DNA methyltransferase homologue TRDMT1 in Plasmodium falciparum specifically methylates endogenous aspartic acid tRNA

In eukaryotes, cytosine methylation regulates diverse biological processes such as gene expression, development and maintenance of genomic integrity. However, cytosine methylation and its functions in pathogenic apicomplexan protozoans remain enigmatic. To address this, here we investigated the presence of cytosine methylation in the nucleic acids of the protozoan Plasmodium falciparum. Interestingly, P. falciparum has TRDMT1, a conserved homologue of DNA methyltransferase DNMT2. However, we found that TRDMT1 did not methylate DNA, in vitro. We demonstrate that TRDMT1 methylates cytosine in the endogenous aspartic acid tRNA of P. falciparum. Through RNA bisulfite sequencing, we mapped the position of 5-methyl cytosine in aspartic acid tRNA and found methylation only at C38 position. P. falciparum proteome has significantly higher aspartic acid content and a higher proportion of proteins with poly aspartic acid repeats than other apicomplexan pathogenic protozoans. Proteins with such repeats are functionally important, with significant roles in host-pathogen interactions. Therefore, TRDMT1 mediated C38 methylation of aspartic acid tRNA might play a critical role by translational regulation of important proteins and modulate the pathogenicity of the malarial parasite.     

Whole-genome validation of high-information-content fingerprinting

Fluorescent-based high-information-content fingerprinting (HICF) techniques have recently been developed for physical mapping. These techniques make use of automated capillary DNA sequencing instruments to enable both high-resolution and high-throughput fingerprinting. In this article, we report the construction of a whole-genome HICF FPC map for maize (Zea mays subsp. mays cv B73), using a variant of HICF in which a type IIS restriction enzyme is used to generate the fluorescently labeled fragments. The HICF maize map was constructed from the same three maize bacterial artificial chromosome libraries as previously used for the whole-genome agarose FPC map, providing a unique opportunity for direct comparison of the agarose and HICF methods; as a result, it was found that HICF has substantially greater sensitivity in forming contigs. An improved assembly procedure is also described that uses automatic end-merging of contigs to reduce the effects of contamination and repetitive bands. Several new features in FPC v7.2 are presented, including shared-memory multiprocessing, which allows dramatically faster assemblies, and automatic end-merging, which permits more accurate assemblies. It is further shown that sequenced clones may be digested in silico and located accurately on the HICF assembly, despite size deviations that prevent the precise prediction of experimental fingerprints. Finally, repetitive bands are isolated, and their effect on the assembly is studied.     

Characterization of three maize bacterial artificial chromosome libraries toward anchoring of the physical map to the genetic map using high-density bacterial artificial chromosome filter hybridization

Three maize (Zea mays) bacterial artificial chromosome (BAC) libraries were constructed from inbred line B73. High-density filter sets from all three libraries, made using different restriction enzymes (HindIII, EcoRI, and MboI, respectively), were evaluated with a set of complex probes including the 185-bp knob repeat, ribosomal DNA, two telomere-associated repeat sequences, four centromere repeats, the mitochondrial genome, a multifragment chloroplast DNA probe, and bacteriophage lambda. The results indicate that the libraries are of high quality with low contamination by organellar and lambda-sequences. The use of libraries from multiple enzymes increased the chance of recovering each region of the genome. Ninety maize restriction fragment-length polymorphism core markers were hybridized to filters of the HindIII library, representing 6x coverage of the genome, to initiate development of a framework for anchoring BAC contigs to the intermated B73 x Mo17 genetic map and to mark the bin boundaries on the physical map. All of the clones used as hybridization probes detected at least three BACs. Twenty-two single-copy number core markers identified an average of 7.4 +/- 3.3 positive clones, consistent with the expectation of six clones. This information is integrated into fingerprinting data generated by the Arizona Genomics Institute to assemble the BAC contigs using fingerprint contig and contributed to the process of physical map construction.     

电针介导的基因转移

基因转移是实现基因治疗的关键技术之一 ,目前尚缺少简便、易行、有效、安全的方法 .首次将我国传统的针刺技术与现代转基因技术结合起来 ,创建了一种电针转基因的方法 .应用针灸针携带外源基因 ,经皮针刺 ,进行直流电刺激 ,可实现有效的基因转移 .     

