Markers for ageing or maturation in woody plants provides the possibility of identifying genotype... more Markers for ageing or maturation in woody plants provides the possibility of identifying genotypes with a prolonged juvenile phase, or to evaluate reinvigoration procedures, such as grafting of adult material. This study focuses specifically on cytokinins (Cks) as markers, due to their role in the transition process from juvenile to adult states. Previous reports from our group disclosed that the ratio of isopentenyladenine-type (iP-type) to zeatin-type (Z-type) Cks decreases during tree maturation, a maturation and ageing index being likely in Pinus radiata. Based on these results, Cks were tested in terminal buds of adult and grafted adult P. radiata material to corroborate the importance of the aforementioned balance as an index in the reinvigoration process of adult trees associated with grafting procedures. Results revealed the reversion of this index pattern parallel to the reactivation of some juvenile traits, namely, increasing values of the ratio throughout the reinvigorati...
Arteriosclerosis, thrombosis, and vascular biology, 2002
Studies in mice have shown that genetic disruption of monocyte chemotactic protein-1 or its recep... more Studies in mice have shown that genetic disruption of monocyte chemotactic protein-1 or its receptor, the C-C chemokine receptor 2 (CCR2), inhibits atherosclerosis, but few data exist in humans to suggest that the monocyte chemotactic protein-1-CCR2 interaction is important in atherogenesis. A common polymorphism in the human CCR2 gene resulting in a substitution of isoleucine for valine (Val64Ile) has been associated with other disease phenotypes in humans. A cohort of first-degree relatives of persons with premature coronary artery disease was recruited and quantitatively phenotyped for the extent of CAC, a marker of coronary atherosclerosis, by using electron beam CT. The extent of CAC was significantly lower in subjects with the CCR2-Ile64 variant (Val/Ile and Ile/Ile genotypes) than in subjects carrying 2 Val64 alleles, even after adjustment for traditional risk factors. This study provides genetic evidence linking CCR2 with coronary atherosclerosis in humans.
A newly-described syndrome called Aneurysm-Osteoarthritis Syndrome (AOS) was recently reported. A... more A newly-described syndrome called Aneurysm-Osteoarthritis Syndrome (AOS) was recently reported. AOS presents with early onset osteoarthritis (OA) in multiple joints, together with aneurysms in major arteries, and is caused by rare mutations in SMAD3. Because of the similarity of AOS to idiopathic generalized OA (GOA), we hypothesized that SMAD3 is also associated with GOA and tested the hypothesis in a population-based cohort. Study participants were derived from the Chingford study. Kellgren-Lawrence (KL) grades and the individual features of osteophytes and joint space narrowing (JSN) were scored from radiographs of hands, knees, hips, and lumbar spines. The total KL score, osteophyte score, and JSN score were calculated and used as indicators of the total burden of radiographic OA. Forty-one common SNPs within SMAD3 were genotyped using the Illumina HumanHap610Q array. Linear regression modelling was used to test the association between the total KL score, osteophyte score, and J...
Low weight at birth has previously been shown to be associated with a number of adult diseases su... more Low weight at birth has previously been shown to be associated with a number of adult diseases such as type 2 diabetes, cardiovascular disease, high blood pressure, and obesity later in life. Genome-wide association studies (GWAS) have been published for singleton-born individuals, but the role of genetic variation in birth weight (BW) in twins has not yet been fully investigated. A GWAS was performed in 4,593 female study participants with BW data available from the TwinsUK cohort. A genome-wide significant signal was found in chromosome 9, close to the NTRK2 gene (OMIM: 600456). QIMR, an Australian twin cohort (n = 3,003), and UK-based singleton-birth individuals from the Hertfordshire cohort (n = 2,997) were used as replication for the top two single nucleotide polymorphism (SNPs) underpinning this signal, rs12340987 and rs7849941. The top SNP, rs12340987, was found to be in the same direction in the Australian twins and in the singleton-born females (fixed effects meta-analysis beta = -0.13, SE = 0.02, and p = 1.48 × 10-8) but not in the singleton-born males tested. These findings provide an important insight into the genetic component of BW in twins who are normally excluded due to their lower BW when compared with singleton births, as well as the difference in BW between twins. The NTRK2 gene identified in this study has previously been associated with obesity.
