SSAHA: a fast search method for large DNA databases

We describe an algorithm, SSAHA (Sequence Search and Alignment by Hashing Algorithm), for performing fast searches on databases containing multiple gigabases of DNA. Sequences in the database are preprocessed by breaking them into consecutive k-tuples of k contiguous bases and then using a hash table to store the position of each occurrence of each k-tuple. Searching for a query sequence in the database is done by obtaining from the hash table the "hits" for each k-tuple in the query sequence and then performing a sort on the results. We discuss the effect of the tuple length k on the search speed, memory usage, and sensitivity of the algorithm and present the results of computational experiments which show that SSAHA can be three to four orders of magnitude faster than BLAST or FASTA, while requiring less memory than suffix tree methods. The SSAHA algorithm is used for high-throughput single nucleotide polymorphism (SNP) detection and very large scale sequence assembly. Also, it provides Web-based sequence search facilities for Ensembl projects.     

Vancomycin-resistant enterococcal bacteremia: comparison of clinical features and outcome between Enterococcus faecium and Enterococcus faecalis.

BACKGROUND AND PURPOSE: Vancomycin-resistant enterococci (VRE) have emerged as important nosocomial pathogens. This study was conducted to clarify the clinical features and outcome of patients with vancomycin-resistant enterococcal bacteremia. METHODS: Patients with vancomycin-resistant enterococcal bacteremia treated at a medical center in northern Taiwan between November 1998 and July 2006 were reviewed. Clinical and bacteriological characteristics of Enterococcus faecium and Enterococcus faecalis were compared. RESULTS: Twelve patients (6 males and 6 females) were included for analyses. The mean age was 69.3 years (range, 40 to 86 years), and 8 cases (66.7%) were older than 65 years. All patients had underlying disease. Two patients received total hip replacement before development of VRE bacteremia. Twelve patients had prior exposure to broad-spectrum antimicrobial therapy. Ten patients had prior intensive care unit stay and prior mechanical ventilation before VRE bacteremia. All of the patients (n = 12) had an intravascular catheter in place. Bacteremia was caused by E. faecalis in 4 patients and by E. faecium in eight. The portals of entry included urinary tract (8.3%), skin, soft tissue and bone (41.7%) and unknown sources (50.0%). E. faecium showed a higher rate of resistance to ampicillin and teicoplanin than E. faecalis (87.5% vs 0.0%, p=0.01). The 60-day mortality rate was higher in patients with E. faecium bacteremia than E. faecalis bacteremia (62.5% vs 0.0%), although statistical significance was not obtained (p=0.08). CONCLUSIONS: VRE bacteremia may have an impact on the mortality and morbidity of hospitalized patients. Patients with bacteremia caused by vancomycin-resistant E. faecium had a grave prognosis, especially immunosuppressed patients. The prudent use of antibiotics and strict enforcement of infection control may prevent further emergence and spread of VRE.     

过继转输胚胎抗原耐受T细胞诱导自然流产孕鼠母胎免疫耐受

探讨过继转输胚胎抗原耐受T细胞对小鼠自然流产模型妊娠预后及宿主孕鼠免疫细胞对父系抗原免疫耐受状态的影响。以CBA/J×BALB/c为正常妊娠模型 ,CBA/J×DBA/ 2为自然流产模型 ,将自然流产模型CBA/J孕鼠于孕 4d (着床期 )分别腹腔注射大鼠抗小鼠CD80和CD86mAb或大鼠同型IgG。于孕 9d ,应用免疫磁珠阴性分选三组孕鼠的脾脏T细胞 ,并将三组T细胞分别转输至孕 4d的CBA/J×DBA/ 2孕鼠。于宿主孕鼠孕第 9天 ,采用单向混合淋巴细胞反应分析宿主孕鼠脾脏免疫细胞对父系抗原的增殖能力 ,并用流式细胞术分析经父系抗原刺激的宿主孕鼠脾脏T细胞内IL 2表达水平。于孕 1 4d分别观察宿主孕鼠的胚胎吸收率。结果显示 ,过继转输胚胎抗原耐受T细胞和转输正常妊娠模型孕鼠的T细胞均可诱导宿主孕鼠脾脏免疫细胞对父系抗原的增殖能力及IL 2的表达显著下降 (P <0 0 5 ) ,孕 1 4d胚胎吸收率也显著下降 (P <0 0 5 )。这些结果表明 ,于孕早期过继转输胚胎抗原耐受T细胞和转输正常妊娠模型孕鼠的T细胞能诱导宿主孕鼠母 胎免疫耐受 ,防止母体对胚胎的免疫排斥 ,从而使自然流产模型的妊娠预后达到正常妊娠水平。     

