candidate to study in Mexican population. The objective of this work was to analyze the association of polymorphisms in ADRB1 (rs1801253) (Arg389Gly) and ADRB3 (Trp64Arg) genes with T2D and metabolic syndrome (MS). METHODS We studied 445 MS patients, 502 with T2D and 552 healthy controls. Anthropometric features and complete biochemical profile were evaluated, and Arg389Gly and Trp64Arg SNPs were determined by TaqMan assays. Data analysis was adjusted by African, Caucasian and Amerindian ancestral percentage. RESULTS The variant Arg389Gly of ADRB1 was statistically associated with an increase of LDL levels (P < 0.008), and the variant ADRB3 Trp64Arg was associated to larger HOMA-IR (P < 0.018) and with an increase of insulin levels (P < 0.001). A multiple logistic regression analysis was made in three grouping models: For ADRB3 in the codominant model Trp/Arg genotype, there was an OR of 1.53 (1.09-2.13, P < 0.003) which was increased up to OR 2.99 (1.44-6.22, P < 0.003) for the Arg/Arg genotype. Similar risk association was found under the dominant model Trp/Arg-Arg/Arg genotype with OR 1.67 (1.21-2.30; P < 0.002). In the recessive model (Arg/Arg genotype), there was also a high association OR 2.56 (1.24-5.26, P < 0.01). CONCLUSIONS The ADRB3 Trp64Arg variant is a susceptibility gene polymorphism for T2D and the ADRB1 Gly389Arg for lipid metabolism disruption. These results show that these variants are potential biomarkers for predicting metabolic alterations and evolution in diabetic and metabolic syndrome patients.