A JEWISH ISOLATE IN SOUTHERN BRAZIL. EFFECTIVE POPULATION, INTERMARRIAGE, FERTILITY, INBREEDING, MORTALITY, TWINNING, SEX RATIO, GENETIC LOAD AND TOTAL MUTATION RATE.
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Abortion, Induced↗
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INBREEDING AND THE MUTATIONAL AND BALANCED LOADS IN NATURAL POPULATIONS OF DROSOPHILA WILLISTONI.
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Animals↗
Chemobiosynthesis of novel 6-deoxyerythronolide B analogues by mutation of the loading module of 6-deoxyerythronolide B synthase 1.
Chemobiosynthesis (J. R. Jacobsen, C. R. Hutchinson, D. E. Cane, and C. Khosla, Science 277:367-369, 1997) is an important route for the production of polyketide analogues and has been used extensively for the production of analogues of 6-deoxyerythronolide B (6-dEB). Here we describe a new route for chemobiosynthesis using a version of 6-deoxyerythronolide B synthase (DEBS) that lacks the loading module. When the engineered DEBS was expressed in both Escherichia coli and Streptomyces coelicolor and fed a variety of acyl-thioesters, several novel 15-R-6-dEB analogues were produced. The simpler "monoketide" acyl-thioester substrates required for this route of 15-R-6-dEB chemobiosynthesis allow greater flexibility and provide a cost-effective alternative to diketide-thioester feeding to DEBS KS1(o) for the production of 15-R-6-dEB analogues. Moreover, the facile synthesis of the monoketide acyl-thioesters allowed investigation of alternative thioester carriers. Several alternatives to N-acetyl cysteamine were found to work efficiently, and one of these, methyl thioglycolate, was verified as a productive thioester carrier for mono- and diketide feeding in both E. coli and S. coelicolor.
Culture Media↗
Role of hepatitis B viral load and basal core promoter mutation in hepatocellular carcinoma in hepatitis B carriers.
BACKGROUND: Several hepatitis B viral factors correlate with the progression of chronic liver disease. However, the independent and interactive effects of each known viral factor on the development of hepatocellular carcinoma (HCC) remain largely unknown. METHODS: In a cross-sectional, retrospective, hospital-based setting, we comprehensively compared viral factors in 160 chronic hepatitis B virus (HBV) carriers and 200 patients with HCC, to clarify the independent and joint effect of each factor. RESULTS: In univariate analysis, statistically significant odds ratios (ORs) were obtained for male sex (P < .001), advanced age (P < .001), HBV genotype C infection (P = .005), the precore A1896 mutation (P < .001), and the basal core promoter (BCP) T1762/A1764 mutation (P < .001). According to the results of multiple logistic-regression analysis, advanced age, male sex, the precore A1896 mutation, the BCP T1762/A1764 mutation, and an HBV load > or = 10(5) copies/mL were independently associated with the development of HCC. Compared with patients with an HBV load < 10(5) copies/mL and the BCP A1762/G1764 wild-type strain, the adjusted OR of developing HCC was > or = 30 in patients with an HBV load > or = 10(5) copies/mL and the BCP T1762/A1764 mutant, irrespective of the presence of the precore A1896 mutation and viral genotype. CONCLUSIONS: HBV load and the BCP T1762/A1764 mutation are important in hepatocarcinogenesis.
Age Factors↗
THE LOAD OF LETHAL MUTATIONS IN WHITE AND NEGRO BRAZILIAN POPULATIONS. I. FIRST SURVEY.
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Abortion, Induced↗
THE LOAD OF LETHAL MUTATIONS IN WHITE AND NEGRO BRAZILIAN POPULATIONS. II. SECOND SURVEY.
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Abortion, Induced↗
Immunoglobulin VH genes of high-grade mucosa-associated lymphoid tissue lymphomas show a high load of somatic mutations and evidence of antigen-dependent affinity maturation.
