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PubMed2006

TRPV6 exhibits unusual patterns of polymorphism and divergence in worldwide populations.

A striking footprint of positive selection was recently identified on chromosome 7q34-35 that spans at least 115 kb and encompasses four known genes (KEL, TRPV5, TRPV6, EPHB6). The signature of selection was observed in only one of the two populations analyzed suggesting the action of geographically restricted selective pressures. However, as only two populations were analyzed, it remains unknown whether the signature of selection extends to additional populations. To address this issue and begin to dissect the evolutionary history of this region in more detail, we performed an in-depth population genetic analysis on TRPV6, which is a calcium-permeable ion channel thought to mediate the rate-limiting step of dietary calcium absorption. We demonstrate that the rate of TRPV6 protein evolution is significantly accelerated in the human lineage, but only for a haplotype defined by three non-synonymous SNPs (C157R, M378V and M681T) that are nearly fixed for the derived alleles in non-African populations. Interestingly, we found that these three non-synonymous SNPs have high posterior probabilities for being targets of positive selection and are therefore strong candidates for mediating the population-specific signatures of selection in this region. In addition, we resequenced the exons corresponding to the C157R, M378V and M681T polymorphisms in 90 geographically diverse individuals and characterized their global allele frequency distribution by genotyping them in 1064 individuals from 52 populations. These data strongly suggest that the TRPV6 haplotype defined by the derived alleles at C157R, M378V and M681T conferred a selective advantage that varied spatially, and perhaps temporally, during human history.

Calcium Channels↗
PubMed2005

Comparative studies on codon usage pattern of chloroplasts and their host nuclear genes in four plant species.

A detailed comparison was made of codon usage of chloroplast genes with their host (nuclear) genes in the four angiosperm species Oryza sativa, Zea mays, Triticum aestivum and Arabidopsis thaliana. The average GC content of the entire genes, and at the three codon positions individually, was higher in nuclear than in chloroplast genes, suggesting different genomic organization and mutation pressures in nuclear and chloroplast genes. The results of Nc-plots and neutrality plots suggested that nucleotide compositional constraint had a large contribution to codon usage bias of nuclear genes in O. sativa, Z. mays, and T. aestivum, whereas natural selection was likely to be playing a large role in codon usage bias in chloroplast genomes. Correspondence analysis and chi-test showed that regardless of the genomic environment (species) of the host, the codon usage pattern of chloroplast genes differed from nuclear genes of their host species by their AU-richness. All the chloroplast genomes have predominantly A- and/or U-ending codons, whereas nuclear genomes have G-, C- or U-ending codons as their optimal codons. These findings suggest that the chloroplast genome might display particular characteristics of codon usage that are different from its host nuclear genome. However, one feature common to both chloroplast and nuclear genomes in this study was that pyrimidines were found more frequently than purines at the synonymous codon position of optimal codons.

Arabidopsis↗
PubMed1998

Variable substitution rates of the 18 domain sequences in Artemia hemoglobin.

The Artemia hemoglobin is a dimer comprising two nine-domain covalent polymers in quaternary association. Each polymer is encoded by a gene representing nine successive globin domains which have different sequences and are presumed to have been copied originally from a single-domain gene. Two different polymers exist as the result of a complete duplication of the nine-domain gene, allowing the formation of either homodimers or the heterodimer. The total population size of 18 domains comprising nine corresponding pairs, coupled with the probability that they reflect several hundred million years of evolution in the same lineage, provides a unique model in which the process of gene multiplication can be analyzed. The outcome has important implications for the reliability of local molecular clocks. The two polymers differ from each other at 11.7% of amino acid sites; however when corresponding individual domains are compared between polymers, amino acid substitution fluctuates by a factor of 2.7-fold from lowest to highest. This variation is not obvious at the DNA level: Domain pair identity values fluctuate by 1. 3-fold. Identity values are, however, uncorrected for multiple substitutions, and both silent and nonsilent changes are pooled. Therefore, to determine the variability in relative substitution rates at the DNA level, we have used the method of Li (1993, J Mol Evol 36:96-99) to determine estimates of nonsynonymous (KA) and synonymous (KS) substitutions per site for the nine pairs of domains. As expected, the overall level of silent substitutions (KS of 56. 9%) far exceeded nonsilent substitutions (KA of 6.7%); however, for corresponding domain pairs, KA fluctuates by 2.3-fold and KS by 1. 7-fold. The large discrepancies reflected in the expressed protein have accrued within a single lineage and the implication is that divergence dates of different genera based on amino acid sequences, even with well-studied proteins of reasonable size, can be wrong by a factor well in excess of 2.

Amino Acid Sequence↗
PubMed2002

The structural basis for amyloid formation by plasma apolipoproteins: a review.

The formation of amyloid and other protein deposits in vivo is synonymous with many pathological conditions such as Alzheimer's disease, Creutzfeldt-Jakob disease and Parkinson's disease. Interestingly, many plasma apolipoproteins are also associated with amyloid deposits, including apolipoprotein (apo) A-I, apoA-II and apoE. Apolipoproteins share a number of structural and conformational properties, namely a large proportion of class A amphipathic alpha-helices and limited conformational stability in the absence of lipid. Other proteins that form amyloid such as alpha-synuclein and serum amyloid A also contain amphipathic alpha-helical domains similar to those found in apolipoproteins. In this review we develop a hypothesis to account for the widespread occurrence of apolipoproteins in amyloid deposits. We describe the conformational stability of human apoC-II and the stabilization of alpha-helical structure in the presence of phospholipid. We propose that lipid-free apoC-II forms partially folded intermediates prone to amyloid formation. Parameters that affect apolipoprotein lipid binding in vivo, such as protein and lipid oxidation or protein truncations and mutations, could promote apolipoprotein-related pathologies including those associated within amyloid deposits of atherosclerotic plaques.

