Novel PTEN germline mutation in a family with mild phenotype: Difficulties in genetic counseling

PTEN gene (phosphatase and tensin homolog deleted on chromosome ten, MIM 601628) is a tumor suppressor gene implicated in PTEN hamartoma tumor syndromes (PHTS) including Cowden syndrome, Bannayan–Riley–Ruvalcaba syndrome and Proteus-like syndrome. PTEN mutations have been more recently reported in children with macrocephaly and autism spectrum disorders or mental retardation, without other symptoms of PHTS. Although tumor risk has not been evaluated in these patients and their relatives, the same surveillance as for Cowden syndrome is usually proposed. We report a family including patients carrying a novel PTEN mutation and presenting with a mild phenotype consisting of macrocephaly, hypotonia during the first year of life and mild learning disabilities, without autistic features. None of these patients exhibited PTHS-related symptoms such as tumors, lipomas, vascular malformations or pigmented macules of the glans penis. This report raises the question of extending the indications of PTEN mutation screening to familial macrocephaly with learning disabilities. Detection of a mutation in this family led to difficult questions about surveillance, genetic counseling and familial information since the mother declined tumor screening and disclosure of genetic risk information to at-risk relatives.     

Rule extraction in gene–disease relationship discovery

Background

Biomedical data available to researchers and clinicians have increased dramatically over the past years because of the exponential growth of knowledge in medical biology. It is difficult for curators to go through all of the unstructured documents so as to curate the information to the database. Associating genes with diseases is important because it is a fundamental challenge in human health with applications to understanding disease properties and developing new techniques for prevention, diagnosis and therapy.

Methods

Our study uses the automatic rule-learning approach to gene–disease relationship extraction. We first prepare the experimental corpus from MEDLINE and OMIM. A parser is applied to produce some grammatical information. We then learn all possible rules that discriminate relevant from irrelevant sentences. After that, we compute the scores of the learned rules in order to select rules of interest. As a result, a set of rules is generated.

Results

We produce the learned rules automatically from the 1000 positive and 1000 negative sentences. The test set includes 400 sentences composed of 200 positives and 200 negatives. Precision, recall and F-score served as our evaluation metrics. The results reveal that the maximal precision rate is 77.8% and the maximal recall rate is 63.5%. The maximal F-score is 66.9% where the precision rate is 70.6% and the recall rate is 63.5%.

Conclusions

We employ the rule-learning approach to extract gene–disease relationships. Our main contributions are to build rules automatically and to support a more complete set of rules than a manually generated one. The experiments show exhilarating results and some improving efforts will be made in the future.     

Is CD36 gene polymorphism in region encoding lipid-binding domain associated with early onset CAD?

CD36 is a fatty acid translocase in striated muscle cells and cardiomyocytes. Some study suggested that alterations in CD36 gene may be associated with coronary artery disease (CAD) risk. The aim of the current study was to compare the frequency of CD36 variants in region encoding lipid-binding domain in Caucasian patients with early-onset CAD, no-CAD adult controls and neonates. The study group comprised 100 patients with early onset CAD. The genetic control groups were 306 infants and 40 no-CAD adults aged over 70 years. Exons 4, 5 and 6 including fragments of flanking introns were studied using the denaturing high-performance liquid chromatography technique and direct sequencing. Changes detected in analyzed fragment of CD36: IVS3-6 T/C (rs3173798), IVS4-10 G/A (rs3211892), C311T (Thr104Ile, not described so far) in exon 5, G550A (Asp184Asn, rs138897347), C572T (Pro191Leu, rs143150225), G573A (Pro191Pro, rs5956) and A591T (Thr197Thr, rs141680676) in exon 6. No significant differences in the CD36 genotype, allele and haplotype frequencies were found between the three groups. Only borderline differences (p = 0.066) were found between early onset CAD patients and newborns in the frequencies of 591T allele (2.00% vs 0.50%) and CGCGCGT haplotype (2.00% vs 0.50%) with both IVS3-6C and 591T variant alleles. In conclusion, CD36 variants: rs3173798, rs3211892, rs138897347, rs5956, rs143150225 rs141680676 and C311T do not seem to be involved in the risk of early-onset CAD in Caucasian population.     

