A modified statistically optimal null filter method for recognizing protein-coding regions

Computer-aided protein-coding gene prediction in uncharacterized genomic DNA sequences is one of the most important issues of biological signal processing.A modified filter method based on a statistically optimal null filter(SONF) theory is proposed for recognizing protein-coding regions.The square deviation gain(SDG) between the input and output of the model is used to identify the coding regions.The effective SDG amplification model with Class I and Class II enhancement is designed to suppress the non-coding regions.Also,an evaluation algorithm has been used to compare the modified model with most gene prediction methods currently available in terms of sensitivity,specificity and precision.The performance for identification of protein-coding regions has been evaluated at the nucleotide level using benchmark datasets and 91.4%,96%,93.7% were obtained for sensitivity,specificity and precision,respectively.These results suggest that the proposed model is potentially useful in gene finding field,which can help recognize protein-coding regions with higher precision and speed than present algorithms.     

Proteins binding to the 5''''-flanking regulatory elements of the human β-globin gene~1

The binding of nuclear proteins prepared from mouse erythroid tissue in different developmental stages to the 5'-flanking regulatory elements of human globin gene, two negative control regions(NCR1, -610 to -490 bp; NCR2,-338 to -233bp), was identified. Two stage specific protein factors corresponding to embryonic and fetal stages were found to be capable of binding to NCR2. These data provided evidence that the cis acting elements of the 5'-flanking region might be involved in the developmental control of globin gene and NCR2 might be responsible in part for the silence of globin gene in the embryonic and fetal stages.     

Polymorphisms in the 5 ′ regulatory region of my-ostatin gene are associated with early growth traits in Yorkshire pigs

Myostatin is a negative regulator of skeletal muscle mass. The present study cloned the 5′ regulatory region of porcine myostatin gene, screened its polymorphisms and analyzed their associations with early growth traits in Yorkshire pigs. The results indicated that a fragment length polymorphism and a polymorphism concerning two nucleotide changes exist in the 5′ regulatory region of porcine my-ostatin gene. At sites 435 and 447, allele A and allele B have the haplotypes of A-G and G-A, respec-tively. The allelic frequency of B is 0.475 in Yorkshire pigs. No homozygous BB genotype was detected in 9 Laiwu Black pigs. Allele B was found to have positive effect on body weight on day 21 (BW21) (P<0.01), body weight on day 28 (BW28) (P<0.05), body weight on day 70 (BW70) (P<0.05), average daily gain from birth to 21 d (ADG1) (P<0.01), average daily gain from birth to 28 d (ADG2) (P<0.05) and av-erage daily gain from 21 d to 70 d (ADG3) (P<0.01), respectively. The additive effect of allele B on BW21, BW28, BW70, ADG1, ADG2 and ADG3 was 0.596±0.205 kg (P=0.0041), 0.498±0.200 kg (P=0.0136), 1.409±0.551 kg (P=0.0112), 28.39±9.74 g P=0.0041), 17.78±7.15 g (P=0.0136) and 37.00±16.92 g (P=0.0304), respectively, whereas its effect on average daily gain from 28 d to 70 d (ADG4) was not significant (P>0.1), although BB individuals are superior in average daily gain to AA and AB.     

Isolation of pea matrix attachment region and study on its function in transgenic tobaccos

A DNA fragment containing consensus sequence of matrix attachment region (MAR) has been isolated from pea genome. Compared with original DNA sequence, one 115 bp-long repeat sequence is deleted in the obtained DNA sequence. DNA fragments located upstream and downstream of repeat DNA sequence respectively share 84% and 93% homology to the corresponding original sequence, and contain A-box or T-box and TATAA sequence, which is characteristics short sequence of MARs. To test the function of the DNA sequence, the plant expression vectors in which β-glucuronidase gene (GUS, uidA) was used as reporter gene were constructed and transferred into tobaccos via Agrobacterium-mediated transformation procedure. Quantitative GUS assay showed that the average level of uidA expression was increased twofold for the presence of MAR, and the highest level of GUS activity of transgenic plants could be increased six times. The results cited above suggest that the isolated DNA sequence contains consensus sequence of MARs and     

Preliminary study on the molecular structure of 3'''' region of Duchenne muscular dystrophy (DMD) gene in Chinese

