Prediction of the packing arrangement of strands in β-sheets of globular proteins

A method is proposed for predicting the adjacency order in which strands pack in a -sheet in a protein, on the basis of its amino acid sequence alone. The method is based on the construction of a predicted contact map for the protein, in which the probability that various residue pairs are close to each other is computed from statistically determined average distances of residue pairs in globular proteins of known structure. Compact regions, i.e., portions of the sequence with many interresidue contacts, are determined on the map by using an objective search procedure. The proximity of strands in a -sheet is predicted from the density of contacts in compact regions associated with each pair of strands. The most probable -sheet structures are those with the highest density of contacts. The method has been tested by computing the probable strand arrangements in a five-strand -sheet in five proteins or protein domains, containing 62–138 residues. Of the theoretically possible 60 strand arrangements, the method selects two to eight arrangements as most probable; i.e., it leads to a large reduction in the number of possibilities. The native strand arrangement is among those predicted for three of the five proteins. For the other two, it would be included in the prediction by a slight relaxation of the cutoff criteria used to analyze the density of contacts.     

The Upper Cave at Zhoukoudian and the origins of the Mongoloids

The best evidence for identifying the inhabitants of northeast Asia in the terminal Pleistocene or early Holocene periods is provided by the human burials from the Upper Cave at Zhoukoudian, and in particular the “Old Man”. Apart from the Minatogawa finds on Okinawa, all Late Pleistocene human remains from East Asia that are reasonably well published are poorly preserved and often have equivocal dates. Since the time the Upper Cave was excavated it has been supposed that the human remains were the link between “Peking Man” and the modern Mongoloid complex. We have carried out multivariate analyses of the “Old Man” cranium employing new measurements of Weidenreich's cast of the skull and comparative data from Howells' survey of modern human groups. Despite our expectations the analyses have not shown the “Old Man” to be closely linked with the Mongoloids. Considering all the evidence available we conclude that the common belief of a close biological relationship between the people buried in the Upper Cave and the modern Mongoloids is not yet adequately demonstrated. Of crucial importance in interpreting the Upper Cave burials is their antiquity, which is still commonly thought to be in the order of at least 18 000 years. We believe that recent C-14 dates of about 11 000 years, determined from animal bones, indicate the earliest possible date for the burials. The time span between the Upper Cave burials and the earliest known modern Mongoloids in north China is in the order of about 4–5000 years. It is possible that a major population shift has occurred in north China between the terminal Pleistocene and the mid Holocene, when farming first appears. If this is so, the Upper Cave people may not have been closely allied to the Mongoloid groups that now inhabit East Asia and the Americas.     

Inheritance and structure of foreign DNA in progenies of transgenic tobacco obtained by direct gene transfer

Summary One of the transformed tobacco plants obtained by direct DNA transformation possessed two marker genes, a chimeric aminoglycoside phosphotransferase and nopaline synthase genes. Selfed progenies of this plant (T3-d) showed stable inheritance of these two genes. The minimum size of foreign DNA integrated into tobacco genome was estimated to be 5.4 kbp. A deleted nopaline synthase gene co-existed with an intact gene. The linkage analysis indicated that two transformants, T1-b and T3-c, possessed foreign DNA inserted in different chromosomes or in different sites of the same chromosome that recombine freely.     

Diversity and evolution of chloroplast DNA in Triticum and Aegilops as revealed by restriction fragment analysis

