The modified wobble nucleoside uridine-5-oxyacetic acid in tRNAPro(cmo5UGG) promotes reading of all four proline codons in vivo

In Salmonella enterica serovar Typhimurium five of the eight family codon boxes are decoded by a tRNA having the modified nucleoside uridine-5-oxyacetic acid (cmo5U) as a wobble nucleoside present in position 34 of the tRNA. In the proline family codon box, one (tRNAProcmo5UGG) of the three tRNAs that reads the four proline codons has cmo5U34. According to theoretical predictions and several results obtained in vitro, cmo5U34 should base pair with A, G, and U in the third position of the codon but not with C. To analyze the function of cmo5U34 in tRNAProcmo5UGG in vivo, we first identified two genes (cmoA and cmoB) involved in the synthesis of cmo5U34. The null mutation cmoB2 results in tRNA having 5-hydroxyuridine (ho5U34) instead of cmo5U34, whereas the null mutation cmoA1 results in the accumulation of 5-methoxyuridine (mo5U34) and ho5U34 in tRNA. The results suggest that the synthesis of cmo5U34 occurs as follows: U34 -->(?) ho5U -->(CmoB) mo5U -->(CmoA?) cmo5U. We introduced the cmoA1 or the cmoB2 null mutations into a strain that only had tRNAProcmo5UGG and thus lacked the other two proline-specific tRNAs normally present in the cell. From analysis of growth rates of various strains and of the frequency of +1 frameshifting at a CCC-U site we conclude: (1) unexpectedly, tRNAProcmo5UGG is able to read all four proline codons; (2) the presence of ho5U34 instead of cmo5U34 in this tRNA reduces the efficiency with which it reads all four codons; and (3) the fully modified nucleoside is especially important for reading proline codons ending with U or C.     

Codon reading by tRNAAla with modified uridine in the wobble position

tRNAs reading four-codon families often have a modified uridine, cmo(5)U(34), at the wobble position of the anticodon. Here, we examine the effects on the decoding mechanism of a cmo(5)U modification in tRNA(1B)(Ala), anticodon C(36)G(35)cmo(5)U(34). tRNA(1B)(Ala) reads its cognate codons in a manner that is very similar to that of tRNA(Phe). As Ala codons are GC rich and Phe codons AU rich, this similarity suggests a uniform decoding mechanism that is independent of the GC content of the codon-anticodon duplex or the identity of the tRNA. The presence of cmo(5)U at the wobble position of tRNA(1B)(Ala) permits fairly efficient reading of non-Watson-Crick and nonwobble bases in the third codon position, e.g., the GCC codon. The ribosome accepts the C-cmo(5)U pair as an almost-correct base pair, unlike third-position mismatches, which lead to the incorporation of incorrect amino acids and are efficiently rejected.     

Association of polymorphic markers I/D of gene ACE and A1166C of gene AT2R1 with ischemic chronic heart failure in the Russian and Tatar populations of Bashkortostan Republic

Polymerase chain reaction was used to study the association of polymorphic markers I/D of the angiotensin-converting enzyme gene (ACE) and A1166C of the angiotensin II type 1 receptor gene (AT2R1) with chronic heart failure (CHF) in Russian and Tatar patients that had had myocardial infarction. In Russian patients aged 50 years or younger that had had macrofocal myocardial infarction, the CC genotype of the A1166C polymorphic marker of gene AT2R1 was associated with an increased risk of CHF (OR = 11.36). Genotype DD and allele D of the I/D polymorphic marker of gene ACE were associated with a more severe CHF (functional class III-IV) in Russian patients (OR = 3.50 and 2.06). In Tatar patients, polymorphic markers I/D of gene ACE and A1166C of gene AT2R1 were not associated with CHF.     

