Indinavir resistance evolution in one human immunodeficiency virus type 1 infected patient revealed by single-genome amplification

Abstract  

Human Immunodeficiency Virus Type 1 exists in vivo as quasispecies, and one of the genome’s characteristics is its diversity. During the antiretroviral therapy, drug resistance is the main obstacle to effective viral prevention. Understanding the molecular evolution process is fundamental to analyze the mechanism of drug resistance and develop a strategy to minimize resistance.     

Occurrence of tetracycline resistance genes tet(M) and tet(S) in bacteria from marine aquaculture sites

Occurrence of tetracycline resistance genes encoding ribosomal protection proteins was examined in 151 tetracycline-resistant bacterial isolates from fish and seawater at coastal aquaculture sites in Japan and Korea. The tet(M) gene was detected in 34 Japanese and Korean isolates, which included Vibrio sp., Lactococcus garvieae, Photobacterium damsela subsp. piscicida, and unidentified Gram-positive bacteria. The majority of these bacterial isolates displayed high-level resistance with a minimum inhibitory concentrations (MICs) equal to or greater than 250 microg/ml of oxytetracycline and only four isolates had MICs less than 31.3 microg/ml. 16S rDNA RFLP typing of tet(M)-positive Vibrio isolates suggests that these are clonal populations of the same phylotype specific to a particular location. One Vibrio clone (phylotype III), however, is widely disseminated, being detected during different sampling years, at different locations, and in different fish species in both Japan and Korea. The tet(S) gene was detected in L. garvieae from yellowtail in Japan and in Vibrio sp. from seawater in Korea. This is the first report of tet(S) occurrence in Gram-negative facultative anaerobes. These results suggest that tet(M) and tet(S) genes are present in fish intestinal and seawater bacteria at aquaculture sites and could be an important reservoir of tetracycline resistance genes in the marine environment.     

Ecomorphological comparisons of sagittae in Mullus barbatus and M. surmuletus

For both Mullus barbatus and M. surmuletus , the relationship between sagitta area (O), sulcus acusticus area (S) throughout postlarval growth was characterized by their negative allometric growth. The adjusted mean S: O ratio differed between the two species. This may be associated with the difference in size and shape of the sagittae, a difference in somatic growth, and differences in food and spatial niches. The inner ear of Mullus cannot be considered as specialized and the interaction of stimuli detected by the sensory barbels and the inner ear together could be a compensatory mechanism that helps in the food search.     

正常人及肝细胞癌患者肝脏及血浆中丙酮酸激酶同工酶免疫测定

 分别从人肝及鼠肝中高度纯化L型和M_1型丙酮酸激酶(Pyk),制备相应的免抗血清。从抗血清中纯化IgG并水解成F(ab')_2,进而还原成Fab',后者与辣根过氧物酶(HRP)交联成Fab'-HRP,再利用这两种复合物建立了各自的高灵敏夹心ELISA来免疫定量L及M_2型(与鼠M_1-Pyk有交叉免疫)Pyk,结果发现:正常人肝中95％的Pyk为L型,M_2-Pyk仅占5％,而肝细胞癌中L-Pyk降至正常肝的3.5％,M_2-Pyk却增至正常的14.6倍,以致M_2-Pyk占总量的95.5％。免疫组化研究进一步证实定量的结果,正常人肝L-Pyk染色呈强阳性。M_2-Pyk染色较弱,而肝细胞癌恰好相反,L-Pyk染色明显减退,而M_2-Pyk不仅癌组织染色很深,癌周组织也明显深于正常,而且愈近癌巢,染色愈深。测定血浆Pyk,发现正常人L-Pyk占89.9％,M-Pyk(以M_2计)仅占10.1％。肝细胞癌患者血浆L-Pyk略见降低,为正常值的79.6％,p值在0.02～0.05之间,但血浆M型Pyk明显升高至正常的4.59倍,占Pyk总量的39.6％,并证明主要来源于肝癌组织中的M_2,故M_2-Pyk有可能成为肝细胞癌诊断的新指标。     

嗜酸乳杆菌表层蛋白提取方法及影响因素的研究

对嗜酸乳杆菌S层蛋白的提取方法进行了改进．用酸性5mol／L LiCl法,中性5mol／L LiCl法和8mol／L尿素法提取嗜酸乳杆菌的表层蛋白,考马斯亮兰法测蛋白浓度,进行常规SDS-PAGE,用Gel—Pro软件进行数据分析,得出其中酸性5mol／L LiCl法提取表层蛋白百分含量最多．分析影响提取条件的因素,设置0、4、室温（25℃）3个温度梯度和10、15、20、25、30min 5个时间梯度,进行常规SDS-PAGE,检测提取表层蛋白的效果．Sephadex G-100柱分离中性5mol／L LiCl法和8mol／L尿素法提取嗜酸乳杆菌的表层蛋白获得SA蛋白．酸性5mol／L LiCl法可用于分析各种表层蛋白;中性5mol／L LiCl法和8mol／L尿素法用于提取43kDa的SA蛋白．25℃处理15min得到最大量的表层蛋白．     

