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PubMed2002

An approach for global scanning of single nucleotide variations.

Efficient global scanning of single nucleotide variations in DNA sequences between related, complex DNA samples remains a challenge. In the present article we present an approach to this problem. We have used immobilized thymidine DNA glycosylases to capture and enrich DNA fragments containing internal mismatched base pairs and separate these fragments as a pool from perfectly base-paired fragments as another pool. Enrichments of up to several hundredfold were obtained with one cycle of treatment, and all of the four groups of single nucleotide mismatches were fully covered by combining use of two thymine DNA glycosylases generated here. We have used a heterohybrid-orientating strategy for selective amplification of duplexes with one strand derived from each of two input DNA samples, which can also be used for selective amplification of duplexes with both strands derived from one of two input samples when desired. By combining these methods, the single nucleotide variations either between two DNA pools or within one DNA pool can be obtained in one process. This approach has been applied to the total cDNA from a human cell line and has several potential applications in mapping genetic variations, particularly global scanning of cDNA single nucleotide variations or polymorphisms, and finally high-throughput mapping of complex genetic traits.

Base Pair Mismatch↗
PubMed1999

Breast carcinoma: vascular density determined using CD105 antibody correlates with tumor prognosis.

Angiogenesis is essential for tumor growth and metastasis. There are conflicting reports as to whether microvessel density (IMD) in breast cancers is associated with prognosis. This could be due to the use of different antibodies to endothelial cell markers, variation in tissue pretreatment protocols, and nonstandardized counting methods. We have assessed the IMD in 106 breast carcinomas using a pan-endothelial marker, CD34, and a recently described mAb to CD105, which preferentially reacts with endothelial cell in angiogenic tissues. IMD values (separated as above or below median) for CD105 expression showed a statistically significant correlation with overall (P = 0.0029) and disease-free survival (P = 0.0362). In contrast, blood vessel counts using a panendothelial marker CD34 did not correlate with overall or disease-free survival (P = 0.2912 and P = 03153, respectively). When IMD values were subdivided into quartiles and assessed for their prognostic values, there was a statistically significant difference in the overall survival across CD105, but not CD34, values (P = 0.0017 and P = 0.7997, respectively) and also disease-free survival (P = 0.0431 and P = 0.5066, respectively). Further analysis of IMD values demonstrated that there were no deaths in the lowest quartile for CD105 and it differed from the other three quartiles. However, examination of clinical details of patients in the lowest quartile failed to reveal clustering of patients known to be associated with low-risk factors. Multivariate analysis confirmed that IMD values using CD105 were an independent prognostic factor. These results suggest that the ability to quantitatively distinguish between tumor neovascularization and preexisting vessels may be important in the assessment of tumor angiogenesis, but requires confirmation in a greater number of patients with a longer follow-up.

Adult↗
PubMed2002

Assessment of dietary adequacy for an elderly population based on a Mediterranean model.

This study analysed whether at different energy levels, a varied diet based on Mediterranean Diet patterns would meet the RDIs for specific nutrients in a population > 65 y. Based on RDIs for elderly persons > 65 y for PRO, FAT CHO, phosphorus, calcium, magnesium, iron, zinc, vitamin C, B6, folate and fibre, menu models based on Mediterranean diet food patterns were calculated for the following calorie levels: 1400, 1500, 1600, 1700 and 1800 kcals. 15 menu variations for each calorie level were then created based on the previously calculated models. Utilising the Program for Alimentation and Nutrition (PAN) database, nutritional analysis was carried out for all menus and the mean nutrient values for a 2 week period were calculated for each calorie level. Intakes at all calorie levels provided adequate amounts of folate, phosphorus, iron and Vitamin B6. Intakes were low in all groups for Calcium, Zinc, Magnesium and Vitamin E, with the exception of the 1800 kcal level for Vitamin E. Results show that at low energy levels, meeting nutrient needs was difficult and that even at higher calorie intakes, contrary to what was expected, certain nutrients were found to be inadequate.

Aged↗
PubMed2002

[Variations in chromosomal number of regenerated melon plants from somatic embryos].

Chromosomal number of different of somatic embryos regenerated plants were investigated in melon variety "xiaomaigua" and "Qingpilurou". Certain variations of chromosomal number were found among the regenerated plants compared with normal sample,and range of variation covered from 2n = 23-24 to 2n = 13-48 with the increase of generation,the rate from 3.3% to 30%. The results indicated that degree of variation in chromosomal number of somatic embryos regenerated melon plants increased with the time of culture, and those cultured in one to two months had the least variation. It was also found that degree of chromosomal number variations varied with melon varieties.

