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PubMed1983

Variable restriction endonuclease sites of herpes simplex virus type 1 isolates from encephalitic, facial and genital lesions and ganglia.

The distribution of restriction endonuclease (RE) sites was compared for 84 herpes simplex virus type 1 (HSV-1) isolates obtained from the ganglia, facial lesions, genital lesions and from brain tissue from herpes encephalitis cases. The isolates came from Canada, the U.K., the U.S.A. and Japan. Out of a total of 224 sites identified, 87 were variable. Three of the 30 most variable sites were at significantly (P less than 0.05) different frequencies in groups of isolates from distinct anatomical sites of isolation; one of these, and a further two sites, were at significantly different frequencies in groups from distinct geographical origins. There are at least two inter-related linkage groups. However, most of the site combinations appear to be random. The variability of RE sites in contiguous genome segments, which include both non-coding and coding sequences, show a marked heterogeneity, indicating that some viral gene sequences are more variable than others. The three RE sites at different frequencies in viral groups from distinct anatomical sites of isolation are in two genome segments: map units 27 to 35 and 50 to 57. We infer from the observed associations with anatomical site of viral isolation that part of at least one of these segments may modulate viral virulence in man following infection.

Base Sequence↗

PubMed1992

Expectation maximization algorithm for identifying protein-binding sites with variable lengths from unaligned DNA fragments.

An Expectation Maximization algorithm for identification of DNA binding sites is presented. The approach predicts the location of binding regions while allowing variable length spacers within the sites. In addition to predicting the most likely spacer length for a set of DNA fragments, the method identifies individual sites that differ in spacer size. No alignment of DNA sequences is necessary. The method is illustrated by application to 231 Escherichia coli DNA fragments known to contain promoters with variable spacings between their consensus regions. Maximum-likelihood tests of the differences between the spacing classes indicate that the consensus regions of the spacing classes are not distinct. Further tests suggest that several positions within the spacing region may contribute to promoter specificity.

Algorithms↗

PubMed2001

Y-chromosome mismatch distributions in Europe.

Ancient demographic events can be inferred from the distribution of pairwise sequence differences (or mismatches) among individuals. We analyzed a database of 3,677 Y chromosomes typed for 11 biallelic markers in 48 human populations from Europe and the Mediterranean area. Contrary to what is observed in the analysis of mitochondrial polymorphisms, Tajima's test was insignificant for most Y-chromosome samples, and in 47 populations the mismatch distributions had multiple peaks. Taken at face value, these results would suggest either (1) that the size of the male population stayed essentially constant over time, while the female population size increased, or (2) that different selective regimes have shaped mitochondrial and Y-chromosome diversity, leading to an excess of rare alleles only in the mitochondrial genome. An alternative explanation would be that the 11 variable sites of the Y chromosome do not provide sufficient statistical power, so a comparison with mitochondrial data (where more than 200 variable sites are studied in Europe) is impossible at present. To discriminate between these possibilities, we repeatedly analyzed a European mitochondrial database, each time considering only 11 variable sites, and we estimated mismatch distributions in stable and growing populations, generated by simulating coalescent processes. Along with theoretical considerations, these tests suggest that the difference between the mismatch distributions inferred from mitochondrial and Y-chromosome data are not a statistical artifact. Therefore, the observed mismatch distributions appear to reflect different underlying demographic histories and/or selective pressures for maternally and paternally transmitted loci.

Alleles↗

PubMed2026

Co-mutation Based Genetic Networks to Infer Temporal Mutation Dynamics in Ancient Human Mitochondrial Genomes.

The evolutionary history of Homo sapiens is marked by complex interactions between environmental, cultural, and genetic factors. To investigate the molecular signatures of these processes, we analyzed ancient mitochondrial DNA (mtDNA) across temporal and geographic contexts using principles of co-occurrence of minor alleles defined as co-mutation, through spatiotemporal co-mutation networks of variable sites. Haplogroup-based assessments of variable sites revealed a major transition from foraging to agrarian lifestyles during the Copper-Bronze Age. Genetic network analyses demonstrated that COX and CYB loci exhibited distinct temporal dynamics, with their interactions modulated by NADH dehydrogenase genes in a geological age-dependent manner. To complement the network approach, we constructed phylogeny-based gene interaction networks and assessed polymorphism-to-divergence from chimpanzee ratios. The tree-based networks displayed topologies consistent with co-mutation analyses but showed reduced gene-gene connectivity. Polymorphism/divergence analysis further indicated that the CYB gene has been under long-term purifying selection, whereas ATP6, COX, and NADH dehydrogenase genes experienced episodic purifying selection aligned with distinct historical phases. Collectively, our findings demonstrate that network-based analysis of ancient mtDNA provides insights into early human lifestyle transitions and haplogroup diversification, contributing to the evolutionary foundations of modern human populations.