Covalent vs. Non‐Covalent Inhibition: Tackling Drug Resistance in EGFR – A Thorough Dynamic Perspective

A persistent challenge in the treatment of non‐small cell lung cancer (NSCLC) with EGFR is the emergence of drug‐resistant caused by somatic mutations. The EGFR L858R/T790 M double mutant (EGFR^DM) was found to be the most alarming variant. Despite the development of a wide range of inhibitors, none of them could inhibit EGFR^DM effectively. Recently, 11h and 45a , have been found to be potent inhibitors against EGFR^DM through two distinctive mechanisms, non‐covalent and covalent binding, respectively. However, the structural and dynamic implications of the two modes of inhibitions remain unexplored. Herein, two molecular dynamics simulation protocols, coupled with free‐energy calculations, were applied to gain insight into the atomistic nature of each binding mode. The comparative analysis confirmed that there is a significant difference in the binding free energy between 11h and 45a (ΔΔG_bind=?21.17 kcal/mol). The main binding force that governs the binding of both inhibitors is vdW, with a higher contribution for 45a . Two residues ARG841 and THR854 were found to have curtailed role in the binding of 45a to EGFR^DM by stabilizing its flexible alcohol chain. The 45a binding to EGFR^DM induces structural rearrangement in the active site to allow easier accessibility of 45a to target residue CYS797. The findings of this work can substantially shed light on new strategies for developing novel classes of covalent and non‐covalent inhibitors with increased specificity and potency.     

Specific recognition in the tertiary structure of β-sheets of proteins

The frequency of occurrence of nearest neighbour residue pairs on adjacent antiparallel (β_A) and parallel (β_P) strands is obtained from 30 known protein structures. The specificity of interstrand recognition due to such pairing as a factor in the folding of β-sheets is studied by statistical methods. Residues of sufficiently high count for statistical analysis are treated individually while the rest are combined into small groups of similar size, polarity, and/or genetic exchangeability. The hypothesis of specific recognition between individuals and small groups is contrasted with the alternative hypothesis of non-specific recognition between broad classes (hydrophobia, neutral, polar) of residues. A χ² test of pair correlations favours specific recognition against non-specific recognition with a high level of confidence. The largest and most significant correlations are: Ser/Thr (1.9 ± 0.3), Ile/Val (1.7 ± 0.3) and Lys-Arg/Asp-Gln (1.8 ± 0.3) in β_A, and Ile/Leu (1.9 ± 0.4) in β_P. The pair Gly/Gly never occurs in any β-sheet. The specific residue-pair correlations derived here may be useful in statistical prediction methods of protein tertiary structure.     

Production of enantiomerically pure (S)-phenyl(pyridin-2-yl)methanol with Lactobacillus paracasei BD101

Abstract

Asymmetric reduction studies of heteroaryl ketones, including phenyl(pyridin-2-yl)methanone in enantioselective form with biocatalysts are very few, and chiral heteroaryl alcohols have been synthesized generally in the small scale. In this study, seven bacterial strains have been used to produce the (S)-phenyl(pyridin-2-yl)methanol in high enantiomeric excess and yield. Among the tested strains, Lactobacillus paracasei BD101, was found to be the best biocatalyst for the reducing phenyl(pyridin-2-yl)methanone to the (S)-phenyl(pyridin-2-yl)methanol at gram scale. The asymmetric bioreduction conditions were systematically optimized using L. paracasei BD101, which demonstrated excellent enantioselectivity and high level of conversion for the bioreduction reaction. (S)-phenyl(pyridin-2-yl)methanol, which is an analgesic, was produced enantiomerically pure form in the first time on gram scale using a biocatalyst. In total, 5.857?g of (S)-phenyl(pyridin-2-yl)methanol in enantiomerically pure form (>99% enantiomeric excess) was obtained in 52?h with 93% yield using whole cells of L. paracasei BD101. Enantiomerically pure (S)-phenyl (pyridin-2-yl)methanol, which is an analgesic, was first produced in the gram scale using a biocatalyst with excellent ee (>99%) and yield (93%).     