High-grade mucosa-associated lymphoid tissue (MALT) B-cell lymphoma of the stomach shares several features with its low-grade counterpart. The latter is nearly invariably associated with Helicobacter pylori, and the tumor cells of all MALT lymphomas normally express surface antigen receptors; thus, it is possible that the high-grade type, like the low-grade type, is still influenced by interaction with antigen. In the present study, we analyzed the immunoglobulin heavy chain variable (V)-region genes from eight cases of high-grade MALT lymphoma and one case of Burkitt's lymphoma of the stomach. The V-region genes revealed somatic mutations in all cases, leading to the conclusion that high-grade MALT lymphomas derive from antigen-experienced (post-) germinal center B-cells. Nonrandom distribution of replacement and silent mutations within the gene segments in seven of the eight MALT lymphomas indicated that these V-region genes were selected by antigen, at least for some period of time. Five of the cases showed an unusual mutation pattern that was suggestive of selection by autoantigen or superantigen rather than heterogeneous antigen. Analysis for intraclonal variations revealed evidence of ongoing mutations in two cases. In these cases, the tumor clones probably derived from cells affected by a germinal center B-cell reaction, as the microenvironment of the germinal center is required for maintenance of an active hypermutation mechanism. On the other hand, in another two cases, no evidence of intraclonal variations was found. Thus, either these tumor clones were derived from postgerminal center B-cells, or the hypermutation mechanism in the germinal center ceased after some period of time. Given the mutation pattern, it is possible that high-grade MALT lymphomas emerge from further transformation of low-grade MALT lymphomas with accumulation of additional mutations in the complementarity-determining regions.
Amino Acid Sequence↗
Genetics of natural populations. 32. Inbreeding and the mutational and balanced genetic loads in natural populations of Drosophila pseudoobscura.
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Animals↗
Role of hepatitis B virus precore/core promoter mutations and serum viral load on noncirrhotic hepatocellular carcinoma: a case-control study.
BACKGROUND: Apart from the presence of liver cirrhosis, hepatitis B virus (HBV) factors have also been shown to play a role in the development of hepatocellular carcinoma (HCC). Studying HBV-related noncirrhotic HCC may help clarify the effect of viral factors. METHODS: In a hospital-based, age- and genotype-matched study, we aimed to determine the role played by basal core promoter (BCP) T1762/A1764 mutation, precore A1896 mutation, and serum viral load in noncirrhotic hepatocarcinogenesis by comparing 44 patients with HBV-related noncirrhotic HCC, 45 patients with chronic hepatitis B, and 42 patients with HBV-related cirrhotic HCC. HBV genotype, precore and BCP mutations, and viral load were determined by molecular assays. RESULTS: In univariate analysis, statistically significant odds ratios were obtained for male sex (P=.005) and BCP T1762/A1764 mutation (P=.0003) in patients with noncirrhotic HCC, compared with patients with chronic hepatitis B. By multiple logistic regression analysis, male sex, BCP T1762/A1764 mutation, and viral load >or=10(5) copies/mL were independently associated with the risk of noncirrhotic HCC. The virologic characteristics were similar between patients with cirrhotic HCC and those with noncirrhotic HCC. CONCLUSIONS: Our results suggest that BCP T1762/A1764 mutation and higher viral load may be involved in the carcinogenesis of cirrhotic and noncirrhotic HCC.
Adult↗
Somatic hypermutation and B-cell lymphoma.
