Circular dichroism spectra of DNA quadruplexes [d(G(5)T(5))](4) as formed with G(4) and T(4) tetrads and [d(G(5)T(5)). d(A(5)C(5))]2 as formed with Watson-Crick-like (G-C)(2) and (T-A)(2) tetrads

We utilize electrophoresis and find that a thermally treated equimolar mixture of the oligonucleotide d(G(5)T(5)) and its complementary oligonucleotide d(A(5)C(5)) exhibits either two bands or a single band in one lane, depending on the conditions of the incubation solutions. The thermally treated d(G(5)T(5)) solution loaded in a different lane exhibits a single band of the parallel quadruplex [d(G(5)T(5))](4), which is composed of homocyclic hydrogen-bonded G(4) and T(4) tetrads previously proposed. For the thermally treated equimolar mixture of d(G(5)T(5)) and d(A(5)C(5)), the fast band is assigned to a Watson-Crick d(G(5)T(5)). d(A(5)C(5)) duplex, so that the slow band with the same low mobility as that of [d(G(5)T(5))](4) may be assigned to either [d(G(5)T(5))](4) itself or a [d(G(5)T(5)). d(A(5)C(5))](2) quadruplex. If the latter compound is true, this may be the antiparallel quadruplex composed of the heterocyclic hydrogen-bonded G-C-G-C and T-A-T-A tetrads proposed previously. After removing these three bands for the duplex and two kinds of hypothetical quadruplexes, we electrophoretically elute the corresponding compounds in the same electrophoresis buffer using an electroeluter. The eluted compounds are ascertained to be stable by electrophoresis. The circular dichroism (CD) and UV absorption spectra measured for the three isolated compounds are found to be clearly different. For the electrophoretic elution of the hypothetical [d(G(5)T(5))](4) quadruplex, the result of the molecularity of n = 4 obtained from the CD melting curve analysis provides further support for the formation of the parallel [d(G(5)T(5))](4) quadruplex already proposed. For the thermally treated equimolar mixture of d(G(5)T(5)) and d(C(5)A(5)), the fast band with a molecularity of n = 2 corresponds to the Watson-Crick duplex, d(G(5)T(5)). d(A(5)C(5)). The slow band with a molecularity of n = 4 indicates the antiparallel quadruplex [d(G(5)T(5)). d(A(5)C(5))](2), whose observed CD and UV spectra are different from those of [d(G(5)T(5))](4). By electrophoresis, after reannealing the eluted compound [d(G(5)T(5)). d(A(5)C(5))](2), a distinct photograph showing the band splitting of this quadruplex band into the lower duplex and upper quadruplex bands is not possible; but by a transilluminator, we occasionally observe this band splitting with the naked eye. The linear response polarizability tensor calculations for the thus determined structures of the [d(G(5)T(5))](4) quadruplex, the McGavin-like [d(G(5)T(5)). d(A(5)C(5))](2) quadruplex, and the Watson-Crick d(G(5)T(5)). d(A(5)C(5)) duplex are found to qualitatively predict the observed CD and UV spectra.     

编码序列的（G＋C）%与蛋白质的耐热性相关性分析

运用计算机统计方法,对以木糖异构酶为主的几个蛋白质家族的核酸和氨基酸序列进行分析,发现密码子各位上的（Ｇ＋Ｃ）％与编码序列的（Ｇ＋Ｃ）％成线性正相关,大多数氨基酸的含量与编码序列的（Ｇ＋Ｃ）％也存在相关性,按其相关性,将氨基酸分为正相关,负相关和不相关３类,对木糖异构酶氨基酸序列和酶的耐热性的统计发现,那些在统计学上显著的,可能提高蛋白质耐热性的氨基酸替换,往往伴随关编码序列中ＧＣ含量的上升,这提     

Co-segregation of the T1095C with the A1555G mutation of the mitochondrial 12S rRNA gene in a patient with non-syndromic hearing loss