Characterization of Odorous Compounds in Rotten Blue-green Algae

An ice-nucleating bacterium, strain KUIN-1, was isolated from the leaves of field beans (Phaseolus vulgaris L.). Strain KUIN-1 was identified as Pseudomonas fluorescens from its taxonomical characteristics. Ice-nucleating activity was obtained when strain KUIN-1 was cultured aerobically in a medium containing Koser citrate broth (pH 7.0) for 24 hr at 18°C. The ice- nucleating activity did not appear until the bacterial cell concentration reached 10⁷ to 10⁸/ml. Nucleation at — 3.0°C was detected in suspensions (1.8 × 10⁹ cells/ml) of cells that had been grown on the medium containing Koser citrate broth. Strain KUIN-1 produced a lower nucleation frequency (i.e. the number of ice nuclei/cell) than did ice-nucleating Pseudomonas syringae No. 31 suspensions, particularly at temperatures above — 5°C. The nucleation frequency of strain KUIN- 1-suspensions was similar to that obtained for an ice-nucleating Erwinia herbicola No. 26 at — 5°C.     

Modification of isolated α and β chains of human hemoglobin by the metal tetrasulfonated phthalocyanines. Studies on hybrid phthalocyanine-heme intermediates

α and β chains of hemoglobin have been modified with cobalt(II) tetrasulfonated phthalocyanine in place of heme. They display properties very similar to those of iron(II) phthalocyanine modified α and β chains. Mixed together they form tetrameric cobalt(II) phthalocyanine hemoglobin.Incorporation of Co(II)L into α and β globins results in stabilization of the protein structure, which is shown by a marked increase in its helicity content. Cobalt phthalocyanine substituted α and β chains are able to combine reversibly with oxygen giving more stable oxygenated species than their native analogues. The rate of both processes is lower in the case of the modified α chain. Recombination of the phthalocyanine α and β chains with the alternate heme containing chains give tetrameric hybrid hemoglobins. These comprise two phthalocyanine modified subunits and two heme containing subunits. The helicity content of the tetrameric hybrid hemoglobin calculated for one subunit is lower that the arithmetic mean of helicities for its isolated subunits. This suggests a destabilizing chain-chain interaction within the tetramer. Unlike in the separated subunits, oxygen binding by hybrid hemoglobins is irreversible. Deoxygenation by argon bubbling leads to the formation of inactive species which in oxygen atmosphere undergo irreversible oxidation with destruction of the complex.     

Use of microsatellite polymorphisms for paternity exclusion in rhesus macaques (Macaca multatta)

A total of 224 infant rhesus macaques and their dams and potential sires in 11 multimale groups in 2 different specific pathogen free breeding colonies were screened for up to 6 different microsatellite polymorphism using cross-species PCR amplification. Observed and expected success of paternity exclusion analysis (based on gene frequencies of sires and dams in each colony) were computed by individual locus and cumulatively. Greater or less success of PEA than expected was observed at most loci due to the nonrandom distribution of genotypes between sires and dams and among breeding groups at each colony and because genotypes at different loci did not provide completely independent information about parentage. The combined success of PEA using all loci, however, was slightly greater than predicted both with and without assuming knowledge of one parent's (i.e. the dam's) genotype and was far greater than that based on protein coding loci or DNA restriction fragment length polymorphisms.     

The SKS of the KMSKS signature of class I aminoacyl-tRNA synthetases corresponds to the GKT/S sequence characteristic of the ATP-binding site of many proteins

On the basis of protein modification studies and primary structure comparison, we propose that the SKS sequence within the KMSKS signature of the class 1 aminoacyl-tRNA synthetases corresponds to the GKT(or S) sequence considered as a signature of the nucleotide triphosphate-binding site of many proteins.     

Pharmacokinetic data of propranolol enantiomers in a comparative human study with (S)- and (R,S)-propranolol

The pharmacokinetics of (S)-propranolol were compared after the oral administration of a 40 mg dose of the pure enantiomer and an 80 mg dose of a racemic mixture of (R,S)-propranolol. The results of this study indicate that the bioavailability of (S)-propranolol, as expressed by the mean area under the concentration-time curve (AUC) and maximum serum concentration, is lower after 40 mg of the optically pure drug than after the racemic drug.     

