Elimination of rNMPs from mitochondrial DNA has no effect on its stability.

Ribonucleotides (rNMPs) incorporated in the nuclear genome are a well-established threat to genome stability and can result in DNA strand breaks when not removed in a timely manner. However, the presence of a certain level of rNMPs is tolerated in mitochondrial DNA (mtDNA) although aberrant mtDNA rNMP content has been identified in disease models. We investigated the effect of incorporated rNMPs on mtDNA stability over the mouse life span and found that the mtDNA rNMP content increased during early life. The rNMP content of mtDNA varied greatly across different tissues and was defined by the rNTP/dNTP ratio of the tissue. Accordingly, mtDNA rNMPs were nearly absent in SAMHD1-/- mice that have increased dNTP pools. The near absence of rNMPs did not, however, appreciably affect mtDNA copy number or the levels of mtDNA molecules with deletions or strand breaks in aged animals near the end of their life span. The physiological rNMP load therefore does not contribute to the progressive loss of mtDNA quality that occurs as mice age.

De novo dNTP production is essential for normal postnatal murine heart development.

The building blocks of DNA, dNTPs, can be produced de novo or can be salvaged from deoxyribonucleosides. However, to what extent the absence of de novo dNTP production can be compensated for by the salvage pathway is unknown. Here, we eliminated de novo dNTP synthesis in the mouse heart and skeletal muscle by inactivating ribonucleotide reductase (RNR), a key enzyme for the de novo production of dNTPs, at embryonic day 13. All other tissues had normal de novo dNTP synthesis and theoretically could supply heart and skeletal muscle with deoxyribonucleosides needed for dNTP production by salvage. We observed that the dNTP and NTP pools in WT postnatal hearts are unexpectedly asymmetric, with unusually high dGTP and GTP levels compared with those in whole mouse embryos or murine cell cultures. We found that RNR inactivation in heart led to strongly decreased dGTP and increased dCTP, dTTP, and dATP pools; aberrant DNA replication; defective expression of muscle-specific proteins; progressive heart abnormalities; disturbance of the cardiac conduction system; and lethality between the second and fourth weeks after birth. We conclude that dNTP salvage cannot substitute for de novo dNTP synthesis in the heart and that cardiomyocytes and myocytes initiate DNA replication despite an inadequate dNTP supply. We discuss the possible reasons for the observed asymmetry in dNTP and NTP pools in WT hearts.

Ribonucleotides incorporated by the yeast mitochondrial DNA polymerase are not repaired.

Incorporation of ribonucleotides into DNA during genome replication is a significant source of genomic instability. The frequency of ribonucleotides in DNA is determined by deoxyribonucleoside triphosphate/ribonucleoside triphosphate (dNTP/rNTP) ratios, by the ability of DNA polymerases to discriminate against ribonucleotides, and by the capacity of repair mechanisms to remove incorporated ribonucleotides. To simultaneously compare how the nuclear and mitochondrial genomes incorporate and remove ribonucleotides, we challenged these processes by changing the balance of cellular dNTPs. Using a collection of yeast strains with altered dNTP pools, we discovered an inverse relationship between the concentration of individual dNTPs and the amount of the corresponding ribonucleotides incorporated in mitochondrial DNA, while in nuclear DNA the ribonucleotide pattern was only altered in the absence of ribonucleotide excision repair. Our analysis uncovers major differences in ribonucleotide repair between the two genomes and provides concrete evidence that yeast mitochondria lack mechanisms for removal of ribonucleotides incorporated by the mtDNA polymerase. Furthermore, as cytosolic dNTP pool imbalances were transmitted equally well into the nucleus and the mitochondria, our results support a view of the cytosolic and mitochondrial dNTP pools in frequent exchange.

Body Mass Index and Association With Caries in School-Aged Children With Orofacial Cleft: A Case-Control Study.

