Some comments on coordinate-free and scale-invariant methods in morphometrics

The unusual strategy for comparing biological shapes is to use some kind of superimposition of the two forms under study and then look at the "residuals" as the shape change. In this paper, I take a careful look at this general strategy and point out some subtle but inherent and important pitfalls. Additionally an alternative approach based on Euclidean Distance Matrix representation is presented. It is applicable to two- as well as three-dimensional objects.     

Topological mirror images in protein structure computation: an underestimated problem.

When calculating three-dimensional structures from NMR data, alternative solutions with very large RMS deviation can be obtained. Sometimes local or global inversions of the protein folding can be observed. We call these different solutions topological mirror images, as they keep the correct amino acid chirality. They are observed when the number of restraints is insufficient and represent different solutions from the same scalar information. Therefore they are common in small peptides where the NMR data are often limited and the secondary structure is not very well defined. They can also be observed in large molecules in regions of higher flexibility. In our experience the observation of topological mirror images is independent of the efficiency of sampling of the algorithm used. We present four examples of proteins with different size and folding. We also discuss ways to distinguish among the different solutions.     

进化距离与相对替代率的比较研究

系统树是描述物种、人种甚至基因间亲缘关系和演化的重要工具,必须以进化距离或(相对)替代率作为重要的参数。但以哪一个参数构建的树更能反映真实的系统树呢?事实上迄今并无人对此作过认真的研究。本文以模拟数据并用方差分析法检验两个参数的异同并讨论其包含的生物学意义。研究结果表明,当氨基酸的替代率和核苷酸的替代率分别为0.18和0.13时,它们的进化距离分别为0.199和0.143。经方差分析证实,若检验的氨基酸和核苷酸最大数目均为75只时,不论以替代率或进化距离中那一个作为构树参数,拓扑树事实上几乎只有一个。这就是说,该时拓扑树可靠性很大,而且随着它们替代率的减少,则检验的氨基酸和核苷酸的数目会随之增加。但是一旦氨基酸的替代率和核苷酸的替代率超过上述数字,则两个参数构建的树在拓扑长度上是不等价的。经分析,若进化距离大致上与进化时间成线性关系的话,则应选用进化距离。用进化距离重建的系统树事实上支持中性学说;若进化距离与进化时间显著地不存在线性关系的话,则可选用替代率,该情况表明中性学说不适用,似更倾向于新达尔文主义。     

Statistical assessment of population variability: a methodological approach

We have implemented a multivariate statistical methodology to assess the degree and pattern of cranial variability in skeletal samples. Specifically, the method is designed to test whether variability in a skeletal sample exceeds "normal within-group variability" defined in the present instance as variability present among crania from a cemetery associated with a village. It involves comparing a covariance matrix derived from a sample of unknown composition to one representing "normal within-group variability." The method has been applied to two Plains Indian craniometric samples. The Leavenworth site (39CO9) represents the remnants of previously autonomous Arikara Indian villages devastated by epidemic diseases in the late 1700s. The Bad River 2 Phase is an archaeological designation grouping together closely related sites in the Bad-Cheyenne region of South Dakota dating from 1740-1795 AD. We were able to show substantial heterogeneity among crania from Leavenworth. District burial areas at Leavenworth account for some of the heterogeneity, supporting the notion that they represent an attempt to maintain former social distinctions. We were unable to differentiate among sites within the Bad River 2 Phase, suggesting that it is a valid biological unit.     

Evolutionary analysis ofα andβ hemoglobin genes by reh theory under the assumption of the equiprobability of genetic events

Summary It is shown how REH theory in conjunction with mRNA or gene sequence data can be used to obtain estimates of the fixation intensity, the number of varions, and the total mutations fixed between homologous pairs of nucleic acids. These estimates are more accurate than those that can be derived from amino acid sequence data. The method is illustrated for and hemoglobin genes and these improved estimates are compared with those made from the amino acid sequences for which those genes code. Significant differences are found between the estimates made by these two methods. For the hemoglobin gene sequences examined here, the fixation intensity is some-what less than the protein data had suggested, and the number of rations is considerably greater. Depending on the gene sequences examined, between 62 and 83% of the codons appear able to fix mutations during the divergences considered. This reflects the constraints of natural selection on acceptable mutations. The total number of base replacements separating the genes for human, mouse, and rabbit hemoglobin varies from 61 to 105 depending on the pair examined. Rabbit and hemoglobin are separated by at least 290 fixed mutations. For such distantly related sequences estimates made from protein and mRNA data differ less, reflecting the higher quality of information from the many observed changes in primary structure. The effects of nonrandom gene structure on these evolutionary estimates and the fact that various genetic events are not equiprobable are discussed.     

