POLG1外显子1、3、4、7突变与弱精子症的相关性及其对mtDNA和4977 bp缺失的影响

为了探索POLG1外显子1、3、4、7突变与弱精子症的相关性及对mtDNA序列突变和4 977 bp缺失的影响,按WHO标准收集了120例弱精子症和101例精子活力正常的精液标本,经PCR测序分析POLG1外显子1、3、4、7突变,继而测序检测9例外显子4 c.948 GA突变的弱精子症标本、9例无c.948 GA突变的弱精子症标本和9例正常对照标本的mtDNA全序列,利用巢式PCR技术分析9例c.948 GA突变标本、9例无c.948 GA突变的弱精子症标本和9例对照标本的4 977 bp缺失。结果显示:在120例弱精子症中发现POLG1外显子4 c.948 GA突变9例(7.5%),显著高于对照组(0%,P0.05)。c.948 GA突变组mtDNA全序中突变率与对照组比无统计学差异(P0.05)。作者关注的两组中,突变数有差异的位点累积突变频次突变组显著高于对照组(P0.05),但与无c.948 GA突变的弱精子症标本的累积突变频次比较无统计学意义;突变组mtDNA 4 977 bp缺失率(7/9,77.8%)显著高于对照组(2/9,22.2%,P0.05)和无c.948 GA突变的弱精子症组(2/9,22.2%,P0.05)。以上结果提示,弱精子症的发生可能与POLG1 c.948 GA突变有相关性,弱精子症线粒体DNA某些位点的累积突变率增高,但可能不是POLG1 c.948 GA突变引起;c.948 GA突变可能会增加mtDNA 4 977 bp缺失,从而影响精子线粒体功能,导致精子活动力下降。     

mtATPase6基因变异与弱精子症的相关分析

为了分析mtATPase6基因突变与弱精子症的相关性,按wHO标准收集了27例弱精子症精液标本和28例精子活力正常精液标本,PCR扩增mtATPase6基因,纯化测序,分析mtATPase6基因突变,比较两组突变频率的差异.结合生物信息学工具分析错义突变位点的氨基酸进化保守性及其蛋白质部分三级结构.结果显示:发现了6个未曾报道过的突变位点;弱精子症组mtATPase6基因平均突变率显著高于对照组,可能与弱精子症有一定的相关性.G8584A、A8701G和G9053A三个错义突变可能是多态性位点,其余8个错义突变中的6个具有进化保守性的位点累计突变频率显著高于对照组,这些位点突变可能与弱精子症有关.     

严重寡精症ICSI精子供体的DAZ基因拷贝缺失研究

DAZ基因拷贝缺失与人类的生精障碍有关。为了解中国正常生精男性和ICSI中严重寡精症精子供体DAZ基因拷贝缺失的分布, 探讨DAZ基因拷贝数检测在严重生精障碍精子供体遗传缺陷筛查中的意义, 本研究运用多重PCR和PCR-RFLP技术, 对128例严重寡精症ICSI精子供体和287个正常生精男性的DAZ基因缺失进行了研究。发现DAZ1/DAZ2、DAZ3/DAZ4和全部4个拷贝缺失等3种拷贝缺失类型, 其中全部4个拷贝缺失仅见于严重寡精症患者, 频率为11.7%; DAZ1/DAZ2缺失的频率在严重寡精症患者中显著高于正常男性(9.4% vs 2.8%, P = 0.004); 在严重寡精症患者中DAZ基因拷贝完全缺失与DAZ1/DAZ2缺失的总发生率为21.1%。DAZ3/DAZ4缺失的频率在两组人群中无显著差异(7.0% vs 3.8%, P > 0.05)。这些结果提示, DAZ基因全部拷贝缺失是严重寡精症患者生精障碍的常见遗传病因, 而DAZ1/DAZ2缺失则可能是一种高风险因素。鉴于上述DAZ基因缺失在严重生精障碍精子供体中较高的发生率, 在应用ICSI进行辅助生育前, 建议对严重寡精症的精子供体进行DAZ基因全缺失与DAZ1/DAZ2共缺失筛查, 以评估其男性后代患病的风险。     