OBJECTIVE: Data on the association between body mass index (BMI) and dental caries in children with orofacial clefts are sparse. Therefore, studies on the impact of BMI on caries frequency in children with cleft lip and/or palate (CL/P) are of importance. The aim of the current study was to investigate the association between BMI and frequency of dental caries in children with and without CL/P. Height, weight, and BMI in children with CL/P were also compared to controls. DESIGN: This study used a cross-sectional case-control design. PARTICIPANTS: One hundred and thirty-nine 5- and 10-year-old children with CL/P and 299 age-matched controls. MAIN OUTCOME MEASURES: Caries was recorded according to the International Caries Detection and Assessment System. Height and weight were recorded, and BMI was calculated as weight/height2. RESULTS: There was no correlation between BMI and caries frequency. Weight, height, and BMI were significantly lower in all children with CL/P compared to controls. After adjustment for international adoption, only BMI was significantly lower in CL/P children compared to controls. Non-adopted children with CL/P were significantly heavier and longer than adopted children with CL/P. CONCLUSIONS: Five- and 10-year-old children with corrected CL/P seemed to have a lower BMI than controls, but there was no association between BMI and caries frequency. Internationally adopted children with CL/P were lighter and shorter than non-adopted CL/P children and controls.

Heterozygous colon cancer-associated mutations of SAMHD1 have functional significance.

Even small variations in dNTP concentrations decrease DNA replication fidelity, and this observation prompted us to analyze genomic cancer data for mutations in enzymes involved in dNTP metabolism. We found that sterile alpha motif and histidine-aspartate domain-containing protein 1 (SAMHD1), a deoxyribonucleoside triphosphate triphosphohydrolase that decreases dNTP pools, is frequently mutated in colon cancers, that these mutations negatively affect SAMHD1 activity, and that several SAMHD1 mutations are found in tumors with defective mismatch repair. We show that minor changes in dNTP pools in combination with inactivated mismatch repair dramatically increase mutation rates. Determination of dNTP pools in mouse embryos revealed that inactivation of one SAMHD1 allele is sufficient to elevate dNTP pools. These observations suggest that heterozygous cancer-associated SAMHD1 mutations increase mutation rates in cancer cells.

Increased and imbalanced dNTP pools symmetrically promote both leading and lagging strand replication infidelity.

The fidelity of DNA replication requires an appropriate balance of dNTPs, yet the nascent leading and lagging strands of the nuclear genome are primarily synthesized by replicases that differ in subunit composition, protein partnerships and biochemical properties, including fidelity. These facts pose the question of whether imbalanced dNTP pools differentially influence leading and lagging strand replication fidelity. Here we test this possibility by examining strand-specific replication infidelity driven by a mutation in yeast ribonucleotide reductase, rnr1-Y285A, that leads to elevated dTTP and dCTP concentrations. The results for the CAN1 mutational reporter gene present in opposite orientations in the genome reveal that the rates, and surprisingly even the sequence contexts, of replication errors are remarkably similar for leading and lagging strand synthesis. Moreover, while many mismatches driven by the dNTP pool imbalance are efficiently corrected by mismatch repair, others are repaired less efficiently, especially those in sequence contexts suggesting reduced proofreading due to increased mismatch extension driven by the high dTTP and dCTP concentrations. Thus the two DNA strands of the nuclear genome are at similar risk of mutations resulting from this dNTP pool imbalance, and this risk is not completely suppressed even when both major replication error correction mechanisms are genetically intact.

Caries prevalence and enamel defects in 5- and 10-year-old children with cleft lip and/or palate: A case-control study.

OBJECTIVE: To determine the prevalence of dental caries and enamel defects in 5- and 10-year-old Swedish children with cleft lip and/or palate (CL(P)) in comparison to non-cleft controls. MATERIALS AND METHODS: The study group consisted of 139 children with CL(P) (80 subjects aged 5 years and 59 aged 10 years) and 313 age-matched non-cleft controls. All children were examined by one of two calibrated examiners. Caries was scored according to the International Caries Detection and Assessment System (ICDAS-II) and enamel defects as presence and frequency of hypoplasia and hypomineralization. RESULTS: The caries prevalence among the 5-year-old CL(P) children and the non-cleft controls was 36% and 18%, respectively (p < 0.05). The CL(P) children had higher caries frequency (initial and cavitated lesions) in the primary dentition than their controls (1.2 vs 0.9; p < 0.05). A significantly higher prevalence of enamel defects was found in CL(P) children of both age groups and anterior permanent teeth were most commonly affected. CONCLUSIONS: Preschool children with cleft lip and/or palate seem to have more caries in the primary dentition than age-matched non-cleft controls. Enamel defects were more common in CL(P) children in both age groups.

Mechanisms of mutagenesis in vivo due to imbalanced dNTP pools.