A 16S rRNA-tRNA product containing a nucleotide phototrimer and specific for tRNA in the P/E hybrid state in the Escherichia coli ribosome

Ribosome complexes containing deacyl-tRNA1(Val) or biotinylvalyl-tRNA1(Val) and an mRNA analog have been irradiated with wavelengths specific for activation of the cmo5U nucleoside at position 34 in the tRNA1(Val) anticodon loop. The major product for both types of tRNA is the cross-link between 16S rRNA (C1400) and the tRNA (cmo5U34) characterized already by Ofengand and his collaborators [Prince et al. (1982) Proc. Natl Acad. Sci. USA, 79, 5450-5454]. However, in complexes containing deacyl-tRNA1(Val), an additional product is separated by denaturing PAGE and this is shown to involve C1400 and m5C967 of 16S rRNA and cmo5U34 of the tRNA. Puromycin treatment of the biotinylvalyl-tRNA1(Val) -70S complex followed by irradiation, results in the appearance of the unusual photoproduct, which indicates an immediate change in the tRNA interaction with the ribosome after peptide transfer. These results indicate an altered interaction between the tRNA anticodon and the 30S subunit for the tRNA in the P/E hybrid state compared with its interaction in the classic P/P state.     

Chorismic acid, a key metabolite in modification of tRNA.

Chorismic acid is the common precursor for the biosynthesis of the three aromatic amino acids as well as for four vitamins. Mutants of Escherichia coli defective in any of the genes involved in the synthesis of chorismic acid are also unable to synthesize uridine 5-oxyacetic acid (cmo5U) and its methyl ester (mcmo5U). Both modified nucleosides are normally present in the wobble position of some tRNA species. Mutants defective in any of the specific pathways leading to phenylalanine, tyrosine, tryptophan, folate, enterochelin, ubiquinone, and menaquinone have normal levels of cmo5U and mcmo5U in their tRNA. The presence of shikimic acid in the growth medium restores the ability of an aroD mutant to synthesize cmo5U, while O-succinylbenzoate, which is an early intermediate in the synthesis of menaquinone, does not. Thus, chorismic acid is a key metabolite in the synthesis of these two modified nucleosides in tRNA. The absence of chorismic acid blocks the formation of cmo5U and mcmo5U at the first step, which might be the formation of 5-hydroxyuridine. This results in an unmodified U in the wobble position of tRNA(1Val) and in most of the tRNAs normally containing cmo5U and mcmo5U. Since cmo5U and mcmo5U are synthesized under anaerobic conditions, the formation of these nucleosides does not require molecular oxygen. One of the carbon atoms of the side chain, --O--CH2--COOH, originates from the methyl group of methionine. The other carbon atom does not originate directly from the C-1 pool, from the carboxyl group methionine, or from bicarbonate. This metabolic link between intermediary metabolism and translation also exists for another member of the family Enterobacteriaceae, Salmonella typhimurium, as well as for the distantly related gram-positive organism Bacillus subtilis.     

Cryptococcus arboriformis Sp. Nov., a novel anamorphic basidiomycetous yeast species isolated from a patient's urine

A basidiomycetous yeast strain isolated from the urine of a 73-year-old Japanese patient with chronic renal failure was revealed to be a novel species by sequencing the D1/D2 26S rDNA and ITS regions of the rRNA gene. The name Cryptococcus arboriformis sp. nov. is proposed for the isolate, with IFM 54862(T) (=CBS 1044(T) =JCM 14201(T)) as the type strain. A phylogenetic analysis positioned Cryptococcus arboriformis in the Trichosporonales lineage and showed that it is closely related to C. haglerorum.     

普通小麦D2型CMS系的育性基因及其遗传特性

通过研究普通小麦D^2型CMS－育性恢复体系中育性基因的种类及其遗传特性。结果表明：（1）D^2型不育系具有较好的不育性保持与恢复特征,在一般的普通小麦品种（系）中具有广泛的恢复（基因）源、可恢复度高（恢复度超过50％的品种或品质占到33．61％）,也能较容易地转育出新的不育系（完全保持不育性的品种或品系占到25．21％）,这一特征明显优于现有T、K、V型等不育系。（2）D^2型不育系的不育性受核内不育基因和抑制基因控制,相应的核基因型分为Al（不育基因）、A2（不育基因＋抑制基因）两类;恢复纱的恢复性受核内主效恢复基因、微效恢复基因和抑制基因控制,相应的核基因型分为C1（主效恢复基因）、C2(驻效恢复基因＋微效恢复基因）、C3（微效恢复基因）、C4（主效恢复基因＋抑制基因）、C5（主效恢复基因＋微效恢复基因＋抑制基因）、C6（微效恢复基因＋抑制基因）6种。环境条件的变化对育性基因、尤其是微效恢复基因和抑制基因的遗传效应有不同程度的影响。D^2型不育有效杂交组合的模型为：A1＋C1`A1 C2、A2＋C2。（3）D^2型不育系等位恢复基因的遗传表现为不完全显性,非等位恢复基因的遗传表现出积效应,这正是强恢复系德育的理论依据之一。     