KATNAL1 基因突变筛查及其与无精症的相关性分析

目的:探讨男性不育症患者Katnal15基因的一个突变位点与男性不育症的关系及意义。方法:运用聚合酶链反应(PCR)结合琼脂糖凝胶电泳和基因序列分析等方法,对77例原发性男性不育患者以及84名已生育的正常男性进行Katnal1基因筛查。结果:与精子形成的关键基因KATNAL1中1个致病突变位点A236G为的男性精子无力症Katnal1基因筛查的主要候选基因。结论:Katnal1基因蛋白质编码序列区A236G可能是特发性少精无精症的诱发因素之一。临床上对原发性不育患者进行A236G基因突变筛查是十分必要的。     

特发性少精子症和无精子症与Pygo2基因蛋白编码区SNPs的相关性

男性不育常伴随精子数量减少。Pygo2基因在染色质重塑的伸长精细胞中表达, 其功能受损会导致精子形成阻滞和精子生成减少而引发不育。文章旨在检测引起人特发性少精子症和无精子症的Pygo2基因突变。从77例正常生育力男性和195例特发性少精子症和无精子症患者静脉血提取DNA, 采用聚合酶链式反应-测序方法对Pygo2基因3个蛋白质编码区进行测序对比, 非同义单核苷酸多态性(Single nucleotide polymorphisms, SNPs)位点分别用SIFT、Polyphen-2和 Mutation Taster软件进行诱发蛋白质结构和表型改变的检测和分析。结果表明, 195例患者中, 178例(30例轻度或中度少精子症, 57例重度少精子症和91例无精子症)基因序列分析报告完好, 无精子症中3例患者分别在2个位点(rs61758740, rs141722381)发生了非同义突变SNPs, 重度少精子症中1例患者在位点rs61758741发生了非同义突变, 3个突变位点在SNPs基因数据库都已有报道, 轻度或中度少精子症患者以及正常生育力男性中不存在SNPs。rs61758740可使PYGO2蛋白第141位蛋氨酸(M)变为异亮氨酸(I), rs61758741使PYGO2蛋白第261位碱性赖氨酸(K)变为酸性谷氨酸(E), rs141722381使PYGO2蛋白第240位亲水侧链天冬酰胺(N)变为疏水侧链异亮氨酸(I)。软件分析表明, 在所发现的3个SNP非同义突变位点中, rs141722381引起的单个氨基酸改变会导致PYGO2蛋白空间结构破坏和诱发相关疾病。因此, Pygo2基因蛋白质编码序列区SNPs可能是特发性少精子症和无精子症的诱发因素之一, 导致男性不育。     

mt ND2基因多态性与弱精子症的相关性分析

为了探讨线粒体ND2(mt ND2)基因多态性与弱精子症的相关性,按WHO标准收集了134例弱精子症和1 12例精子活力正常的精液标本,PCR测序或双向等位基因PCR(Bi-PASA)技术分析ND2基因多态性,统计ND2基因4个位点多态性在两组间的差异。应用变性高效液相色谱(DHPLC)分析m.5442TC和m.5466AG多态性变异的异质性。结果发现了34个变异位点,其中6个位点未曾报道;ND2基因m.5351AG、m.5460GA和m.5466AG变异率弱精子症组显著高于对照组(P0.05),m.5442TC变异率对照组显著高于弱精子症组(P0.05);进一步分析m.5460GA和m.5466AG突变阳性标本精子活力显著低于突变阴性标本(P0.001),m.5442TC突变阳性标本精子活力显著高于突变阴性标本(P0.001)。提示:ND2基因一些核苷酸变异(m.5351AG、m.5460GA和m.5466AG)可能与弱精子症有关,m.5460GA和m.5466AG错义突变可能是精子活力的有害因素,而m.5442TC多态性可能对精子活力具有一定的帮助。     