We reported here the clinical and molecular characterization of a Chinese subject with childhood-onset hearing impairment. Clinical evaluations showed that the patient suffered from profound and non-syndromic sensorineural hearing loss with flat configurations. Sequence analysis of the mitochondrial 12S rRNA and tRNA^Ser(UCN) genes led to the identification of double deafness-associated mutations of A1555G and T1095C in the 12S rRNA gene which apparently in the homoplasmic forms. In additional, there was no other functionally significant nucleotide variants found in this subject. As previous studies have indicated that the A1555G mutation was a primary contributing factor underlying the development of deafness but not sufficient to produce clinical phenotype, the co-segregation of two mitochondrial DNA mutations raises the possibility that the T to C transition at position 1095 plays a role in the phenotypic expression of deafness-associated A1555G mutation. Actually, the T1095C mutation disrupted an evolutionarily conserved base-pair at stem-loop of helix 25 of 12S rRNA, resulting in impaired translation in mitochondrial protein synthesis and a significant reduction of cytochrome c oxidase activity. As a result, it may enhance the biochemical defect in patient carrying the A1555G mutation, thus changing the age of onset and the severity of hearing impairment.     

Silent nucleotide substitutions and G+C content of some mitochondrial and bacterial genes

Summary The G+C content of DNA varies widely in different organisms, especially microorganisms. This variation is accompanied by changes in the nucleotide composition of silent positions in codons. (Silent positions are defined and explained in the text.) These changes are mostly neutral or near neutral, and appear to result from mutation pressure in the direction of increasing either A+T (AT pressure) or G+C(GC pressure) content. Variations in G+C content are also accompanied by substitutions at replacement positions in codons. These substituions produce changes in the amino acid content of homologous proteins. The examples studied were genes for 13 mitochondrial proteins in five species, and A and B genes for bacterial tryptophan synthase in four species.In microorganisms, varying AT and GC mutational pressures, presumably resulting from shifts in the DNA polymerase system, exert strong effects on molecular evolution by changing the G+C content of DNA. These effects may be greater than those of random drift. The effects of GC pressure on silent substitutions in the systems examined are several times as great as the effects on replacement substitutions.GC pressure is exerted on noncoding as well as coding regions in mitochondrial DNA. This is shown by the close correlation (correlation coefficient, 0.99) of the G+C content of the noncoding D loop of mitochondria with the G+C content of silent positions in the corresponding mitochondrial genes.     

The novel G10680A mutation is associated with complete penetrance of the LHON/T14484C family

We report the clinical and genetic characterization of a Chinese Leber′s hereditary optic neuropathy (LHON) family with complete penetrance and high percentage of recovery. Sequence analysis of the complete mitochondrial DNA revealed the presence of heteroplasmic ND6/T14484C mutation and 27 other variants, belonging to the East-Asian haplogroup B4b′d. Of those variants, a novel homoplasmic G10680A mutation substituted a threonine for a highly conserved alanine at ND4L amino acid 71, which was not found in unaffected family members and 100 normal controls. It indicated that G10680A may play a synergistic role with the primary mutation T14484C, leading to the complete penetrance of LHON in the presenting family. In addition, the other modifier factors including nuclear background, mitochondrial haplotypes and other environmental factors should account for the phenotypic variability of visual impairment in this family.     