CHOP T/C and C/T haplotypes contribute to early-onset type 2 diabetes in Italians

Type 2 diabetes (T2D) is characterized by impaired insulin secretion, insulin insensitivity and decreased beta-cell mass. Multiple genes contribute to T2D. The chromosome 12q13.1 region is in linkage to T2D in different populations, including our Italian dataset. CHOP is a candidate gene for the linkage, as it is located in the chromosome 12q13.1 region, and may contribute to T2D by increasing beta-cell apoptosis susceptibility and by impairing insulin sensitivity. Our goal was to identify any potential CHOP gene variants contributing to T2D in our Italian early-onset T2D families, which show linkage to the CHOP region. We directly sequenced the CHOP gene in 28 Italian probands of the linked T2D families and in 115 control subjects. We performed genotype and haplotype association tests with T2D of the identified single nucleotide polymorphisms (SNPs). We performed model-free and parametric association haplotype tests with T2D. We identified three SNPs [5'UTR-c.279T > C, 5'UTR-c.120A > G and + nt30C > T (F10F)] in CHOP. These SNPs are in complete linkage disequilibrium. The genotype association test showed an association trend with T2D of TT (F10F) and AG (-c.120A > G). The haplotype association test provided significant results for the haplotypes T/C (frequency = 0.33) and C/T (frequency = 0.01) (at 5'UTR-c.279T > C and + nt30C > T, respectively) under non-parametric analysis (P-value = 0.0000), recessive model (P-value = 0.0000) and additive model (P-value = 0.0014). Our data show that CHOP described haplotypes T/C and C/T, as an additive and as a homozygous variant, contribute significantly to T2D in our Italian early-onset group. We conclude that the CHOP T/C and C/T haplotype contributes to our T2D linkage signal on chromosome 12q13.1.     

Whole-Body Diffusion-Weighted Imaging in Chronic Recurrent Multifocal Osteomyelitis in Children

Objective

Chronic recurrent multifocal osteomyelitis/ chronic non-bacterial osteomyelitis (CRMO/ CNO) is a rare auto-inflammatory disease and typically manifests in terms of musculoskeletal pain. Because of a high frequency of musculoskeletal disorders in children/ adolescents, it can be quite challenging to distinguish CRMO/ CNO from nonspecific musculosketetal pain or from malignancies. The purpose of this study was to evaluate the visibility of CRMO lesions in a whole-body diffusion-weighted imaging (WB-DWI) technique and its potential clinical value to better characterize MR-visible lesions.

Material and Methods

Whole-body imaging at 3T was performed in 16 patients (average: 13 years) with confirmed CRMO. The protocol included 2D Short Tau Inversion Recovery (STIR) imaging in coronal and axial orientation as well as diffusion-weighted imaging in axial orientation. Visibility of lesions in DWI and STIR was evaluated by two readers in consensus. The apparent diffusion coefficient (ADC) was measured for every lesion and corresponding reference locations.

Results

A total of 33 lesions (on average 2 per patient) visible in STIR and DWI images (b = 800 s/mm² and ADC maps) were included, predominantly located in the long bones. With a mean value of 1283 mm²/s in lesions, the ADC was significantly higher than in corresponding reference regions (782 mm²/s). By calculating the ratio (lesion to reference), 82% of all lesions showed a relative signal increase of 10% or higher and 76% (25 lesions) showed a signal increase of more than 15%. The median relative signal increase was 69%.