Experimental determination of the anisotropy function for the model 200 103Pd "light seed" and derivation of the anisotropy constant based upon the linear quadratic model

Since the publication of the AAPM Task Group 43 report in 1995, Model 200 103Pd seed, which has been widely used in prostate seed implants and other brachytherapy procedures, has undergone some changes in its internal geometry resulting from the manufacturer's transition from lower specific activity reactor-produced 103Pd ("heavy seeds") to higher specific activity accelerator-produced radioactive material ("light seeds"). Based on previously reported theoretical calculations and measurements, the dose rate constants and the radial dose functions of the two types of seeds are nearly the same and have already been reported. In this work, the anisotropy function of the "light seed" was experimentally measured and an averaging method for the determination of the anisotropy constant from distance-dependent values of anisotropy factors is presented based upon the continuous low dose rate irradiation linear quadratic model for cell killing. The anisotropy function of Model 200 103Pd "light seeds" was measured in a Solid Water phantom using 1 X 1 x 1 mm micro LiF TLD chips at radial distances of 1, 2, 3, 4, 5, and 6 cm and at angles from 0 to 90 degrees with respect to the longitudinal axis of the seeds. At a radial distance of 1 cm, the measured anisotropy function of the 103Pd "light seed" is considerably lower than that of the 103Pd "heavy seed" reported in the TG 43 report. Our measured values at all radial distances are in excellent agreement with the results of a Monte Carlo simulation reported by Weaver, except for points along and near the seed longitudinal axis. The anisotropy constant of the 103Pd "light seed" was calculated using the linear quadratic biological model for cell killing in 30 clinical implants. For the model 200 "light seed," it has a value of 0.865. However, our biological model calculations lead us to conclude that if the anisotropy factors of an interstitial brachytherapy seed vary significantly over radial distances anisotropy constant should not be used as an approximation for anisotropy characteristics of a brachytherapy seed.     

TRP超家族与肾脏

TRP(Transient receptor potentical)家族是非选择性阳离子通道家族，近来发现其与肾脏关系密切，如调节肾小管离子转运，肾脏微循环等。TRP通道异常可导致遗传性局灶节段硬化性肾病（FSGS），常染色体显性遗传多囊肾(ADPKD)，低镁血症继发低钙血症(HSH)等，对TRP通道的进一步研究将有助于临床肾脏病的防治。     

中晚期重型乙型肝炎血浆置换与内科治疗生存率的比较

观察血浆置换、内科治疗对中晚期重型乙型病毒性肝炎生存率的影响,探索中晚期重型肝炎的治疗方法。方法观察在内科治疗基础上给予血浆置换患者的肝功能、并发症及疾病的转归,与同期仅予内科综合治疗的患者相比较,对相应的临床资料进行统计学分析,从而了解两种治疗方法的疗效。结果血浆置换组36例,18例好转、18例死亡,内科治疗组32例,13例好转、19例死亡,两组之间患者生存情况无统计学差异;肝功能指标(ALT、AST、SB、ALB、TC、ChE和凝血酶原时间(PT)也无统计学差异。结论与内科治疗相比较,在其基础上给予血浆置换并不能提高中晚期重型病毒性肝炎生存率;中晚期重型肝炎患者的预后决定于其肝功能衰竭的程度。     