The relationship between the presence of ADHD and certain candidate gene polymorphisms in a Turkish sample

Due to the high heritability of attention-deficit hyperactivity disorder (ADHD), parents of children with ADHD appear to represent a good sample group for investigating the genetics of the disorder. The aim of this study was to investigate the association between ADHD and six polymorphisms in five candidate genes [5-HT2A (rs6311), NET1 (rs2242447), COMT (rs4818), NTF3 (rs6332), SNAP-25 (rs3746544) and (rs1051312)]. We included 228 parents of children diagnosed with ADHD and 109 healthy parents as the control group. The polymorphisms were genotyped using polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) assays and analyzed using the chi-square test and the multinomial logit model. SNAP-25 (rs3746544) polymorphism was associated with loading for ADHD, while 5-HT2A (rs6311) and NET1 (rs2242447) polymorphisms were associated with ADHD. On the other hand, there was no significant association between the SNAP-25 (rs1051312), NTF3 (rs6332), or COMT (rs4818) gene polymorphisms and ADHD.     

人工管理和自然驱动下盐城海滨湿地互花米草沼泽演变及空间差异

将盐城国家级自然保护区核心区划分为人工管理区和自然湿地区两种模式,根据2000年、2006年、2011年3个时相的ETM+影像,运用RS、GIS技术和景观生态学方法,分析不同驱动力下互花米草沼泽景观变化的差异.结果表明:(1)人工管理区,2000-2011年,互花米草沼泽面积由272hm2增加到781hm2;平均分维数呈下降的趋势,聚合度指数呈上升的趋势,表明互花米草沼泽在空间上趋于聚集,在形状上趋于规则;从互花米草沼泽增长速率看,2000-2011年,呈现先快后慢的特征.在景观空间演变上,互花米草沼泽的平均宽度从598.679m增加到1719.002m,表现出向海陆两个方向扩张的特征.(2)自然湿地区,2000-2011年互花米草沼泽面积由2023hm2增加到3974hm2;平均分维数和聚合度指数呈先上升后下降的趋势;米草沼泽增长稳定,年增长约160-180 hm2/a,单位长度岸线年增长面积约为15 hm2· km-1·a-1左右;比较发现,自然湿地区互花米草沼泽的增长速度高于人工管理区的增长速度.在景观空间演变上,互花米草沼泽平均宽度从1625.586m增加到3193.317m,2000-2006年表现出向海洋单方向扩张的特征,2006-2011年表现出向海陆两个方向扩张的性质.(3)在自然条件下互花米草沼泽扩张受到气候、地貌过程、水文过程、植被类型及种间竞争的影响,表现出明显的带状特征.在人工管理下,通过建设拦水堤坝等,阻止了潮汐作用下海水的扩散能力,生态过程发生改变,致使生态系统类型向淡水湿地方向演变,抑制了互花米草沼泽的扩张,表现出一定的镶嵌格局.     

卧龙巴郎山川滇高山栎群落植物叶特性海拔梯度特征

川滇高山栎林是中国植被非常特殊的亚高山硬叶栎林类型,广泛分布在横断山地区。为了阐明植物群落植物叶型组成对海拔梯度的响应,对卧龙自然保护区巴朗山阳坡川滇高山栎群落植物叶型特征随海拔梯度（15海拔梯度,海拔2200～3600 m）的变化进行了研究。卧龙自然保护区巴朗山各个梯度川滇高山栎群落维管束植物的叶级以小型叶为主,占总种数的平均百分率为36.09％;细型叶和中型叶的维管束植物比例相当,分别为25.64％,25.22％;大型叶和巨型叶维管束植物分别占6.82％～9.94%和0.00％～0.71%;微型叶植物比例在1.28～5.59%;小型叶维管束植物的比例随海拔先降低后升高再降低,最低值出现在海拔3000 m左右。各个海拔梯度川滇高山栎林内维管束植物的叶型以单叶为主,平均占总种数的75.89％,其余为复叶植物,占总种数的24.11％;维管束单叶型植物物种比例随海拔升高变幅较小,在73.84％～78.78％之间,但在海拔2500 m有一个最低值,其比例为73.85％;复叶维管束植物在各海拔梯度群落物种数比例在21.21％～26.15％之间。各海拔川滇高山栎林内维管束植物的叶质以纸叶型为主,平均占总种数的46.03％,其次为薄叶植物（29.17％）,革质（22.00%）和厚革质植物（2.79％）。川滇高山栎群落内纸质与厚革质维管束植物种类的比例随海拔升高而降低;革质与薄叶型维管束植物种类的比例随海拔升高而升高。全缘维管束和非全缘维管束植物种类分别占总数的50.50％和49.50％;全缘类维管束植物随海拔升高呈正二项式分布,而非全缘维管束植物则呈相反的分布格局。     