During the B-cell response to T-cell-dependent antigens, the B cells undergo a rapid proliferative phase in the germinal centre. This is accompanied by the introduction of mutations into the immunoglobulin (Ig) variable region (V) genes. The B cells are then selected according to the affinity of the encoded immunoglobulin for antigen, resulting in affinity maturation of the response. Analysis of mutations in IgV genes has given insight into the history of individual B cells and their malignancies. In most cases, analysis of mutations confirms classifications of B-cell lineage designated by studies of cellular morphology and surface antigen expression. However, of particular interest is the subdivision of groups of malignancies by analysis of somatic hypermutation. It is now apparent that there are two subsets of chronic lymphocytic leukaemia (CLL), one with a low load of mutations and poor prognosis. and one with a heavy load of mutations with a much more favourable prognosis. In addition, in Burkitt's lymphoma, sporadic and endemic subtypes are now considered possibly to have a different pathogenesis, reflected in differences in the numbers of mutations. Hodgkin's disease, which was a mystery for many years, has now been shown to be a B-cell tumour. Although in many cases the Ig genes are crippled by somatic hypermutation, it is thought that failure to express Ig is more likely to be associated with problems of transcription. It has been proposed that the distribution of mutations in a B-cell lymphoma can be used to determine whether a lymphoma is selected. We have investigated the load and distribution of mutations in one group of lymphomas--marginal zone B-cell lymphomas of mucosa-associated lymphoid tissues (MALT-type lymphoma), which are dependent on Helicobacter pylori for disease progression, to investigate the limits of information that can be derived from such studies. Comparison of the load of mutations demonstrates that these tumours have approximately the same load of mutations as normal mucosal marginal zone B cells from the Peyer's patches and mucosal plasma cells. This is consistent with the origin of these cells from mucosal marginal zone B cells with plasma cell differentiation. To investigate selection in MALT lymphomas we compared a region of the framework region three in ten MALT lymphomas which use the V(H4) family, with the same codons in groups of V(H4) genes that are out of frame between V and J. The latter accumulate mutations but are not used and are not selected. A group of V(H4) genes are in-frame between V and J were also included for comparison. There were no obvious differences in the distribution of mutations between the groups of genes; the same hot spots and cold spots were apparent in each. In the MALT lymphomas, selection was apparent in the framework regions only and the tendency was to conserve. We therefore feel that there is selection to conserve antibody structure and that this does not reflect selection for antigen. We do not believe that antigen selection can be deduced reliably from sequence information alone. It is possible that somatic hypermutation could be a cause of malignancy since it has been shown that the process may generate DNA strand breaks and is known to be able to generate insertions and deletions. Such events may mediate the translocation of genes--a process that is pivotal in the evolution of many lymphomas.
Antigens↗
Common gardens reveal genomic susceptibility and vulnerability to climate change in Eucalyptus.
Accelerated global climate change and increased species introduction across international scales have raised concerns about the potential for trees to experience maladaptation or lagging adaptation in response to these environmental shifts. However, our knowledge regarding the relationship between the genomic metrics used to predict maladaptation and actual fitness proxies in trees remains limited. Here, we present a population genomic analysis of 295 families from 28 provenances of Eucalyptus pellita, a widely cultivated fast-growing tree species, and conducted two common garden experiments. Genomic susceptibility encompassing individual heterozygosity (H), genomic inbreeding (FROH), and genomic load (inferred from deleterious mutations) exhibited distinct geographic patterns, shedding light on the origin and evolutionary history of E. pellita. The genetic basis of local adaptation was elucidated through genotype-environment associations and genome-wide association studies, including 198 loci associated with climate and 2388 loci regulating different traits. Furthermore, Australian provenances have higher genomic vulnerability under prospective climate alterations than Papua New Guinea and Indonesia provenances. By integrating phenotypic data across two common gardens, the relationship between leaf functional traits and predicted metrics of maladaptation was closer than growth attributes. Notably, pronounced natural selection signals linked to leaf morphogenesis have been identified by comparing two lineages spanning the oceans. This study underscores the immense potential of leveraging genomic susceptibility and genomic vulnerability to decipher the local (mal)adaptation of forest trees.
Eucalyptus↗
Host-parasite arms race in mutation modifications: indefinite escalation despite a heavy load?