Amyloid↗
PubMed2007

Leucine-rich repeat kinase 1: a paralog of LRRK2 and a candidate gene for Parkinson's disease.

Leucine-rich repeat kinase 1 gene (LRRK1) on chromosome 15q26.3 is a paralog of LRRK2 in which multiple substitutions were recently linked to Parkinson's disease. We have examined the exon-intron structure of the gene and the expressed mRNA sequence in brain. LRRK1 sequencing analysis in 95 probands from families with autosomal dominant Parkinson's disease identified 23 variants, 14 of which are novel, with four resulting in non-synonymous amino acid substitutions. These four substitutions are rare and do not clearly segregate with disease within our families or associate with sporadic Parkinson's disease in a US case-control series. Subsequent sequencing of exon 26 encoding the kinase activation segment in an additional 360 probands identified one further synonymous variant, suggesting that LRRK1 variants are not a frequent cause of Parkinson's disease. The relative absence of substitutions within LRRK1 highlights a greater conservation of sequence than observed for LRRK2. Comparison of evolutionary interspecies sequences of LRRK1 and LRRK2 suggests they diverged from a common founder gene.

Alternative Splicing↗
PubMed1999

Directional substitution and evolution of nucleotide content in the cytochrome oxidase II gene in earwigs (dermapteran insects).

The cytochrome oxidase subunit II (COII) gene was sequenced for six dermapteran species. The nucleotide composition of this gene is biased in most animals. While the CG content of other insect orders is low (mean, 27.6%; range, 19.5%-33.1%), species from the Forficula genus showed unusually high values (mean, 42.4%; range, 37.3%-44.1%), mostly due to high CG frequencies at third codon positions: the mean CG content at these positions was around 45% (range, 43.9%-46.9%) for Forficula, compared with only 13.3% for other insects. This effect was so strong that in one species, Forficula lesnei, there was no significant difference between the frequencies of the four bases. During evolution, this loss of bias has involved a significant increase in the synonymous substitution rate and an increase of transitions over transversions compared with other insects. A strong directionality of substitutions has favored T-->C and A-->G changes. This phenomenon was also observed between two conspecific populations of Forficula auricularia. A species from a closely related genus, Anechura bipunctata, was intermediate between Forficula and other insects for these parameters, while two remotely related dermapteran species, Labidura riparia and Euborellia moesta, were similar to other insects. These results suggest that the evolution of Forficula DNA content has been both rapid and recent.

Animals↗
PubMed1999

NTP Toxicology and Carcinogenesis Studies of Glutaraldehyde (CAS NO. 111-30-8) in F344/N Rats and B6C3F1 Mice (Inhalation Studies).

Glutaraldehyde is used in large volume in a variety of industries as a disinfectant, preservative, fixative and cross-linking agent, and as a chemical intermediate in the synthesis of pharmaceuticals and pesticides. Glutaraldehyde was nominated by the National Cancer Institute, the Occupational Safety and Health Administration, and the National Institute of Environmental Health Sciences for carcinogenicity studies because of potential occupational exposure. Male and female F344/N rats and B6C3F1 mice were exposed to glutaraldehyde (25% aqueous solution) (approximately 93% pure) by inhalation for 2 years. In vitro genetic toxicology studies were conducted in Salmonella typhimurium, L5178Y mouse lymphoma cells, and cultured Chinese hamster ovary cells; in vivo studies were conducted to measure sex-linked recessive lethal mutations in Drosophila melanogaster, chromosomal aberrations and micronucleated erythrocytes in mouse bone marrow, and micronucleated erythrocytes in mouse peripheral blood. The results of 13-week inhalation studies with glutaraldehyde were reported previously (NTP, 1993 -- TOX-25 ). 2-YEAR STUDY IN RATS: Groups of 50 male and 50 female F344/N rats were exposed to 0, 250, 500, or 750 ppb glutaraldehyde vapor by inhalation, 6 hours per day, 5 days per week, for 104 weeks. Survival of 500 and 750 ppb female rats was less than that of the chamber controls. Mean body weights of all exposed groups of male rats and 500 and 750 ppb female rats were generally less than those of the chamber controls. Some female rats exposed to 750 ppb were thin to emaciated at the time they were killed moribund. Increased incidences of nonneoplastic nasal lesions occurred primarily within the anterior section of the nose in 500 and 750 ppb rats and to a lesser extent in 250 ppb rats. The more significant lesions included hyperplasia and inflammation of the squamous and respiratory epithelia and squamous metaplasia of the respiratory epithelium. 2-YEAR STUDY IN MICE: Groups of 50 male and 50 female B6C3F1 mice were exposed to 0, 62.5, 125, or 250 ppb glutaraldehyde vapor by inhalation, 6 hours per day, 5 days per week, for 104 weeks. Survival of exposed mice was similar to that of the chamber controls. Mean body weights of female mice exposed to 250 ppb were generally less than those of the chamber controls throughout the study. Incidences of squamous meta-plasia of the respiratory epithelium were increased in 250 ppb males and females and 125 ppb females. Incidences of hyaline degeneration of the respiratory epithelium were increased in all exposed groups of females. The incidence of inflammation of the nose was marginally increased in 250 ppb females. GENETIC TOXICOLOGY: In genetic toxicity studies, glutaraldehyde was muta-genic with and without S9 metabolic activation in S. typhimurium strains TA100, TA102, and TA104. Glutaraldehyde was mutagenic in mouse L5178Y lymphoma cells in the absence of S9 and induced sister chromatid exchanges in cultured Chinese hamster ovary cells with and without S9. No increase in chromosomal aberrations was induced by glutaraldehyde in cultured Chinese hamster ovary cells with or without S9 at one laboratory; at another laboratory, chromosomal aberrations were induced in the absence of S9 only. Glutaraldehyde did not induce sex-linkedrecessive lethal mutations in germ cells of male D. melanogaster treated as adults by feeding or injection or treated as larvae by feeding. In vivo, glutaraldehyde induced a significant increase in chromosomal aberrations in mouse bone marrow cells 36 hours after a single intraperitoneal injection. In a subset of the 36-hour chromosomal aberrations test, there was a small increase in the number of micronucleated bone marrow polychromatic eryth-rocytes, which was judged to be equivocal. Addi-tional short-term (3-day) and subchronic (13-week) micronucleus tests in mice, using the intraperitoneal or inhalation routes, respectively, yielded negative results. CONCLUSIONS: Under the conditions of these 2-year inhalation studies, there was no evidence of carcinogenic activinogenic activity of glutaraldehyde in male or female F344/N rats exposed to 250, 500, or 750 ppb. There was no evidence of carcinogenic activity in male or female B6C3F1 mice exposed to 62.5, 125, or 250 ppb. Incidences of nonneoplastic lesions of the nose were significantly increased in male and female rats and mice. Synonyms: 1,3-Diformylpropane; glutaral; glutardialdehyde; glutaric dialdehyde; 1,5-pentanedial; 1,5-pentanedione; potentiated acid glutaraldehyde Trade names: Cidex; Sonacide.