The journals of gerontology. Series A, Biological sciences and medical sciences, Jan 14, 2014
To elucidate the proteomic features of aging in plasma, the subproteome targeted by the SOMAscan ... more To elucidate the proteomic features of aging in plasma, the subproteome targeted by the SOMAscan assay was profiled in blood samples from 202 females from the TwinsUK cohort. Findings were replicated in 677 independent individuals from the AddNeuroMed, Alzheimer's Research UK, and Dementia Case Registry cohorts. Results were further validated using RNAseq data from whole blood in TwinsUK and the most significant proteins were tested for association with aging-related phenotypes after adjustment for age. Eleven proteins were associated with chronological age and were replicated at protein level in an independent population. These were further investigated at gene expression level in 384 females from the TwinsUK cohort. The two most strongly associated proteins were chordin-like protein 1 (meta-analysis β [SE] = 0.013 [0.001], p = 3.66 × 10(-46)) and pleiotrophin (0.012 [0.005], p = 3.88 × 10(-41)). Chordin-like protein 1 was also significantly correlated with birthweight (0.06 [0...
The analysis of rich catalogues of genetic variation from population-based sequencing provides an... more The analysis of rich catalogues of genetic variation from population-based sequencing provides an opportunity to screen for functional effects. Here we report a rare variant in APOC3 (rs138326449-A, minor allele frequency ~0.25% (UK)) associated with plasma triglyceride (TG) levels (-1.43 s.d. (s.e.=0.27 per minor allele (P-value=8.0 × 10(-8))) discovered in 3,202 individuals with low read-depth, whole-genome sequence. We replicate this in 12,831 participants from five additional samples of Northern and Southern European origin (-1.0 s.d. (s.e.=0.173), P-value=7.32 × 10(-9)). This is consistent with an effect between 0.5 and 1.5 mmol l(-1) dependent on population. We show that a single predicted splice donor variant is responsible for association signals and is independent of known common variants. Analyses suggest an independent relationship between rs138326449 and high-density lipoprotein (HDL) levels. This represents one of the first examples of a rare, large effect variant ident...
Age-related changes in DNA methylation have been implicated in cellular senescence and longevity,... more Age-related changes in DNA methylation have been implicated in cellular senescence and longevity, yet the causes and functional consequences of these variants remain unclear. To elucidate the role of age-related epigenetic changes in healthy ageing and potential longevity, we tested for association between whole-blood DNA methylation patterns in 172 female twins aged 32 to 80 with age and age-related phenotypes. Twin-based DNA methylation levels at 26,690 CpG-sites showed evidence for mean genome-wide heritability of 18%, which was supported by the identification of 1,537 CpG-sites with methylation QTLs in cis at FDR 5%. We performed genome-wide analyses to discover differentially methylated regions (DMRs) for sixteen age-related phenotypes (ap-DMRs) and chronological age (a-DMRs). Epigenome-wide association scans (EWAS) identified age-related phenotype DMRs (ap-DMRs) associated with LDL (STAT5A), lung function (WT1), and maternal longevity (ARL4A, TBX20). In contrast, EWAS for chronological age identified hundreds of predominantly hyper-methylated age DMRs (490 a-DMRs at FDR 5%), of which only one (TBX20) was also associated with an age-related phenotype. Therefore, the majority of age-related changes in DNA methylation are not associated with phenotypic measures of healthy ageing in later life. We replicated a large proportion of a-DMRs in a sample of 44 younger adult MZ twins aged 20 to 61, suggesting that a-DMRs may initiate at an earlier age. We next explored potential genetic and environmental mechanisms underlying a-DMRs and ap-DMRs. Genome-wide overlap across cis-meQTLs, genotype-phenotype associations, and EWAS ap-DMRs identified CpG-sites that had cis-meQTLs with evidence for genotype-phenotype association, where the CpG-site was also an ap-DMR for the same phenotype. Monozygotic twin methylation difference analyses identified one potential environmentally-mediated ap-DMR associated with total cholesterol and LDL (CSMD1). Our results suggest that in a small set of genes DNA methylation may be a candidate mechanism of mediating not only environmental, but also genetic effects on age-related phenotypes.
A Trypanosoma cruzi small subunit ribosomal RNA gene was sequenced from genomic recombinant plasm... more A Trypanosoma cruzi small subunit ribosomal RNA gene was sequenced from genomic recombinant plasmid clones. The assigned coding region was 2319 bp, the longest SSU rRNA gene described to date. On the basis of comparisons with published sequences from Crithidiafasciculata, Trypanosoma brucei, and Leishmania donovani, we conclude that the extra nucleotides in the T. cruzi gene occur in highly variable regions of rRNA genes. A phylogenetic analysis was performed with the SSU rRNA sequences from these four trypanosomatids and from Euglena gracilis as an outgroup. The Leishmania and Crithidia sequences were remarkably similar to each other (not separable statistically). Given the standard errors associated with the branching order of the two Trypanosoma species and the Leishmania-Crithidia branch, the actual topology cannot be unequivocally determined using only the ribosomal sequences analyzed here.