Ancient humans↗

PubMed2002

[DNA sequencing and molecular identification of Patchouli and its substitute wrinkled gianthyssop].

AIM: To analyze sequences of the nuclear ribosomal RNA small subunit (18S rRNA) gene and the chloroplast matK gene of crude drug Patchouli (Pogostemon cablin) in order to provide molecular evidence for identification of Patchouli drug. METHODS: To sequence the entire 18S rRNA gene and partial matK gene of Patchouli from Guangzhou and its substitute Wrinkled Gianthyssop (Agastache rugosa) from Sichuan using PCR direct sequencing and to detect the homology of two gene sequences between these two crude drugs. RESULTS: The complete 18S rRNA gene sequence is 1,805 bp in length for Patchouli from Guangzhou whereas 1,794 bp for Wrinkled Gianthyssop from Sichuan. The 3'-end sequence of matK gene is 521 bp (747-1,268 nt from upstream of matK gene) for these two crude drugs. Based on multiple sequence alignment, it is found that there are 18 variable sites and 11 aligned gap sites in 18S rRNA sequence, 49 variable sites in 3'-matK sequence between these two crude drugs. The homology is 98.4% for 18S rRNA and 90.6% for 3'-matK between two crude drugs, respectively. CONCLUSION: DNA sequencing can provide an accurate and reliable tool in the crude drug identification of Patchouli and its substitute Wrinkled Gianthyssop.

Agastache↗

PubMed1985

Identification of five new variable restriction sites in HSV-1 DNA.

Restriction endonuclease analysis of herpes simplex virus type 1 (HSV-1) DNA has shown that individual strains differ from one another. The differences can be recognized by the presence or absence of cleavage sites due to base changes, small insertions and occasional deletions. In a study in which 13 HSV-1 isolates from South Africa were analysed, a total of 5 new variable restriction sites were identified using the restriction endonucleases Hind III, Eco RI and Bgl II.

Bacterial Proteins↗

PubMed2004

Microbial, nutritional and physical quality of commercial and hospital prepared tube feedings in Saudi Arabia.

OBJECTIVE: Blenderized tube feedings (BTF) may present disadvantages over commercially prepared formulas (CPF). This study compares the microbial safety, nutritional content, and physical properties of BTF versus CPF. METHODS: A total of 18 samples of BTF were collected from 3 hospitals in the Kingdom of Saudi Arabia from August 1999 through to November 1999. Samples of a CPF were collected for comparison. All samples were analyzed for nutritional content, microbial quality (aerobic plate counts, coliform counts, microorganism growth) and physical characteristics (viscosity, osmolality). RESULTS: The nutrient content of BTF varied significantly within and between sites. The average intra site variability for all sites ranged from 16-50%. The average variability of the CPF was 4-7%. Between sites, the mean concentration of most nutrients varied by 2-3 fold. The BTF had considerable differences between actual and expected nutrient concentrations, reaching statistical significance in 12 nutrients. The measured concentration of most nutrients in the CPF was within 10% of expected values. The BTF samples had higher viscosity and osmolality than the CPF. All samples of BTF had detectable aerobic plate counts that increased significantly over 4 hours (p<0.0005). Coliform contamination varied between sites, with 100% contamination at one site. No aerobic plate counts or coliform counts were detected in the CPF samples. CONCLUSION: There is a high degree of variability in nutrient content and physical properties with BTF. Furthermore, BTF are highly contaminated, increasing the risk of nosocomial infections. For these reasons, CPF should replace BTF.

Colony Count, Microbial↗

PubMed1989

Apolipoprotein B amino acid 3611 substitution from arginine to glutamine creates the Ag (h/i) epitope: the polymorphism is not associated with differences in serum cholesterol and apolipoprotein B levels.