Fas cDNA克隆、表达及重组蛋白纯化的研究

目的:获得高质量及充足的Fas重组蛋白。方法:采用PCR构建表达重组质粒,亲和层析纯化Fas重组蛋白,ELISA检测其免疫学功能。结果:①PCR扩增获得目的片段约 470 bp。②Sanger双脱氧链终止法测序表明,该 DNA序列仅 174位由A→G突变,属于同义突变,与已知的Fas膜外区氨基酸完全一致。③重组质粒经IPTG诱导有一蛋白得以表达,其目的融合蛋白占细菌总蛋白的17. 4%,分子量约为 34．3 kD。④经 Factor Xa切割 Fas融合蛋白,纯化获得 Fas重组蛋白,Western印迹出现特异性Fas蛋白带,分子量为21．3kD,与预测结果相吻合。⑤ELISA检测 Fas重组蛋白,具有抗体的免疫学活性。结论:成功地表达并纯化了Fas重组蛋白,解决了Fas不易获得的难题,为研究Fas提供了良好的实验材料。     

Cariporide对兔心房电重构的影响

目的：探讨钠氢交换体Ⅰ型(NHE-1)特异性抑制剂cariporide对快速起搏所致兔心房电重构的影响。 方法： 30只兔随机等分为3组：对照组、起搏组和cariporide组。起搏组和cariporide组给予6 h 600 beats/min的快速心房起搏。测定各组不同时点的心房有效不应期（AERP200，AERP150，AERP130），连续刺激6 h后取左右心耳组织，用Western blotting测定NHE-1的含量。 结果： 在快速起搏后1 h后，起搏组的AERP200较起搏前明显缩短，2 h时达高峰，相对缩短量为（15.63±9.04）ms，而对照组和cariporide组AERP未发生明显变化，起搏2h时相对缩短量为(1.43±2.44)ms和(1.43±6.90)ms（P<0.05，与起搏组相比），这些变化一直保持至快速起搏后6 h；起搏组的AERP频率适应性下降, 起搏前AERP130较AERP200缩短(11.88±15.57)ms，起搏后6 h只缩短(4.38±5.63)ms。而cariporide组的AERP频率适应性则未发生显著变化。起搏组右心耳组织的NHE-1含量显著少于对照组（P<0.05），cariporide组的右心耳组织NHE-1含量与对照组差异不显著。 结论： Cariporide可有效阻止快速心房起搏引起的AERP缩短，但不影响起搏引起的NHE-1含量的下降。     

CTT triplex系统各基因座位等位基因在葡萄胎基因组中的分布及其意义

我们对采用PCR和聚丙烯酰胺凝胶电泳鉴别出的37例DNA完全来自父方的遗传学完全性葡萄胎(g-CHM)进行基因组中CTTtriplex系统各基因座位(CSF1PO、TPOX和TH01)等位基因分布的分析,并初步研究了这些等位基因分布与临床预后的关系。结果显示,在37例g-CHM中,CSF1PO座位中3个等位基因(11,12和14)和TPOX座位中的1个等位基因(11)的出现率与它们在北京地区人群中的基因频率差异显著;g-CHM中CSF1PO、TPOX和TH01基因座位杂合度显著低于北京地区人群的杂合度(P值均远小于0.01);在23例良性g-CHM和10例侵袭性g-CHM中:CSF1PO座位的等位基因10、11在良性中的出现率高于在侵袭性g-CHM中(P=0.026148),等位基因12在良性中的出现率低于在侵袭性g-CHM中(P=0.023879);TPOX座位的等位基因8在良性中的出现率高于在侵袭性g-CHM中(P=0.004322),而等位基因11在良性中的出现率低于其在侵袭性g-CHM中(P=0.008671)。上述结果提示,葡萄胎基因组中存在某些等位基因分布与在人群中的分布不同,而且葡萄胎是否具有侵袭性也和某些等位基因的出现率过高或过低有相关性,这些与侵袭性有关的等位基因可能成为预测葡萄胎是否具有侵袭性的标志物。     

以傅立叶频谱滤波为手段的振荡电位波形分离方法

为克服传统方法(Calliper-square)和带通放大器在测量振荡电位(OPs)中的不足,应用计算机傅立叶频谱滤波技术,从ERG中分离出振荡电位波形。分离出的OPs能够摆脱a-波,b-波对它的影响而独立地表现出来,使得对OPs的测量变得直观、方便、准确,并把对ERG、OPs的研究,从时域分析扩展到频域分析。