POLG1外显子1、3、4、7突变与弱精子症的相关性及其对mtDNA和4977bp缺失的影响

为了探索POLG1外显子1、3、4、7突变与弱精子症的相关性及对mtDNA序列突变和4977bp缺失的影响,按WHO标准收集了120例弱精子症和101例精子活力正常的精液标本,经PCR测序分析POLG1外显子1、3、4、7突变,继而测序检测9例外显子4c．948G〉A突变的弱精子症标本、9例无C．948G〉A突变的弱精子症标本和9例正常对照标本的mtDNA全序列,利用巢式PCR技术分析94Pie．948G〉A突变标本、9例无C．948G〉A突变的弱精子症标本和9例对照标本的4977bp缺失。结果显示：在120例弱精子症中发现P说G,外显子4c．948G〉A突变9例（7．5％）,显著高于对照组（0％,P〈0．05）。c．948G〉A突变组mtDNA全序中突变率与对照组比无统计学差异俨〉0．05）。作者关注的两组中,突变数有差异的位点累积突变频次突变组显著高于对照组俨〈0．05）,但与无C．948G〉A突变的弱精子症标本的累积突变频次比较无统计学意义;突变组mtDNA4977bp缺失率（7／9,77．8％）显著高于对照组（2／9,22．2％,P〈0．05）和无c．948G〉A突变的弱精子症组（2／9,22．2％,P〈0．05）。以上结果提示,弱精子症的发生可能与POLG,c．948G〉A突变有相关性,弱精子症线粒体DNA某些位点的累积突变率增高,但可能不是POLGlc．948G〉A突变引起;c．948G〉A突变可能会增加mtDNA4977bp缺失,从而影响精子线粒体功能,导致精子活动力下降。     

不明原因男性不育人群中睾丸特异性乳酸脱氢酶基因突变的发现及其意义

为了研究睾丸特异性乳酸脱氢酶,即乳酸脱氢酶C4(LDH-C4)基因突变在男性不育发病中的作用,利用LDH-C4特异性底物对100名不明原因男性不育症患者的精子LDH-C4进行活性显色,用变性高效液相色谱(DHPLC)技术对LDH-C4活性低下的患者进行LDHC基因PCR产物的突变筛查,对DHPLC峰形异常的PCR产物进行序列测定.筛选到一组精子LDH-C4活性明显下降的患者,其中1名患者的LDHC基因PCR产物在DHPLC中呈异常洗脱峰.对这一PCR产物进行序列测定,发现患者LDHC基因第5外显子的115位碱基发生了T→A的杂合改变(GenBank登录号GU479375),该突变使LDHC基因的178位密码子由原来的TTG(编码亮氨酸)变为TAG(终止密码子),形成截短的C亚基.T克隆-测序进一步证实了该无义突变的杂合状态.这是在人类LDHC基因上发现的第一个突变,提示LDHC基因突变可能是男性不育发病的原因之一.     

PCR-RFLP和PCR-SSCP方法对弱精子症精子mtATPase6基因突变的检测

为了检测弱精子症精子mtATPase6基因突变,采用PCR方法扩增了17例弱精子症mtDNA8602～9416区域815bp目的片段,用MspI和HaeⅢ限制性内切酶酶切,分别用琼脂糖凝胶电泳、聚丙烯酰胺凝胶电泳和单链构像多态性(SSCP)筛查突变。筛选出3例突变标本,经测序确认突变位点和突变性质。结果显示17例标本全部扩增出mtDNA8602～9416的815bp目的片段,PCR产物经MspI限制性内切酶酶切后电泳结果与剑桥序列预期酶切图谱相一致。PCR产物经HaeⅢ酶切,聚丙烯酰胺凝胶电泳图谱上出现泳动带的异常,在17例弱精子症中共筛选出2例酶切片段异常标本。PCR-HaeⅢ酶切产物的SSCP电泳图谱分析结果显示,在PCR-RFLP(HaeⅢ)电泳图谱正常的15例弱精子症标本中筛选出1例异常。两种方法在弱精子症精子标本中筛选出mtATPase6基因突变3例(3/17,17.7%)。3例测序结果发现A8701G、C8943T、C8964T、T8966C、G9053A、C9060A、C9075T、A9120G、C9296T共9个点突变,其中A8701G、T8966C、G9053A三个突变为错义突变,其余均为同义突变。上述结果提示,弱精子症精子mtATPase6基因存在较高突变率;PCR-RFLP和PCR-SSCP能简单、快速、灵敏地筛选mtATPase6基因突变。     