English Abstract↗
PubMed2006

[Relationship between quality of life and TCM syndrome types in patients with diabetes mellitus].

OBJECTIVE: To explore the relationship between the syndrome types differentiated by traditional Chinese medicine and the quality of life (QOL) in patients with diabetes mellitus (DM). METHODS: The QOL in patients was investigated with Short Form-36 questionnaire (SF-36), and compared with that of healthy subjects for control; the TCM syndrome type was differentiated at the same time by the outcomes of symptoms acquired from the questionnaire. RESULTS: The score of all the domains of QOL was respectively lower in the DM patients than that in the healthy subjects. The score of some domains of QOL showed correlation with different TCM syndrome types. CONCLUSION: QOL of DM patients significantly decreased. The variation of syndrome types could significantly influence some domains of QOL.

Adult↗
PubMed1991

Intraspecific variation and sexual dimorphism in cranial and dental variables among higher primates and their bearing on the hominid fossil record.

The extent and nature of dental and cranial sexual dimorphisms in extant hominoids have been investigated using reliably sexed samples of Homo sapiens (n = 75), Pan troglodytes (n = 51), Gorilla gorilla (n = 64) and Pongo pygmaeus (n = 43). Seventy nine measurements (35 dental, 16 mandibular and 28 cranial) formed the basis of the study. The patterns of mean differences and dispersions between the taxa were compared across the anatomical regions and the group structures of the separate sex samples were analysed using multivariate (PCA and CVA) analysis. Within and between group variations were compared across the taxa to investigate whether any variables were consistently effective sex or taxonomic discriminators. The study confirmed that there were differences in degree and pattern of sexual dimorphism between the extant higher primates, but the results did not substantiate the distribution of patterns as suggested by Oxnard et al. (1985); in particular there was no evidence of the dispersion differences noted by those authors. There were sufficient consistencies in the behaviour of variables across the four taxa to suggest that all canine dimensions, postcanine crown buccolingual dimensions and mandibular and cranial breadths are generally good sex discriminators, whereas some incisor dimensions, postcanine crown mesiodistal dimensions and facial heights are more effective at discriminating between the four extant taxa included in this study.

Animals↗
PubMed2004

High variety of different simian T-cell leukemia virus type 1 strains in chimpanzees (Pan troglodytes verus) of the Taï National Park, Côte d'Ivoire.

We found human T-cell leukemia virus type 1- and simian T-cell leukemia virus type 1 (STLV-1)-related infections in 5 of 10 chimpanzees originating from three groups of wild chimpanzees. The new virus isolates showed a surprising heterogeneity not only in comparison to STLV-1 described previously in other primate species but also between the different chimpanzee groups, within a group, or even between strains isolated from an individual animal. The interdisciplinary combination of virology, molecular epidemiology, and long-term behavioral studies suggests that the primary route of infection might be interspecies transmission from other primates, such as red colobus monkeys, that are hunted and consumed by chimpanzees.

Animals↗
PubMed1988

Seasonal modulation of the circadian time structure of circulating T and natural killer lymphocyte subsets from healthy subjects.

A seasonal modulation of the circadian time structure of circulating T and natural killer (NK) lymphocyte subtypes was documented in five healthy men aged 24-36 yr. Venous blood was obtained every 4 h for 24 h from each subject in January, March, June, August, and November 1984. Three subjects were also studied in April and/or August and/or November 1983 for the T subsets only. Mononuclear cells were isolated on Ficoll-Paque gradient and aliquots were incubated with OKT3, OKT4, OKT8, or HNK-1 monoclonal antibodies for characterizing all, T, T helper, T suppressor-cytotoxic, and NK lymphocytes, respectively, under an epifluorescence microscope. An effect of both sampling time and study month was statistically validated (P less than 0.01) with both two-way analysis of variance and cosinor for the peripheral counts in total, pan-T, T helper, and NK lymphocytes (cells per cubic millimeter). Seasonal changes affected both the circadian patterns and the 24-h mean values. Thus the double amplitude (total extent of variation) of the circadian rhythm in circulating total, T and T helper lymphocytes varied between 0 in March (P greater than 0.30; no rhythm) and up to 46-68% of the 24-h-mean (M) in November, with acrophases (times of maximum, 0) localized in the first half of the night (P less than 0.001). Maximal values were found at 8:30 h for both T suppressor-cytotoxic and NK lymphocytes; a smaller second peak was also found at 20:30 h, and a 12-h rhythm was validated by cosinor (P less than 0.0001), with no patient change in waveform along the year scale. A circannual rhythm was statistically validated by cosinor for total (0 in November), pan-T (0 in March), T suppressor-cytotoxic (0 in December), and NK lymphocytes (0 in October). A rhythm with a period equal to 6 mo was found for circulating T helper cells with 0 occurring both in April and October. Seasonal variations in the incidence of several immunologically related diseases may correspond to an endogenous circannual time structure.