Two Aspects of DNA Base Composition: G+C Content and Translation-Coupled Deviation from Intra-Strand Rule of A=T and G=C

The relative contribution of mutation and selection to the G+C content of DNA was analyzed in bacterial species having widely different G+C contents. The analysis used two methods that were developed previously. The first method was to plot the average G+C content of a set of nucleotides against the G+C content of the third codon position for each gene. This method was used to present the G+C distribution of the third codon position and to assess the relative neutrality of a set of nucleotides to that of the G+C content of the third codon position. The second method was to plot the intrastrand bias of the third codon position from Parity Rule 2 (PR2), where A=T and G=C. It was found that whereas intragenomic distributions of the DNA G+C content of these bacteria are narrow in the majority of species, in some species the G+C content of the minor class of genes distributes over wider ranges than the major class of genes. On the other hand, ubiquitous PR2 biases are amino acid specific and independent of the G+C content of DNA, so that when averaged over the amino acids, the biases are small and not correlated with the DNA G+C content. Therefore, translation coupled PR2-biases are unlikely to explain the wide range of G+C contents among different species. Considering all data available, it was concluded that the amino acid-specific PR2 bias has only a minor effect, if any, on the average G+C content. In addition, PR2 bias patterns of different species show phylogenetic relationships, and the pattern can be as a taxal fingerprint. Received: 5 November 1998 / Accepted: 1 March 1999     

FramePlot: a new implementation of the Frame analysis for predicting protein-coding regions in bacterial DNA with a high G+C content

FramePlot is a web-based tool for predicting protein-coding regions in bacterial DNA with a high G + C content, such as Streptomyces. The graphical output provides for easy distinction of protein-coding regions from non-coding regions. The plot is a clickable map. Clicking on an ORF provides not only the nucleotide sequence but also its deduced amino acid sequence. These sequences can then be compared to the NCBI sequence database over the Internet. The program is freely available for academic purposes at http://www.nih.go.jp/jun/cgi-bin/frameplot.pl.     

The effect of tumor necrosis factor alpha (-308G/a) and interferon gamma (+874T/a) polymorphisms on susceptibility to coronary heart disease

Abstract

Background: Coronary heart disease (CHD) is a chronic inflammatory disease, which is still regarded as a major cause of morbidity and mortality worldwide. Several studies have suggested that polymorphisms in cytokine genes are associated with the pathogenesis of CHD. The genotype distribution of Tumor necrosis factor alpha (TNF-α) and interferon gamma (IFN-γ) genes polymorphisms have been shown to be different in various ethnic populations. This study was aimed to investigate the association of TNF-α-308?G/A and IFN-γ?+?874T/A polymorphisms with risk of CHD in an Iranian population.

Methods: A total of 187 unrelated subjects comprised 96 CHD patients and 91 healthy controls were enrolled in this cross-sectional study. The TNF-α-308?G/A and IFN-γ?+?874T/A polymorphisms were genotyped using amplification refractory mutation system-PCR (ARMS-PCR). The chi-square and logistic regression tests were used to calculate the odds ratios (ORs) as a measure of differences in genotype frequencies.

Results: A significant differences in the allelic and genotypic distribution of TNF-α-308?G/A and IFN-γ?+?874T/A polymorphisms was found between CHD patients and healthy controls (P?=?0.017, P?=?0.011, P?=?0.006 and P?=?0.002, respectively). Logistic regression analyses were also revealed statistically significant risk for CHD with respect to TNF-α-308?A and IFN-γ?+?874?T carriers either in crude or after adjustment for potential confounders (P?=?0.003 and P?=?0.006, respectively).

Conclusion: This study provides strong evidence supporting the association of TNF-α-308G/A and IFN-γ?+?874T/A polymorphisms with the increased risk of CHD. Therefore, these two cytokine polymorphisms may play a role in predisposition to coronary heart disease.     

