An examination of Nubian and Egyptian biological distances: Support for biological diffusion or in situ development?

Many authors have speculated on Nubian biological evolution. Because of the contact Nubians had with other peoples, migration and/or invasion (biological diffusion) were originally thought to be the biological mechanism for skeletal changes in Nubians. Later, a new hypothesis was put forth, the in situ hypothesis. The new hypothesis postulated that Nubians evolved in situ, without much genetic influence from foreign populations. This study examined 12 Egyptian and Nubian groups in an effort to explore the relationship between the two populations and to test the in situ hypothesis. Data from nine cranial nonmetric traits were assessed for an estimate of biological distance, using Mahalanobis D² with a tetrachoric matrix. The distance scores were then input into principal coordinates analysis (PCO) to depict the relationships between the two populations. PCO detected 60% of the variation in the first two principal coordinates. A plot of the distance scores revealed only one cluster; the Nubian and Egyptian groups clustered together. The grouping of the Nubians and Egyptians indicates there may have been some sort of gene flow between these groups of Nubians and Egyptians. However, common adaptation to similar environments may also be responsible for this pattern. Although the predominant results in this study appear to support the biological diffusion hypothesis, the in situ hypothesis was not completely negated.     

Genetic diversity and differentiation of Indian isolates of Phytophthora infestans as revealed by RAPD analysis

Sixty-seven isolates of Phytophthora infestans collected from Himalayan hill regions and subtropical planes of India were characterized by RAPD markers to assess diversity and differentiation based on location of origin. Ten random decamer primers generated 161 polymorphic fragments. Association of P. infestans isolates on the dendrogram and PCO plot revealed two clear grouping based on geographical location of origin-hill isolates and plane isolates. Quantification of diversity by Shannon index of diversity analysis demonstrated that most of the diversity was present with a particular population (hill or plane) of P. infestans isolates, with 85% variation being within and 15% being between hill and plane isolates. Subtropical plane isolates of P. infestans exhibited higher variability compared to hill isolates and they were more dispersed on the PCO plot. No clear differentiation of isolates based on mating type was reflected on the dendrogram and PCO plot.     

A method for estimating the diffusion resistance of the unstirred layer of microorganisms

A general enzyme-mediated flux equation which incorporates diffusion resistance was derived. By fitting the model to phosphate flux data from a blue-green alga, Anacystis nidulans, diffusion resistance, the half-saturation constant and maximal uptake velocity were estimated. Diffusion resistance for this organism was estimated to be 29 s / cm with a relative precision of about 10%. The parameters were also estimated by graphical analysis of a Woolf plot, but this method was less precise and tended to yield biased estimates.     

Rapid and sensitive dot-matrix methods for genome analysis

MOTIVATION: Dot-matrix plots are widely used for similarity analysis of biological sequences. Many algorithms and computer software tools have been developed for this purpose. Though some of these tools have been reported to handle sequences of a few 100 kb, analysis of genome sequences with a length of >10 Mb on a microcomputer is still impractical due to long execution time and computer memory requirement. RESULTS: Two dot-matrix comparison methods have been developed for analysis of large sequences. The methods initially locate similarity regions between two sequences using a fast word search algorithm, followed with an explicit comparison on these regions. Since the initial screening removes most of random matches, the computing time is substantially reduced. The methods produce high quality dot-matrix plots with low background noise. Space requirements are linear, so the algorithms can be used for comparison of genome size sequences. Computing speed may be affected by highly repetitive sequence structures of eukaryote genomes. A dot-matrix plot of Yeast genome (12 Mb) with both strands was generated in 80 s with a 1 GHz personal computer.     