Conclusion

This study shows that WB-DWI can be reliably performed in children at 3T and predominantly, the ADC values were substantially elevated in CRMO lesions. WB-DWI in conjunction with clinical data is seen as a promising technique to distinguish benign inflammatory processes (in terms of increased ADC values) from particular malignancies.     

SEMA3B基因在鼻咽癌组织中的表达、杂合性丢失和甲基化分析

SEMA3B基因定位于鼻咽癌高频缺失区域3p21.3上,最近被证明具有抑瘤基因的功能.分析了鼻咽癌组织中SEMA3B基因的表达、杂合性丢失(LOH)和甲基化情况.首先应用逆转录-聚合酶链式反应(RT-PCR)方法检测了33例鼻咽癌组织和15例慢性鼻咽炎组织中SEMA3B基因的表达,结果显示75.8%(25/33)鼻咽癌组织中SEMA3B基因表达缺失或下调,显著低于慢性鼻咽炎组织中的表达(P=0.001).进一步选取3个微卫星位点D3S1568、D3S1621和D3S4597分析了20例鼻咽癌组织中SEMA3B基因LOH的情况,结果表明3个位点的丢失率分别为10%、20%和15%,总的丢失率为45%,统计分析发现LOH与基因表达之间存在明显相关(P=0.023).最后,采用甲基化特异性PCR方法分析了SEMA3B基因启动子区甲基化,结果发现在100%的鼻咽癌组织和73.3%的慢性鼻咽炎组织中检测到SEMA3B基因启动子区高甲基化.由此得出结论,SEMA3B基因在鼻咽癌组织中表达缺失或下调,LOH是引起其表达异常的原因之一.     

Virological Characteristics of Acute Hepatitis B in Eastern India: Critical Differences with Chronic Infection

Hepatitis B Virus (HBV) manifests high genetic variability and is classifiable into ten genotypes (A-J). HBV infection can lead to variable clinical outcomes, ranging from self-limiting acute hepatitis to active chronic hepatitis, cirrhosis and hepatocellular carcinoma. The present study characterizes HBV strains circulating among patients with acute (AHB) and chronic HBV infection (CHB). Among a total of 653 HBsAg positive cases, 40 manifested acute infection. After sequencing the surface(S), basal core promoter/pre-core(BCP/PC) and the X gene regions, phylogenetic tree was constructed using MEGA4 by neighbor-joining method. Statistical robustness was established with bootstrap analysis. Nucleotide diversity was determined by Shannon entropy per site using the Entropy program of the Los Alamos National Laboratories. Analyses of acute patients revealed that HBV/D2 is the major circulating sub-genotype and commonly associated with sexual promiscuity and the age group between15-30 years. Comparison of AHB and CHB patients revealed that HBeAg positivity, ALT levels and genotype D were significantly high in AHB, whereas CHB patients were predominantly male, had a high viral load, and were commonly associated with genotype C. The frequencies of mutations in the S, BCP/PC, and X gene were low in AHB as compared to CHB. Drug resistant mutations were not detectable in the polymerase gene of AHB. Average nucleotide diversity in AHB was considerably low as compared to CHB. Further, the highest average ΔH (average difference in entropy between chronic and acute infection) was observed in the BCP/PC region implying that this region was most vulnerable to mutations upon HBV persistence, especially in case of genotype C. Additionally, among all substitutions, the A1762T and G1764A BCP mutations were the strongest indicators of chronicity. In conclusion, the study exhibits a general portrait of HBV strains circulating among acute hepatitis B patients in Eastern India and their intricate differences with chronic patients which should be useful from the clinical point of view.     

