Exact and heuristic algorithms for the Indel Maximum Likelihood Problem.

Given a multiple alignment of orthologous DNA sequences and a phylogenetic tree for these sequences, we investigate the problem of reconstructing the most likely scenario of insertions and deletions capable of explaining the gaps observed in the alignment. This problem, that we called the Indel Maximum Likelihood Problem (IMLP), is an important step toward the reconstruction of ancestral genomics sequences, and is important for studying evolutionary processes, genome function, adaptation and convergence. We solve the IMLP using a new type of tree hidden Markov model whose states correspond to single-base evolutionary scenarios and where transitions model dependencies between neighboring columns. The standard Viterbi and Forward-backward algorithms are optimized to produce the most likely ancestral reconstruction and to compute the level of confidence associated to specific regions of the reconstruction. A heuristic is presented to make the method practical for large data sets, while retaining an extremely high degree of accuracy. The methods are illustrated on a 1-Mb alignment of the CFTR regions from 12 mammals.     

酵母转录因子PHO81基因的上游序列功能分析

利用ＰＨＯ８１ｌａｃＺ融合基因,对它的上游进行缺失分析,发现有两个区域对ＰＨＯ８１基因的表达是必需的：－４０１～－２８９ｂｐ和－１０１２～－８０１ｂｐ。比较ＰＨＯ８１和ＰＨＯ５,ＰＨＯ８４基因上游,未发现有较高同源性的序列存在,但在－４０１～－２８９ｂｐ区域有ＰＨＯ４蛋白结合位点的核心序列５′ＣＡＣＧＴＧ／Ｔ３′,以及ＣＡＣＧＴＧ／Ｔ两侧富含Ａ／Ｔ的序列（可能是ＰＨＯ２结合位点）。推测－４０１～－２８９ｂｐ包含了ＰＨＯ８１的上游激活序列（ＵＡＳ）,－１０１２～－８０１ｂｐ可能起增强的作用。用酵母总蛋白质对－１０１２～－８０１ｂｐ进行凝胶阻抑电泳分析,证明有未知的蛋白因子结合在这个区域。     

三峡水库蓄水前后香溪河氮磷污染状况研究

分别于三峡水库蓄水前的上世纪1996—1997年及蓄水后的2004年采集了香溪河水样及沉积物样,研究了蓄水前后香溪河氮磷的污染状况。结果表明,蓄水前上游总磷浓度低于0.05mg/L,下游在0.22—0.34mg/L之间,其浓度与生活污水及工业废水排放有关;总氮浓度变化不大,在0.7—1.1mg/L之间。蓄水后磷、氮浓度明显升高,但总磷在回水区由于沉降作用反而低于蓄水前。蓄水后下游氮磷比普遍高于10,加之水流变缓,使香溪河库湾发生“水华”的可能性增加。香溪河沉积物磷污染严重,总磷含量高达1221mg/kg,主要以无机磷污染为主。三峡水库蓄水后,对上游库湾水环境的不利影响已开始显现出来,必须采取有效措施,防止水环境的恶化。     

干旱胁迫下华北驼绒藜种子大小及苞片对萌发和幼苗生长的影响

干旱是影响荒漠区植物种子萌发和幼苗生长的关键因素.以多年生强旱生半灌木华北驼绒藜为对象,研究了不同干旱程度(0、100、200、300和400g·L-1PEG6000)下,种子大小及苞片有无对种子萌发及幼苗生长的影响.结果表明:干旱胁迫显著抑制了种子萌发和幼苗地上部的生长.100和200 g ? L-1 PEG6000...     

Variation in soil carbon stocks and their determinants across a precipitation gradient in West Africa