FKBP6基因单核苷酸多态性与原发性无精症相关研究

目的:对Fkbp6基因的编码外显子进行突变和多态性分析,初步探讨其与原发性无精症相关性。方法:运用聚合酶链反应(PCR)结合琼脂糖凝胶电泳和基因序列分析等方法,对65例原发性男性不育患者以及96名已生育的正常男性进行了Fkbp65基因的外显子区域序列分析。结果:基因FKBP6中1个突变位点T141G在无精症患者和正常生育男性中的基因多态性可能是特发性少精无精症的诱发因素之一。因此临床上对原发性不孕不育患者进行FKBP6基因突变筛查是十分必要的。     

Quantitative evaluation of smooth pursuit eye movements by personal computer. I) Normative data and effect of aging

We recorded the smooth pursuit eye movements (SPEM) of 52 healthy subjects by binocular electrooculographic technique. The 52 subjects were homogeneously distributed from the 2nd to the 6th decade. The target moved over 60 deg of amplitude at constant velocity (ramp); different target velocities were used ranging from 10 to 50 deg/sec. All subjects were tested with the same 58 pseudo-random ramp sequence under the control of a Personal Computer (PC). The quantitative analysis of SPEM was carried out by an interactive program implemented on the same PC. Different equations were tested by a multiple regression analysis in order to describe the relationship between SPEM gain values and target velocities; two of these equations were chosen and used in order to find out if SPEM gain was influenced by target direction (the direction effect) and/or by subject age (the age effect). The statistical analyses we performed, demonstrated that SPEM gain values were influenced by aging but not by target direction: SPEM gain decreased as age increased.     

Single‐nucleotide polymorphism c.474G>A in the SEPT12 gene is a predisposing factor in male infertility

SEPT12 is a testis‐specific gene involved in the terminal differentiation of male germ cells. SEPT12 protein is required for sperm head‐tail formation and acts as a fundamental constituent of sperm tail annulus. In this study, we screened genetic variations in exons 5, 6, 7 of the SEPT12 and assessed the annulus status in teratozoospermic, globozoospermic, and patients with immotile short tail sperm. DNA sequencing was performed for 90 teratozoospermic and 30 normozoospermic individuals. Immunocytochemistry, transmission electron microscopy and western blotting were conducted to evaluate annulus status and the expression level of SEPT12 in patients with a distinct exonic variation (c.474G>A), respectively. Five polymorphisms identified within the desired regions of the SEPT12, among them c.474G>A had the potential to induce aberrant splicing results in the expression of a truncated protein. The annulus was detected in most of the spermatozoa from teratozoospermic and normozoospermic men with c.474G>A. In contrast, in the patient with short tail sperm defect carrying c.474G>A, 99% of spermatozoa were devoid of the annulus. Based on our findings there would be no association between exons 5, 6, 7 polymorphisms of the SEPT12 gene and the occurrence of mentioned disease but c.474G>A would be a predisposing factor in male infertility.     

