Structural analysis based on state-space modeling.

A new method has been developed to compute the probability that each amino acid in a protein sequence is in a particular secondary structural element. Each of these probabilities is computed using the entire sequence and a set of predefined structural class models. This set of structural classes is patterned after Jane Richardson''s taxonomy for the domains of globular proteins. For each structural class considered, a mathematical model is constructed to represent constraints on the pattern of secondary structural elements characteristic of that class. These are stochastic models having discrete state spaces (referred to as hidden Markov models by researchers in signal processing and automatic speech recognition). Each model is a mathematical generator of amino acid sequences; the sequence under consideration is modeled as having been generated by one model in the set of candidates. The probability that each model generated the given sequence is computed using a filtering algorithm. The protein is then classified as belonging to the structural class having the most probable model. The secondary structure of the sequence is then analyzed using a "smoothing" algorithm that is optimal for that structural class model. For each residue position in the sequence, the smoother computes the probability that the residue is contained within each of the defined secondary structural elements of the model. This method has two important advantages: (1) the probability of each residue being in each of the modeled secondary structural elements is computed using the totality of the amino acid sequence, and (2) these probabilities are consistent with prior knowledge of realizable domain folds as encoded in each model. As an example of the method''s utility, we present its application to flavodoxin, a prototypical alpha/beta protein having a central beta-sheet, and to thioredoxin, which belongs to a similar structural class but shares no significant sequence similarity.     

Can the Study of Natural Vegetation Succession Assist in the Control of Soil Erosion on Abandoned Croplands on the Loess Plateau,China?

In the Loess Plateau, China, arable cultivation of slope lands is common and associated with serious soil erosion. Planting trees or grass may control erosion, but planted species may consume more soil water and can threaten long‐term ecosystem sustainability. Natural vegetation succession is an alternative ecological solution to restore degraded land, but there is a time cost, given that the establishment of natural vegetation, adequate to prevent soil erosion, is a longer process than planting. The aims of this study were to identify the environmental factors controlling the type of vegetation established on abandoned cropland and to identify candidate species that might be sown soon after abandonment to accelerate vegetation succession and establishment of natural vegetation to prevent soil erosion. A field survey of thirty‐three 2 × 2–m plots was carried out in July 2003, recording age since abandonment, vegetation cover, and frequency of species together with major environmental and soil variables. Data were analyzed using correspondence analysis, classification tree analysis, and species response curves. Four vegetation types were identified and the data analysis confirmed the importance of time since abandonment, total P, and soil water in controlling the type of vegetation established. Among the dominant species in the three late‐successional vegetation types, the most appropriate candidates for accelerating and directing vegetation succession were King Ranch bluestem (Bothriochloa ischaemum) and Lespedeza davurica (Leguminosae). These species possess combinations of the following characteristics: tolerance of low water and nutrient availability, fibrous root system and strong lateral vegetative spread, and a persistent seed bank.     

内蒙古多伦县土地沙漠化景观格局变化特征

利用景观分析软件Fragstats 3.3和内蒙古多伦县1960、1975、1987、1995、2000、2005年6期遥感影像解译结果,分析了1960—2005年间土地沙漠化景观格局变化.结果表明:1960—1995年间研究区土地沙漠化面积呈先增后减趋势,总沙漠化面积增加212.70km2,沙漠化斑块数先增多后减少,景观多样性和均匀性上升,轻度、中度、重度沙漠化斑块形状趋向简单;1995—2005年间研究区沙漠化斑块数大幅增加,景观多样性和均匀性下降,轻度、中度、重度沙漠化斑块形状趋向复杂;严重沙漠化斑块形状在1960年以后一直趋向复杂化.整个景观在研究期间表现为完整-破碎-完整-破碎的趋势,由轻度到严重沙漠化,其景观类型的破碎化程度逐渐降低.     