Osteoarthritis (OA) is the most prevalent form of arthritis in the elderly. A large body of evide... more Osteoarthritis (OA) is the most prevalent form of arthritis in the elderly. A large body of evidence, including familial aggregation and classic twin studies, indicates that primary OA has a strong hereditary component that is likely polygenic in nature. Traits related to OA, such as longitudinal changes in cartilage volume and progression of radiographic features, are also under genetic control. In recent years several linkage analyses and candidate gene studies have been performed and unveiled some of the specific genes involved in disease risk, such as FRZB and GDF5. This article discusses the impact that future genome-wide association scans can have on our understanding of the pathogenesis of OA and on identifying individuals at high risk for developing severe OA.
We evaluated the capacity of the plant growth regulator thidiazuron (TDZ), a substituted phenylur... more We evaluated the capacity of the plant growth regulator thidiazuron (TDZ), a substituted phenylurea with high cytokinin-like activity, to promote organogenesis in petals and leaves of several carnation cultivars (Dianthus spp.), combined with 1-naphthaleneacetic acid (NAA). The involvement of the endogenous auxin indole-3-acetic acid (IAA) and purine-type cytokinins was also studied. Shoot differentiation was found to depend on the explant, cultivar and balance of growth regulators. TDZ alone (0.5 and 5.0 µmol/L) as well as synergistically with NAA (0.5 and 5.0 µmol/L) promoted shoot organogenesis in petals, and was more active than N 6 -benzyladenine. In petals of the White Sim cultivar, TDZ induced cell proliferation in a concentration-dependent manner and, on day 7 of culture, the proportion of meristematic regions in those petals allowed the prediction of shoot regeneration capacity after 30 days of culture. Immunolocalization of CK ribosides, N 6 -(∆ 2 -isopentenyl)adenosine, zeatin riboside (ZR) and dihydrozeatin riboside (DHZR), in organogenic petals showed them to be highly concentrated in the tips of bud primordia and in the regions with proliferation capacity. All of them may play a role in cell proliferation, and possibly in differentiation, during the organogenic process. After seven days of culture of White Sim petals, NAA may account for the changes found in the levels of IAA and DHZR, whereas TDZ may be responsible for the remarkable increases in N 6 -(∆ 2 -isopentenyl)adenine (iP) and ZR. ZR is induced by low TDZ concentrations (0.0 -0.005 µmol/L), whereas iP, that correlates with massive cell proliferation and the onset of shoot differentiation, is associated with high TDZ levels (0.5 µmol/L). In addition to the changes observed in quantification and in situ localization of endogenous phytohormones during TDZ-induced shoot organogenesis, we propose that TDZ also promotes growth directly, through its own biological activity. To our knowledge, this study is the first to evaluate the effect of TDZ on endogenous phytohormones in an organogenic process.
The Journals of Gerontology Series A: Biological Sciences and Medical Sciences, 2013
Fine structural details of glycans attached to the conserved N-glycosylation site significantly n... more Fine structural details of glycans attached to the conserved N-glycosylation site significantly not only affect function of individual immunoglobulin G (IgG) molecules but also mediate inflammation at the systemic level. By analyzing IgG glycosylation in 5,117 individuals from four European populations, we have revealed very complex patterns of changes in IgG glycosylation with age. Several IgG glycans (including FA2B, FA2G2, and FA2BG2) changed considerably with age and the combination of these three glycans can explain up to 58% of variance in chronological age, significantly more than other markers of biological age like telomere lengths. The remaining variance in these glycans strongly correlated with physiological parameters associated with biological age. Thus, IgG glycosylation appears to be closely linked with both chronological and biological ages. Considering the important role of IgG glycans in inflammation, and because the observed changes with age promote inflammation, changes in IgG glycosylation also seem to represent a factor contributing to aging.