An S-System Parameter Estimation Method (SPEM) for biological networks

Advances in experimental biology, coupled with advances in computational power, bring new challenges to the interdisciplinary field of computational biology. One such broad challenge lies in the reverse engineering of gene networks, and goes from determining the structure of static networks, to reconstructing the dynamics of interactions from time series data. Here, we focus our attention on the latter area, and in particular, on parameterizing a dynamic network of oriented interactions between genes. By basing the parameterizing approach on a known power-law relationship model between connected genes (S-system), we are able to account for non-linearity in the network, without compromising the ability to analyze network characteristics. In this article, we introduce the S-System Parameter Estimation Method (SPEM). SPEM, a freely available R software package (http://www.picb.ac.cn/ClinicalGenomicNTW/temp3.html), takes gene expression data in time series and returns the network of interactions as a set of differential equations. The methods, which are presented and tested here, are shown to provide accurate results not only on synthetic data, but more importantly on real and therefore noisy by nature, biological data. In summary, SPEM shows high sensitivity and positive predicted values, as well as free availability and expansibility (because based on open source software). We expect these characteristics to make it a useful and broadly applicable software in the challenging reconstruction of dynamic gene networks.     

Altered velocity processing in schizophrenia during pursuit eye tracking

Smooth pursuit eye movements (SPEM) are needed to keep the retinal image of slowly moving objects within the fovea. Depending on the task, about 50%-80% of patients with schizophrenia have difficulties in maintaining SPEM. We designed a study that comprised different target velocities as well as testing for internal (extraretinal) guidance of SPEM in the absence of a visual target. We applied event-related fMRI by presenting four velocities (5, 10, 15, 20°/s) both with and without intervals of target blanking. 17 patients and 16 healthy participants were included. Eye movements were registered during scanning sessions. Statistical analysis included mixed ANOVAs and regression analyses of the target velocity on the Blood Oxygen Level Dependency (BOLD) signal. The main effect group and the interaction of velocity×group revealed reduced activation in V5 and putamen but increased activation of cerebellar regions in patients. Regression analysis showed that activation in supplementary eye field, putamen, and cerebellum was not correlated to target velocity in patients in contrast to controls. Furthermore, activation in V5 and in intraparietal sulcus (putative LIP) bilaterally was less strongly correlated to target velocity in patients than controls. Altered correlation of target velocity and neural activation in the cortical network supporting SPEM (V5, SEF, LIP, putamen) implies impaired transformation of the visual motion signal into an adequate motor command in patients. Cerebellar regions seem to be involved in compensatory mechanisms although cerebellar activity in patients was not related to target velocity.     

Association of Neuregulin 1 rs3924999 genotype with antisaccades and smooth pursuit eye movements

Neuregulin 1 (NRG1) has been identified as one of the leading candidate genes for schizophrenia. However, its functional mechanisms and its effects on neurocognition remain unclear. In this study, we used two well‐established oculomotor endophenotypes, the antisaccade (AS) and smooth pursuit eye movement (SPEM) tasks, to investigate the functional mechanisms of a single nucleotide polymorphism (SNP) in NRG1 (rs3924999) at the neurocognitive level in a healthy volunteer sample. A total of 114 healthy Caucasian volunteers completed genotyping for NRG1 rs3924999 and infrared oculographic assessment of AS and SPEM (at target velocities of 12°, 24° and 36° per second). Additionally, self‐report questionnaires of schizotypy, neuroticism, attention deficit hyperactivity and obsessive‐compulsive traits were included. A significant effect of rs3924999 genotype, with gender as a covariate, was found for AS amplitude gain (P < 0.01), with an increasing number of A alleles being associated with increasingly hypermetric performance. No statistically significant associations were found for other AS and SPEM variables or questionnaire scores. These findings indicate that NRG1 rs3924999 affects spatial accuracy on the AS task, suggesting an influence of the gene on the neural mechanisms underlying visuospatial sensorimotor transformations, a mechanism that has been previously found to be impaired in patients with schizophrenia and their relatives.     