Oligonucleotides replacing the roles of repetitive sequences pAs1, pSc119.2, pTa-535, pTa71, CCS1, and pAWRC.1 for FISH analysis

Hybrids derived from wheat (Triticum aestivum L.) × rye (Secale cereale L.) have been widely studied because of their important roles in wheat cultivar improvement. Repetitive sequences pAs1, pSc119.2, pTa-535, pTa71, CCS1, and pAWRC.1 are usually used as probes in fluorescence in situ hybridization (FISH) analysis of wheat, rye, and hybrids derived from wheat × rye. Usually, some of these repetitive sequences for FISH analysis were needed to be amplified from a bacterial plasmid, extracted from bacterial cells, and labeled by nick translation. Therefore, the conventional procedure of probe preparation using these repetitive sequences is time-consuming and labor-intensive. In this study, some appropriate oligonucleotide probes have been developed which can replace the roles of repetitive sequences pAs1, pSc119.2, pTa-535, pTa71, CCS1, and pAWRC.1 in FISH analysis of wheat, rye, and hybrids derived from wheat × rye. These oligonucleotides can be synthesized easily and cheaply. Therefore, FISH analysis of wheat and hybrids derived from wheat × rye using these oligonucleotide probes becomes easier and more economical.     

Diversity of bacteria and polyketide synthase associated with marine sponge Haliclona sp.

The microbial community associated with a marine sponge (Haliclona sp.) collected from Tateyama city, Japan was studied using 16S rRNA gene clone libraries. Two DNA templates were prepared using methods recommended for Gram-positive and Gram-negative bacteria in the Qiagen kit manual. From each DNA template, two 16S rRNA genes were PCR amplified, using the combination of universal bacterial primer 27f and primers 1385r and 1492r, respectively. A total of 347 clones were sequenced and compared with those available in DNA data banks. These sequences were members of ten bacterial phyla. Interestingly, more than 30 % of the clones represent novel sequences. A comparison of these sequences with sequences in a library prepared from DNA extracted from the surrounding water shows minimum DNA contamination. Taxonomically, the highest diversity was detected in the clone library prepared using a combination of primers 27f and 1492r and DNA isolated using the Gram-positive bacteria protocol. The potential of Haliclona sp.-associated bacteria to produce secondary metabolites was studied by cloning and sequencing the polyketide synthase (PKS, type 1) gene using the same DNA samples. Analysis of partial sequences derived from the sponge metagenome revealed 27 unique ketosynthase domains of PKS type I. This study suggests strongly that this Haliclona sp. plays host to diverse novel bacteria with a potential to produce novel polyketides.     

Protein structure alignment

A new method of comparing protein structures is described, based on distance plot analysis. It is relatively insensitive to insertions and deletions in sequence and is tolerant of the displacement of equivalent substructures between the two molecules being compared. When presented with the co-ordinate sets of two structures, the method will produce automatically an alignment of their sequences based on structural criteria. The method uses the dynamic programming optimization technique, which is widely used in the comparison of protein sequences and thus unifies the techniques of protein structure and sequence comparison. Typical structure comparison problems were examined and the results of the new method compared to the published results obtained using conventional methods. In most examples, the new method produced a result that was equivalent, and in some cases superior, to those reported in the literature.     

The use of AFLPs to examine genetic relatedness in barley

The generation of AFLPs in spring barley cultivars provided genetic information relating to the development of the crop in the UK since 1953. Principal co-ordinate (PCO) analysis of genetic similarities (gs) confirmed the marked contrast in the cultivars used in the 1970s and 1980s. The earliest cultivars, many derived from Proctor, were succeeded by tall-strawed, disease-resistant types with high yield but poor malting potential. In the 1980s they were in turn replaced by short-strawed cultivars with excellent yield and good malting quality, which originated from Triumph. A PCO plot of gs provided insight into the effects of selection for disease resistance and the antagonism between malting quality and particular resistance genes. The analysis of gs was more useful than pedigrees and estimates of kinship in revealing the genetic relationship between cultivars. Theoretical considerations for maximising the efficiency of an AFLP genotyping programme are discussed in the context of the number of primer pairs required to distinguish genotypes at varying levels of similarity.     

Development of 5006 Full-Length CDNAs in Barley: A Tool for Accessing Cereal Genomics Resources