The Journal of Clinical Endocrinology & Metabolism, 2006
Leukocyte telomere length is inversely correlated with age, insulin resistance, serum leptin, and... more Leukocyte telomere length is inversely correlated with age, insulin resistance, serum leptin, and smoking. We explored whether menopausal status modifies the relations between leukocyte telomere length and insulin resistance. In addition, we examined the effect of menopause on the relation between leukocyte telomere length and C-reactive protein (CRP), an index of inflammation. This was an observational cohort study. The study setting was community based. A total of 1517 women aged 18-79 yr selected only for belonging to a twin pair and representative of the general population participated in the study. Leukocyte telomere restriction fragment length (TRFL) was measured. Insulin resistance (expressed in the homeostasis model assessment), leptin, and CRP were inversely correlated with leukocyte TRFL in premenopausal but not postmenopausal women. Insulin resistance, CRP, but not leptin independently accounted for variation in white blood cell TRFL in premenopausal women. Menopausal status impacts leukocyte telomere length and its relation with insulin resistance and inflammation in women.
Codon bias and base composition in major histocompatibility complex (MHC) sequences have been stu... more Codon bias and base composition in major histocompatibility complex (MHC) sequences have been studied for both class I and II loci in Homo sapiens and Pan troglodytes. There is low to moderate codon bias for the MHC of humans and chimpanzees. In the class I loci, the same level of moderate codon bias is seen for HLA-B, HLA-C, Patr-A, Patr-B, and Patr-C, while at HLA-A the level of codon bias is lower. There is a correlation between codon usage bias and G+C content in the A and B loci in humans and chimps, but not at the C locus. To examine the effect of diversifying selection on codon bias, we subdivided class I alleles into antigen recognition site (ARS) and non-ARS codons. ARS codons had lower bias than non-ARS codons. This may indicate that the constraint of codon bias on nucleotide substitution may be selected against in ARS codons. At the class II loci, there are distinct differences between alpha and beta chain genes with respect to codon usage, with the beta chain genes being much more biased. Species-specific differences in base composition were seen in exon 2 at the DRB1 locus, with lower GC content in chimpanzees. Considering the complex evolutionary history of MHC genes, the study of codon usage patterns provides us with a better understanding of both the evolutionary history of these genes and the evolution of synonymous codon usage in genes under natural selection.
DNA diagnostics has been progressively moving from expensive, low-throughput, multi-step methods ... more DNA diagnostics has been progressively moving from expensive, low-throughput, multi-step methods towards inexpensive, robust, and high-throughput methods. Here we describe the further validation and refinement of a recently described novel genotyping method that has the latter characteristics. An evolved form of allele-specific PCR, the method generates a fluorescent signal through the use of universal labeled primers, which can be quantified directly from microplates using standard plate readers. We have applied the method successfully to a test set of 12 novel single nucleotide polymorphisms (SNPs) on a panel of 47 individuals using low reaction volumes. We demonstrate that the method is extremely accurate, robust, and can be optimized in a simple and predictable manner. By conducting the assay in closed-tube format, the potential for contamination is reduced to a minimum. By virtue of its simplicity, the method is versatile and cost-effective with potential for use in industrial-scale genetic studies or in the clinical diagnostic setting.
HTLVI/ HTLVII are human oncoviridae causally associated with adult T cell leukaemia /lymphoma. Th... more HTLVI/ HTLVII are human oncoviridae causally associated with adult T cell leukaemia /lymphoma. They are endemic in Central/South-America where they show geographic clustering: HTLVI among native Amerindians (Andean highlands and Brazilian coast); HTLVII predominates in the lowlands, its prevalence in Yucatan, Mexico is 0.3%. The aim of this study was to assess the prevalence of HTLV I/II antibodies in the Mexican Mestizo and in several native groups: Mixteco from Oaxaca, of the southwest (Nϭ55), Seri from Sonora of the northwest (Nϭ102), Lacandon from the jungle of Chiapas in the southeast (Nϭ175) and Mestizo (Nϭ118). We used the Innogenetics INNO-LIA HTLV I/II Score. It allows the detection of HTLV I/II antibodies in serum/plasma. It also differentiates between HTLVI/HTLVII types.The assay uses recombinant/synthetic peptides derived from HTLVI/II immunodominant proteins. The type-specific antigens for HTLV-I (gag p19-I, env gp46-I) and for HTLV-II (env gp46-II) differentiate between types. The intensity of the reaction on the control lines on each strip is the baseline to assign the reactivity for each antigen on that strip. All populations showed negative results except for the Lacandon in whom 1 individual was found positive and 5 were indeterminates (0.03% including the latter). Every individual was typed for DRB1/DQA1/ DQB1 and most of them for A*; B*, C* alleles. Interestingly, the 4/6 Lacandon typed for class I loci, shared B*4002. The data are concordant with those found in Latin America. The expectation was to detect HTLVI/II in the Southeast more than in the rest of Mexico, being a tropical area. The relation with class I alleles in them, agrees with the genetic control of humoral response against viruses.