Quantitative analysis of smooth pursuit eye movements by personal computer. II. Evaluation of individual performance and clinical applicability

In a previous report on quantitative analysis of smooth pursuit eye movements (SPEM) we assessed two equations in order to describe the SPEM gain/target velocity relationship, and we demonstrated that this relationship is age-related. This report presents a method to evaluate normality of a single subject SPEM performance. Three points have been considered: 1) The control of gain asymmetries depending on target direction (leftward vs rightward SPEM) 2) The definition of age-related control values 3) The subject vs control values comparison An example to explain how our method actually works and its clinical applicability is shown. Finally, the reasons why no choice has been made between the two equations are discussed.     

Testicular testosterone: Estradiol ratio in domestic cats and its relationship to spermatogenesis and epididymal sperm morphology

The phenomenon of teratozoospermia in felids is not fully understood. In this study, we investigated the testicular androgen:estrogen balance in domestic cats and correlated these data with epididymal sperm morphology and the degree of spermatogenic activity. During spring and summer, testes and blood samples were obtained from 37 mixed-breed domestic cats (12 to 48 mo). The epididymal sperm were harvested and evaluated for sperm counts, motility, and morphology. Distal cytoplasmic droplets were not considered a defect, and samples were considered normozoospermic if they contained more than 60% normal sperm (N = 25) or teratozoospermic if they contained less than 45% normal sperm (N = 12). The testicular and serum concentrations of testosterone (T) and 17β-estradiol (E2) were determined with an enzyme immunoassay. The gonadosomatic index and epididymal sperm numbers and motility did not differ between groups. The percentage of normal sperm was higher in normozoospermic (74.3 ± 2.0, mean ± SEM) than in teratozoospermic samples (43.1 ± 1.4). The most prevalent sperm defects in the teratozoospermic group were abnormal acrosomes (9.7 ± 2.0) and bent midpieces (12.2 ± 2.0) or tails (24.0 ± 2.7) with cytoplasmic droplets. Histomorphometric data were similar between groups, although there was a lower Leydig cell nuclear volume in teratozoospermic samples. Normozoospermic samples contained a higher percentage of haploid cells and had a higher index of total spermatogenic transformation than teratozoospermic samples. Serum concentrations of T (0.5 ± 0.1 vs. 0.8 ± 0.4 ng/mL) and E2 (9.5 ± 1.2 vs. 11.4 ± 2.3 pg/mL) and testicular T concentrations (471.6 ± 65.3 vs. 313.4 ± 57.6 ng/g) were similar between groups. However, compared with normozoospermic samples, teratozoospermic samples had higher testicular E2 concentrations (8.5 ± 3.6 vs. 5.4 ± 0.5 ng/g) and a lower T:E2 ratio (31.8 ± 4.1 vs. 87.2 ± 11.6). There were significant correlations between testicular E2 values and percentages of normal sperm (r = −0.55) as well as those with primary sperm defects (r = 0.58) or abnormal acrosomes (r = 0.64). The T:E2 ratio was also correlated with meiotic index (r = 0.45) and percentage of normal sperm (r = 0.58). In conclusion, a high testicular E2 concentration and a reduced T:E2 ratio were significantly associated with higher ratios of abnormal sperm types, suggesting that the balance between androgens and estrogens is an important endocrine component in the genesis of teratozoospermia in felids.     

Gli1 Deletion Prevents Helicobacter-Induced Gastric Metaplasia and Expansion of Myeloid Cell Subsets