Adult↗
PubMed1976

Phylogenetic variability of serum lipids and lipoproteins in non-human primates fed diets with different contents of dietary cholesterol.

The response of serum lipids and lipoproteins to different levels of dietary cholesterol (0.05% to 1.5% w/w) was measured in six nonhuman primate species. Relative response of serum cholesterol in different species, measured in terms of response, index, varied with dietary cholesterol concentration. The overall response for the different diets allowed ranking of the species as follows: Squirrel is greater than green is greater then spider is approximately thesus is approximately patas is greater than chimpanzee The serum cholesterol response was reflected not only in an increase in beta + pre-beta-lipoprotein cholesterol but also in alpha-lipoprotein cholesterol, with significant differences among species in the amount of cholesterol transported in the lipoprotein classes.

Animals↗
PubMed2006

Comparative genomic analysis of human and chimpanzee indicates a key role for indels in primate evolution.

Sequence comparison of humans and chimpanzees is of interest to understand the mechanisms behind primate evolution. Here we present an independent analysis of human chromosome 21 and the high-quality BAC clone sequences of the homologous chimpanzee chromosome 22. In contrast to previous studies, we have used global alignment methods and Ensembl predictions of protein coding genes (n = 224) for the analysis. Divergence due to insertions and deletions (indels) along with substitutions was examined separately for different genomic features (coding, noncoding genic, and intergenic sequence). The major part of the genomic divergence could be attributed to indels (5.07%), while the nucleotide divergence was estimated as 1.52%. Thus the total divergence was estimated as 6.58%. When excluding repeats and low-complexity DNA the total divergence decreased to 2.37%. The chromosomal distribution of nucleotide substitutions and indel events was significantly correlated. To further examine the role of indels in primate evolution we focused on coding sequences. Indels were found within the coding sequence of 13% of the genes and approximately half of the indels have not been reported previously. In 5% of the chimpanzee genes, indels or substitutions caused premature stop codons that rendered the affected transcripts nonfunctional. Taken together, our findings demonstrate that indels comprise the majority of the genomic divergence. Furthermore, indels occur frequently in coding sequences. Our results thereby support the hypothesis that indels may have a key role in primate evolution.

Animals↗
PubMed2002

PKLR- GBA region shows almost complete linkage disequilibrium over 70 kb in a set of worldwide populations.

Haplotype diversity in a genomic region of approximately 70 kb in 1q21 between genes PKLR and GBA was characterized by typing one single nucleotide polymorphism (SNP) in PKLR, two SNPs in GBA and one short tandem repeat polymorphism (STRP) in PKLR in 1792 chromosomes from 17 worldwide populations. Two other SNPs in GBA were typed in three African populations. Most chromosomes carried one of either two phylogenetically distinct haplotypes with different alleles at each site. Allele diversity at the STRP was tightly linked to haplotype background. Linkage disequilibrium (LD) was highly significant for all SNP pairs in all populations, although it was, on average, slightly higher in non-African populations than in sub-Saharan Africans. Variation at PKLR-GBA was also tightly linked to that at the GBA pseudogene, 16 kb downstream from GBA. Thus, a 90 kb-long LD block was observed, which points to a low recombination rate in this region. Detailed haplotype phylogeny suggests that the chimpanzee GBA haplotype is not one of the two most frequent haplotypes. Based on variability at the PKLR STRP and on the geographical distribution of LD, the expansion of the two main haplotypes may have predated the "Out of Africa" expansion of anatomically modern humans. LD and STRP variability in non-Africans are approximately 87% of those in Africans, in contrast with other loci; this implies that the "out of Africa" bottleneck may have had a broad distribution of effects across loci.

Africa↗
PubMed2004

Tau gene (MAPT) sequence variation among primates.