Markers for ageing or maturation in woody plants provides the possibility of identifying genotype... more Markers for ageing or maturation in woody plants provides the possibility of identifying genotypes with a prolonged juvenile phase, or to evaluate reinvigoration procedures, such as grafting of adult material. This study focuses specifically on cytokinins (Cks) as markers, due to their role in the transition process from juvenile to adult states. Previous reports from our group disclosed that the ratio of isopentenyladenine-type (iP-type) to zeatin-type (Z-type) Cks decreases during tree maturation, a maturation and ageing index being likely in Pinus radiata. Based on these results, Cks were tested in terminal buds of adult and grafted adult P. radiata material to corroborate the importance of the aforementioned balance as an index in the reinvigoration process of adult trees associated with grafting procedures. Results revealed the reversion of this index pattern parallel to the reactivation of some juvenile traits, namely, increasing values of the ratio throughout the reinvigorati...
Arteriosclerosis, thrombosis, and vascular biology, 2002
Studies in mice have shown that genetic disruption of monocyte chemotactic protein-1 or its recep... more Studies in mice have shown that genetic disruption of monocyte chemotactic protein-1 or its receptor, the C-C chemokine receptor 2 (CCR2), inhibits atherosclerosis, but few data exist in humans to suggest that the monocyte chemotactic protein-1-CCR2 interaction is important in atherogenesis. A common polymorphism in the human CCR2 gene resulting in a substitution of isoleucine for valine (Val64Ile) has been associated with other disease phenotypes in humans. A cohort of first-degree relatives of persons with premature coronary artery disease was recruited and quantitatively phenotyped for the extent of CAC, a marker of coronary atherosclerosis, by using electron beam CT. The extent of CAC was significantly lower in subjects with the CCR2-Ile64 variant (Val/Ile and Ile/Ile genotypes) than in subjects carrying 2 Val64 alleles, even after adjustment for traditional risk factors. This study provides genetic evidence linking CCR2 with coronary atherosclerosis in humans.
A newly-described syndrome called Aneurysm-Osteoarthritis Syndrome (AOS) was recently reported. A... more A newly-described syndrome called Aneurysm-Osteoarthritis Syndrome (AOS) was recently reported. AOS presents with early onset osteoarthritis (OA) in multiple joints, together with aneurysms in major arteries, and is caused by rare mutations in SMAD3. Because of the similarity of AOS to idiopathic generalized OA (GOA), we hypothesized that SMAD3 is also associated with GOA and tested the hypothesis in a population-based cohort. Study participants were derived from the Chingford study. Kellgren-Lawrence (KL) grades and the individual features of osteophytes and joint space narrowing (JSN) were scored from radiographs of hands, knees, hips, and lumbar spines. The total KL score, osteophyte score, and JSN score were calculated and used as indicators of the total burden of radiographic OA. Forty-one common SNPs within SMAD3 were genotyped using the Illumina HumanHap610Q array. Linear regression modelling was used to test the association between the total KL score, osteophyte score, and J...
Low weight at birth has previously been shown to be associated with a number of adult diseases su... more Low weight at birth has previously been shown to be associated with a number of adult diseases such as type 2 diabetes, cardiovascular disease, high blood pressure, and obesity later in life. Genome-wide association studies (GWAS) have been published for singleton-born individuals, but the role of genetic variation in birth weight (BW) in twins has not yet been fully investigated. A GWAS was performed in 4,593 female study participants with BW data available from the TwinsUK cohort. A genome-wide significant signal was found in chromosome 9, close to the NTRK2 gene (OMIM: 600456). QIMR, an Australian twin cohort (n = 3,003), and UK-based singleton-birth individuals from the Hertfordshire cohort (n = 2,997) were used as replication for the top two single nucleotide polymorphism (SNPs) underpinning this signal, rs12340987 and rs7849941. The top SNP, rs12340987, was found to be in the same direction in the Australian twins and in the singleton-born females (fixed effects meta-analysis beta = -0.13, SE = 0.02, and p = 1.48 × 10-8) but not in the singleton-born males tested. These findings provide an important insight into the genetic component of BW in twins who are normally excluded due to their lower BW when compared with singleton births, as well as the difference in BW between twins. The NTRK2 gene identified in this study has previously been associated with obesity.