HCV-specific interleukin-21+CD4+ T cells responses associated with viral control through the modulation of HCV-specific CD8+ T cells function in chronic hepatitis C patients

Interleukin-21 (IL-21)+CD4+ T cells are involved in the immune response against hepatitis B virus (HBV) by secreting IL-21. However, the role of IL-21+CD4+ T cells in the immune response against chronic hepatitis C (CHC) virus infection is poorly understood. This study aimed to investigate the role of IL-21+CD4+ T cells in CHC patients and the potential mechanisms. The study subjects included nineteen CHC patients who were grouped by viral load (low, < 10⁶ RNA copies/ml, n = 8; high, > 10⁶ RNA copies/ml, n = 11). The peripheral frequency of HCV-specific IL-21+CD4+ T cells was higher in the low viral load group and was negatively correlated with the serum HCV RNA viral load in all CHC patients. Meanwhile, IL-21+ cells accumulated in the liver in the low viral load group. In vitro, IL-21 treatment increased the expression of proliferation markers and cytolytic molecules on HCV-specific CD8+ T cells. In summary, these findings suggest that HCV-specific IL-21+CD4+ T cells might contribute to HCV control by rescuing HCV-specific CD8+ T cells in CHC patients.     

On the correlation between genomic G+C content and optimal growth temperature in prokaryotes: data quality and confounding factors

The correlation between genomic G+C content and optimal growth temperature in prokaryotes has gained renewed interest after Musto et al. [H. Musto, H. Naya, A. Zavala, H. Romero, F. Alvarex-Valin, G. Bernardi, Correlations between genomic GC levels and optimal growth temperatures in prokaryotes, FEBS Lett. 573 (2004) 73-77], reported that positive correlations exist in 15 families studied. We have reanalyzed their data and found that when genome size and data quality were adjusted for, there was no significant evidence of relationship between optimal temperature and GC content for two of the families that had previously shown strongly significant correlations. Using updated temperature optima for Halobacteriaceae species we found the correlation is insignificant in this family. For the family Enterobacteriaceae when genome size and optimal temperature are included in a multiple linear regression, only genome size is significant as a predictor of GC content. We showed that more profound statistical methods than simple two factor correlation analysis should be used for analyzing complex intrinsic and extrinsic factors that affect genomic GC content. We further found that a positive correlation between temperature and genomic GC is only evident in free-living species of low optimal growth temperatures.     

The longest (A+T) and (G+C) blocks in the human and other genomes

We analysed complete or almost complete nucleotide sequences of the human, chimp, mouse, rat, chicken, dog, and other genomes to find that they contain extremely long (A+T) a (G+C) blocks that do not occur at all in the corresponding randomized sequences. The longest is an (A+T) block containing 1040 consecutive AT pairs that occurs in the 16th human chromosome. The longest human (G+C) block has 261 bp in length. About a half of the longest blocks occur in introns. The (A+T) blocks are discrete units whereas the (G+C) blocks are diffuse. They are imbedded in the genome through connectors longer than 1 kilobase where the (G+C) content gradually decreases to the value of 50%. Remarkably, the (A+T) as well as (G+C) blocks are substantially shorter in the chimp genome. Chicken is characteristic by very long (G+C) blocks that are even longer than in the human genome. Though much shorter, long (G+C) and especially (A+T) blocks occur in lower organisms as well, which means that AT and GC pair clustering is an ancient property that has evolved into large scales in higher eukaryote genomes and the human genome in particular. Very long (A+T) and (G+C) blocks confer specific biophysical properties on DNA that are likely to influence genome folding in cell nuclei and its functional properties.     

G+C3 structuring along the genome: a common feature in prokaryotes

The heterogeneity of gene nucleotide content in prokaryotic genomes is commonly interpreted as the result of three main phenomena: (1) genes undergo different selection pressures both during and after translation (affecting codon and amino acid choice); (2) genes undergo different mutational pressure whether they are on the leading or lagging strand; and (3) genes may have different phylogenetic origins as a result of lateral transfers. However, this view neglects the necessity of organizing genetic information on a chromosome that needs to be replicated and folded, which may add constraints to single gene evolution. As a consequence, genes are potentially subjected to different mutation and selection pressures, depending on their position in the genome. In this paper, we analyze the structuring of different codon usage measures along completely sequenced bacterial genomes. We show that most of them are highly structured, suggesting that genes have different base content, depending on their location on the chromosome. A peculiar pattern of genome structure, with a tendency toward an A+T-enrichment near the replication terminus, is found in most bacterial phyla and may reflect common chromosome constraints. Several species may have lost this pattern, probably because of genome rearrangements or integration of foreign DNA. We show that in several species, this enrichment is associated with an increase of evolutionary rate and we discuss the evolutionary implications of these results. We argue that structural constraints acting on the circular chromosome are not negligible and that this natural structuring of bacterial genomes may be a cause of overestimation in lateral gene transfer predictions using codon composition indices.     