Chronic inflammation in the stomach induces metaplasia, the pre-cancerous lesion that precedes inflammation-driven neoplastic transformation. While Hedgehog signaling contributes to the initiation of some cancers, its role in gastric transformation remains poorly defined. We found that Helicobacter-infected C57BL/6 mice develop extensive mucous cell metaplasia at 6 month but not at 2 months post-infection. Gastric metaplasia coincided with the appearance of CD45⁺MHCII⁺CD11b⁺CD11c⁺ myeloid cells that were normally not present in the chronic gastritis at 2 months. The myeloid regulatory gene Schlafen-4 was identified in a microarray analysis comparing infected WT versus Gli1 null mice and was expressed in the CD11b⁺CD11c⁺ myeloid population. Moreover this same population expressed IL-1β and TNFα pro-inflammatory cytokines. By 6 months, the mucous neck cell metaplasia (SPEM) expressed IL-6, phosphorylated STAT3 and the proliferative marker Ki67. Expression was not observed in Gli1 mutant mice consistent with the requirement of Gli1 to induce this pre-neoplastic phenotype. Ectopic Shh ligand expression alone was not sufficient to induce SPEM, but with Helicobacter infection synergistically increased the histologic severity observed with the inflammation. Therefore Hedgehog signaling is required, but is not sufficient to generate pre-neoplastic changes during chronic gastritis. Gli1-dependent myeloid cell differentiation plays a pivotal role in the appearance of myeloid cell subtypes ostensibly required for SPEM development. Moreover, it suggests that therapies capable of targeting this phenotypic switch might prevent progression to metaplasia, the pre-neoplastic change that develops prior to dysplasia and gastric cancer, which also occurs in other epithelial-derived neoplasias initiated by chronic inflammation.     

Altered metaplastic response of waved-2 EGF receptor mutant mice to acute oxyntic atrophy

Metaplastic cell lineages are putative precursors for the development of gastric adenocarcinoma. The loss of parietal cells (oxyntic atrophy) is the initiating step in the evolution of gastric fundic mucosal lineage changes including metaplasia and hyperplasia. However, the intrinsic mucosal factors that promote and modulate the emergence of metaplastic phenotypes remain obscure. Over the past several years, we have studied pharmacologically induced, reversible oxyntic atrophy in rodents treated with DMP-777, a drug that acts as a parietal cell secretory membrane protonophore. DMP-777 elicits a rapid loss of parietal cells followed by the emergence of foveolar hyperplasia and spasmolytic polypeptide (SP)-expressing metaplasia (SPEM). The objective of the present study was to provide further insights into the intrinsic mucosal factors regulating the emergence of SPEM in the setting of oxyntic atrophy. We therefore studied the effects of DMP-777 administration on both SP/trefoil factor (TFF)2-deficient mice, which lack SP/TFF2, a marker of SPEM, and waved-2 mice, which harbor a point mutation in the EGF receptor that attenuates its tyrosine kinase activity. As in wild-type mice, treatment with DMP-777 for 7 days did elicit SPEM in SP/TFF2-deficient mice. These results suggest that SP/TFF2 does not impact on the development of metaplasia after the induction of parietal cell loss. In contrast, waved-2 homozygous mice displayed accelerated SPEM development by 3 days of treatment with DMP-777. These findings indicate that attenuation of EGF receptor signaling in waved-2 mice does elicit a more rapid emergence of SPEM. The results support a role for EGF receptor ligands in the regulation of gastric metaplasia.     

SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures

MOTIVATION: Multiple sequence alignment is an essential part of bioinformatics tools for a genome-scale study of genes and their evolution relations. However, making an accurate alignment between remote homologs is challenging. Here, we develop a method, called SPEM, that aligns multiple sequences using pre-processed sequence profiles and predicted secondary structures for pairwise alignment, consistency-based scoring for refinement of the pairwise alignment and a progressive algorithm for final multiple alignment. RESULTS: The alignment accuracy of SPEM is compared with those of established methods such as ClustalW, T-Coffee, MUSCLE, ProbCons and PRALINE(PSI) in easy (homologs) and hard (remote homologs) benchmarks. Results indicate that the average sum of pairwise alignment scores given by SPEM are 7-15% higher than those of the methods compared in aligning remote homologs (sequence identity <30%). Its accuracy for aligning homologs (sequence identity >30%) is statistically indistinguishable from those of the state-of-the-art techniques such as ProbCons or MUSCLE 6.0. AVAILABILITY: The SPEM server and its executables are available on http://theory.med.buffalo.edu.