北京松山自然保护区森林群落物种多样性及其神经网络预测

物种多样性是群落结构和功能复杂性的一种度量,物种多样性的空间分布格局受许多环境因子的影响.运用多样性指数,多层感知器网络,分析了松山保护区森林群落物种多样性与群落类型、结构和生境之间的关系.结果表明:(1)大果榆+山杨混交林、油松+青杨混交林物种丰富度、多样性和均匀度均较高,而大果榆林、华北落叶松林的各项指数值均较低.Patrick指数和Shannon-Weiner指数在森林群落中均表现为草本层＞灌木层＞乔木层;Pielou指数在榆林中表现为草本层＞乔木层＞灌木层,而在其他森林群落中表现为灌木层＞草本层＞乔木层.(2)功能层物种多样性在海拔梯度上的变化趋势不同,在乔木层,丰富度、多样性和均匀度随海拔的升高逐渐降低;在灌木层,丰富度、多样性和均匀度均呈比较明显的单峰曲线变化趋势;在草本层,丰富度和多样性随海拔的升高都呈下降趋势,而在草本层,均匀度变化不大.(3)用多层感知器网络预测功能层多样性效果很好,结果发现坡向对乔木层和灌木层物种多样性的影响最大,而海拔高度对草本层物种多样性的影响最大.     

河漫滩湿地生态阈值——以二卡自然保护区为例

以典型河漫滩湿地 —— 二卡自然保护区为研究区域,进行生态阈值研究。根据湿地补给河流 —— 海拉尔河的月均流量频率分布特征,选取58.72 m³/s(P=74.6%)、119.26 m³/s(P=44.4%)、190.35 m³/s(P=23.8%)分别代表河流的低、中、高径流期,分析各径流期湿地分布特征。结果表明,低、中径流期内草本沼泽及盐化沼泽所占比例较高,而高径流期则以季节性河流湿地及湖泊湿地为主。低径流期内,作为湿地中心区的湖泊湿地景观破碎度出现一个较明显的跃变,由中径流期的0.57增加到1.37。此时的湿地状态可近似的作为区域的生态阈值,即维持湿地面积占全区域面积的43.03%。而中、高径流期湿地面积比例可近似作为保护区湿地面积的适宜值和理想值,分别为53.66%和69.53%。其研究结果为二卡自然保护区的管理及保护提供支持,并为河漫滩湿地研究提供思路。     

内蒙古达赉湖西岸地区大鵟巢穴特征和巢址选择

2010年和2011年3月-6月,对内蒙古达赉湖国家级保护区达赉湖西岸地区大鵟(Buteo hemilasius)的巢穴结构和巢址选择因子进行了调查研究.采用野外观察和样方法定位了13个大鵟巢址,并对巢址样方的20个生态因子进行测量,运用主成分分析法对影响大鵟巢址选择的主要因子进行了分析.测量显示,大鵟巢穴的基本结构特征为:外径(94.7+4.2) cm;巢高度(46.1±2.7) cm;内径(24.8±1.5)cm;巢深(14.0±+0.9)cm.生境因子分析结果表明,达赉湖西岸地区大鵟的巢集中分布在湖岸或水塘附近的悬崖,营巢点坡度为15°-45°之间的阳坡或半阳坡;隐蔽度高于20％;草本密度大于5株/m2;植被均高大于30cm;巢距悬崖上部距离2-5m;距水源l00m以内;距居民点距离大于lkm;距草原道路的距离大于0.5km;而对于物种丰富度没有特殊要求.主成分分析显示,影响大鵟巢址选择的主要因子有3个,依次为:隐蔽性因子(主要包括巢址区域的植物特征和地形特征)、干扰因子和食物因子.各主成分中,相对系数绝对值最高的变量依次是:植被盖度、距居民点距离、巢的高度和距草原道路距离.