The journals of gerontology. Series A, Biological sciences and medical sciences, Jan 14, 2014
To elucidate the proteomic features of aging in plasma, the subproteome targeted by the SOMAscan ... more To elucidate the proteomic features of aging in plasma, the subproteome targeted by the SOMAscan assay was profiled in blood samples from 202 females from the TwinsUK cohort. Findings were replicated in 677 independent individuals from the AddNeuroMed, Alzheimer's Research UK, and Dementia Case Registry cohorts. Results were further validated using RNAseq data from whole blood in TwinsUK and the most significant proteins were tested for association with aging-related phenotypes after adjustment for age. Eleven proteins were associated with chronological age and were replicated at protein level in an independent population. These were further investigated at gene expression level in 384 females from the TwinsUK cohort. The two most strongly associated proteins were chordin-like protein 1 (meta-analysis β [SE] = 0.013 [0.001], p = 3.66 × 10(-46)) and pleiotrophin (0.012 [0.005], p = 3.88 × 10(-41)). Chordin-like protein 1 was also significantly correlated with birthweight (0.06 [0...
The analysis of rich catalogues of genetic variation from population-based sequencing provides an... more The analysis of rich catalogues of genetic variation from population-based sequencing provides an opportunity to screen for functional effects. Here we report a rare variant in APOC3 (rs138326449-A, minor allele frequency ~0.25% (UK)) associated with plasma triglyceride (TG) levels (-1.43 s.d. (s.e.=0.27 per minor allele (P-value=8.0 × 10(-8))) discovered in 3,202 individuals with low read-depth, whole-genome sequence. We replicate this in 12,831 participants from five additional samples of Northern and Southern European origin (-1.0 s.d. (s.e.=0.173), P-value=7.32 × 10(-9)). This is consistent with an effect between 0.5 and 1.5 mmol l(-1) dependent on population. We show that a single predicted splice donor variant is responsible for association signals and is independent of known common variants. Analyses suggest an independent relationship between rs138326449 and high-density lipoprotein (HDL) levels. This represents one of the first examples of a rare, large effect variant ident...
Age-related changes in DNA methylation have been implicated in cellular senescence and longevity,... more Age-related changes in DNA methylation have been implicated in cellular senescence and longevity, yet the causes and functional consequences of these variants remain unclear. To elucidate the role of age-related epigenetic changes in healthy ageing and potential longevity, we tested for association between whole-blood DNA methylation patterns in 172 female twins aged 32 to 80 with age and age-related phenotypes. Twin-based DNA methylation levels at 26,690 CpG-sites showed evidence for mean genome-wide heritability of 18%, which was supported by the identification of 1,537 CpG-sites with methylation QTLs in cis at FDR 5%. We performed genome-wide analyses to discover differentially methylated regions (DMRs) for sixteen age-related phenotypes (ap-DMRs) and chronological age (a-DMRs). Epigenome-wide association scans (EWAS) identified age-related phenotype DMRs (ap-DMRs) associated with LDL (STAT5A), lung function (WT1), and maternal longevity (ARL4A, TBX20). In contrast, EWAS for chronological age identified hundreds of predominantly hyper-methylated age DMRs (490 a-DMRs at FDR 5%), of which only one (TBX20) was also associated with an age-related phenotype. Therefore, the majority of age-related changes in DNA methylation are not associated with phenotypic measures of healthy ageing in later life. We replicated a large proportion of a-DMRs in a sample of 44 younger adult MZ twins aged 20 to 61, suggesting that a-DMRs may initiate at an earlier age. We next explored potential genetic and environmental mechanisms underlying a-DMRs and ap-DMRs. Genome-wide overlap across cis-meQTLs, genotype-phenotype associations, and EWAS ap-DMRs identified CpG-sites that had cis-meQTLs with evidence for genotype-phenotype association, where the CpG-site was also an ap-DMR for the same phenotype. Monozygotic twin methylation difference analyses identified one potential environmentally-mediated ap-DMR associated with total cholesterol and LDL (CSMD1). Our results suggest that in a small set of genes DNA methylation may be a candidate mechanism of mediating not only environmental, but also genetic effects on age-related phenotypes.
A Trypanosoma cruzi small subunit ribosomal RNA gene was sequenced from genomic recombinant plasm... more A Trypanosoma cruzi small subunit ribosomal RNA gene was sequenced from genomic recombinant plasmid clones. The assigned coding region was 2319 bp, the longest SSU rRNA gene described to date. On the basis of comparisons with published sequences from Crithidiafasciculata, Trypanosoma brucei, and Leishmania donovani, we conclude that the extra nucleotides in the T. cruzi gene occur in highly variable regions of rRNA genes. A phylogenetic analysis was performed with the SSU rRNA sequences from these four trypanosomatids and from Euglena gracilis as an outgroup. The Leishmania and Crithidia sequences were remarkably similar to each other (not separable statistically). Given the standard errors associated with the branching order of the two Trypanosoma species and the Leishmania-Crithidia branch, the actual topology cannot be unequivocally determined using only the ribosomal sequences analyzed here.