A G- to A-DNA sequence change in exon 26 of the human apolipoprotein B (apo B) gene leads to a glutamine substitution for arginine at codon 3611 of the mature apolipo-protein B100 and causes a loss of an MspI site. In 106 Finnish individuals, a complete correspondence exists between this MspI polymorphic site and the Ag (h/i) immunochemical polymorphism. Linkage disequilibrium was found between this MspI polymorphic site and the apo B XbaI and EcoRI variable sites and the Ag (al/d) and (c/g) epitope pairs; there is apparent linkage equilibrium with the apo B PvuII variable site. Based on three population studies (samples from London. Finland and Italy), no significant association was found between this RFLP and serum cholesterol and apo B levels. These data suggest that the arginine 3611----glutamine 3611 substitution has no significant effect on apo B function.

Adult↗

PubMed2006

Molecular systematics of Vampyressine bats (Phyllostomidae: Stenodermatinae) with comparison of direct and indirect surveys of mitochondrial DNA variation.

Approximately 29 species in seven genera (Chiroderma, Mesophylla, Platyrrhinus, Uroderma, Vampyressa, Vampyriscus, and Vampyrodes) compose the Subtribe Vampyressina, a group of New World leaf-nosed bats (Phyllostomidae) specialized in fruit-eating. A recent study of restriction-site variability within the mitochondrial ND3-ND4 gene region contrasts with other molecular data, including sequence data from other mitochondrial genes, by suggesting that the monotypic genus Ectophylla (E. alba) also is member of the group and is related closely to Mesophylla. In this study, we address possible explanations for why the restriction-site data appear to contradict other molecular data by performing phylogenetic analysis of DNA sequence variation (direct survey) in the ND3-ND4 region and cytochrome b gene and by re-assessing ND3-ND4 restriction-site variability in the known sequences (indirect survey). Results from analysis of sequence data reject the Ectophylla-Mesophylla hypothesis (P<0.001) and suggest four primary lineages within Vampyressina: (1) Mesophylla-Vampyressa; (2) Chiroderma-Vampyriscus; (3) Platyrrhinus-Vampyrodes; and (4) Uroderma. We also find no support for the Ectophylla-Mesophylla hypothesis in our re-analysis of ND3-ND4 restriction-site variability, and suggest the differences between molecular studies have a methodological basis.

Animals↗

PubMed1990

Metastatic adenocarcinomas of unknown primary site. Prognostic variables and treatment results.

As part of a Phase II chemotherapy trial using mitomycin-C, adriamycin, and vindesine, 57 patients with adenocarcinoma of unknown primary site were assessed for prognostic variables predictive of response and survival. They were also evaluated for response and toxicity, usefulness of screening techniques, and eventual definition of primary site and pattern of progression. Only gender predicted response, with women being more likely to respond than men. Visceral metastases below the diaphragm, or the presence of liver metastases, predicted poor survival. Responding patients were highly likely to relapse first at sites of initial disease. Hemolytic-uremic syndrome was the most severe toxicity; other side effects were moderate. The response rate was 30% (three complete responders), which is similar to other current regimens. This study suggests that patients with better prognosis characteristics of single site of disease and without intraabdominal tumor may benefit from a policy of expectant observation after local control has been established. Patients with multiple sites of disease and/or intraabdominal tumor are appropriate candidates for investigational chemotherapy.

Adenocarcinoma↗

PubMed2004

Generalized boundary conditions for periodic lattice systems: application to the two-dimensional Ising model on a square lattice.

We show that the thermal properties of periodic lattice systems can be approximated to that of a finite cluster with appropriate boundary conditions which include a modified Hamiltonian for the boundary variables. Imposing lattice invariance on the correlation of the local site variables is sufficient to obtain the free parameters of the boundary Hamiltonian. The degree of accuracy of the calculation depends on the interaction range allowed in the boundary Hamiltonian and the range up to which the correlation of the site variables are made lattice invariant. The Bethe approximation can be considered a trivial case of this general method for clusters of one lattice site. The reliability of the method is demonstrated with the results obtained for the two-dimensional Ising model, where a cluster of four spins and invariance conditions up to second neighbors is sufficient to reproduce some nonuniversal thermal properties of the model with an accuracy comparable or better than other more complex numerical methods.

Journal Article↗

PubMed1986

Genetic control over fragile X chromosome expression.