Number and order of HindⅢ exon-containing fragments (Hd) at 3' region of DMD gene were studied systematically using 16 partly-overlapping cDNA subprobes which were produced from dystrophin cDNA 9- 14 with each of 9 restriction endonudeases. There are 25 Hd fragments corresponding to cDNA 9 -14 in DMD gene. Since then, the exact length and the new order of Hd fragments are established. A new 2.1 kb fragment (Hd 55) is revealed, a 5.2 kb fragment (formely designated as Hd 59) is excluded and the existence of a controversial 3.2 kb fragment (Hd 64) is confirmed. Besides, three new exons were revealed by comparing the PvuⅡ and the XbaⅠ hybridization patterns with the Hindlll hybridization patterns for these cDNA subprobes. It is concluded that there are at least 66 Hd fragments, or 79 exons in DMD gene basing on the discovery of three additional exons. The corresponding relationship between the 66 Hd fragments and the SfiⅠ large scale physical map has been studied, and at least 17 Hd fragments or 19 exo     

Bohaidina(沟鞭藻)古口之新见

在光学显微镜及扫描电镜下对采自辽河断陷西部拗陷的61块岩芯样品中的沟鞭藻Bohaidlna进行了观察,在相当数量的化石囊孢上发现了保存较完好的古口。大量标本的仔细观察和比较研究表明,虽然多数Bohaidina的囊孢上不见古口构造,但确有一定数量的囊孢具前间式古口,2a或3I型。对古口的新认识将有可能导致Bohaidina这类囊孢的重新分类。     

豌豆肌动蛋白异型体的表达与系统发生分析

豌豆(Pisum sativum Linn.)肌动蛋白基因至少可以分为3类异型体: PEAcⅠ、PEAcⅡ和PEAcⅢ,它们的编码区序列相似性很高,而非编码区序列存在显著的差异.RT-PCR和以3′端非翻译区作探针的Southern杂交结果显示豌豆肌动蛋白异型体基因在根、茎、叶、卷须、花粉和幼嫩果实中均表达,但表达强度存在明显差异.利用连续稀释电泳对PEAcⅠ的转录本水平进行分析后发现它倾向于在幼嫩的器官中表达,且在7 d的茎中表达最强;在一个月内的叶片中表达也较强,此后明显下降;卷须中表达变化不显著,在花粉中表达很弱,在幼嫩荚果中的表达亦较多.PEAcⅡ表达特点与PEAcⅠ具有某些相似性.根据肌动蛋白序列重建的系统发生树表明豌豆肌动蛋白3类异型体间的分歧明显,但起源于单、双子叶植物分化前的共同基因祖先.推测豌豆肌动蛋白异型体基因在转录调控和细胞功能上存在差异.     

Species Account of Anura ns from the Western Slope of Mt. Kita nglad,Mindanao Island,Philippines

The Mt. Kitanglad Range is one of the country’s important key biodiversity sites;however, information about anuran diversity in this protected area remains depauperate. Herein we provided accounts of anuran species from high-elevation forests, in three sites of the western slope of Mt. Kitanglad range. The combined belt-transect sampling and microha bitat searches accounted for 13 species representing five families. The most represented family was Rhacophoridae with five representative species of the genus Philautus. Twelve out of the 13 species documented in the current survey are endemic. Four previously unaccounted species(Pelophr yne brevipes, Pulchrana grandocula, Sanguirana mearnsi, and Philautus surrufus) were added and brought the total anurans known from Mt. Kitanglad to 26 species. Most of the species were also recorded in forested sites, suggestive of their lesser affinity to non-forested ecosystems. The additional species detected during our survey may also imply that full understanding of anuran diversity of Mt. Kitanglad remains far from complete.     

斜纹夜蛾核多角体病毒(SpltNPV)基因组EcoR I-G片段的序列分析

斜纹夜蛾核多角体病毒(SpltNPV)基因组EcoR I-G片段全长7 450bp,包括7个开放读码框vp39、lef-4、cg30、p91、vp33、tlp20、AcMNPV ORF81同源基因和一个同源区(hr).基因组排列比较分析发现,这些基因在基因组中的排列,在所有已知序列的杆状病毒中都比较保守.     