Comparative nuclear and mitochondrial genome diversity in humans and chimpanzees

Restriction mapping and sequencing have shown that humans have substantially lower levels of mitochondrial genome diversity (d) than chimpanzees. In contrast, humans have substantially higher levels of heterozygosity (H) at protein-coding loci, suggesting a higher level of diversity in the nuclear genome. To investigate the discrepancy further, we sequenced a segment of the mitochondrial genome control region (CR) from 49 chimpanzees. The majority of these were from the Pan troglodytes versus subspecies, which was underrepresented in previous studies. We also estimated the average heterozygosity at 60 short tandem repeat (STR) loci in both species. For a total sample of 115 chimpanzees, d = 0.075 +/0 0.037, compared to 0.020 +/- 0.011 for a sample of 1,554 humans. The heterozygosity of human STR loci is significantly higher than that of chimpanzees. Thus, the higher level of nuclear genome diversity relative to mitochondrial genome diversity in humans is not restricted to protein-coding loci. It seems that humans, not chimpanzees, have an unusual d/H ratio, since the ratio in chimpanzees is similar to that in other catarrhines. This discrepancy in the relative levels of nuclear and mitochondrial genome diversity in the two species cannot be explained by differences in mutation rate. However, it may result from a combination of factors such as a difference in the extent of sex ratio disparity, the greater effect of population subdivision on mitochondrial than on nuclear genome diversity, a difference in the relative levels of male and female migration among subpopulations, diversifying selection acting to increase variation in the nuclear genome, and/or directional selection acting to reduce variation in the mitochondrial genome.      

Skeletal muscle glycogenolysis, glycolysis, and pH during electrical stimulation in men

Glycogenolytic and glycolytic rates were estimated and muscle pH (pHm) was measured in electrically stimulated quadriceps femoris muscles of seven men. Leg blood flow was occluded and muscles were stimulated 64 times at 20 Hz, with contractions lasting 1.6 s and separated by pauses of 1.6 s. Muscle biopsies were obtained at rest and following 16, 32, 48, and 64 contractions. Glycolytic intermediates and several modulators of the glycolytic enzyme phosphofructokinase (PFK) were measured. Glycogenolytic and glycolytic rates were 1.68 and 1.26 mmol glucosyl units X kg dry muscle-1 X S-1 contraction time during the initial 16 contractions and pHm decreased from 7.00 +/- 0.01 to 6.70 +/- 0.03. During the subsequent 32 contractions both glycogenolytic and glycolytic rates were maintained at approximately 0.70 mmol X kg-1 X S-1 and pHm decreased to 6.45 +/- 0.04. In the final 16 contractions, both rates were very low and pHm was unchanged. Therefore, PFK remained active despite increasing acidity until pHm decreased to approximately 6.45. We conclude that increases in the concentrations of several positive modulators partially reverses pH-dependent ATP inhibition of PFK in vivo, permitting glycolytic activity to continue in the pHm range of 6.70-6.45.     

Metabolic activation of 1,2-dibromo-3-chloropropane: evidence for the formation of reactive episulfonium ion intermediates

The nematocide and soil fumigant 1,2-dibromo-3-chloropropane (DBCP) is a carcinogen and a mutagen and displays target-organ toxicity to the testes and the kidney. It has been proposed that both cytochrome P-450 mediated activation and glutathione (GSH) conjugation pathways are operative in DNA damage and organotropy induced by DBCP. To determine the chemical mechanisms involved in the bioactivation of DBCP and to assess a role for an episulfonium ion intermediate, the mechanism of formation of GSH conjugate metabolites of DBCP was investigated. Five biliary GSH conjugates of DBCP were isolated from rats and identified by fast atom bombardment tandem mass spectrometry: S-(2,3-dihydroxy-propyl)glutathione (I), S-(2-hydroxypropyl)glutathione (IIA), S-(3-chloro-2-hydroxypropyl)glutathione (III), 1,3-di(S-glutathionyl)propan-2-ol (IV), and 1-(glycyl-S-cysteinyl)-3- (S-glutathionyl)propan-2-ol (V). The mechanisms of conjugate formation were addressed by assessing deuterium retention in conjugates derived from [1,1,2,3,3-2H5] DBCP (D5-DBCP). GSH conjugates I, III, IV, and V displayed quantitative retention of deuterium, an observation consistent with the formation of an episulfonium ion intermediate. GSH conjugate IIA, however, retained three atoms of deuterium, thus invoking a P-450 mechanism in its genesis. The involvement of glutathione transferase (GST) and sequential episulfonium ion intermediates in the formation of metabolites I, III, and IV was demonstrated in vitro. Upon incubation of DBCP with GST, metabolites I, III, and IV were identified by tandem mass spectrometry and were found to arise with quantitative retention of deuterium when D5-DBCP was employed as a substrate. An additional GSH conjugate, 1,2,3-tri(S-glutathionyl)propane (VI), was observed as the major metabolite in incubations of GST with DBCP. When the incubations of DBCP with GST were performed in H2(18)O, metabolite I incorporated two atoms of 18O, and metabolites III and IV incorporated one atom of 18O. The ability of GST to catalyze the formation of the four GSH conjugates observed in vivo, with quantitative retention of deuterium and incorporation of 18O from H2(18)O, may be rationalized by a mechanism invoking the initial formation of S-(2-bromo-3-chloropropyl)glutathione. Rearrangement of this unstable conjugate via several reactive episulfonium ions, with either hydrolysis by water or alkylation of GSH at various stages, would account for the pattern of metabolites and their status of isotopic enrichment observed under various incubation conditions.(ABSTRACT TRUNCATED AT 400 WORDS)