A collection of 5006 full-length (FL) cDNA sequences was developed in barley. Fifteen mRNA samples from various organs and treatments were pooled to develop a cDNA library using the CAP trapper method. More than 60% of the clones were confirmed to have complete coding sequences, based on comparison with rice amino acid and UniProt sequences. Blastn homologies (E<1E-5) to rice genes and Arabidopsis genes were 89 and 47%, respectively. Of the 5028 possible amino acid sequences derived from the 5006 FLcDNAs, 4032 (80.2%) were classified into 1678 GreenPhyl multigenic families. There were 555 cDNAs showing low homology to both rice and Arabidopsis. Gene ontology annotation by InterProScan indicated that many of these cDNAs (71%) have no known molecular functions and may be unique to barley. The cDNAs showed high homology to Barley 1 GeneChip oligo probes (81%) and the wheat gene index (84%). The high homology between FLcDNAs (27%) and mapped barley expressed sequence tag enabled assigning linkage map positions to 151–233 FLcDNAs on each of the seven barley chromosomes. These comprehensive barley FLcDNAs provide strong platform to connect pre-existing genomic and genetic resources and accelerate gene identification and genome analysis in barley and related species.Key words: full-length cDNA, Hordeum vulgare, mRNA, gene ontology     

Babesia bovis: A comprehensive phylogenetic analysis of plastid-encoded genes supports green algal origin of apicoplasts

Apicomplexan parasites commonly contain a unique, non-photosynthetic plastid-like organelle termed the apicoplast. Previous analyses of other plastid-containing organisms suggest that apicoplasts were derived from a red algal ancestor. In this report, we present an extensive phylogenetic study of apicoplast origins using multiple previously reported apicoplast sequences as well as several sequences recently reported. Phylogenetic analysis of amino acid sequences was used to determine the evolutionary origin of the organelle. A total of nine plastid genes from 37 species were incorporated in our study. The data strongly support a green algal origin for apicoplasts and Euglenozoan plastids. Further, the nearest green algae lineage to the Apicomplexans is the parasite Helicosporidium, suggesting that apicoplasts may have originated by lateral transfer from green algal parasite lineages. The results also substantiate earlier findings that plastids found in Heterokonts such as Odontella and Thalassiosira were derived from a separate secondary endosymbiotic event likely originating from a red algal lineage.     

Identification and relationships of cultivated accessions fromLolium-Festuca complex based on RAPD fingerprinting

Randomly Amplified Polymorphic DNA (RAPD) technique with 15 arbitrary primers was used to identify and reveal relationships of the accessions comprising 4 species ofLolium-Festuca complex. Altogether 252 RAPD markers were considered in statistical treatment, 60 of which could be identified as potentially taxon-specific. All analyzed taxa were fully distinguishable using RAPD markers.Lolium-Festuca relationships based on RAPD data were evaluated using cluster analysis (UPGMA) and principle coordinate analysis (PCO). The results of UPGMA as well as PCO performed on data pooled from all RAPD profiles support separation of the two generaLolium andFestuca.     

Integrated biosorption and photocatalytic oxidation treatment of di(2-ethylhexyl)phthalate

Di(2-ethylhexyl)phthalate (DEHP), a toxic phthalate ester, is a ubiquitous contaminant due to its extensive use and persistence. No available treatment method can cost-effectively remove it from industrial wastewater. In a previous study, DEHP was effectively removed from aqueous solution by adsorption onto the biomass of selected seaweed, i.e., beached seaweed and Sargassum siliquastrum. Since biosorption cannot detoxify DEHP, the degradation (and detoxification) of desorbed DEHP from seaweed biomass by photocatalytic oxidation (PCO) was attempted. The first part of this study was to optimize the conditions for the degradation of desorbed DEHP in aqueous solution by PCO. Under optimized conditions, a total degradation of 20 mg/L of DEHP was achieved within 45 min. The degradation intermediates/products such as phthalic anhydride and 2-ethyhexanol were identified by GC-MS analysis. Total organic carbon analysis was also used to ensure the complete mineralization of DEHP. The Microtox^® test was used to assess the toxicities of the parent and degraded compounds. In the second part of this study, DEHP was first removed and concentrated by adsorption onto seaweed biomass under the conditions optimized in the previous study. It was then desorbed from seaweed biomass and degraded by PCO. Results indicate that the treatment for DEHP by integrating biosorption and PCO is feasible.     

DNA sequence representation without degeneracy

Graphical representation of DNA sequence provides a simple way of viewing, sorting and comparing various gene structures. A new two-dimensional graphical representation method using a two- quadrant Cartesian coordinates system has been derived for mathematical denotation of DNA sequence. The two-dimensional graphic representation resolves sequences’ degeneracy and is mathematically proven to eliminate circuit formation. Given x-projection and y-projection of any point on the graphical representation, the number of A, G, C and T from the beginning of the sequence to that point could be found. Compared with previous methods, this graphical representation is more in-line with the conventional recognition of linear sequences by molecular biologists, and also provides a metaphor in two dimensions for local and global DNA sequence comparison.     