If constantly changing genotypes are favorable in host and parasite coevolution, an indefinite escalation of mutation rates would result despite heavy mutational loads. We theoretically study this possibility by examining the mutation modifier dynamics of host and parasite that engage in genotype-specific epidemiological interaction. In the first model, we study the evolutionarily stable (ESS) mutation rate or switching rate if two alleles in a single locus are subjected to frequency-dependent selection favoring the rarer of the two. Mutation modifier locus is either tightly linked or unlinked to the selected locus. Sufficiently strong frequency-dependent selection may cause cycles in allele frequencies and a modifier with higher mutation rate enjoys the long-term advantage by randomizing the genotype of their offspring. Through the repeated events of invasion and replacement of mutation modifiers, the mutation rate continues to increase until the allele frequencies are stabilized. If some fraction of mutations are deleterious, there is no longer a pure ESS mutation rate: the evolutionarily stable population then consists of multiple strains concerning mutation modifier, typically one with a very high mutation rate and the other with a very low rate, stably coexisting and fighting off invasion by any other modifiers. These results are almost independent of the linkage between the selected and the modifier loci. In the second model, we consider the joint evolution of host and parasite mutation modifiers, assuming that a specific pair of host and parasite genotype densities change following the Nicholson-Bailey type model. If there is no cost of deleterious mutations, mutation rates of both species are escalated indefinitely by modifier evolution until they completely suppress the fluctuation of genotype densities. However, a small cost of deleterious mutation is enough to collapse this coevolutionary equilibrium of inflated mutations. Typical coevolutionary outcome is that the parasite mutation rate is accelerated to a high level; whereas the host mutation rate is driven to zero. Extension of our results to host-parasite coevolution of recombination modifier evolution is discussed.
Animals↗
Inverse relationship between viral load and genotypic resistance mutations in Korean patients with primary HIV type 1 infections.
The transmission of antiretroviral-resistant HIV-1 strains is associated with suboptimal virological responses to initial antiretroviral therapy. However, certain types of resistance mutations are known to be associated with decreased viral fitness, which confers a lower replication capacity than that of the wild-type virus in the absence of antiretroviral drugs. Therefore, we evaluated the relationship between antiretroviral resistance mutations and viral replication in the primary HIV-1 infection (PHI) period. From January 2002 to March 2005, 52 PHI patients were identified in the Republic of Korea. HIV-1 RNA genotyping was performed, and the resistance mutation score was obtained from the HIV Drug Resistance Database of Stanford University. We defined the sum of the average resistance mutation scores (SARMS) for each antiretroviral drug class as a measure of the degree of resistance of any specific strain. The overall mean SARMS was 2.00 +/- 2.74, and the annual mean did not change significantly during the study period. No critical resistance mutation gene was identified in the study group. The SARMS showed a weak negative correlation with the viral load log10 during PHI, but without statistical significance (r = -0.274, p = 0.051). But the mean SARMS of patients with a viral load exceeding 100,000 copies/ml was significantly lower than that of patients with a viral load of less than 100,000 copies/ml (p = 0.03). Evaluation of the potency of antiretroviral resistance revealed a weak negative correlation with viral replication in the PHI period. This could be one reason why the transmission of resistant strains in PHI patients is not increasing significantly despite the widespread use of highly active antiretroviral therapy (HAART).
Adolescent↗
Analysis of the mutant HLA-A*0201 heavy chain H74L: impaired TAP-dependent peptide loading.
A mutation of the HLA-A*0201 heavy chain at position 74 from histidine to leucine (H74L) resulted in a molecule with an interesting phenotype. H74L-expressing targets were recognized by peptide-specific HLA-A*0201-restricted cytotoxic T lymphocytes at lower peptide concentrations than wild type HLA-A*0201. H74L's improved ability to sensitize cells for tysis was due to its enhanced capability to bind exogenous peptide. Furthermore, this phenotype of improved exogenous binding and functional recognition was not peptide-specific. In contrast, the H74L molecule failed to present the HIV- HLA-A2-restricted pol peptide when expressed and processed endogenously. The inability to bind endogenous pol could be rescued by preceding the pol peptide with a signal sequence. The defect affecting endogenous presentation, therefore, appeared to be limited to the TAP-dependent pathway. Surprisingly, the H74L heavy chain was able to enter the defined MHC class I pathway and associate with beta2M, calreticulin, tapasin, and TAP. Despite the presence of the H74L heavy chain at the TAP complex, H74L was functionally inefficient at loading TAP-dependent peptides. H74L may help elucidate further steps in the process of loading TAP-dependent peptides into the class I cleft.