Isolation of Plant Gene Space-Related Sequence Elements by High C+G Patch (HCGP) Filtration: Model Study on Rice

For the isolation of gene space representative sequence elements, a new methodology—high C+G patch (HCGP) filtration—has been developed using rice as a model. The method is based on the fragmentation of the genomic DNA by methylation-sensitive HpaII and MspI restriction endonucleases having exclusively G/C base pair-containing recognition sites. These enzymes fragment the genome at high C+G content and hypomethylated regions. Cloning fragments spanning such regions in close vicinity (200–2,000 bp) revealed that about 60% of the clones represented gene space sequences resulting in twofold enrichment of these sequences, which is close to the theoretical maximum in rice. The sequence information of clones used in the present study was deposited in the NCBI database under the accession numbers EI 365676–EI 366364.     

嗜血细胞综合征患儿外周血CD_4~+CD_(25)~+调节性T细胞变化及临床意义

目的观察嗜血细胞综合征(hemophagocytic syndrome,HPS)患儿外周血中调节性T细胞(RegulatoryTcells,Treg细胞)的变化,探讨其在HPS发病中的作用及临床意义。方法应用流式细胞仪检测17例初诊HPS患者(初诊组)、11例经诱导治疗后临床缓解者(缓解组)及20例健康人群(对照组)外周血中CD4+CD25+调节性T细胞。结果与对照组相比较,HPS患者初诊组及缓解组外周血CD4+CD25+调节性T细胞均升高(P0.05)。与初诊组相比较,缓解组CD4+CD25+Treg细胞降低(P0.05),但仍高于正常对照组(P0.05)。结论CD4+CD25+Treg细胞增多可能是HPS患者免疫功能受抑的重要原因之一,其变化对于HPS的预后判断有一定的意义。     

Relationship between G + C in silent sites of codons and amino acid composition of human proteins

Summary We have investigated the relationship between the G + C content of silent (synonymous) sites in codons and the amino acid composition of encoded proteins for approximately 1,600 human genes. There are positive correlations between silent site G + C and the proportions of codons for Arg, Pro, Ala, Trp, His, Gln, and Leu and negative ones for Tyr, Phe, Asn, Ile, Lys, Asp, Thr, and Glu. The median proteins coded by groups of genes that differ in silent-site G + C content also differ in amino acid composition, as do some proteins coded by homologous genes. The pattern of compositional change can be largely explained by directional mutation pressure, the genetic code, and differences in the frequencies of accepted amino acid substitutions; the shifts in protein composition are likely to be selectively neutral.Offprint requests to: D.W. Collins     

冻干A+C群脑膜炎球菌多糖疫苗安全性和免疫原性观察

为了评价冻干A+C群脑膜炎球菌多糖疫苗(MPV)的安全性和免疫原性,按随机、盲法的原则,评价疫苗免疫后不良反应发生率、抗体阳转率及抗体几何平均滴度(GMT)。将606名健康观察者分为2～5岁、6～12岁、13～17岁、18～60岁四个年龄组,结果显示,该疫苗全身反应发生率2.64%,局部反应发生率1.32%,四个年龄组疫苗免疫后杀菌抗体阳性率分别为100%、100%、99.3%和100%,免疫后A群杀菌抗体GMT分别为1:250.47、1:190.61、1:144.22和1:205.79,免疫后C群杀菌抗体GMT分别为1:273.33、1:551.18、1:788.26和1:809.81,冻干A+C群多糖疫苗在≥2岁人群中具有良好的安全性和免疫原性,建议推广使用A+C群MPV。     