The mechanisms by which imbalanced dNTPs induce mutations have been well characterized within a test tube, but not in vivo. We have examined mechanisms by which dNTP imbalances induce genome instability in strains of Saccharomyces cerevisiae with different amino acid substitutions in Rnr1, the large subunit of ribonucleotide reductase. These strains have different dNTP imbalances that correlate with elevated CAN1 mutation rates, with both substitution and insertion-deletion rates increasing by 10- to 300-fold. The locations of the mutations in a strain with elevated dTTP and dCTP are completely different from those in a strain with elevated dATP and dGTP. Thus, imbalanced dNTPs reduce genome stability in a manner that is highly dependent on the nature and degree of the imbalance. Mutagenesis is enhanced despite the availability of proofreading and mismatch repair. The mutations can be explained by imbalanced dNTP-induced increases in misinsertion, strand misalignment and mismatch extension at the expense of proofreading. This implies that the relative dNTP concentrations measured in extracts are truly available to a replication fork in vivo. An interesting mutational strand bias is observed in one rnr1 strain, suggesting that the S-phase checkpoint selectively prevents replication errors during leading strand replication.

Quantitative Analysis of Nucleoside Triphosphate Pools in Mouse Muscle Using Hydrophilic Interaction Liquid Chromatography Coupled with Tandem Mass Spectrometry Detection.

Defects in deoxyribonucleoside triphosphate (dNTP) metabolism are associated with a number of mitochondrial DNA (mtDNA) depletion syndromes (MDS). These disorders affect the muscles, liver, and brain, and the concentrations of dNTPs in these tissues are already normally low and are, therefore, difficult to measure. Thus, information about the concentrations of dNTPs in tissues of healthy animals and animals with MDS are important for mechanistic studies of mtDNA replication, analysis of disease progression, and the development of therapeutic interventions. Here, we present a sensitive method for the simultaneous analysis of all four dNTPs as well as all four ribonucleoside triphosphates (NTPs) in mouse muscles using hydrophilic interaction liquid chromatography coupled with triple quadrupole mass spectrometry. The simultaneous detection of NTPs allows them to be used as internal standards for the normalization of dNTP concentrations. The method can be applied for measuring dNTP and NTP pools in other tissues and organisms.

Highly mutagenic and severely imbalanced dNTP pools can escape detection by the S-phase checkpoint.

A balanced supply of deoxyribonucleoside triphosphates (dNTPs) is one of the key prerequisites for faithful genome duplication. Both the overall concentration and the balance among the individual dNTPs (dATP, dTTP, dGTP, and dCTP) are tightly regulated, primarily by the enzyme ribonucleotide reductase (RNR). We asked whether dNTP pool imbalances interfere with cell cycle progression and are detected by the S-phase checkpoint, a genome surveillance mechanism activated in response to DNA damage or replication blocks. By introducing single amino acid substitutions in loop 2 of the allosteric specificity site of Saccharomyces cerevisiae RNR, we obtained a collection of strains with various dNTP pool imbalances. Even mild dNTP pool imbalances were mutagenic, but the mutagenic potential of different dNTP pool imbalances did not directly correlate with their severity. The S-phase checkpoint was activated by the depletion of one or several dNTPs. In contrast, when none of the dNTPs was limiting for DNA replication, even extreme and mutagenic dNTP pool imbalances did not activate the S-phase checkpoint and did not interfere with the cell cycle progression.

The integrity and assay performance of tissue mitochondrial DNA is considerably affected by choice of isolation method.

The integrity of mitochondrial DNA (mtDNA) isolated from solid tissues is critical for analyses such as long-range PCR, but is typically assessed under conditions that fail to provide information on the individual mtDNA strands. Using denaturing gel electrophoresis, we show that commonly-used isolation procedures generate mtDNA containing several single-strand breaks per strand. Through systematic comparison of DNA isolation methods, we identify a procedure yielding the highest integrity of mtDNA that we demonstrate displays improved performance in downstream assays. Our results highlight the importance of isolation method choice, and serve as a resource to researchers requiring high-quality mtDNA from solid tissues.

Genome-wide linkage scan of common stroke in families from northern Sweden.