ATP Binding Cassette Transporter, Subfamily B, Mem↗
The influence of neighborhood size and habitat shape on the accumulation of deleterious mutations.
To examine the impact of genetic neighborhood size and habitat shape on genetic load and the accumulation of deleterious mutation, individual-based simulations were performed in continuously distributed habitats. The risk of extinction increased as both the area of the habitat and the neighborhood size decreased. When the neighborhood area became smaller than the habitat area, habitat shape also began to influence the risk of extinction by mutation loads, expected time to extinction being shorter in longer and narrower habitats than in a square habitat. Both the number of homozygous deleterious loci per individual and the mutation load in the population increased as the neighborhood size and total population size decreased. Neighborhood size and total population size both independently affected the average number of homozygous deleterious loci per individual. In addition, as the ratio of the long to the short side of the rectangle of a habitat increased, the average number of homozygous deleterious loci increased. When the areas of the habitats were held constant, the average number of homozygous loci and the mutation loads were smallest for a regular square and largest for the longest, narrowest habitat. These results suggest that the spatial genetic structure of an individual is an important factor in the accumulation of deleterious mutations and the risk of extinction by mutation meltdown.
Animals↗
Pattern and distribution of immunoglobulin VH gene usage in a cohort of B-CLL patients from a Northeastern region of Italy.
We analyzed individual VH gene rearrangements in 55 consecutive B-chronic lymphocytic leukemia (B-CLL) patients collected from a northeastern region of Italy, stressing the possible differences related to geographic characteristics of the cohorts studied. Considering the percentage of somatic mutations present in the VH gene sequences and using the 98% cut-off value, 38 of the 55 B-CLL (69%) patients displayed somatic hypermutations and 17 (31%) had a germline configuration. Our results confirm and extend the observations of a bias in the use of certain VH, DH, and JH genes among B-CLL cells. The most frequently used VH genes were VH1-69 (12.7%) with VH3-23 (12.7%) and VH4-34 (10.9%). Collectively these genes accounted for 36.3% of the cases. In the mutated cases, the range of mutations varied from 2% to 15%, with a median of 6.5%. VH1-69 (7 cases, all unmutated) carried few mutations as opposed to VH3-23 (7 cases, 5 of which mutated), VH4-34 (6 cases, all mutated), and VH3-30 (5 cases, all mutated), which show a high load of mutations. D3 family genes were found frequently (38.1%) followed by D2 (27.2%) and D6 (18.1%). The individual D segment most frequently used was D3-3, which was present in 16.3% of cases. There was predominance of the JH4 gene (49%) followed by JH6 (40%). Analysis of the distribution of replacement and silent mutations in the mutated sequences using the method of Lossos showed in 39.4% of cases evidence of antigen selection in the framework region and/or complementary determining regions. In comparison with a recent study on B-CLL patients from the Mediterranean area, the VH4-34 gene was significantly overused in the mutated group at a percentage double that of the Italian cohort reported in this study (10.9% vs. 5%), but at a frequency similar to the entire Mediterranean region (10.7%). We also found an over-representation of VH1-69 usage in the germline group, at a frequency (12.7%) higher than previously described by the same authors (Italian 8%, Mediterranean 10.7%). On the contrary, VH3-07 and VH3-49 were not much used in our study (5.4% and 1.8%, respectively) compared with the Italian group (8% and 5.1%). In our study, VH3-23 gene segment was frequently expressed, at frequency as high as that of VH1-69, a finding in keeping with reported B-CLL Italian data, but higher than the entire series of the Mediterranean area (12.7% vs. 9.2%); VH3-21 gene, frequently expressed in northern European CLL but rarely in the Mediterranean area, was completely absent. This biased usage of VH family genes may reflect a geographic leukemic repertoire, perhaps owing to a peculiar genetic background, depending on variations in germline composition of the IgVH locus or to the effect of a potential environmental element less frequently encountered in different regions.
