Neutral mutations and repetitive DNA

We have previously shown that computer simulations of processes that generate selectively advantageous changes together with random duplications and deletions give rise to genomes with many different genes embedded in a large amount of dispensable DNA sequence. We now explore the consequences of neutral changes on the evolution of genomes. We follow the consequences of sequence divergences that are neutral when they occur in dispensable sequences or extra copies of genes present in multigene families. We find that when divergence occurs at about the same frequency as duplication/deletion events, genomes carry repetitive sequences in proportion to their size. Inspection of the genomes as they evolved showed that multigene families were generated by relatively recent duplications of single genes and so would be expected to be highly homogeneous.     

Comparison of properties of tests for assessing tumor clonality

SUMMARY: In a recent article Begg et al. (2007, Biometrics 63, 522-530) proposed a statistical test to determine whether or not a diagnosed second primary tumor is biologically independent of the original primary tumor, by comparing patterns of allelic losses at candidate genetic loci. The proposed concordant mutations test is a conditional test, an adaptation of Fisher's exact test, that requires no knowledge of the marginal mutation probabilities. The test was shown to have generally good properties, but is susceptible to anticonservative bias if there is wide variation in mutation probabilities between loci, or if the individual mutation probabilities of the parental alleles for individual patients differ substantially from each other. In this article, a likelihood ratio test is derived in an effort to address these validity issues. This test requires prespecification of the marginal mutation probabilities at each locus, parameters for which some information will typically be available in the literature. In simulations this test is shown to be valid, but to be considerably less efficient than the concordant mutations test for sample sizes (numbers of informative loci) typical of this problem. Much of the efficiency deficit can be recovered, however, by restricting the allelic imbalance parameter estimate to a prespecified range, assuming that this parameter is in the prespecified range.     

Driver mutations of cancer epigenomes

Epigenetic alterations are associated with all aspects of cancer, from tumor initiation to cancer progression and metastasis. It is now well understood that both losses and gains of DNA methylation as well as altered chromatin organization contribute significantly to cancerassociated phenotypes. More recently, new sequencing technologies have allowed the identification of driver mutations in epigenetic regulators, providing a mechanistic link between the cancer epigenome and genetic alterations. Oncogenic activating mutations are now known to occur in a number of epigenetic modifiers (i.e. IDH1/2, EZH2, DNMT3A), pinpointing epigenetic pathways that are involved in tumorigenesis. Similarly, investigations into the role of inactivating mutations in chromatin modifiers (i.e. KDM6A, CREBBP/EP300, SMARCB1) implicate many of these genes as tumor suppressors. Intriguingly, a number of neoplasms are defined by a plethora of mutations in epigenetic regulators, including renal, bladder, and adenoid cystic carcinomas. Particularly striking is the discovery of frequent histone H3.3 mutations in pediatric glioma, a particularly aggressive neoplasm that has long remained poorly understood. Cancer epigenetics is a relatively new, promising frontier with much potential for improving cancer outcomes. Already, therapies such as 5-azacytidine and decitabine have proven that targeting epigenetic alterations in cancer can lead to tangible benefits. Understanding how genetic alterations give rise to the cancer epigenome will offer new possibilities for developing better prognostic and therapeutic strategies.     

Mitochondrial impairment observed in fibroblasts from South African Parkinson’s disease patients with parkin mutations

Parkinson’s disease (PD), defined as a neurodegenerative disorder, is characterized by the loss of dopaminergic neurons in the substantia nigra in the midbrain. Loss-of-function mutations in the parkin gene are a major cause of autosomal recessive, early-onset PD. Parkin has been implicated in the maintenance of healthy mitochondria, although previous studies show conflicting findings regarding mitochondrial abnormalities in fibroblasts from patients harboring parkin-null mutations. The aim of the present study was to determine whether South African PD patients with parkin mutations exhibit evidence for mitochondrial dysfunction. Fibroblasts were cultured from skin biopsies obtained from three patients with homozygous parkin-null mutations, two heterozygous mutation carriers and two wild-type controls. Muscle biopsies were obtained from two of the patients. The muscle fibers showed subtle abnormalities such as slightly swollen mitochondria in focal areas of the fibers and some folding of the sarcolemma. Although no differences in the degree of mitochondrial network branching were found in the fibroblasts, ultrastructural abnormalities were observed including the presence of electron-dense vacuoles. Moreover, decreased ATP levels which are consistent with mitochondrial dysfunction were observed in the patients’ fibroblasts compared to controls. Remarkably, these defects did not manifest in one patient, which may be due to possible compensatory mechanisms. These results suggest that parkin-null patients exhibit features of mitochondrial dysfunction. Involvement of mitochondria as a key role player in PD pathogenesis will have important implications for the design of new and more effective therapies.     