中国人α珠蛋白基因3’HVR多态分布的研究

本文以3’HVR为探针,对来自全国17省市的51名无血缘关系的健康人进行P vuⅡ限制性片段长度的多态分析,发现3’HVR在片段大小的变异范围及基因频率的分布均有中国人的特点。结果表明,纯合子占15.7%,杂合子占84 .3%,102个等位基因共有34个长度不同的等位片段,大小从2.0-7.0kb之间呈连续分布, 主要分布在2.0-2.5kb及4.0-6.0kb,频率分别为0.43和0.34。并与刘国仰、余裕炉等的资料进行综合比较,初步揭示了中国人群中3’HVR的多态特点。 Abstract: 51 unrelated Chinese individuals from 17 different provinces and cities were typed for PvuII restiction fragment length polymorphism with the probe 3’HVR.The frequencies of homozygotes and heterozygotes were estimated as 15.7% and 84.3%,34 distinguishable allele sizes showed a continue distribution from 2.0-7.0kb.The main alleles of 2.0-2.5kb and 4.0-6.0kb gave the gene frequencies of 0.43 and 0.34 respectively.The preliminary characteristics of 3’HVR locus in Chinese population were revealed.     

亚热带典型常绿阔叶树种叶片叶绿素含量与其高光谱特征间的关系

叶绿素在植物的生理生态过程中非常重要.利用高光谱数据,揭示光谱反射率上特征光谱与叶绿素含量间的关系将有助于理解叶绿素光谱反射特征的规律.选取了6种亚热带常绿阔叶树种,抽取一定数量的叶片样品,分别测量了叶片的光谱反射率及其叶绿素含量,并建立了光谱反射率曲线上的红边位置附近的光谱反射率和叶绿素总量间的回归模型.结果显示:对所研究的树种而言,红边位置处一窄波长范围内的平均光谱反射率与叶绿素总量间的相关性普遍较高,回归效果显著.从高光谱遥感的角度结合植物的生理生态特点分析了其机理.建立的有关红边位置处的光谱反射率与叶绿素总量间的回归模型普遍具有较高的拟合度,其应用前景较好.     

阜平山区草莓错季栽培的生物表现及适宜区域

通过田间试验和平行观测气象资料,利用地理信息技术和气候要素计算模型,研究了阜平山区种植草莓的生物表现及适宜种植区域.结果表明:在阜平山区种植草莓能够安全越冬、开花、结果,草莓发育期滞后于河北平原,从而达到错季生产的目的;其草莓品质优良,果实中可溶性固形物和维生素C含量均高于河北平原对应的草莓品种;阜平山区错季草莓的适宜发展区域为海拔900～1 200 m的地区.     

太湖河网地区农村非点源氮负荷——以宜兴市大浦镇为例

采用野外试验与实地调查相结合,利用泥沙流失方程和GIS平台,定量估算了江苏宜兴市大浦镇农村非点源氮排放负荷.结果表明:大浦镇农村非点源氮排放负荷为207.0 t·a-1,其中农田、生活污水、养殖、垃圾和非农田泥沙流失的排放负荷分别为80.6、61.1、49.3、10.5和5.4 t·a-1,分别占39.0%、29.5%、23.8%、5.1%和2.6%;5种排放源中,农田、生活污水和养殖为优先控制因子;方钱、大浦、浦北和浦南4村平均氮排放负荷为80.4、73.0、60.4和52.3kg·hm-2·a-1,远高于其他区域,为优先控制区.     

喀斯特峰丛洼地桂牧一号杂交象草对不同追施氮肥水平的响应

利用田间试验,研究了桂牧一号杂交象草对不同氮肥水平的响应.结果表明:3个追施氮肥处理株高、分蘖数、干草产量、粗蛋白含量和可溶性糖含量均高于对照处理;高氮追肥处理株高显著高于对照处理,中氮追肥处理分蘖数和干草产量显著高于对照处理,3个追施氮肥处理粗蛋白和可溶性糖年产量显著高于对照处理;追施氮肥有利于促进桂牧一号杂交象草的生长和营养物质的积累;高氮追肥处理的年净收入低于对照处理;中氮追肥处理为最佳经济施肥量,其年净收入显著高于对照处理.     