Wide intra-genomic G+C heterogeneity in human and chicken is mainly due to strand-symmetric directional mutation pressures: dGTP-oxidation and symmetric cytosine-deamination hypotheses

The intra-strand Parity Rule 2 of DNA (PR2) states that A=T and G=C within each strands. Useful corollaries of PR2 are G/(G+C)=A/(A+T)=0.5, G/(G+A)=C/(C+T)=G+C, G/(G+T)=C/(C+A)=G+C. Here. A, T, G, and C represent relative contents of the four nucleotide residues in a specific strand of DNA, so that A+T+G+C=1. Thus, deviations from the PR2 is a sign of strand-specific (or asymmetric) mutation and/or selection pressures. The present study delineates the symmetric and asymmetric effects of mutations on the intra-genomic heterogeneity of the G+C content in the human genome. The results of this study on the human genome are: (1) When both two- and four-codon amino acids were combined, only slight departures from the PR2 were observed in the total ranges of G+C content of the third-codon position. Thus, the G+C heterogeneity is likely to be caused by symmetric mutagenesis between the two strands. (2) The above result makes the deamination of cytosine due to double-strand breathing of DNA [Mol. Biol. Evol. 17 (2000) 1371] and/or incorporation of the oxidized guanine (8-oxo-guanine) opposite adenine during DNA replication (dGTP-oxidation hypothesis) as the most likely candidates for the major cause of the diversities of the G+C content. (3) Patterns of amino acid-specific PR2-biases detected by plotting PR2 corollaries against the G+C content of third codon position revealed that eight four-codon amino acids can be divided into three types by the second codon letter: (a) C₂-type (Ala, Pro, Ser4, and Thr), (b) G₂-type (Arg4 and Gly), and (c) T₂-type (Leu4 and Val). (4) Most of the asymmetric plot patterns of the above three classes in PR2 biases can be explained by C₂→T₂ deamination of C₂pG₃ of C₂-type to T₂pG₃ (T₂-type) in both human and chicken. This explains the existence of some preferred codons in human and chicken. However, these biases (asymmetric) hardly contribute to the overall G+C content diversity of the third codon position.     

HIV/AIDS患者机会性感染与CD4+ T淋巴细胞间的关联性

目的 研究人免疫缺陷病毒（HIV）感染者及艾滋病（AIDS）患者发生机会性感染的概率与自身CD4+ T淋巴细胞之间的关系,为HIV患者机会性感染的防治提供参考。方法 以2016年6月至2017年6月我院400例HIV患者为研究对象,回顾性分析不同CD4+T淋巴细胞计数HIV患者发生机会性感染的情况。结果 400例HIV患者发生机会性感染178例,总感染率为44.5%。CD4+T淋巴细胞计数≤50个/μL的患者机会性感染发生率（86.67%）最高,与其他各组比较差异有统计学意义（P<0.05）。随着CD4+ T淋巴细胞计数的减少,HIV患者机会性感染率升高。178例机会性感染者中,单一感染82例,2部位感染52例,3部位感染28例,4部位以上感染16例。感染病原体检测显示,细菌感染84例（47.19%）,结核杆菌感染36例（20.22%）,病毒感染30例（16.85%,包括巨细胞病毒感染18例、单纯疱疹病毒感染12例）,真菌感染77例（43.25%,包括假丝酵母感染35例,肺孢子菌感染20例,马尔尼菲青霉菌感染12例,新型隐球菌感染10例）,未明确病原体性质34例（19.10%）,复合感染多见。结论 CD4+ T淋巴细胞水平与HIV患者继发机会性感染的概率关系密切。HIV患者CD4+ T淋巴细胞水平的监测对其继发机会性感染的防控具有重要临床意义。