BACKGROUND AND PURPOSE: Taking advantage of low genetic variations in northern Sweden, we performed a genome-wide linkage scan to investigate the susceptibility loci for common forms of stroke. METHODS: Fifty-six families, containing multiple cases of stroke and whose data had been previously used to replicate linkage to the phosphodiesterase 4D locus on chromosome 5q, were genotyped in a genome-wide scan. Fine mapping was performed, and subsequently 53 additional families from the same region were genotyped over the candidate regions. RESULTS: Linkage calculations were performed by using 3 different disease models, from a very broad (all stroke cases defined by World Health Organization MONICA criteria) to a narrower (ischemic stroke only) stroke phenotype. With all models, nonparametric multipoint linkage analysis yielded allele-sharing log of the odds (LOD) scores >1.2 at 9 locations: 1p34, 5q13, 7q35, 9q22, 9q34, 13q32, 14q32, 18p11, and 20q13. The highest allele-sharing LOD scores were obtained on chromosomes 5q (previously reported), 1p (LOD=2.09), and 18p (LOD=2.14). Fine mapping resulted in increased allele-sharing LOD scores for chromosome 5q (previously reported) and 9q22 (LOD=1.56), but all others decreased. Combining these initial results with a subsequent analysis of 53 additional families, we obtained the highest allele-sharing LOD scores on chromosomes 5q, 13q, and 18p, although none reached the initial genome-wide allele-sharing LOD scores. CONCLUSIONS: Genetic analysis of stroke in families from northern Sweden did not identify any new major stroke loci. This indicates that multiple minor susceptibility loci in addition to the previously known locus on chromosome 5 could contribute to the disease.

Linkage of ischemic stroke to the PDE4D region on 5q in a Swedish population.

BACKGROUND AND PURPOSE: Recent Icelandic studies have demonstrated linkage for common forms of stroke to chromosome 5q12 and association between phosphodiesterase4D (PDE4D) and ischemic stroke. Using a candidate region approach, we wanted to test the validity of these findings in a different population from northern Sweden. METHODS: A total of 56 families with 117 affected individuals were included in the linkage study. Genotyping was performed with polymorphic microsatellite markers with an average distance of 4.5 cM on chromosome 5. In the association study, 275 cases of first-ever stroke were included together with 550 matched community controls. Polymorphisms were tested individually for association of PDE4D to stroke. RESULTS: Maximum allele-sharing lod score in favor of linkage was observed at marker locus D5S424 (lod score=2.06; P=0.0010). Conditional logistic regression calculations revealed no significant association of ischemic stroke to the defined at-risk allele in PDE4D (odds ratio, 1.1; 95% confidence interval, 0.84 to 1.45). A protective effect may though be implied for 2 of the polymorphisms analyzed in PDE4D. CONCLUSIONS: Using a candidate region approach in a set of stroke families from northern Sweden, we have replicated linkage of stroke susceptibility to the PDE4D gene region on chromosome 5q. Association studies in an independent nested case-control sample from the same geographically located population suggested that different alleles confer susceptibility/protection to stroke in the Icelandic and the northern Swedish populations.

Lasting improvement of hyperglycaemia and bodyweight: low-carbohydrate diet in type 2 diabetes--a brief report.

UNLABELLED: In two groups of obese patients with type 2 diabetes the effects of 2 different diet compositions were tested with regard to glycaemic control and bodyweight. A group of 16 obese patients with type 2 diabetes was advised on a low-carbohydrate diet, 1800 kcal for men and 1600 kcal for women, distributed as 20 % carbohydrates, 30 % protein and 50 % fat. Fifteen obese diabetes patients on a high-carbohydrate diet were control group. Their diet, 1600-1800 kcal for men and 1400-1600 kcal for women, consisted of approximately 60 % carbohydrates, 15 % protein and 25 % fat. Positive effects on the glucose levels were seen very soon. After 6 months a marked reduction in bodyweight of patients in the low-carbohydrate diet group was observed, and this remained one year later. After 6 months the mean changes in the low-carbohydrate group and the control group respectively were (+/-SD): fasting blood glucose (f-BG): -3.4+/-2.9 and -0.6+/-2.9 mmol/l; HBA1c: -1.4+/-1.1 % and -0.6+/-1.4 %; Body Weight: -11.4+/-4 kg and -1.8+/-3.8 kg; BMI: -4.1+/-1.3 kg/m_ and -0.7+/-1.3 kg/m_. Large changes in blood glucose levels were seen immediately. CONCLUSION: A low-carbohydrate diet is an effective tool in the treatment of obese patients with type 2 diabetes.