Journal Article↗
PubMed1999

NTP Toxicology and Carcinogenesis Studies of AZT (CAS No. 30516-87-1) and AZT/alpha-Interferon A/D B6C3F1 Mice (Gavage Studies).

3'-Azido-3'-deoxythymidine (AZT) is the most widely used and evaluated chemotherapeutic agent for the treatment of persons with acquired immune deficiency syndrome (AIDS) and persons seropositive for human immunodeficiency virus (HIV). The National Cancer Institute nominated AZT for toxicity and carcinogenicity studies because of the impending large-scale use of AZT in the treatment of adult patients with AIDS or AIDS-related complex. alpha-Interferon A/D, which displays antiviral activity in mice, is a hybrid molecule composed of the N-terminal portion of human alpha-interferon A and the C-terminal portion of human alpha-interferon D. AZT and alpha-interferon A/D combination studies were conducted because in vitro studies of AZT and alpha-interferon have demonstrated that the combination is more effective in blocking HIV infection than either agent alone. Male and female B6C3F1 mice received AZT (approximately 98% pure) in 0.5% aqueous methylcellulose by gavage for 14 weeks or 2 years. In addition, male and female B6C3F1 mice received alpha-interferon A or alpha-interferon A/D by subcutaneous injection for 2 years, and male and female B6C3F1 mice received AZT in 0.5%% aqueous methylcellulose by gavage in combination with alpha-interferon A/D by subcutaneous injection for 2 years. Genetic toxicology studies were conducted in Salmonella typhimurium, cultured Chinese hamster ovary cells, mouse bone marrow erythrocytes, and mouse peripheral blood erythrocytes. 14-WEEK AZT STUDY: Groups of 10 male and 10 female mice received AZT in 0.5% methylcellulose by gavage at doses of 0, 50, 100, 200, 800, or 2,000 mg/kg daily for 14 weeks. Additional groups of 10 male and 10 female mice received AZT in 0.5% methylcellulose by gavage at doses of 0, 100, 800, or 2,000 mg/kg daily for 14 weeks and then were held without treatment for an additional 4 weeks before necropsy. One female receiving 100 mg/kg and two females receiving 200 mg/kg died during week 1 as a result of gavage trauma; one female receiving 2,000 mg/kg also died prior to the end of the 14-week dosing period. One female receiving 2,000 mg/kg in the recovery study also died from gavage trauma during week 1. The final mean body weights of dosed mice were similar to those of the vehicle control groups at the end of the dosing period and at the end of the recovery period. Female mice receiving 200, 800, or 2,000 mg/kg gained less weight than the vehicle controls during the 14-week dosing period. Exposure to AZT was toxic to the bone marrow, resulting in significant changes in the peripheral blood (decreased hematocrit values, erythrocyte counts, and hemoglobin concentrations, and increased mean cell volume and mean cell hemoglobin) and bone marrow (erythroid hypoplasia) characteristic of a dose- and time-dependent, minimal to moderate, poorly regenerative macrocytic anemia. At the end of the 4-week recovery period, the hematology parameters had returned to normal, indicating that the hematotoxicity was reversible. 2-YEAR STUDIES: AZT Groups of 95 male and 95 female mice received AZT in 0.5% methylcellulose by gavage at daily doses of 0, 30, 60, or 120 mg/kg body weight, administered as two equal doses at least 6 hours apart, 5 days per week for 105 weeks. Each group of 95 animals was composed of a core group of 50 animals for evaluation of carcinogenic response, a group of 30 animals for evaluation of hematology and bone marrow cellularity, and a group of 15 animals from which blood was drawn for determination of plasma AZT concentrations at week 54. alpha-Interferon A/D and AZT/alpha-Interferon A/D Studies Groups of 80 male and 80 female mice received AZT in 0.5% aqueous methylcellulose by gavage at daily doses of 0, 30, 60, or 120 mg/kg body weight, given in two equal doses, 5 days per week for 105 weeks. Those groups receiving AZT also received sub-cutaneous injections of 500 or 5,000 U alpha-interferon A/D three times per week for 105 weeks. Additional groups of 80 male and 80 female mice received subcutaneous injections of the vehicle, 500 U alpha-interferon A/D, 5,000 Uutaneous injections of the vehicle, 500 U α-interferon A/D, 5,000 U α-interferon A/D, or 5,000 U α-interferon A, three times per week for 105 weeks. Each group of 80 animals was composed of a core group of 50 animals for evaluation of carcinogenic response and a group of 30 animals for evaluation of hematology and bone marrow cellularity. Because of the large number of animals involved, the 2-year studies were started in four phases and, for clarity, are presented as follows: the AZT study, the α-interferon A/D study, the AZT/500 U α-interferon A/D study, and the AZT/5,000 U α-interferon A/D study. Design of the 2-year AZT, AZT/α-Interferon A/D, and α-Interferon A/D Studies AZT Dose AZT Study AZT/500 U α-Interferon A/D Study AZT/5,000 U α-Interferon A/D Study 500 or 5,000 U α-Interferon A/D or 5,000 U α-Interferon A Study Vehicle Control 95 male and 95 female micea 80 male and 80 female miceb 80 male and 80 female miceb 80 male and 80 female miceb 30 mg/kg AZT 95 male and 95 female mice 80 male and 80 female mice 80 male and 80 female mice none 60 mg/kg AZT 95 male and 95 female mice 80 male and 80 female mice 80 male and 80 female mice none 120 mg/kg AZT 95 male and 95 female mice 80 male and 80 female mice 80 male and 80 female mice none aFor the AZT study, there were 95 male and 95 female mice; these were divided into 50 males and 50 females in the core groups, 30 males and 30 females in the clinical pathology groups (hematology and bone marrow analyses only), and 15 males and 15 females for plasma AZT concentration