天山北坡生态经济的脆弱性

根据脆弱性的理论内涵,以土地利用变化引起的生态系统服务功能变化为影响力;从资源、经济与社会发展水平三方面选取了14个指标,利用层次分析法、模糊综合评价法确定了社会经济系统的适应能力.在此基础上,应用GIS等手段评价了天山北坡15个市、县生态经济的脆弱性.按级数越大,区域越具有脆弱性的原则,将研究区的生态经济脆弱性划分为5级：一级区为乌苏市和昌吉市;二级区包括呼图壁县、米泉县、阜康市、吉木萨尔县、奇台县和木垒县;三级区为克拉玛依市和乌鲁木齐市:四级区为奎屯市和沙湾县;五级区包括精河县、石河子市和玛纳斯县.生态经济系统脆弱性是区域生态环境变化与社会经济发展的综合反映,脆弱性评估是深化可持续发展理论研究的重要途径.各区域应以降低区域脆弱性为目标,从自身脆弱性影响因素入手制定生态经济协调发展策略,以促进区域的可持续发展.     

内蒙古中部地区土壤金龟子群落特征

2003-2004年,采用土壤样方法和粪诱捕法调查了内蒙古中部地区7个不同生境中的土壤金龟子群落特征,并以群落系数、欧氏距离、百分率相似系数和因子分析等方法对不同土壤金龟子群落之间的相似性进行了分析.共计捕获土壤金龟子101 788头,分属于7科22属59种.其中,植食性种类3科12属18种,主要为鳃金龟科和丽金龟科的种类;粪食腐食性种类4科10属41种,主要为金龟科、蜉金龟科和粪金龟科的种类.对几种群落相似性聚类分析方法所得结果的对比表明,因子分析方法所得的结果是较为合理的,因子分析排序的结果将7个土壤金龟子群落分为2类:一类为典型草原、草甸草原、荒漠草原和沙地;另一类为农田、退耕地和人工林地.     

千岛湖库区岛屿面积对植物分布的影响及植物物种多样性保护研究

修建大坝形成水库蓄水是造成景观破碎化的原因和形式之一.本研究选取了浙江千岛湖库区景观破碎化的典型区域小金山林场,调查了74个大小不一的岛屿,研究了面积对植物物种分布的影响,并比较了使物种多样性最大化的几种植物物种保护方案:小岛组合、中岛组合、大岛组合、大中小组合岛.调查共记录到乔木物种56种,灌木物种79种.将岛屿按照面积由大到小排序,将相对应分布的乔木、灌木绘制成植物物种分布表.结果显示:乔木中分布不受面积影响的物种有15种,受面积影响的有11种,介于两者之间的有30种;灌木物种中不受面积影响的有24种,受面积影响的有16种,介于两者之间的有39种.将乔木、灌木和总物种数分别累加,同时将相对应的岛屿面积按不同组合累加,绘制累加物种和面积关系图,发现在特定的相同累加面积下,组合岛的累加乔木、灌木、总物种数最多,小岛组合次之,大岛组合最少.因此,建立相同面积的保护区时,组合岛有利于保护更多的物种.     

CLUE-S模型在南京市土地利用变化研究中的应用

土地利用/覆盖变化模型是研究区域景观动态并解释其驱动机制的重要技术手段.应用CLUE-S模型,在Landsat TM影像等相关数据支持下,对南京地区1998-2006年土地利用的时空动态变化进行了研究.结果表明:各土地利用类型变化受地形因素影响最大,人均GDP与城镇用地和农业用地的分布呈显著相关,城乡主干道对土地利用变化的贡献显著大于省级及以上道路;海拔较高区域林地的发生比率较高,而地形低平区域农田、城建用地的发生比率较高.经检验,在300 m空间分辨率水平,对南京地区2003年、2006年土地利用状况模拟的精度分别达到了85.7%和84.1%;而通过将研究区分成若干子区,分别修正模型参数并重新模拟,准确率提高到89.7%和88.3%,分区赋值法有效地提高了模拟精度.研究表明,CLUE-S模型对城市发展的空间结构也有较强的预测能力,对指导城市规划、分析景观动态的驱动机制有重要参考价值.