Summary Restriction fragment analysis of chloroplast (cp) DNAs from 35 wheat (Triticum) and Aegilops species, including their 42 accessions, was carried out with the use of 13 restriction enzymes to clarify variation in their cpDNAs. Fourteen fragment size mutations (deletions/insertions) and 33 recognition site changes were detected among 209 restriction sites sampled. Based on these results, the 42 accessions of wheat-Aegilops could be classified into 16 chloroplast genome types. Most polyploids and their related diploids showed identical restriction fragment patterns, indicating the conservatism of the chloroplast genome during speciation, and maternal lineages of most polyploids were disclosed. This classification of cpDNAs was principally in agreement with that of the plasma types assigned according to phenotypes arising from nucleus-cytoplasm interactions. These mutations detected by restriction fragment analysis were mapped on the physical map of common wheat cpDNA, which was constructed with 13 restriction endonucleases. Length mutations were more frequently observed in some regions than in others: in a 16.0 kilo base pairs (kbp) of DNA region, including rbcL and petA genes, 6 of 14 length mutations were concentrated. This indicates that hot spot regions exist for deletions/insertions in chloroplast genome. On the other hand, 33 recognition site mutations seemed to be distributed equally throughout the genome, except in the inverted repeat region where only one recognition site change was observed. Base substitution rate (p) of cpDNA was similar to that of other plants, such as Brassica, pea and Lycopersicon, showing constant base substitution rates among related taxa and slow evolution of cpDNA compared with animal mitochondrial DNA. Phylogenetic relationships among Triticum and Aegilops species were discussed, based on the present data.Contributions no. 45 and no. 490 from the Kihara Institute for Biological Research, Yokohama City University and the Laboratory of Genetics, Faculty of Agriculture, Kyoto University, respectively.     

Linear and non-linear regression analysis of genotype X environment interactions in pearl millet

Summary Regression analysis was computed on the grain yield of 15 single cross F₁ hybrids of pearl millet (Pennisetum typhoides (Burm.) S. & H.) evaluated in 20 environments at 19 sites in India to assess the nature of genotype X environment interactions. Linear, quadratic, cubic, twoand three-intersecting straight line models were examined for fit. The interactions of six hybrids viz. MH 110, MH 113, MH 114, MH 115, MH 120 and MBH 110 were explained by the linear regression model. The response of the remaining nine hybrids was largely non-linear. The two and three-intersecting straight line models fit better than the quadratic and cubic models and explained non-linearity of response. The two-intersecting straight line models fit for 6 hybrids MH 106, MH 107, MH 112, MH 116, MH 117 and BJ 104. The response of MH 109 was best explained by a three-intersecting straight line model, but there still existed a significant remainder variation. The truncation of environmental range by assuming moving division points was more efficient than the fixed division points for the segmental regression models. The stability of hybrid varieties on the best fitting model has been discussed.     

Trace elements in human parotid saliva

Although various proteins and some electrolytes have been measured in human saliva, little systematic data about the major and minor elemental components of this body fluid have been obtained. In order to obtain such data, concentrations of C, Na, P, Cl, K, Ca, Sc, Cr, Fe, Co, Zn, Se, Br, Rb, Sb, I, and Cs in human parotid saliva were measured by instrumental nuclear methods. The data obtained confirmed the relative lack of Zn in saliva of patients with hypogeusia (decreased taste acuity) and suggested that concentrations of Na, Cl, Br, and Ca followed the order: normals > hypogeusia > hyposmia (decreased smell acuity). To compare concentrations of elements in saliva with those in blood and urine, absolute concentrations were normalized to that of Na through the use of a concept called an enrichment factor. On this basis, parotid saliva is relatively depleted in Se, Zn, and Fe and enriched for most other elements relative to blood plasma indicating that the fluid is not simply a transudate of blood plasma. Using this same technique, saliva composition was found more similar to urine than blood plasma, being relatively depleted in Se, Cs, and Co, being enriched in I, Br, and Cr and having about the same relative concentrations of P, Cl, Zn, Fe, Ca, K, and Rb. As the total body concentrations of many of the enriched elements in saliva are extremely small, their enrichment in saliva suggests special roles for these elements in the oral cavity. Because of its accessibility, ease of collection, and interaction with some body constituents, saliva represents a useful, albeit neglected, tool in the diagnosis of some physiological and pathological changes in body function and in understanding important aspects of trace metal metabolism.     