Osteoarthritis (OA) is the most prevalent form of arthritis in the elderly. A large body of evide... more Osteoarthritis (OA) is the most prevalent form of arthritis in the elderly. A large body of evidence, including familial aggregation and classic twin studies, indicates that primary OA has a strong hereditary component that is likely polygenic in nature. Traits related to OA, such as longitudinal changes in cartilage volume and progression of radiographic features, are also under genetic control. In recent years several linkage analyses and candidate gene studies have been performed and unveiled some of the specific genes involved in disease risk, such as FRZB and GDF5. This article discusses the impact that future genome-wide association scans can have on our understanding of the pathogenesis of OA and on identifying individuals at high risk for developing severe OA.
We evaluated the capacity of the plant growth regulator thidiazuron (TDZ), a substituted phenylur... more We evaluated the capacity of the plant growth regulator thidiazuron (TDZ), a substituted phenylurea with high cytokinin-like activity, to promote organogenesis in petals and leaves of several carnation cultivars (Dianthus spp.), combined with 1-naphthaleneacetic acid (NAA). The involvement of the endogenous auxin indole-3-acetic acid (IAA) and purine-type cytokinins was also studied. Shoot differentiation was found to depend on the explant, cultivar and balance of growth regulators. TDZ alone (0.5 and 5.0 µmol/L) as well as synergistically with NAA (0.5 and 5.0 µmol/L) promoted shoot organogenesis in petals, and was more active than N 6 -benzyladenine. In petals of the White Sim cultivar, TDZ induced cell proliferation in a concentration-dependent manner and, on day 7 of culture, the proportion of meristematic regions in those petals allowed the prediction of shoot regeneration capacity after 30 days of culture. Immunolocalization of CK ribosides, N 6 -(∆ 2 -isopentenyl)adenosine, zeatin riboside (ZR) and dihydrozeatin riboside (DHZR), in organogenic petals showed them to be highly concentrated in the tips of bud primordia and in the regions with proliferation capacity. All of them may play a role in cell proliferation, and possibly in differentiation, during the organogenic process. After seven days of culture of White Sim petals, NAA may account for the changes found in the levels of IAA and DHZR, whereas TDZ may be responsible for the remarkable increases in N 6 -(∆ 2 -isopentenyl)adenine (iP) and ZR. ZR is induced by low TDZ concentrations (0.0 -0.005 µmol/L), whereas iP, that correlates with massive cell proliferation and the onset of shoot differentiation, is associated with high TDZ levels (0.5 µmol/L). In addition to the changes observed in quantification and in situ localization of endogenous phytohormones during TDZ-induced shoot organogenesis, we propose that TDZ also promotes growth directly, through its own biological activity. To our knowledge, this study is the first to evaluate the effect of TDZ on endogenous phytohormones in an organogenic process.
The Journals of Gerontology Series A: Biological Sciences and Medical Sciences, 2013
Fine structural details of glycans attached to the conserved N-glycosylation site significantly n... more Fine structural details of glycans attached to the conserved N-glycosylation site significantly not only affect function of individual immunoglobulin G (IgG) molecules but also mediate inflammation at the systemic level. By analyzing IgG glycosylation in 5,117 individuals from four European populations, we have revealed very complex patterns of changes in IgG glycosylation with age. Several IgG glycans (including FA2B, FA2G2, and FA2BG2) changed considerably with age and the combination of these three glycans can explain up to 58% of variance in chronological age, significantly more than other markers of biological age like telomere lengths. The remaining variance in these glycans strongly correlated with physiological parameters associated with biological age. Thus, IgG glycosylation appears to be closely linked with both chronological and biological ages. Considering the important role of IgG glycans in inflammation, and because the observed changes with age promote inflammation, changes in IgG glycosylation also seem to represent a factor contributing to aging.