Effects of somatic mutations on CDR loop flexibility during affinity maturation

Prior studies suggest that antibody affinity maturation is achieved, in part, via prearranging the CDRs for binding. The implication is that the entropy cost of binding is reduced and that this rigidification occurs as a consequence of somatic mutations during maturation. However, how these mutations modulate CDR flexibility is unclear. Here, molecular dynamics simulations captured CDR flexibility differences between four mature antibodies (7G12, AZ28, 28B4, and 48G7) and their germline predecessors. Analysis of their trajectories: (1) rationalized how mutations during affinity maturation restrict CDR motility, (2) captured the equilibrium between bound and unbound conformations for the H3 loop of unliganded 7G12, and (3) predicted a set of new mutations that, according to our simulations, should diminish binding by increasing flexibility.     

An evolutionary perspective on pathogenic mtDNA mutations: haplogroup associations of clinical disorders

More than 75 human diseases have been associated with mitochondrial dysfunction, and many of these are directly caused by overtly pathogenic mutations in the mitochondrial genome (mtDNA). In addition, there have been a number of reports that posit a different, subtler role for mtDNA substitutions in the disease process. As we review here, mtDNA evolution has resulted in the distribution of sequences into continent-specific haplogroups, which are defined by a relatively small number of polymorphisms. Thus, mtDNA sequences can be assigned to European, African, or Asian/Native American haplogroups. There are numerous reports that various diseases are haplogroup-associated, and it has been suggested that some of these haplogroup-associated polymorphisms act as risk factors in these disorders. It has also been suggested that there are haplogroup-associations for aging. As we note here, however, such associations have usually been observed only in single studies and it is difficult to draw broad conclusions on the basis of the available evidence. At a minimum, we suggest that, a haplogroup-group association must be detected in multiple subpopulations or in a large, carefully controlled population survey.     

How various factors influence the CO2/O2 specificity of ribulose-1,5-bisphosphate carboxylase/oxygenase

Temperature, activating metal ions, and amino-acid substitutions are known to influence the CO₂/O₂ specificity of the chloroplast enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase. However, an understanding of the physical basis for enzyme specificity has been elusive. We have shown that the temperature dependence of CO₂/O₂ specificity can be attributed to a difference between the free energies of activation for the carboxylation and oxygenation partial reactions. The reaction between the 2,3-enediolate of ribulose 1,5-bisphosphate and O₂ has a higher free energy of activation than the corresponding reaction of this substrate with CO₂. Thus, oxygenation is more responsive to temperature than carboxylation. We have proposed possible transition-state structures for the carboxylation and oxygenation partial reactions based upon the chemical natures of these two reactions within the active site. Electrostatic forces that stabilize the transition state of the carboxylation reaction will also inevitably stabilize the transition state of the oxygenation reaction, indicating that oxygenase activity may be unavoidable. Furthermore, the reduction in CO₂/O₂ specificity that is observed when activator Mg²⁺ is replaced by Mn²⁺ may be due to Mg²⁺ being more effective in neutralizing the negative charge of the carboxylation transition state, whereas Mn²⁺ is a transition-metal ion that can overcome the triplet character of O₂ to promote the oxygenation reaction.Abbreviations CABP 2-carboxyarabinitol 1,5-bisphosphate - enol-RuBP 2,3-enediolate of ribulose 1,5-bisphosphate - K_c K_mfor CO₂ - K_o K_mfor O₂ - Rubisco ribulose-1,5-bisphosphate carboxylase/oxygenase - RuBP ribulose 1,5-bisphosphate - V_c V _max for carboxylation - V_o V _max for oxygenation     