We examine the influence of climate, soil properties and vegetation characteristics on soil organic carbon (SOC) along a transect of West African ecosystems sampled across a precipitation gradient on contrasting soil types stretching from Ghana (15°N) to Mali (7°N). Our findings derive from a total of 1108 soil cores sampled over 14 permanent plots. The observed pattern in SOC stocks reflects the very different climatic conditions and contrasting soil properties existing along the latitudinal transect. The combined effects of these factors strongly influence vegetation structure. SOC stocks in the first 2 m of soil ranged from 20 Mg C ha^?1 for a Sahelian savanna in Mali to over 120 Mg C ha^?1 for a transitional forest in Ghana. The degree of interdependence between soil bulk density (SBD) and soil properties is highlighted by the strong negative relationships observed between SBD and SOC (r² > 0.84). A simple predictive function capable of encompassing the effect of climate, soil properties and vegetation type on SOC stocks showed that available water and sand content taken together could explain 0.84 and 0.86 of the total variability in SOC stocks observed to 0.3 and 1.0 m depth respectively. Used in combination with a suitable climatic parameter, sand content is a good predictor of SOC stored in highly weathered dry tropical ecosystems with arguably less confounding effects than provided by clay content. There was an increased contribution of resistant SOC to the total SOC pool for lower rainfall soils, this likely being the result of more frequent fire events in the grassier savannas of the more arid regions. This work provides new insights into the mechanisms determining the distribution of carbon storage in tropical soils and should contribute significantly to the development of robust predictive models of biogeochemical cycling and vegetation dynamics in tropical regions.     

辽西北部主要绿化树种对粉尘污染的生理响应研究

为探究乡土和外来树种对城市不同污染环境的适应性,选取阜新市工业区、道路、矿区和公园绿地共有的10种树种作为研究对象,采用洗脱法测定了各树种单位叶面积滞尘量,并测定了叶片滞尘前后生理指标的变化,探讨不同种树叶片滞尘效应,以及叶片滞尘后对植物生理活动的影响。结果表明：(1)在4个功能区的不同树种单位叶面积滞尘量均不同,其中新疆杨单位叶面积滞尘量都较高、均值为1.45 g/m²,银杏单位叶面积滞尘量都较低、均值仅有0.92 g/m²。(2)叶片滞尘之后生理指标分析显示,叶片SPAD值呈显著下降趋势,渗透调节物质(脯氨酸、可溶性蛋白、可溶性糖)含量和细胞膜透性(MDA、Rec)均呈上升趋势,而抗氧化酶活性(SOD和POD)呈下降趋势但下降率不明显。(3)银杏和五角枫滞尘量与各生理指标之间有显著相关关系,更适合从生理方面检测城市粉尘污染环境指示物。(4)4个功能区不同树种滞尘能力与抗尘能力聚类分析显示,新疆杨、紫丁香、山皂荚和臭椿的滞尘能力和抗尘能力均较强;阜新市外来树种新疆杨、紫叶李、臭椿等的滞尘和抗尘能力均与乡土树种相当。研究认为,在长期粉尘污染胁迫下,各绿化树种可能通过提高渗透调节物质含量和抗氧化酶的活性等来缓解粉尘污染的伤害,外来树种与乡土树种同样在各污染环境中表现出较强的适应能力;在不造成生物入侵危害的前提下应该积极引进能够有效滞尘和治沙防风的外来树种。     

Hot-water pretreatment of cattails for extraction of cellulose

To date in the US, production of renewable fuels, particularly ethanol, is primarily from food crops that are high in sugar and starch. The use of arable land for fuel rather than food production and the use of a food source for fuel rather than food have created issues in pricing and availability of traditional foods and feed. The use of cattails to produce biofuel will add value to land and also reduce emissions of greenhouse gases by replacing petroleum products. In order to investigate the feasibility of converting cattails into cellulosic ethanol, a hot-water pretreatment process was studied using a Dionex accelerated solvent extractor (ASE) varying treatment temperature and time. The pretreatment at 190°C for more than 10 min could effectively dissolve the xylan fraction of cattails as soluble oligomers. Both the glucose yield and xylose yield obtained from the pretreated cattails increased with the escalation of the final pretreatment temperature, treatment time or enzyme loading. When cattails were pretreated at 190°C for 15 min, the highest glucose yield of 77.6% from the cellulose was achieved in 48 h using a cellulase loading of 60 FPU/g glucan. The yeast Saccharomyces cerevisiae (ATCC 24858) was able to ferment glucose released by cattail cellulose, resulting in approximately 88.7 ± 2.8% of the theoretical ethanol yield. The higher enzyme loading of 60 FPU/g glucan will significantly increase costs. It is recommended that further studies be carried out using cattails as a feedstock for bio-fuels, especially to optimize the economics of biological conversion processes for cattails with regard to reducing enzyme usage, energy input, glucose yield and xylose yield.     