Filamentous tau deposits are a defining feature of a number of human neurodegenerative diseases. Apes and monkeys have been reported to be differentially susceptible to developing tau pathology. Despite this, only little is known about the organisation and sequence of Tau from nonhuman primates. Here we have sequenced Tau exons 1-13, including flanking intronic regions, and the region in intron 9 that contains Saitohin in chimpanzees, gorillas, and gibbons. Partial sequences were obtained for cynomolgus macaque and green monkey. Chimpanzee brain tau was 100% identical to human tau. Identities were 99.5% for gorilla tau and 99.0% for gibbon tau. Chimpanzee DNA was polymorphic for a repeat in intron 9, which was present in human and gorilla tau, and for the nucleotide at position +29 of the intron that follows exon 10. As was the case of the other nonhuman primates examined, chimpanzee DNA was homozygous for nucleotides used to define the H2 haplotype in human Tau. These differences between human and chimpanzee Tau may contribute to the apparent resistance of chimpanzee brain to developing tau pathology. Sequencing of Saitohin revealed an intact open reading frame in chimpanzee and gorilla, but not in gibbon or macaque.

Alternative Splicing↗
PubMed2000

Conservation in decay accelerating factor (DAF) structure among primates.

The decay accelerating factor (DAF, CD55) protects self cells from activation of autologous complement on their surfaces. It functions to disable the C3 convertases, the central amplification enzymes of the cascade. Its active site(s) are contained within four approximately 60 amino acid long units, termed complement control protein repeats (CCPs), which are suspended above the cell surface on a 68 amino acid long serine/threonine (S/T)-rich cushion that derives from three exons. We previously proposed a molecular model of human DAF's four CCPs in which certain amino acids were postulated to be recognition sites for the interaction between DAF and the C3 convertases. In the current study, we characterized DAF in five non-human primates: the great apes, gorilla and common chimpanzee, and the Old World monkeys: hamadryas baboon, Rhesus macaque, and patas monkey. Amino acid homology to human DAF was approximately 98% for the two great apes and 83% for the three Old World monkeys. The above cited putative ligand interactive residues were found to be fully conserved in all of the non-human primates, although there were amino acid changes outside of these areas. In the chimpanzee, alternative splicing of the S/T region was found potentially to be the source of multiple protein isoforms in erythrocytes, whereas in the patas monkey, similar alternative splicing was observed but only one protein band was seen. Interestingly, a Rhesus macaque was found to exhibit a phenomenon paralleling the human Cromer Dr(a-) blood group, in which a 44-base pair deletion in CCP3 leads to a frameshift and early STOP codon.

Alternative Splicing↗
PubMed2001

Novel alleles at the lymphotoxin alpha (LTalpha) locus mark extended HLA haplotypes in native Africans.

Genetic variations at the closely related tumor necrosis factor alpha (TNFalpha or TNF) and lymphotoxin alpha (LTalpha, formerly TNFbeta) loci have been well documented in various human populations, and several haplotypes spanning the MHC class I and class II loci are known to carry specific TNF alleles. Genotyping of the TNFc microsatellite within the first intron of LTalpha in 285 Rwandans and 319 Zambians revealed two predominant alleles, c1 at frequencies of 0.598 and 0.683 and c2 at 0.384 and 0.307, respectively. Overall, the distribution of TNFc genotypes containing the major alleles conformed well to the Hardy-Weinberg equilibrium in both cohorts. Two previously unrecognized minor TNFc alleles were also detected: the first, designated c0, was found in 10 native Africans and was the only allele present in 10 chimpanzees; the second, designated c3, was seen in 6 other African patients. Further genotyping at loci for HLA class I, class II, and for transporters associated with antigen processing, subunit 1 (TAP1) in those 16 individuals suggested a tight, stable extended haplotype involving c0 and 26Asn (LTalpha)-TNF3 (TNF promoter -238A and -308G)-DRB1*1503-DQB1*0602-TAP1.2 (333Val)-TAP1.4 (637Gly). The c3 allele was observed on another extended haplotype with 26Thr (LTalpha)-TNF1 (TNF promoter -238G and -308G)-DQB1*0102-DQB1*0501-TAP1*0101 (333Ile and 637Asp). The c3-tagged haplotype further extended to Cw*15 at the HLA class I C locus, but no specific A or B alleles could be unambiguously assigned. Positive associations between c2 homozygosity and HIV-1 seronegative status in both Rwandans and Zambians (odds ratio = 2.03 and 2.00, p = 0.04 and 0.07, respectively) had little effect on the haplotype assignments. These findings suggest a preferential expansion of the human TNFc dinucleotide (CT/AG) repeat sequence and further imply the existence of two extended MHC lineages that have not been disrupted by recombinations.