determinations. bFor the α-interferon A/D study and the AZT/α-interferon A/D studies, there were 80 male and 80 female mice for each study; these were divided into 50 males and 50 females in the core groups and 30 males and 30 females in the clinical pathology groups (hematology and bone marrow analyses only). Survival and Body Weights Survival and mean body weights of mice exposed to AZT, α-interferon A, α-interferon A/D, or AZT plus α-interferon A/D were generally similar to those of the vehicle control groups. Hematology and Bone Marrow Analyses All groups of male and female mice receiving AZT exhibited changes in peripheral blood and bone marrow characteristic of a dose- and time-dependent, minimal to mild, macrocytic, nonresponsive anemia. In females, these changes were evident throughout the study. In males, the macrocytic anemia had resolved by week 80 in the 30 mg/kg group; at study termination erythrocyte macrocytosis was present only in males receiving 60 or 120 mg/kg AZT or AZT plus α-interferon A/D. There were no treatment-related alterations in hematology or bone marrow parameters in groups that received only α-interferon A or A/D. Pathology Findings Incidences of squamous cell carcinoma and squamous cell papilloma or carcinoma (combined) of the vagina occurred with a positive trend and were significantly increased in groups of female mice receiving 60 or 120 mg/kg AZT alone or in combination with α-interferon A/D. Epithelial hyperplasia was observed in all dosed groups of females, and the incidence was significantly increased in the 120 mg/kg AZT group. Three renal tubule adenomas and one renal tubule carcinoma were observed in male mice receiving 120 mg/kg AZT; the combined incidence in this group exceeded the range in historical controls. A renal tubule adenoma was observed in one male receiving 60 mg AZT/kg and 500 U α-interferon A/D; how ever, none were observed in other groups. Evaluation of step sections revealed a few more renal tubule hyperplasias but no additional neoplasms. The incidence of harderian gland adenoma was increased in male mice receiving 120 mg/kg AZT and exceeded the range in historical controls. Harderian gland neoplasms were observed in other groups but did not follow a treatment-related pattern. Overall Incidences of Vaginal Neoplasms and Hyperplasia of the Vaginal Epithelium in Female Mice in the 2-Year Gavage Studies of AZT and AZT/α-Interferon A/Da Vehicle Control 30 mg AZT/kg 60 mg AZT/kg 120 mg AZT/kg AZT alone 2/197 (1%)b 1/197 0/49 (0%) 3/49 5/45 (11%%) 4/45 11/49 (22%%) 11/49 500 U α-Interferon A/D 0/49 (0%%) 0/49 0/44 (0%) 4/44 5/48 (10%) 8/48 6/48 (13%) 12/48 5,000 U α-Interferon A/D 1/50 (2%) 1/50 1/48 (2%) 4/48 5/48 (10%) 8/48 4/50 (8%) 15/50 aData are presented as number of vaginal neoplasms/number of animals microscopically examined (first line) and number of vaginal hyperplasias/number of animals microscopically examined (second line) bCombined incidences of controls from the AZT alone study and the AZT/α-interferon A/D studies; incidences in the vehicle control group from the AZT alone study are 0/50 (0%%) (neoplasms) and 0/50 (hyperplasia) Overall Incidence of Harderian Gland Neoplasms in Male Mice in the 2-Year Gavage Studies of AZT and AZT/α-Interferon A/Da Vehicle Control 30 mg AZT/kg 60 mg AZT/kg 120 mg AZT/kg AZT alone 13/200 (6%%)b 5/50 (10%%) 2/50 (4%) 10/50 (20%%) 500 U α-Interferon A/D 3/50 (6%) 3/50 (6%) 1/50 (2%%) 4/50 (8%%) 5,000 U α-Interferon A/D 3/50 (6%) 9/50 (18%%) 4/50 (8%%) 4/50 (8%) aData are presented as number of harderian gland neoplasms/number of animals necropsied bCombined incidences of controls from the AZT alone study and the AZT/α-interferon A/D studies; incidence in the vehicle control group from the AZT alone study is 3/50 (6%) Male mice had a pattern of nonneoplastic liver lesions along with silver-staining helical organisms within the liver consistent with an infection with Helicobacter hepaticus. An organism compatible with H. hepaticus was confirmed by polymerase chain reaction-restriction fragment length polymorphism-based assays. Detection of dose-related differences in neoplasm incidences in these studies was not considered to have been significantly impacted by the infection with H. hepaticus or its associated hepatitis. GENETIC TOXICOLOGY: AZT is mutagenic in vitro and in vivo. It induced gene mutations in Salmonella typhimurium strain TA102, with and without S9; no increases in mutations were noted in the other tested strains of S. typhimurium. AZT induced sister chromatid exchanges, but not chromosomal aberrations, in cultured Chinese hamster ovary cells, with and without S9. In vivo studies with male mice administered AZT by gavage showed highly significant increases in micronucleated erythrocytes in bone marrow and peripheral blood after exposure periods that ranged from 72 hours to 14 weeks. CONCLUSIONS: Under the conditions of these 2-year gavage studies there was equivocal evidence of carcinogenic activity of AZT in male mice based on increased incidences of renal tubule and harderian gland neoplasms in groups receiving AZT alone. There was clear evidence of carcinogenic activity of AZT in female mice based on increased incidences of squamous cell neoplasms of the vagina in groups that received AZT alone or in combination with α-interferon A/D. Hematotoxicity occurred in all groups that received AZT. Treatment with AZT alone and AZT in combination with α-interferon A/D resulted in increased incidences of epithelial hyperplasia of the vagina in all dosed groups of females. Synonyms: AZT; 3'-azido-2',3'-dideoxythymidine; azidodeoxythymidine; azidothymidine; 3'-azidothymidine; 3'-deoxy-3'-azidothymidine; 3'-deoxy-(8CI) (9CI); BW A509U; Compound S; ZDV; zidovudine Trade name: Retrovir®