不同分布区文冠果物候期的差异及其与地理-气候因子和结实性状的相关性

为明确文冠果(Xanthoceras sorbifolium Bunge)物候期的地理变异规律,在文冠果的主要分布区(内蒙古自治区、河北省和河南省)选择6个样地,采用定株观测方法,于2012年对文冠果的物候期进行观测,并分析了物候期与经度和纬度、气候因子和结实性状间的相关性.结果表明:在供试6个样地中,文冠果的芽萌动期、初花期、盛花期、末花期、展叶期、果速生期、果熟期、落果期、落叶期及总生长期均存在明显差异;其中,盛花期相差天数最多(40 d),果速生期相差天数最少(26 d).产自河南省三门峡市陕县(分布区南缘)的文冠果落叶期最晚,但其他各物候期均最早,总生长期最长(199 d);而产自内蒙古自治区赤峰市阿鲁科尔沁旗坤都镇(分布区北缘)的文冠果落叶期最早,但其他各物候期均最晚,总生长期最短(148 d).从结实性状看,6个样地文冠果的座果率和单位投影面积种子质量差异均较大,而种子含油率差异不明显;其中,产自河南省三门峡市陕县的文冠果座果率和单位投影面积种子质量均最低.相关性和回归分析结果表明:文冠果的大多数物候期间呈正相关,仅落叶期与其他物候期呈负相关;其中,除盛花期与果速生期无显著相关性外,花期的各物候期(初花期、盛花期和末花期)与果期的各物候期(果速生期、果熟期和落果期)均呈显著或极显著正相关.多数物候期与经度和纬度呈显著或极显著正相关,仅落叶期与经度和纬度分别呈显著和极显著负相关.总体上看,除落叶期外,文冠果各物候期与年均日照时数呈正相关,与其他气候因子多数呈负相关;其中,除果速生期和落果期外,其他物候期与年均温呈显著或极显著负相关.此外,仅总生长期与文冠果的座果率呈显著负相关,其他物候期与结实性状则无显著相关性.综合分析结果表明:文冠果的物候期呈现明显的地理变异规律,且气温是影响其物候期的主要气候因子.     

Interactions between hepatitis B virus infection and exposure to aflatoxins in the development of hepatocellular carcinoma: a molecular epidemiological approach.

Aflatoxins and hepatitis B virus (HBV) are major risk factors for hepatocellular carcinoma (HCC) in high incidence areas for this cancer, namely southeast Asia and parts of Africa. There is evidence from both epidemiological studies and animal models that the two factors can act synergistically to increase the risk of HCC. The cellular and molecular mechanism of the interaction between these two factors is as yet undefined. However, one possible mechanism attested to by studies in HBV transgenic mice is that chronic liver injury alters the expression of specific carcinogen metabolising enzymes thus modulating the binding of aflatoxin to DNA in hepatocytes. The high levels of aflatoxin exposure which occur in many areas of the world where chronic HBV infection is endemic indicate that measures to reduce aflatoxin exposure would contribute to reducing HCC incidence. In preliminary studies, Guinea-Conakry have established baseline data for the implementation of a community-based intervention study to evaluate the effectiveness of improved post-harvest processing and storage of the groundnut crop, a major source of aflatoxins. Aflatoxin-albumin adducts were measured in 423 sera from individuals living in the four natural geographic zones of Guinea. More than 95% of the serum samples were positive for this biomarker and highest exposures were found in Lower Guinea where groundnuts are consumed as a dietary staple. Variations in mean levels between villages within a geographic region did not vary greatly. HBV infection was endemic in all regions with an overall prevalence of 16.7% chronic carriers. Thus in this population both HBV vaccination and reduction in aflatoxin exposure would be beneficial in decreasing morbidity and mortality from liver disease.     

Value of Cricetomys gambianus in the study of experimental trypanosomiasis from Trypanosoma gambiense. Methods for mass preparation of antigen and purification of serum exoantigen]

Methods for mass preparation of crude antigen and exoantigen of Trypanosoma gambiense from experimentally infected Cricetomys gambianus are described. The size of this animal and the hyperparasitism obtained make it a remarkable source of trypanosomian antigens.