The Journal of Clinical Endocrinology & Metabolism, 2006
Leukocyte telomere length is inversely correlated with age, insulin resistance, serum leptin, and... more Leukocyte telomere length is inversely correlated with age, insulin resistance, serum leptin, and smoking. We explored whether menopausal status modifies the relations between leukocyte telomere length and insulin resistance. In addition, we examined the effect of menopause on the relation between leukocyte telomere length and C-reactive protein (CRP), an index of inflammation. This was an observational cohort study. The study setting was community based. A total of 1517 women aged 18-79 yr selected only for belonging to a twin pair and representative of the general population participated in the study. Leukocyte telomere restriction fragment length (TRFL) was measured. Insulin resistance (expressed in the homeostasis model assessment), leptin, and CRP were inversely correlated with leukocyte TRFL in premenopausal but not postmenopausal women. Insulin resistance, CRP, but not leptin independently accounted for variation in white blood cell TRFL in premenopausal women. Menopausal status impacts leukocyte telomere length and its relation with insulin resistance and inflammation in women.
Codon bias and base composition in major histocompatibility complex (MHC) sequences have been stu... more Codon bias and base composition in major histocompatibility complex (MHC) sequences have been studied for both class I and II loci in Homo sapiens and Pan troglodytes. There is low to moderate codon bias for the MHC of humans and chimpanzees. In the class I loci, the same level of moderate codon bias is seen for HLA-B, HLA-C, Patr-A, Patr-B, and Patr-C, while at HLA-A the level of codon bias is lower. There is a correlation between codon usage bias and G+C content in the A and B loci in humans and chimps, but not at the C locus. To examine the effect of diversifying selection on codon bias, we subdivided class I alleles into antigen recognition site (ARS) and non-ARS codons. ARS codons had lower bias than non-ARS codons. This may indicate that the constraint of codon bias on nucleotide substitution may be selected against in ARS codons. At the class II loci, there are distinct differences between alpha and beta chain genes with respect to codon usage, with the beta chain genes being much more biased. Species-specific differences in base composition were seen in exon 2 at the DRB1 locus, with lower GC content in chimpanzees. Considering the complex evolutionary history of MHC genes, the study of codon usage patterns provides us with a better understanding of both the evolutionary history of these genes and the evolution of synonymous codon usage in genes under natural selection.
DNA diagnostics has been progressively moving from expensive, low-throughput, multi-step methods ... more DNA diagnostics has been progressively moving from expensive, low-throughput, multi-step methods towards inexpensive, robust, and high-throughput methods. Here we describe the further validation and refinement of a recently described novel genotyping method that has the latter characteristics. An evolved form of allele-specific PCR, the method generates a fluorescent signal through the use of universal labeled primers, which can be quantified directly from microplates using standard plate readers. We have applied the method successfully to a test set of 12 novel single nucleotide polymorphisms (SNPs) on a panel of 47 individuals using low reaction volumes. We demonstrate that the method is extremely accurate, robust, and can be optimized in a simple and predictable manner. By conducting the assay in closed-tube format, the potential for contamination is reduced to a minimum. By virtue of its simplicity, the method is versatile and cost-effective with potential for use in industrial-scale genetic studies or in the clinical diagnostic setting.
HTLVI/ HTLVII are human oncoviridae causally associated with adult T cell leukaemia /lymphoma. Th... more HTLVI/ HTLVII are human oncoviridae causally associated with adult T cell leukaemia /lymphoma. They are endemic in Central/South-America where they show geographic clustering: HTLVI among native Amerindians (Andean highlands and Brazilian coast); HTLVII predominates in the lowlands, its prevalence in Yucatan, Mexico is 0.3%. The aim of this study was to assess the prevalence of HTLV I/II antibodies in the Mexican Mestizo and in several native groups: Mixteco from Oaxaca, of the southwest (Nϭ55), Seri from Sonora of the northwest (Nϭ102), Lacandon from the jungle of Chiapas in the southeast (Nϭ175) and Mestizo (Nϭ118). We used the Innogenetics INNO-LIA HTLV I/II Score. It allows the detection of HTLV I/II antibodies in serum/plasma. It also differentiates between HTLVI/HTLVII types.The assay uses recombinant/synthetic peptides derived from HTLVI/II immunodominant proteins. The type-specific antigens for HTLV-I (gag p19-I, env gp46-I) and for HTLV-II (env gp46-II) differentiate between types. The intensity of the reaction on the control lines on each strip is the baseline to assign the reactivity for each antigen on that strip. All populations showed negative results except for the Lacandon in whom 1 individual was found positive and 5 were indeterminates (0.03% including the latter). Every individual was typed for DRB1/DQA1/ DQB1 and most of them for A*; B*, C* alleles. Interestingly, the 4/6 Lacandon typed for class I loci, shared B*4002. The data are concordant with those found in Latin America. The expectation was to detect HTLVI/II in the Southeast more than in the rest of Mexico, being a tropical area. The relation with class I alleles in them, agrees with the genetic control of humoral response against viruses.
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