The cytogenetic expression of fragile sites is highly variable. Sites are seen in differing proportions of cells. To determine if part of this variability is genetic, the proportions of lymphocytes manifesting the fragile X were examined in a large cohort of males with the fragile X chromosome. The number of fragile X cells was solely determined by genetic factors: the heritability as determined from the correlation between brothers as well as between cousins was 99.6% and 94.4%, respectively, as compared with 0% in unrelated males with the fragile X. This is consistent with pure genetic determination without any environmental influence over the expression of the fragile X chromosome in males.

Alleles↗

PubMed1994

PCR assays of variable nucleotide sites for identification of conservation units.

A number of authors have recently suggested that the best approach for identifying units of conservation is to follow a systematics model of character analysis (Amato, 1991; Cracraft, 1991; Vogler and DeSalle, 1994). This approach necessitates the use of an operational, typological, evolutionary species concept. The use of the phylogenetic species concept has the utility and philosophical logic appropriate for this task. Additionally, there is a large body of literature that uses this framework, along with a parsimony based character analysis to identify patterns of phylogeny (Cracraft, 1983; Nelson and Platnick, 1981; Nixon and Wheeler, 1990). While we advocate this approach, we recognize that one of its limiting factors is sample size. We propose that by selective direct sequencing plus rapid sampling of variable target characters by polymerase chain reaction (PCR) assays of specific sites, sufficiently large numbers of individuals can be accurately, inexpensively, and quickly surveyed for diagnostic characters. This procedure is demonstrated by a survey of variable nucleotide sites in the Caiman crocodilus complex.

Alligators and Crocodiles↗

PubMed1988

Antigenic analysis of African measles virus field isolates: identification and localisation of one conserved and two variable epitope sites on the NP protein.

Measles virus isolates from epidemics in the Cameroons (1983) and Gabon (1984) were analysed by a panel of monoclonal antibodies against four of the virion proteins. We observed no antigenic variation in the haemagglutinin, the fusion glycoprotein, or in the matrix protein. However, both inter- and intra-epidemic variation was observed in the nucleoprotein (NP). On the basis of strain reactivity and a competition binding assay, three epitopic sites were designated on the NP. One site was found on all the measles virus strains examined, whereas the other two were variable. Examination of proteolytic cleavage of the NP in situ (on the ribonucleoparticle) showed that the conserved site is located on a large fragment which remains bound to the viral genome. The peptide removed by proteolysis contained the two variable epitopes. The variability of the NP is discussed in relationship to its biological activity.

Animals↗

PubMed1992

Phylogenetic studies of ribosomal RNA variation in higher moths and butterflies (Lepidoptera: Ditrysia).

The selection of exemplars has been shown both theoretically and empirically to affect tree topology, but the importance of the number and nature of taxa used to represent higher taxonomic lineages in molecular studies is rarely stressed. In our rRNA study of higher moths and butterflies (Lepidoptera: Ditrysia), the selection of different exemplars and outgroups caused major tree rearrangements. We also examined the effectiveness with which conserved rRNA regions track the diversification of Lepidoptera. Homoplasy is as prevalent at the few variable sites of conserved regions (18E, 18J, 28F) as at the many variable sites of a more rapidly evolving region (28B). Finally, 28B sequence variation differs qualitatively among lepidopteran superfamilies of presumed comparable age, the Papilionoidea (true butterflies) and Noctuoidea (cutworm moths and relatives).

Animals↗

PubMed2003

Molecular characterization of the mitochondrial cytochrome oxidase I gene of Oestridae species causing obligate myiasis.

A 688-bp region of the mitochondrial cytochrome oxidase I gene was sequenced from larvae of 18 species of Oestridae causing obligate myiasis. Larvae belonged to the four Oestridae subfamilies (Cuterebrinae, Gasterophilinae, Hypodermatinae and Oestrinae), which are commonly found throughout the world. Analysis of both nucleotide and amino acid data was performed. Nucleotide sequences included 385 conserved sites and 303 variable sites; mean nucleotide variation between all species was 18.1% and variation within each subfamily ranged from 5.3% to 13.34%. Intraspecific pairwise divergences ranged from 0.14% to 1.59%, and interspecific variation ranged from 0.7% to 27%. Of the 229 amino acids, 76 were variable (60 of which were phylogenetically informative), with some highly conserved residues identified within each subfamily. Phylogenetic analysis showed a strong divergence among the four subfamilies, concordant with classical taxonomy based on morphological and biological features. This study provides the first molecular data set for myiasis-causing Oestridae species, providing an essential database for the molecular identification of these parasites and the assessment of phylogenetic relationships within family Oestridae.