Africa↗
PubMed2000

Genetic polymorphism of IL-12 p40 gene in immune-mediated disease.

Understanding of the genetic basis of autoimmune diseases is currently incomplete. Cytokine gene polymorphisms warrant consideration as factors explaining variation in the human immune and inflammatory responses and as candidate susceptibility genes for related pathological states. Interleukin 12 (IL-12) is a key regulator of the polarisation of immune responses to T helper 1 or 2 categories and plays a role in autoimmune and infectious diseases. Using a bioinformatic strategy, we aligned cDNA and expressed sequence tag sequences to identify putative polymorphic regions of the IL-12 p40 gene. Position 1188 in the 3' untranslated region (UTR) was polymorphic with the frequency of the common allele around 80% in healthy UK Caucasoids. PCR genotyping of multiple Caucasoid groups and an African group showed significant population variation. In a case-control design, the polymorphism was not associated with rheumatoid arthritis, Felty's syndrome or large granular lymphocyte syndrome with arthritis or multiple sclerosis. A nonsignificant increase in the B allele frequency was observed in the rare large granular lymphocyte syndrome without arthritis (odds ratio 2.02 95% CI 0.95-4.3). This new genetic marker could be useful in anthropological studies and should be investigated in other autoimmune, allergic, inflammatory and infectious diseases.

Alleles↗
PubMed2001

Unusual haplotypic structure of IL8, a susceptibility locus for a common respiratory virus.

Interleukin-8 (IL8) is believed to play a role in the pathogenesis of bronchiolitis, a common viral disease of infancy, and a recent U.K. family study identified an association between this disease and the IL8-251A allele. In the present study we report data, from a different set of families, which replicate this finding; combined analysis of 194 nuclear families through use of the transmission/disequilibrium test gives P = .001. To explore the underlying genetic cause, we identified nine single-nucleotide polymorphisms (SNPs) in a 7.6-kb segment spanning the IL8 gene and its promoter region and used six of these SNPs to define the haplotypic structure of the IL8 locus. The IL8-251A allele resides on two haplotypes, only one of which is associated with disease, suggesting that this may not be the functional allele. Europeans show an unusual haplotype genealogy that is dominated by two common haplotypes differing at multiple sites, whereas Africans have much greater haplotypic diversity. These marked haplotype-frequency differences give an F(ST) of.25, and, in the European sample, both Tajima's D statistic (D = 2.58, P = .007) and the Hudson/Kreitman/Aguade test (chi(2) = 4.9, P = .03) reject neutral equilibrium, suggesting that selective pressure may have acted on this locus.

Africa↗
PubMed2003

A neutral explanation for the correlation of diversity with recombination rates in humans.

One of the most striking findings to emerge from the study of genomic patterns of variation is that regions with lower recombination rates tend to have lower levels of intraspecific diversity but not of interspecies divergence. This uncoupling of variation within and between species has been widely interpreted as evidence that natural selection shapes patterns of genetic variability genomewide. We revisited the relationship between diversity, divergence, and recombination in humans, using data from closely related species and better estimates of recombination rates than previously available. We show that regions that experience less recombination have reduced divergence to chimpanzee and to baboon, as well as lower levels of diversity. This observation suggests that mutation and recombination are associated processes in humans, so that the positive correlation between diversity and recombination may have a purely neutral explanation. Consistent with this hypothesis, diversity levels no longer increase significantly with recombination rates after correction for divergence to chimpanzee.

Animals↗
PubMed1996

Nonneutral mitochondrial DNA variation in humans and chimpanzees.

We sequenced the NADH dehydrogenase subunit 3 (ND3) gene from a sample of 61 humans, five common chimpanzees, and one gorilla to test whether patterns of mitochondrial DNA (mtDNA) variation are consistent with a neutral model of molecular evolution. Within humans and within chimpanzees, the ratio of replacement to silent nucleotide substitutions was higher than observed in comparisons between species, contrary to neutral expectations. To test the generality of this result, we reanalyzed published human RFLP data from the entire mitochondrial genome. Gains of restriction sites relative to a known human mtDNA sequence were used to infer unambiguous nucleotide substitutions. We also compared the complete mtDNA sequences of three humans. Both the RFLP data and the sequence data reveal a higher ratio of replacement to silent nucleotide substitutions within humans than is seen between species. This pattern is observed at most or all human mitochondrial genes and is inconsistent with a strictly neutral model. These data suggest that many mitochondrial protein polymorphisms are slightly deleterious, consistent with studies of human mitochondrial diseases.

Amino Acid Sequence↗