Lasting improvement of hyperglycaemia and bodyweight: low-carbohydrate diet in type 2 diabetes. A brief report.

In two groups of obese patients with type 2 diabetes the effects of 2 different diet compositions were tested with regard to glycaemic control and bodyweight. A group of 16 obese patients with type 2 diabetes was advised on a low-carbohydrate diet, 1800 kcal for men and 1600 kcal for women, distributed as 20% carbohydrates, 30% protein and 50% fat. Fifteen obese diabetes patients on a high-carbohydrate diet were control group. Their diet, 1600-1800 kcal for men and 1400-1600 kcal for women, consisted of approximately 60% carbohydrates, 15% protein and 25% fat. Positive effects on the glucose levels were seen very soon. After 6 months a marked reduction in bodyweight of patients in the low-carbohydrate diet group was observed, and this remained one year later. After 6 months the mean changes in the low-carbohydrate group and the control group respectively were (+/-SD): fasting blood glucose (f-BG): -3.4 +/- 2.9 and -0.6 +/- 2.9 mmol/l; HBA1c: -1.4 +/- 1.1% and -0.6 +/- 1.4%; Body Weight: -11.4 +/- 4 kg and -1.8 +/- 3.8 kg; BMI: -4.1 +/- 1.3 kg/m_ and -0.7 +/- 1.3 kg/m_. Large changes in blood glucose levels were seen immediately. A low-carbohydrate diet is an effective tool in the treatment of obese patients with type 2 diabetes.

Telomere length homeostasis responds to changes in intracellular dNTP pools.

Telomeres, the ends of linear eukaryotic chromosomes, shorten due to incomplete DNA replication and nucleolytic degradation. Cells counteract this shortening by employing a specialized reverse transcriptase called telomerase, which uses deoxyribonucleoside triphosphates (dNTPs) to extend telomeres. Intracellular dNTP levels are tightly regulated, and perturbation of these levels is known to affect DNA synthesis. We examined whether altering the levels of the dNTP pools or changing the relative ratios of the four dNTPs in Saccharomyces cerevisiae would affect the length of the telomeres. Lowering dNTP levels leads to a modest shortening of telomeres, while increasing dNTP pools has no significant effect on telomere length. Strikingly, altering the ratio of the four dNTPs dramatically affects telomere length homeostasis, both positively and negatively. Specifically, we find that intracellular deoxyguanosine triphosphate (dGTP) levels positively correlate with both telomere length and telomerase nucleotide addition processivity in vivo. Our findings are consistent with in vitro data showing dGTP-dependent stimulation of telomerase activity in multiple organisms and suggest that telomerase activity is modulated in vivo by dGTP levels.

Denial in patients with a first-time myocardial infarction: relations to pre-hospital delay and attendance to a cardiac rehabilitation programme.

BACKGROUND: Survival of a myocardial infarction and subsequent prognosis are highly dependent on the time between onset of symptoms and medical intervention. DESIGN: This cross-sectional study examines whether patients who used the psychological defence mechanism of denial when faced with symptoms of a first-time myocardial infarction tended to also show a prolonged delay in going to the hospital and to be less willing to participate in a cardiac rehabilitation programme. METHODS: One hundred and seven patients, 78 men and 29 women, were enrolled in this study. The sample was divided into two groups depending on whether the patients sought medical help within 4 h after they began experiencing myocardial infarction symptoms (non-delayers) or whether they waited longer (delayers). Denial was measured with the Hackett and Cassem semi-structured interview 3-5 days after the patients entered the hospital. Data on participation (attenders) or not (non-attenders) in the rehabilitation programme was also obtained. RESULTS: Forty-nine patients exhibited a prolonged delay and 76 patients did not attend the rehabilitation programme. Both prolonged delay and a lesser readiness to attend the rehabilitation programme that was offered were related to a greater use of denial. In addition, the great majority of the patients categorized as being high deniers were found to also be both delayers and non-attenders. CONCLUSIONS: The results suggest denial to increase the health risks of persons potentially prone to myocardial infarction. If our knowledge about this psychological defence mechanism is increased, we might be able to reach more patients in alternative and individually based cardiac rehabilitation programmes.