Natural occurrence of Fusarium species and fumonisin-production by toxigenic strains isolated from poultry feeds in Argentina

Fusarium species and fumonisin production by toxigenic strains were investigated. During 1996–1998, 158 samples of poultry feeds were collected from a factory located in the department of Río Cuarto Córdoba province, Argentina. The most common species of Fusarium were F. moniliforme (60.7%) and F. nygamai (35.4%) followed by F. semitectum, F. subglutinans, F. proliferatum, F. dlamini, F. solani, F. oxysporum and F. napiforme. Fungal counts ranged from 1 × 10³ to 8 × 10⁵ CFU/g with mean values from 1.5 × 10³ to 2.3 × 10⁵ CFU/g. The highest counts were for F. dlamini, F. subglutinans, F. moniliforme and F. nygamai. Strains of F. moniliforme, F. nygamai, and F. proliferatum were screened for their potential to produce fumonisin B₁ (FB₁), fumonisin B₂ (FB₂) and fumonisin B₃ (FB₃) in corn grain. The samples were analysed using a modified high performance liquid chromatography method. The strains assayed, 43 strains, produced three fumonisins. There was a high degree of variability in the quantities of FB₁, FB₂, and FB₃ produced. The toxin produced in highest levels by the majority of the strains was FB₁. The range of concentration varied from 5.4 to 3,991, 1.01 to 189 and 0.4 to 765 ppm per gram of corn for FB₁, FB₂ and FB₃ respectively. The toxigenic pattern of strains was normal, although two strains of F. moniliforme produced exceptionally high concentrations of FB₃ and minor concentrations of FB₂ and FB₁. This is the first report from Argentina on Fusarium species in poultry feeds and fumonisin production by these strains.This revised version was published online in October 2005 with corrections to the Cover Date.     

广西百色和永乐盆地的始新世猪类化石──兼论早期猪类的分类和演化(英文)

描述了广西百色及永乐盆地发现的中始新世最晚期一晚始新世的猪类化石。这批已知最早的猪超科化石,大大丰富了亚洲地区的早期猪类,对了解全球猪类的早期演化有着重要价值。广西的材料被确定为两个新属新种：萨氏始新猪Ｅｏｃｅｎｃｈｏｅｒｕｓ ｓａｖａｇｅｉ和广西华夏猪Ｈｕａｘｉａｃｈｏｅｒｕｓ ｇｕａｎｇｘｉｅｎｓｉｓ,一个新种：粗壮暹罗猪Ｓｉａｍｏｃｈｏｅｒｕｓ　ｖｉｒｉｏｓｕｓ和一个未定属种：Ｔａｙａｓｓｕｉｄａｅ　ｇｅｎ．ｅｔ　ｓｐ．ｉｎｄｅｔ。加上已发表的单尖旅猪Ｏｄｉｏｃｈｏｅｒｕｓ　ｕｎｉｃｏｎｕｓ,百色、永乐盆地共计发现了５种始新世猪类化石。新属Ｅｏｃｅｎｃｈｏｅｒｕｓ虽然臼齿结构简单,与原始的古猪类（ｐａｉａｅｏｃｈｏｅｒｉｄ）接近,但因其Ｍ３具有一个明显的跟座而被归入猪科。早期猪科动物非常原始的臼齿形式证明,猪科动物的起源并不晚于古猪科（Ｐａｌａｅｏｃｈｏｅｒｉｄａｅ）和西科（Ｔａｙａｓｓｕｉｄａｅ）。旧大陆的古猪类长期以来被认为与新大陆的西类（ｔａｙａｓｓｕｉｄ）更为接近,多数学者将其归入西科。笔者认为两者共有的近祖特征,并不能支持它们更近的亲缘关系,而且古猪类缺乏典型西类的近裔特征,因而支持将Ｐａｌａ?     