Journal Article↗
PubMed1991

NTP Toxicology and Carcinogenesis Studies of dl-Amphetamine Sulfate (CAS No. 60-13-9) in F344/N Rats and B6C3F1 Mice (Feed Studies).

dl-Amphetamine sulfate is used for the treatment of narcolepsy in adults and behavioral syndromes in children. Toxicology and carcinogenesis studies were conducted by administering dl-amphetamine sulfate (USP grade) in feed to groups of F344/N rats and B6C3F1 mice of each sex for 14 days, 13 weeks, or 2 years. Genetic toxicology studies were conducted in Salmonella typhimurium and Chinese hamster ovary (CHO) cells. 14-Day Studies: The chemical was administered at dietary concentrations of 0, 47, 94, 188, 375, or 750 ppm for rats and 0, 125, 250, 500, 1,000, or 2,000 ppm for mice. Decreased body weight gain was seen at the higher concentrations, but no chemical-related deaths or toxic lesions were observed. 13-Week Studies: The chemical was administered at dietary concentrations of 0, 47, 94, 188, 375, or 750 ppm for rats and 0, 125, 250, 500, 1,000, or 2,000 ppm for mice. None of the rats died, but 6/10 male mice and 7/10 female mice that received 2,000 ppm, 3/10 male mice that received 1,000 ppm, and 8/10 male mice that received 500 ppm died before the end of the studies. Decreased body weight gain and hyperactivity were seen in dosed rats and mice. Final body weights of rats receiving 188 ppm or more were 62% to 89% those of controls, and final body weights of mice receiving 250 ppm or more were 70% to 86% those of controls. There were no lesions that were considered to be a primary effect of the chemical. Based on decreased body weight gain and hyperactivity in the 13-week studies, 2-year studies were conducted by feeding diets containing 0, 20 or 100 ppm dl-amphetamine sulfate to groups of 50 rats or 50 mice of each sex. Body Weights and Survival in the 2-Year Studies: No significant differences in survival were observed between any groups of rats or mice (male rats: control, 30/50; low dose, 31/50; high dose, 33/50; female rats: 33/50; 42/50; 37/50; male mice: 48/50; 48/50; 49/50; female mice: 35/50; 36/50; 44/50). Final body weights of dosed rats and mice were decreased relative to those of controls. Final body weights were 92% and 86% those of controls for low- and high-dose male rats, 89% and 70% those of controls for low- and high-dose female rats, 85% and 72% those of controls for low- and high-dose male mice, and 81% and 66% those of controls for low- and high-dose female mice. Hyperactivity was observed in all dosed groups. Feed consumption was similar among control and exposed groups with the exception of high-dose female rats (84% of controls) and high-dose male mice, for which hyperactivity resulted in scattering of feed and overestimation of feed consumption. The average amount of dl-amphetamine sulfate consumed per day was estimated to be 1 or 5 mg/kg for low- and high-dose rats, 4 or 30 mg/kg for low- or high-dose male mice, and 3 or 19 mg/kg for low- or high-dose female mice. Nonneoplastic and Neoplastic Effects in the 2-Year Studies: Myelofibrosis, cataracts, and retinal atrophy in female rats, and ovarian atrophy in female mice occurred in a larger proportion of high-dose animals than in controls. Dose-related increases in neoplasms did not occur in rats or mice receiving amphetamine. The administration of dl-amphetamine sulfate was associated with decreases in the incidence of total neoplasms and in the incidences of certain site-specific neoplasms, including pheochromocytomas of the adrenal gland in male rats (23/49, 15/44, 7/50), fibroadenomas of the mammary gland in female rats (21/50, 11/50, 2/50), adenomas of the anterior pituitary gland in male and female rats and female mice (male rats: 15/49, 15/48, 9/49; female rats: 31/50, 24/48, 19/50; female mice: 12/49, 6/49, 1/46), endometrial stromal polyps of the uterus of female rats (10/50, 6/50, 3/50), adenomas or carcinomas (combined) of the liver in male and female mice (male: 14/50, 12/50, 2/50; female: 5/50, 1/50, 1/47), adenomas of the harderian gland in male and female mice (male: 4/50, 2/50, 0/50; female: 5/50, 2/50, 0/47), and adenomas or carcinomas (combined) of the lung in male and female mice (male: 8/50, 3/50, 4/50; female: 8/50, 6/50 (combined) of the lung in male and female mice (male: 8/50, 3/50, 4/50; female: 8/50, 6/50, 1/47). Genetic Toxicology: dl-Amphetamine sulfate was tested for induction of gene mutations in Salmonella typhimurium strains TA98, TA100, TA1535, and TA1537 with and without exogenous metabolic activation (S9); the only response observed was