Animals↗

PubMedDate not supplied

Identification of types and primary sites of malignant tumors by examination of exfoliated tumor cells in serous fluids. Comparison with the diagnostic accuracy on small histologic biopsies.

The accuracy of identification of tumor type and primary site of malignant tumors by examination of exfoliated tumor cells was cytologically studied in 448 malignant effusions from 366 patients for whom the primary tumor site had been confirmed by histology. Ninety-seven corresponding small biopsies from metastases were separately reviewed histopathologically. In four fluids, the cells were too scanty or too poorly preserved for tumor typing. The cytologic tumor typing was performed with nearly 100% accuracy in the remaining 444 fluids, except for those of intermediate-cell anaplastic carcinomas (0 of 3) and poorly differentiated squamous (epidermoid) carcinomas (1 of 5). Adenocarcinoma was correctly identified in 98% of 285 fluids, large-cell carcinoma in 97% of 108 fluids, oat-cell carcinoma in 94% of 16 fluids, well-differentiated (keratinizing) squamous carcinoma in 100% of 3 fluids, malignant lymphoma in 100% of 22 fluids and sarcoma in 100% of 2 fluids. The criteria and the failures are discussed at length. In the investigation of the accuracy of cytologic and histologic diagnoses with respect to the primary tumor site, tumors with variable sites of origin (sarcomas and lymphomas) and those with usually singular sites of origin (e.g., small-cell anaplastic carcinoma of the lung) were excluded, leaving 387 cytologic and 83 histologic specimens available for review. The breast as a primary site was correctly identified in 70% of both the cytologic and histologic specimens; the primary cytodiagnostic criteria included a uniform cell pattern, finely granular chromatin, dense cytoplasm and cell balls with smooth borders. Ovarian primaries were correctly identified in 70% of the fluids and 83% of the biopsy samples on the basis of very irregular clusters of large pleomorphic tumor cells, large nucleoli and psammoma bodies. Lung primaries, identified in 50% of the fluids and 29% of the biopsy samples, showed quite variable cell patterns, most often including large pleomorphic cells with or without mucus formation and prominent multinucleation. Gastric cancers of the diffuse type were accurately identified in 52% of the corresponding fluids, which showed mainly isolated cells with dense cytoplasmic rims, occasional signet-ring cells, "embryo-shaped" nuclei, marked hyperchromasia and densely granular chromatin.(ABSTRACT TRUNCATED AT 400 WORDS)

Adenocarcinoma↗

PubMed1987

Genetic architecture of inter-individual variability in apolipoprotein, lipoprotein and lipid phenotypes.

Phenotypes that predict coronary heart disease (CHD) are the consequence of interactions between many genetic and environmental factors. Quantitative measures of plasma apolipoproteins, lipoproteins and lipids are examples of phenotypes that link genetic and environmental factors to the CHD end-point. Population studies in Hawaii, Michigan and elsewhere have established that a significant fraction of variability in these phenotypes is attributable to genetic differences among individuals. Recent advances in molecular biology provide measures of the gene loci that code for the apolipoproteins, the cellular receptors for lipoprotein particles and the catalysts and cofactors in lipoprotein metabolism. By measuring polymorphic protein variability and restriction site variability in small regions of DNA known to contain genes that code for the proteins involved in these functions, it is possible to assign polygenetic effects to specific alleles or haplotypes. This 'measured genotype' approach may be used to study the genetic architecture (number of loci involved, the frequencies and effects of their alleles, and the type of loci, i.e., structural or regulatory) of quantitative variation in the plasma apolipoproteins, lipoproteins and lipids. This paper reviews statistical models, sampling designs and results of studies designed to estimate the genetic architecture of selected apolipoproteins, lipoproteins and lipids. The usefulness of these studies for answering questions about the prediction of CHD in the population, the family and the individual are discussed and the directions that human quantitative genetic studies will take in the future are considered.

Apolipoproteins↗