The relationship between the golden spiny mouse circadian system and its diurnal activity: an experimental field enclosures and laboratory study

Examples of animals that switch activity times between nocturnality and diurnality in nature are relatively infrequent. Furthermore, the mechanism for switching activity time is not clear: does a complete inversion of the circadian system occur in conjunction with activity pattern? Are there switching centers downstream from the internal clock that interpret the clock differently? Or does the switch reflect a masking effect? Answering these key questions may shed light on the mechanisms regulating activity patterns and their evolution. The golden spiny mouse (Acomys russatus) can switch between nocturnal and diurnal activity. This study investigated the relationship between its internal circadian clock and its diurnal activity pattern observed in the field. The goal is to understand the mechanisms underlying species rhythm shifts in order to gain insight into the evolution of activity patterns. All golden spiny mice had opposite activity patterns in the field than those under controlled continuous dark conditions in the laboratory. Activity and body temperature patterns in the field were diurnal, while in the laboratory all individuals immediately showed a free-running rhythm starting with a nocturnal pattern. No phase transients were found toward the preferred nocturnal activity pattern, as would be expected in the case of true entrainment. Moreover, the fact that the free-running activity patterns began from the individuals' subjective night suggests that golden spiny mice are nocturnal and that their diurnality in their natural habitat in the field results from a change that is downstream to the internal clock or reflects a masking effect.     

VPMCD: variable interaction modeling approach for class discrimination in biological systems

Data classification algorithms applied for class prediction in computational biology literature are data specific and have shown varying degrees of performance. Different classes cannot be distinguished solely based on interclass distances or decision boundaries. We propose that inter-relations among the features be exploited for separating observations into specific classes. A new variable predictive model based class discrimination (VPMCD) method is described here. Three well established and proven data sets of varying statistical and biological significance are utilized as benchmark. The performance of the new method is compared with advanced classification algorithms. The new method performs better during different tests and shows higher stability and robustness. The VPMCD is observed to be a potentially strong classification approach and can be effectively extended to other data mining applications involving biological systems.     

基于GS和GIS的春尺蠖种群分布动态研究

本文利用杀虫灯诱杀春尺蠖雄成虫的数据,采用地统计学空间插值方法,借助遥感（RS）和地理信息系统（GIS）技术,得出2001～2003年和田地区春尺蠖种群空间分布格局及其动态。结果显示,3年中春尺蠖种群均为聚集分布,但聚集程度、种群空间分布和数量处于动态变化之中。通过TM卫片解译提取和田地区森林图层,在ARCGIS中完成对插值模拟图的切割,从而把春尺蠖种群动态的年际分布显示在具体的森林斑块内。研究结果可作为进一步研究春尺蠖种群暴发机理和系统控制的基础。     

荒漠生态系统对大气CO2浓度升高响应的干湿年差异

利用一个基于详细生理学过程的生态系统模型PALS-FT,通过模拟实验分析了美国亚利桑那州(Arizona)首府凤凰城(Phoenix)市西郊的Larreatridentata荒漠生态系统在干湿年份(1988-2002年)对大气CO2浓度升高响应的差别。结果表明,生态系统地上净初级生产力(ANPP)和土壤有机质年累积速率(SOM)均随大气CO2浓度升高而呈非线性(湿年)或线性(正常年和干年)增加;所有年份的土壤N含量(Nsoil)则呈非线性显著下降。ANPP与SOM的绝对变化量总是湿年大于正常年和干年,相对变化量则与所分析的CO2处理水平有关;Nsoil的绝对变化量和相对变化量均为湿年大于正常年和干年。不同功能型的植物ANPP对大气CO2浓度升高的绝对变化量均为湿年大于正常年和干年;相对变化量则因具体植物功能型而异,灌木和亚灌木为干年大于正常年和湿年,一年生C3和C4草本均为湿年大于正常年和干年。因此,无论是生态系统水平还是植物功能型(或物种)水平,荒漠生态系统对未来大气CO2浓度升高的响应都将受降水格局的显著影响。