Synthesis of ribulose 1,5-bisphosphate carboxylase by isolatedSorghum mesophyll chloroplasts

Chloroplasts isolated fromSorghum vulgare are active in light-dependent, organelle protein synthesis. Intact chloroplasts can use light as an energy source; photosynthetically inactive chloroplasts require the addition of ATP for this protein synthesis. Preincubation of chloroplasts in light at 25°C for 1 h depleted the endogenous templates completely; such preincubated chloroplasts translated exogenously added heterologous templates efficiently. When total cellular RNA fromChlorella protothecoides, a C₃ plant, was used as template for translation in a cell-free light-dependent system of isolated mesophyll chloroplasts fromSorghum vulgare, a C₄ type plant, polypeptides of 55 kDa (large subunit) and 15 kDa (small subunit) were detectable in the fluorographic profile of the newly synthesized proteins; these polypeptides were absent in the products obtained with endogenous RNA. Evidence for the fidelity of the system was obtained by immunological analysis of ribulose 1, 5-bisphosphate carboxylase obtained by the translation ofChlorella cellular RNAs.     

Molecular evolution among someDrosophila species groups as indicated by two-dimensional electrophoresis

Summary The evolutionary and phylogenetic relationships of sevenDrosophila species groups (represented byD. melanogaster, D. mulleri, D. mercatorum, D. robusta, D. virilis, D. immigrans, D. funebris, andD. melanica) were investigated by the use of two-dimensional electrophoresis. The resulting phylogeny is congruent with the current views of evolution among these groups based on morphological characters and immunological distances. Previous studies indicated that the ability of one-dimensional electrophoresis to resolve relationships between distantly related taxa extended to about the Miocene [25 million years (Myr) ago], but the present study demonstrates that two-dimensional electrophoresis is a useful indicator of phylogeny even back to the Paleocene (65 Myr ago). In addition, two-dimensional electrophoresis is shown to be a useful technique for detecting slowly evolving structural proteins such as actins and tropomyosins.     

Morphological variation among widely dispersed larval populations of anadromous southern hemisphere lampreys (Geotriidae and Mordaciidae)

Larvae of all three southern hemisphere anadromous parasitic lampreys were collected from rivers in Australia, New Zealand and South America. Body intervals were measured, trunk myomeres counted and the frequency of pigmentation in different body regions recorded. Morphometric data were subjected to multiple group principal components analysis (MGPCA) which took into account changes during growth. The components (together with myomere counts) and the pigmentation data were both subjected to discriminant analysis. Ordination and rank correlation tests revealed no evidence for either latitudinal clines or a continuum of circumpolar change amongst larval lamprey populations. Clustering of population centroids clearly distinguished between Mordacia lapicida (Gray) from Chile and M. mordax (Richardson) from south-eastern Australia. Populations of Geotria australis Gray divided into groups representing three geographical regions, namely Argentina, Chile and Australasia (Western Australia, Tasmania and New Zealand). Ammocoetes from Argentina were the most divergent, possessing a more posterior cloaca, taller dorsal fins, a greater gap between dorsal fins, and distinctive pigmentation on the head and caudal fin. Within the Australasian group, Western Australian and New Zealand populations clustered closer than either did with those from Tasmania. The cluster analyses for larval populations of G. australis suggest that, during their marine trophic phase, the adults of this species originating from Argentinian and Chilean rivers follow different migratory routes, whereas those from Western Australia, New Zealand and, to a lesser extent, Tasmania intermix.     

The convergent trajectories of bird communities along ecological successions in european forests

Summary There is much more variation in the composition of bird communities in the earlier open and semi-open seral stages of ecological successions in forested landscapes of Europe than later on in preforested and forested climactic stages. The demonstration of this trend is achieved from the study of four habitat gradients, two in the mediterranean region (Provence and Corsica) and two in central Europe (Burgundy, France and Poland). A multivariate analysis has been used to illustrate the dynamics of communities along these succession. Displays of the results in bivariate space as well as an illustration of the distributional profiles of some of the most characteristic species show that: i) there is a discrimination between the two mediterranean gradients and the two medioeuropean ones and ii) each succession starts with a very distinct set of species and then the four gradients regularly converge in the last climactic stage where there is almost no discrimination between communities. These results are discussed in the light of the history of European biotas during the Pleistocene. The reason why there is more variation in species composition in the earlier seral stages than in the later forested stages are discussed according to current theories on the role of habitat selection on speciation processes.