腓肠肌皮瓣联合负压封闭引流治疗胫骨慢性骨髓炎及软组织缺损的临床研究

目的:研究腓肠肌皮瓣联合负压封闭引流治疗胫骨慢性骨髓炎及软组织缺损的临床疗效。方法:选取2013年10月到2014年10月我院收治的胫骨慢性骨髓炎及软组织缺损患者68例,按照手术方式不同将患者分为研究组(n=39例)和对照组(n=29例),其中研究组给予腓肠肌皮瓣联合负压封闭引流治疗,对照组给予常规手术方法治疗,比较两组临床疗效、C反应蛋白(CRP)变化、治愈时间以及复发率。结果:研究组治愈率94.9%(37/39)显著高于对照组的75.9%(22/29),两组比较差异具有统计学意义(P0.05);研究组CRP变化和治愈时间均显著优于对照组,两组比较差异具有统计学意义(P0.05);研究组复发率显著低于对照组,两组比较差异具有统计学意义(P0.05)。结论:腓肠肌皮瓣联合负压封闭引流治疗胫骨慢性骨髓炎及软组织缺损具有较高治愈率,能显著降低炎性反应,缩短愈合时间,降低复发率。     

Chronic bacterial osteomyelitis suppression of tumor growth requires innate immune responses

Clinical studies over the past several years have reported that metastasis-free survival times in humans and dogs with osteosarcoma are significantly increased in patients that develop chronic bacterial osteomyelitis at their surgical site. However, the immunological mechanism by which osteomyelitis may suppress tumor growth has not been investigated. Therefore, we used a mouse model of osteomyelitis to assess the effects of bone infection on innate immunity and tumor growth. A chronic Staphylococcal osteomyelitis model was established in C3H mice and the effects of infection on tumor growth of syngeneic DLM8 osteosarcoma were assessed. The effects of infection on tumor angiogenesis and innate immunity, including NK cell and monocyte responses, were assessed. We found that osteomyelitis significantly inhibited the growth of tumors in mice, and that the effect was independent of the infecting bacterial type, tumor type, or mouse strain. Depletion of NK cells or monocytes reversed the antitumor activity elicited by infection. Moreover, infected mice had a significant increase in circulating monocytes and numbers of tumor associated macrophages. Infection suppressed tumor angiogenesis but did not affect the numbers of circulating endothelial cells. Therefore, we concluded that chronic localized bacterial infection could elicit significant systemic antitumor activity dependent on NK cells and macrophages.     

Mapping of Charcot-Marie-Tooth Disease Type 1C to Chromosome 16p Identifies a Novel Locus for Demyelinating Neuropathies

Charcot-Marie-Tooth (CMT) neuropathy represents a genetically heterogeneous group of diseases affecting the peripheral nervous system. We report genetic mapping of the disease to chromosome 16p13.1-p12.3, in two families with autosomal dominant CMT type 1C (CMT1C). Affected individuals in these families manifest characteristic CMT symptoms, including high-arched feet, distal muscle weakness and atrophy, depressed deep-tendon reflexes, sensory impairment, slow nerve conduction velocities, and nerve demyelination. A maximal combined LOD score of 14.25 was obtained with marker D16S500. The combined haplotype analysis in these two families localizes the CMT1C gene within a 9-cM interval flanked by markers D16S519 and D16S764. The disease-linked haplotypes in these two pedigrees are not conserved, suggesting that the gene mutation underlying the disease in each family arose independently. The epithelial membrane protein 2 gene (EMP2), which maps to chromosome 16p13.2, was evaluated as a candidate gene for CMT1C.     

Significance of Vitamin D Receptor Gene Polymorphisms for Risk of Hepatocellular Carcinoma in Chronic Hepatitis C

BACKGROUND/AIMSBiological and epidemiological data suggest that vitamin D levels may influence cancer development. Several single nucleotide polymorphisms have been described in the vitamin D receptor (VDR) gene in association with cancer risk. We aimed to investigate the association of VDR gene polymorphisms with hepatocellular carcinoma (HCC) development in chronic hepatitis C patients.METHODSIn a cross-sectional, hospital-based setting, 340 patients (201 chronic hepatitis, 47 cirrhosis and 92 HCC) and 100 healthy controls receiving VDR genotyping (bat-haplotype: BsmI rs1544410 C, ApaI rs7975232 C and TaqI rs731236 A) were enrolled.RESULTSPatients with HCC had a higher frequency of ApaI CC genotype (P = 0.027) and bAt[CCA]-haplotype (P = 0.037) as compared to control subjects. There were no differences in BsmI and TaqI polymorphisms between two groups. In patients with chronic hepatitis C, HCC subjects had a higher frequency of ApaI CC genotype and bAt[CCA]-haplotype than those with chronic hepatitis (P = 0.001 and 0.002, respectively) and cirrhosis (P = 0.019 and 0.026, respectively). After adjusting age and sex, logistic regression analysis showed that ApaI CC genotype (odds ratio: 3.02, 95% confident interval: 1.65-5.51) was independently associated with HCC development.CONCLUSIONVDR ApaI polymorphism plays a role in the development of HCC among chronic hepatitis C patients. Further explorations of this finding and its implications are required.     