Identification of specific binding sites for leukotriene C4 in human fetal lung

Specific leukotriene C₄ (LTC₄) binding sites were identified in membrane preparations from human fetal lung. Specific binding of [³H]-LTC₄ represented 95 percent of total binding, reached steadystate within 10 minutes and was rapidly reversible upon addition of excess unlabeled LTC₄. Binding assays were performed at 4°C under conditions which prevented metabolism of [³H]-LTC₄ (80 mM serineborate, 10 mM cysteine, 10 mM glycine). Under these conditions, greater than 95 percent of the membrane bound radioactivity, as analyzed by high performance liquid chromatography, co-eluted with the LTC₄ standard. Computer-assisted analyses of saturation binding data showed a single class of binding sites with a dissociation constant (K_d) of 26 + 6 nM and a density (B_max) of 84 ± 18 pmol/mg protein. Pharmacological specificity was demonstrated by competition studies in which specific binding of [³H]-LTC₄ was displaced by LTC₄ and its structural analogs with inhibition constants (K_j) of 10 to 30 nM, whereas LTD₄, diastereoisomers of LTD₁, LTE₄ and the end organ antagonist FPL 55712 were 150 to 700 fold less potent competitors than LTC₄. These results provide evidence for specific, reversible, saturable, high affinity binding sites for [³H]-LTC₄ in human fetal lung membranes.     

Conformation of acetylaminofluorene and aminofluorene modified guanosine and guanosine derivatives

Acetylaminofluorene and aminofluorene modified Guo, GMP, d(GpA) and d(ApG) have been studied by circular dichroism and ¹H nuclear magnetic resonance. Aminofluorene modified Guo is preferentially in the $\text{anti}$ conformation and acetylaminofluorene modified Guo in the $\text{syn}$ conformation. It is proposed that the $\text{anti}$ conformation of aminofluorene modified Guo is stabilized by an intra molecular hydrogen bond between the NH group of aminofluorene residue and the 5′-OH group of the sugar. The results on the modified dinucleoside monophosphates are analyzed according to this hypothesis.     

PATCHY CONTRAST OF HABITAT AFFECTS INTRACLONAL DIVISION OF LABOR OF POTENTILLA ANSERINA

 相互连接的克隆植物分株分别处于资源互补性的不同斑块时, 将可能发生形态结构的特化, 以更有效地吸收利用所处斑块中丰富的资源, 形成分株的功能分化, 即克隆内分工。生境的斑块对比度, 作为资源或环境异质性的主要素, 在一定程度上决定克隆内分工的发生状况。该文以鹅绒委陵菜(Potentilla anserina)为材料, 在自然条件下将多组分株对置于不同的斑块对比度处理下, 比较了它们克隆内分工的发生状态, 试图发现分工与斑块对比度的关系, 同时考察在克隆分工过程中分株的可塑性变化及其与分工的关系。该实验的理论假设是: 分株发生分工的程度与分株所处斑块的资源对比度成正相关。研究结果表明, 鹅绒委陵菜分株的高度和叶面积对局部光照环境产生强烈的可塑性反应, 反应的结果是增加了对匮乏的光资源的获取。从分株根冠比和我们提出的分工指数来看, 分工的程度在一定的斑块对比度范围内随斑块对比度的增强而增强, 但到达一个最大值后又迅速降低。鹅绒委陵菜分株之间的分工和结构特化往往滞后于分株对所处局部环境的适应性可塑性变化, 而后者往往在分株之间具有独立性和局部特征。克隆内分工主要依赖于生物量分配的调节而实现, 其发生状态都是分株系统在分工收益、分工代价与分工风险之间权衡的结果, 而这种结果在很大程度上取决于分株所处的斑块对比度。     

Skp2参与HeLa细胞G_2/M周期检查点的调控

具癌基因特性的Skp2在大多数肿瘤组织和肿瘤细胞中异常高表达,它作为SCFSkp2复合物的底物识别亚基调控p27KIP蛋白的稳定性而促进细胞G1/S期转换.为进一步明确Skp2与G2/M周期检查点的关系,在HeLa细胞中过表达Skp2以及通过反义寡核苷酸抑制Skp2表达.结果发现:Skp2能促进细胞周期运转,表现为S期细胞增多和G2/M期细胞减少,其中F-box结构域具有重要的功能意义;反义寡核苷酸抑制Skp2表达后,HeLa细胞发生显著的G2/M期阻滞;MTT检测结果表明,400nmol/L的Skp2的反义寡核苷酸能明显抑制HeLa细胞的增殖活性;Western印迹结果表明,HeLa细胞中Skp2可能通过负调控p21WAF的稳定性来参与G2/M检查点调控,这在用放线菌素D处理HeLa细胞的实验中得到验证.这些结果初步揭示了Skp2参与HeLa细胞G2/M周期检查点调控的分子机制.