The blacks of Panama: their genetic diversity as assessed by 15 inherited biochemical systems

Panama's black citizens are culturally and historically divisible into two groups, the Spanish-speaking coloniales and the English-speaking anglos or afro-antillanos. Until recently these groups have been geographically as well as culturally isolated one from the other, although both are predominantly of West and Southwest African origin. Assessment of the genetic diversity within-villages and within language groups reveals as much, possibly somewhat more, diversity in 15 inherited biochemical markers within villages and language groups as that which obtains between villages and language groups. A number of rare variants at the 6-phosphogluconate dehydrogenase, lactate dehydrogenase, and esterase D loci were encountered and are described.     

Interpersonal relationships and personal space: Research review and theoretical model

This article reviews research concerning interpersonal distance as a function of interpersonal relationships, attraction, and reactions to spatial invasion. To integrate research findings, we propose a simple model, based on the idea that people seek an optimal distance from others that becomes smaller with friends and larger for individuals who do not expect to interact. The model describes comfort-discomfort as a function of interaction distance in three situations: interacting friends, interacting strangers, and strangers who do not expect interaction. These three personal space profiles are discussed in terms of qualifying variables, such as seated vs. standing interaction, sex composition of the dyad, intimacy of conversation topics, and situational variables.A version of the theoretical section of this article was presented at the 82nd annual convention of the American Psychological Association in a symposium entitled Getting Close: Personal Space and Privacy, New Orleans, 1974. An earlier version of the material appears in a book by Irwin Altman (1975).     

Genetic structure of a tribal population, the Yanomama Indians. XIII. Dental microdifferentiation.

Data are presented on the frequency of the following eight dental traits in 635 Yanomama and 65 Makiritare Indians: upper central incisor rotation or winging, shoveling of maxillary incisors, maxillary molar hypocone reduction, Carabelli's trait, mandibular molar cusp number, mandibular molar cusp pattern rotation of second lower premolar, and pattern of second lower premolar cusps. Yanomama dentition is unusual in the high frequency of six cusps on the mandibular molars. There is marked dental microdifferentiation between villages; significant agreement was observed between a matrix of pairwise "dental distances" based on six morphological traits and corresponding matrices based on 11 genetic systems and on geographic location.     

Arabica coffee and olive oils mitigate malathion-induced nephrotoxicity in rat: In silico,immunohistochemical and biochemical evaluation

Malathion (MAL) is an organophosphate insecticide that disrupts the body's antioxidant system; it is one of the earliest organophosphate insecticides extensively used as dust, emulsion, and vapor control a wide variety of insect pests under different conditions. This experimentation aims to evaluate the influence of Arabica coffee oil and olive oil on MAL-induced nephrotoxicity in male rat. 6 sets bearing the same number of animals were applied to this experiment. Each set comprised 10 rats. The first set of rats was used as the control group; rats in the second set were exposed to MAL measured at 100 mg/kg body weight for 7 weeks. Animals in the third and fourth set were treated with 400 mg/kg body weight of Arabica coffee oil and olive oil, and 100 mg/kg body weight of MAL. The fifth, together with the sixth set, were fed with a similar proportion of Arabica coffee oil and olive oil as administered to the third set of rats. After the experimental duration, rats of group 2 showed severe biochemical alterations, including significant increases of creatinine, uric acids, and urea nitrogen (BUN), resulting in marked decreases in serum albumin values and total protein (TP). Severe histopathological and immunohistochemical alterations of kidney tissues were observed in exposed MAL-intoxicated rats. Administration of these oils reduced the detected biochemical, histopathological modifications caused by MAL intoxication. Two active ingredients in Arabica coffee oil (oleic acid) and olive oil (hydroxytyrosol) showed good cyclooxygenase-2 (COX 2) interaction. Moreover, oleic acid from coffee oil and olive oil exhibited impressive association with xanthine oxidase (XO). The current finding showed that coffee oil and olive oil could be appraised as possible and a likely deterrence component against nephrotoxicity brought about by MAL.     

Correlation between the compact regions predicted by the Average Distance Map (ADM) and the biologically active sites in atrial natriuretic peptide

The prediction of the short-range compact regions of human atrial natriuretic peptide (a-hANP), one of the biologically active peptides, has been made by means of the Average Distance Map(ADM). We found out that the location of the predicted short-range compact regions is consistent with the structural units determined by the NMR analysis (Kobayashiet al., 1988). Furthermore, the short-range compact regions correspond well to the biologically active areas of atriopeptin (103–125)-amide (which is homologous peptide toa-hANP), detected by the glycine substitution technique (Konishiet al., 1987). The results suggest that a predicted short-range compact region can be regarded as a possible active site in a biologically active peptide.