播散性浅表性光线性汗孔角化症DSAP1位点的精细定位和候选基因的突变检测

播散性浅表性光线性汗孔角化症(DSAP)是一种以多个浅表的角化性皮损,边缘轻微嵴状角化性隆起为特征的少见的慢性角化性皮肤病,呈常染色体显性遗传。以往的研究将该病基因定位于12q23．2—24．1区域(DSAP1)和15q25．1-26．1区域(DSAP2)。本研究对2个无关的六代DSAP家系进行了全基因组扫描和连锁分析,结果显示,这2个DSAP家系在D12窝4位点的最高累积LOD值为8．28(θ=0．00)。单倍型分析结果显示,这2个DSAP家系致病基因位于12q24．1-q24．2(D12S330和D12S354)之间8．0cM的区域内。该区域与DSAP1的致病区域部分重叠。对重叠区域内6个候选基因(CRY1,PWP1,ASCL4,PRDM4,KIAA0789和CMKLR1)的编码区进行序列分析,在DSAP病人中未发现突变位点。提示该6个候选基因可能与这2个DSAP家系的发病机理无关。     

A visfatin promoter polymorphism is associated with low-grade inflammation and type 2 diabetes

Visfatin (also known as pre-B cell colony-enhancing factor, or PBEF) is a pro-inflammatory adipokine expressed predominantly in visceral fat. We investigated whether polymorphisms at the visfatin/PBEF locus influence the risk of type 2 diabetes (T2D). Linkage disequilibrium analysis of 52 single nucleotide polymorphisms spanning the entire gene (34.7 kb) plus 20.5 kb of the upstream region and 25.5 kb of the downstream region revealed a single haplotype block that could be tagged by seven single nucleotide polymorphisms. These seven tags were typed in a group of T2D patients (n = 814) and a group of non-diabetic controls (n = 320) of white origin. A significant association was observed at -948C>A, with minor allele frequencies of 0.157 in T2D cases and 0.119 in non-diabetic controls (p = 0.021). In a non-diabetic population (n = 630), the same -948 allele that conferred increased risk of T2D was significantly associated with higher plasma levels of fibrinogen and C-reactive protein (p = 0.0022 and 0.0038, respectively). However, no significant associations were observed with BMI, waist circumference, serum glucose levels, or fasting insulin levels. Our findings suggest that the visfatin/PBEF gene may play a role in determining T2D susceptibility, possibly by modulating chronic, low-grade inflammatory responses.     

TYMS,MTHFR, p53 and MDR1 gene polymorphisms in breast cancer patients treated with adjuvant therapy

Purpose: The distribution of TSER (TYMS), C677T (MTHFR), Arg72Pro (p53) and C3435T (MDR1) gene polymorphisms was investigated in 80 consecutive breast cancer patients treated with adjuvant chemotherapy. Results: Observed allelic frequencies were: TSER, (2) 0.55 and (3) 0.45; MTHFR C677T, (C) 0.65 and (T) 0.35; p53 Arg72Pro, (Arg) 0.76 and (Pro) 0.24; MDR1 C3435T, (C) 0.51 and (T) 0.49. MTHFR C677T was found to be a strong predictor of the presence of multifocal tumour (odds ratio, 4.1; 95% CI, 1.1–15.7; P = 0.035). Conclusion: Our data indicate that breast cancer patients with the C/C variant may present multifocal tumour most frequently.