in strain TA98 in the presence of S9, and it was judged to be equivocal. No induction of sister chromatid exchanges or chromosomal aberrations occurred in Chinese hamster ovary cells treated with amphetamine sulfate in either the presence or the absence of S9. Conclusions: Under the conditions of these 2-year feed studies, there was no evidence of carcinogenic activity of dl-amphetamine sulfate for male or female F344/N rats or male or female B6C3F1 mice fed 20 or 100 ppm. The administration of dl-amphetamine sulfate was associated with decreased body weight. There were decreased incidences of total neoplasms in dosed rats and mice, of adrenal pheochromocytomas in male rats, of mammary gland fibroadenomas and uterine polyps in female rats, of pituitary gland adenomas in male and female rats and female mice, and of harderian gland adenomas, liver neoplasms, and lung neoplasms in male and female mice. Synonyms: (±)-amphetamine sulfate; (±)-2-amino-1-phenylpropane sulfate; amphetamine sulfate; deoxynorephedrine; desoxynorephedrine; (±)-a-methylphenethylamine sulfate; (±)-phenisopropylamine sulfate; b-phenyl isopropylamine Trade Names: Acedron; Adipan; Adiparthrol; Aketdrin; Aktedrin; Alentol; Amfetamina; Amphaetamin; Amphamed; Amphatamin; Amphate; Amphedrine; Amphetaminum; Amphezamin; Amphoids-S; Anara; Anfetamina; Anorexine; Astedin; Benzafinyl; Benzamphetamine; Benzebar; Benzedrina; Benzedryna; Benzolone; Benzpropamine;Betafen; Betaphen; Bluzedrin; Centramina; Didrex; Dietamine; Durophet; Elastonin; Elastonon; Euphobine; Euphodine; Euphodyn; Fabedrine; Fenamin; Fenara; Fenedrin; Fenopromin; Halloo-Wach; Ibiozedrine; Isamin; Isoamin; Isoamyne; Isomyn; Leodrin; Levonor; Linampheta; Mecodrin; Mimetina; Monetamine; Noclon; Norephedrane; Norphedrane; Novydrine; Oktedrin; Oraldrina; Ortenal; Orthedrin; Percomon; Pharmamedrine; Pharmedrine; Phenamine; Phenedrine; Phenopromin; Phenpromin; Profamina; Profetamine; Propenyl; Propisamine; Psychedrine; Psychedryna; Psychedrinum; Psychoton; Racephen; Rhinalator; Sedolin; Simpamina; Simpamine; Simpatedrin; Stimulan; Sympametin; Sympamine; Sympatedrine; Synsatedrine; Theptine; Vapedrine; Weckamine; Zedrine Slang for Amphetamines: bennies; benzies; cartwheels; hearts; peaches; roses

Journal Article↗
PubMed2006

QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species.

BACKGROUND: Single nucleotide polymorphisms (SNPs) are important tools in studying complex genetic traits and genome evolution. Computational strategies for SNP discovery make use of the large number of sequences present in public databases (in most cases as expressed sequence tags (ESTs)) and are considered to be faster and more cost-effective than experimental procedures. A major challenge in computational SNP discovery is distinguishing allelic variation from sequence variation between paralogous sequences, in addition to recognizing sequencing errors. For the majority of the public EST sequences, trace or quality files are lacking which makes detection of reliable SNPs even more difficult because it has to rely on sequence comparisons only. RESULTS: We have developed a new algorithm to detect reliable SNPs and insertions/deletions (indels) in EST data, both with and without quality files. Implemented in a pipeline called QualitySNP, it uses three filters for the identification of reliable SNPs. Filter 1 screens for all potential SNPs and identifies variation between or within genotypes. Filter 2 is the core filter that uses a haplotype-based strategy to detect reliable SNPs. Clusters with potential paralogs as well as false SNPs caused by sequencing errors are identified. Filter 3 screens SNPs by calculating a confidence score, based upon sequence redundancy and quality. Non-synonymous SNPs are subsequently identified by detecting open reading frames of consensus sequences (contigs) with SNPs. The pipeline includes a data storage and retrieval system for haplotypes, SNPs and alignments. QualitySNP's versatility is demonstrated by the identification of SNPs in EST datasets from potato, chicken and humans. CONCLUSION: QualitySNP is an efficient tool for SNP detection, storage and retrieval in diploid as well as polyploid species. It is available for running on Linux or UNIX systems. The program, test data, and user manual are available at http://www.bioinformatics.nl/tools/snpweb/ and as Additional files.

Base Sequence↗
PubMed2005

Analysis of microsatellite markers and single nucleotide polymorphisms in candidate genes for susceptibility to bipolar affective disorder in the chromosome 12Q24.31 region.