Resistance outside the substrate envelope: hepatitis C NS3/4A protease inhibitors

Direct acting antivirals have dramatically increased the efficacy and tolerability of hepatitis C treatment, but drug resistance has emerged with some of these inhibitors, including nonstructural protein 3/4?A protease inhibitors (PIs). Although many co-crystal structures of PIs with the NS3/4A protease have been reported, a systematic review of these crystal structures in the context of the rapidly emerging drug resistance especially for early PIs has not been performed. To provide a framework for designing better inhibitors with higher barriers to resistance, we performed a quantitative structural analysis using co-crystal structures and models of HCV NS3/4A protease in complex with natural substrates and inhibitors. By comparing substrate structural motifs and active site interactions with inhibitor recognition, we observed that the selection of drug resistance mutations correlates with how inhibitors deviate from viral substrates in molecular recognition. Based on this observation, we conclude that guiding the design process with native substrate recognition features is likely to lead to more robust small molecule inhibitors with decreased susceptibility to resistance.     

Nuclear-cytoplasmic interactions in restoration of male fertility in the ‘9E’ and A4 CMS-inducing cytoplasms of sorghum

 The genetics of male-fertility restoration in sorghum in the “9E” and A4 CMS-inducing cytoplasms, was studied by crossing a number of fertility restorer lines of A1 cytoplasm to CMS lines [9E]T×398 and [A4]T×398 and the line [9E]Milo-10, which was obtained by backcrossing Milo-10 to [9E]T×398. It was revealed that both A4 and “9E” cytoplasms are characterized by a sporophytic mode of restoration of male fertility. Depending on the nuclear background of the male parents, fertility restoration was controlled by one or two dominant genes. Fertility-restorer genes of one of the tester lines, KVV-114, were effective in [9E]T×398 but could not restore [9E]Milo-10. A fertile line obtained from the fertile hybrid [9E]T×398/KVV-112, with “9E” cytoplasm, also failed to restore [9E]Milo-10. In a number of hybrid combinations with both A4 and “9E” cytoplasms a novel and unusual phenomenon of gradual restoration of male fertility in subsequent backcross generations was observed. Pollen from the fertile revertants did not transmit fertility restoration in progeny from crosses with the original CMS line and was poorly transmitted in sib-crosses. The appearance of fertile revertants and the different reactions of different CMS lines with the same cytoplasm in test-crosses may be caused by the action of recessive nuclear genes of the recurrent male parents that were accumulated during backcrossing; these may induce changes in cytoplasmic genes controlling CMS. Received: 5 March 1998 / Accepted: 7 April 1998     

中微量元素和有益元素对水稻生长和吸收镉的影响

采用盆栽试验,研究了中微量元素和有益元素对水稻生长和吸收镉的影响。结果表明,在所有测试的元素和施用方法中,硅酸钠叶面喷施显著增加稻谷产量,而碳酸钙、硼酸、硅酸钠土施和亚硒酸钠显著降低了稻谷产量。镁、锌、铁的盐酸盐形态对水稻籽粒的增产效果优于硫酸盐形态,而钙、铜的硫酸盐形态增产效果略高于盐酸盐形态。在钙、镁、硫三种中量元素中,钙增加了水稻籽粒中的Cd浓度和吸收量,而镁和硫则降低了籽粒中的Cd浓度和吸收量,以硫磺粉处理为最低。稻草中的Cd浓度和总量均以氯化镁处理为最高,硫磺粉处理最低。镁能有效抑制Cd从秸秆向籽粒的转移,其盐酸盐优于硫酸盐。在微量元素中,锌对水稻Cd的吸收抑制作用最为显著,其次是铜,而有益元素肥料硅酸钠叶面喷施则显著增加了稻谷中的Cd浓度和吸收量。硫酸亚铁、氯化锰、氯化铜、硼酸和硼砂处理都能有效地抑制Cd从秸秆向籽粒的转移,而硅酸钠叶面喷施和锌处理则促进了Cd的转移,表明硅酸钠抑制水稻吸收Cd的机制很可能发生在土壤中,而非在植株体内或地上部分。在Cd污染土壤上选用适宜的中微量和有益元素肥料及其施用方法,能有效降低水稻对镉的吸收和稻米中的Cd含量。