Aged↗
Effects of drug resistance on viral load in patients failing antiretroviral therapy.
Previous studies on patients who develop drug resistant HIV-1 variants have shown that continued use of failing regimens might provide clinical benefit. However, the effect of long-term exposure to drug resistant variants may lead to emergence of compensatory mutations that may jeopardize this effect. In this study, we assess associations among type and number of drug resistant mutations, viral load and disease progression in patients with long-term follow up. Patients with genotypic testing performed at the time of treatment failure were enrolled. Comparison of viral load and CD4 cell count between different resistance groups was performed using analysis of variance. Multiple linear regression analysis was performed to assess the simultaneous effects of the presence of particular mutations and their accumulation on viral load. Data from 475 patients who were followed for a median of 43 months from October 1999 to July 2005 were studied. A "V shape" relationship was observed between the number of mutations and viral load. Specifically, in patients harboring up to five mutations, viral load was reduced by 0.8 log/copies when compared to wild-type variants. However, with more than six mutations viral load progressively increased. Certain reverse transcriptase mutations such as M184V/I, K70R, V108I, and protease mutations such as L33FIV, M84V, and M36I were associated with reduced viral load. Together, these findings suggest that long-term maintenance of a sub-optimal antiretroviral regimen may have deleterious consequences for the patient.
Adult↗
The prognostic significance of serum viral load, codon 215 reverse transcriptase mutation and CD4+ T cells on progression of HIV disease in a double-blind study of thymopentin.
OBJECTIVE: To determine in asymptomatic HIV-infected subjects the prognostic value of virion reverse transcriptase (RT) codon 215 mutation, serum HIV RNA level, CD4+ T-cell count and immune complex dissociated (ICD) p24 level. The retrospective evaluation of thymopentin treatment effect on subjects in high risk groups for progression was a secondary objective. PARTICIPANTS: Zidovudine (ZDV)-experienced asymptomatic HIV-infected subjects (n = 352) who had been enrolled in a 48-week placebo-controlled double-blind trial of thymopentin treatment were studied. METHODS: Post hoc analyses were conducted to determine which subjects at study entry were at greater risk for progression to AIDS-related complex (ARC), AIDS or death, and to determine the effect of treatment on these subjects. Four potential prognostic variables (virion RT codon 215 mutation, circulating HIV virion RNA copies, CD4+ T-cell count, and ICD p24) were evaluated by dichotomizing subjects for each variable based on the median of the observed values. CD4+ T-cell count was evaluated prospectively, whereas frozen samples were evaluated under blinded conditions for the other variables after the study was completed. RESULTS: The presence of the codon 215 mutation [P = 0.044; relative hazard (RH), 2.6], > or = 20,000 HIV RNA copies/ml (P = 0.002; RH, 5.5), and < 350 CD4+ cells 10(6)/l (P = 0.042; RH, 2.2) were prognostic factors, and > or = 30 pg/ml ICD p24 level (P = 0.52; RH, 1.4) was not a prognostic factor in predicting progression. Subjects were prestratified by previous ZDV use (< or = 6 or > 6 months). Across both strata thymopentin delayed treatment progression to ARC, AIDS, or death (P = 0.015; RH, 3.0). This effect was magnified in the ZDV-experienced subjects at greater risk, where thymopentin delayed progression compared to placebo in the presence of the codon 215 mutation (P = 0.007; RH, 10.1), > or = 20,000 RNA copies/ml (P = 0.012; RH, 8.9), and CD4+ T-cell count < 350 x 10(6)/l (P = 0.005; RH, 10.4). CONCLUSIONS: Codon 215 mutation, serum HIV RNA and CD4 T-cell count are independent predictors of progression in ZDV-experienced asymptomatic subjects. Furthermore, thymopentin delays HIV disease progression in the presence of a key ZDV resistance mutation as well as high viral load and low CD4+ T-cell counts.
Adjuvants, Immunologic↗