Previous results from our genetic analyses using pedigrees from a French Canadian population suggested that the interval delimited by markers D12S86 and D12S378 on chromosome 12 was the most probable genomic region to contain a susceptibility gene for affective disorders. Here we present a more detailed genetic analysis of a 7.7 Mb genomic region located on 12q24.31. This region was saturated with 20 microsatellite markers to refine the candidate region and linkage analysis performed in 41 families from the Saguenay-Lac-St-Jean (SLSJ) region of Quebec. The results of two point parametric analysis using MFLINK supported the presence of a susceptibility locus on chromosome 12q24.31. Association studies with microsatellite markers using a case/control sample from the same population (n = 401) and analyzed with CLUMP revealed significant allelic associations between the bipolar phenotype and markers NBG6 (P = 0.008) and NBG12 (P < 10(-3)). According to these results, we investigated candidate genes in the NBG12 area. We analyzed 32 genes for the presence of polymorphisms in coding sequences and intron/exon junctions and genotyped 22 non-synonymous SNPs in the SLSJ case/control sample. Two uncommon polymorphisms (minor allele frequency < or = 0.03) found in KIAA1595 and FLJ22471 genes, gave P-values below 0.05 with the T1 statistic. Moreover, using haplotype analysis, a nearly significant haplotypic association was observed at the HM74 gene. These results do not give strong support for a role in the susceptibility to bipolar disorder of any of these genes analyzed. However, the significance of rare polymorphisms should be explored by further analyses.

Alleles↗
PubMed2006

Reduced activity of the hypertension-associated Lys528Arg mutant of human adipocyte-derived leucine aminopeptidase (A-LAP)/ER-aminopeptidase-1.

The adipocyte-derived leucine aminopeptidase (A-LAP)/ER aminopeptidase-1 is a multi-functional enzyme belonging to the M1 family of aminopeptidases. It was reported that the polymorphism Lys528Arg in the human A-LAP gene is associated with essential hypertension. In this study, the role of Lys528 in the enzymatic activity of human A-LAP was examined by site-directed mutagenesis. Among non-synonymous polymorphisms tested, only Lys528Arg reduced enzymatic activity. The replacement of Lys528 with various amino acids including Ala, Met, His and Arg caused a significant decrease in the enzymatic activity. Molecular modeling of the enzyme suggested that Lys528 is located near the entrance of the substrate pocket. These results suggest that Lys528 is important for maximal activity of A-LAP by maintaining the appropriate structure of the substrate pocket of the enzyme. The reduced enzymatic activity of A-LAP may cause high blood pressure and the observed association between the polymorphism and hypertension.

Adipocytes↗
PubMed1994

Molecular population genetics of sex determination genes: the transformer gene of Drosophila melanogaster.

The transformer locus (tra) produces an RNA processing protein that alternatively splices the doublesex pre-mRNA in the sex determination hierarchy of Drosophila melanogaster. Comparisons of the tra coding region among Drosophila species have revealed an unusually high degree of divergence in synonymous and nonsynonymous sites. In this study, we tested the hypothesis that the tra gene will be polymorphic in synonymous and nonsynonymous sites within species by investigating nucleotide sequence variation in eleven tra alleles within D. melanogaster. Of the 1063 nucleotides examined, two synonymous sites were polymorphic and no amino acid variation was detected. Three statistical tests were used to detect departures from an equilibrium neutral model. Two tests failed to reject a neutral model of molecular evolution because of low statistical power associated with low levels of genetic variation (Tajima/Fu and Li). The Hudson, Kreitman, and Aguade test rejected a neutral model when the tra region was compared to the 5'-flanking region of alcohol dehydrogenase (Adh). The lack of variability in the tra gene is consistent with a recent selective sweep of a beneficial allele in or near the tra locus.

Animals↗
PubMed2004

DNA variability and divergence at the notch locus in Drosophila melanogaster and D. simulans: a case of accelerated synonymous site divergence.

DNA diversity in two segments of the Notch locus was surveyed in four populations of Drosophila melanogaster and two of D. simulans. In both species we observed evidence of non-steady-state evolution. In D. simulans we observed a significant excess of intermediate frequency variants in a non-African population. In D. melanogaster we observed a disparity between levels of sequence polymorphism and divergence between one of the Notch regions sequenced and other neutral X chromosome loci. The striking feature of the data is the high level of synonymous site divergence at Notch, which is the highest reported to date. To more thoroughly investigate the pattern of synonymous site evolution between these species, we developed a method for calibrating preferred, unpreferred, and equal synonymous substitutions by the effective (potential) number of such changes. In D. simulans, we find that preferred changes per "site" are evolving significantly faster than unpreferred changes at Notch. In contrast we observe a significantly faster per site substitution rate of unpreferred changes in D. melanogaster at this locus. These results suggest that positive selection, and not simply relaxation of constraint on codon bias, has contributed to the higher levels of unpreferred divergence along the D. melanogaster lineage at Notch.

Animals↗
PubMed1996

Ribosome-mediated translational pause and protein domain organization.

Because regions on the messenger ribonucleic acid differ in the rate at which they are translated by the ribosome and because proteins can fold cotranslationally on the ribosome, a question arises as to whether the kinetics of translation influence the folding events in the growing nascent polypeptide chain. Translationally slow regions were identified on mRNAs for a set of 37 multidomain proteins from Escherichia coli with known three-dimensional structures. The frequencies of individual codons in mRNAs of highly expressed genes from E. coli were taken as a measure of codon translation speed. Analysis of codon usage in slow regions showed a consistency with the experimentally determined translation rates of codons; abundant codons that are translated with faster speeds compared with their synonymous codons were found to be avoided; rare codons that are translated at an unexpectedly higher rate were also found to be avoided in slow regions. The statistical significance of the occurrence of such slow regions on mRNA spans corresponding to the oligopeptide domain termini and linking regions on the encoded proteins was assessed. The amino acid type and the solvent accessibility of the residues coded by such slow regions were also examined. The results indicated that protein domain boundaries that mark higher-order structural organization are largely coded by translationally slow regions on the RNA and are composed of such amino acids that are stickier to the ribosome channel through which the synthesized polypeptide chain emerges into the cytoplasm. The translationally slow nucleotide regions on mRNA possess the potential to form hairpin secondary structures and such structures could further slow the movement of ribosome. The results point to an intriguing correlation between protein synthesis machinery and in vivo protein folding. Examination of available mutagenic data indicated that the effects of some of the reported mutations were consistent with our hypothesis.

Bacterial Proteins↗
PubMed2006

Molecular population genetics of the gene encoding the human fertilization protein zonadhesin reveals rapid adaptive evolution.

A hallmark of positive selection (adaptive evolution) in protein-coding regions is a d(N)/d(S) ratio >1, where d(N) is the number of nonsynonymous substitutions/nonsynonymous sites and d(S) is the number of synonymous substitutions/synonymous sites. Zonadhesin is a male reproductive protein localized on the sperm head, comprising many domains known to be involved in cell-cell interaction or cell adhesion. Previous studies have shown that VWD domains (homologous to the D domains of the von Willebrand factor) are involved directly in binding to the female zona pellucida (ZP) in a species-specific manner. In this study, we sequenced 47 coding exons in 12 primate species and, by using maximum-likelihood methods to determine sites under positive selection, we show that VWD2, membrane/A5 antigen mu receptor, and mucin-like domains in zonadhesin are rapidly evolving and, thus, may be involved in binding to the ZP in a species-specific manner in primates. In addition, polymorphism data from 48 human individuals revealed significant polymorphism-to-divergence heterogeneity and a significant departure from equilibrium-neutral expectations in the frequency spectrum, suggesting balancing selection and positive selection occurring in zonadhesin (ZAN) within human populations. Finally, we observe adaptive evolution in haplotypes segregating for a frameshift mutation that was previously thought to indicate that ZAN was a potential pseudogene.

Animals↗
PubMed1998

Differences in the evolutionary pattern of feline panleukopenia virus and canine parvovirus.

Canine parvovirus (CPV) suddenly appeared in the late 1970s after which it showed continuous antigenic changes. Virological and molecular genetic analyses mainly focused on feline panleukopenia virus (FPLV) were conducted in this study because FPLV is the suspected ancestor of CPV; the way in which FPLV evolves may help to explain the emergence of CPV. Analysis of escape mutants against FPLV-specific monoclonal antibody showed that viruses possessing CPV-like properties were not easily detected in FPLV virus stocks. Phylogenetic analysis revealed that the nonstructural protein 1 (NS1) and capsid protein 2 (VP2) genes of FPLV changed with time. A similar tendency, however, was not observed in the FPLV VP2 proteins. In contrast, the topology of the phylogenetic tree of VP2 proteins of CPV basically concurred with that of the VP2 genes. Analysis of the ratio of nonsynonymous and synonymous substitutions revealed that synonymous substitutions exceeded nonsynonymous substitutions in both the NS1 and VP2 genes of FPLV, even when the analysis focused on specific regions in the VP2 gene that are known to be located on the capsid surface. Comparison of the CPV VP2 genes revealed that nonsynonymous substitution was found to dominate over synonymous substitution in one specific region in the VP2 gene. These results suggested that FPLV has changed mainly by random genetic drift. In contrast, after the appearance of CPV, changes in the CPV VP2 gene appear to be partly selected by certain positive selection forces. CPV and FPLV are known to be closely related viruses genetically and biologically, but the evolutionary mechanisms of the two viruses appeared to be different.

Amino Acid Substitution↗
PubMed2026

Tackling non-canonical splicing in arrhythmogenic cardiomyopathy to reduce the uncertain significance variants burden.

BACKGROUND: Splice-altering variants (SAVs), particularly those outside canonical splice sites, are an underappreciated contributor to inherited cardiovascular diseases. In arrhythmogenic cardiomyopathy (ACM), these variants frequently remain classified as of uncertain significance (VUS) due to limited predictive power and lack of transcript-level evidence, constraining genetic yield and clinical management. Our study aimed to determine the functional impact of SAVs in ACM genes and refine their classification using ACMG/AMP and ClinGen SVI criteria. METHODS: SAVs identified in 200 ACM probands underwent SpliceAI prediction, GTEx cardiac exon-usage annotation, and functional assessment using pSPL3-based minigene assays. Aberrant transcripts were quantified using Percent Splicing Alteration (PSA). Segregation data and ACMG/AMP criteria refined by ClinGen SVI were applied to integrate functional and clinical evidence for classification. RESULTS: Aberrant splicing was confirmed in 9/20 variants (45%), including synonymous, missense, and non-canonical intronic changes. SpliceAI scores correlated strongly with PSA values (R&#xb2;=0.86). Case-control burden testing revealed significant enrichment of splice-altering variants in DSP, DSG2, DSC2 and FLNC. Integrating predictive algorithms with experimental validation and segregation analysis markedly enhances reclassification of 16/20 variants (80%). CONCLUSION: Splicing defects beyond canonical sites significantly shape ACM genetic landscape. Integrating predictive models with experimental validation clarifies uncertain variants bridging the gap between genomic uncertainty and clinical decision-making.

Humans↗