Successive mapping of dune slack vegetation

Summary The succession of the dune slack vegetation around an artificial lake was studied by means of successive mapping. A succession scheme was prepared on the basis of comparison of the maps made in various years. This scheme was discussed in terms of systems theory, with reference to a kinematic graph prepared on the basis of the transformations. The succession derived from the vegetation maps was compared with that derived from the permanent plots; the results of this comparison indicated that only a small proportion of the total number of succession lines could be detected with the aid of the permanent plots. In addition, the information that could be derived from the permanent plot analysis depended on the degree of change of the vegetation in the area; more information could be derived from drier areas which showed the least degree of change. The best method for the investigation of the succession proved to be a combination of a restricted number of permanent plots and successive mapping. Nomenclature of species follows Heukels-van Ooststroom Flora van Nederland, 16 ed. 1970. R.I.N.-Comm. nr. 107.     

Isolation and translation of plant messenger RNA

A fraction of the RNA species isolated from Lemna gibba G-3 consists of molecules with attached sequences of polyadenylic acid. This polyadenylic acid-containing fraction, separated from total RNA by adsorption onto oligothymidylic acid-cellulose, was shown to be mRNA by its ability to serve as template in a cell-free translation system derived from wheat germ. The products of translation were characterized by electrophoresis. This method permitted the comparison of mRNA from plants grown under different light conditions. Such plants were shown to possess qualitative and quantitative differences in their mRNA complements.     

Determining the overall merit of protein identification data sets: rho-diagrams and rho-scores

This paper described a simple heuristic method for determining the merit of a set of peptide sequence assignments made using tandem mass spectra. The method involved comparing a prediction based on the known stochastic behavior of a sequence assignment algorithm with the assignments generated from a particular data set. A particular formulation of this comparison was defined through the construction of a plot of the data, the rho-diagram, as well as a parameter derived from this plot, the rho-score. This plot and parameter were shown to be able to readily characterize the relative quality of a set of peptide sequence assignments and to allow the straightforward determination of probability threshold values for the interpretation of proteomics data. This plot is independent of the algorithm or scoring scheme used to estimate the statistical significance of a set of experimental results; rather, it can be used as an objective test of the correctness of those estimates. The rho-score can also be used as a parameter to evaluate the relative merit of protein identifications, such as those made across proteome species taxonomic categories.     

Diversity and genetic differentiation among populations of Indian and Kenyan tea (Camellia sinensis (L.) O. Kuntze) revealed by AFLP markers

AFLP markers were successfully employed to detect diversity and genetic differentiation among Indian and Kenyan populations of tea (Camellia sinensis (L.) O. Kuntze). Shannon's index of diversity was used to partition the total phenotypic variation into between and within population components. On average, most of the diversity was detected within populations, with 79% of the variation being within and 21% being between populations of Indian and Kenyan tea. A dendrogram constructed on the basis of band sharing distinctly separated the three populations of tea into China type (sinensis), Assam type (assamica) and Cambod type (assamica ssp. lasiocalyx) in a manner consistent with the present taxonomy of tea, the known pedigree of some of the genotypes and their geographical origin. Principal coordinate (PCO) analysis grouped Assam genotypes both from India and Kenya supporting the suggestion that the Kenyan clones have been derived from collections made in this region. The China types were more dispersed on the PCO plot which is a reflection of wider genetic variation. As would be expected, clones collected from the same region exhibited less overall genetic variation. AFLP analysis discriminated all of the tested genotypes from India and Kenya, even those which cannot be distinguished on the basis of morphological and phenotypic traits. Received: 2 May 1996 / Accepted: 14 June 1996     

GenomeFingerprinter: The Genome Fingerprint and the Universal Genome Fingerprint Analysis for Systematic Comparative Genomics

Background

No attention has been paid on comparing a set of genome sequences crossing genetic components and biological categories with far divergence over large size range. We define it as the systematic comparative genomics and aim to develop the methodology.

Results

First, we create a method, GenomeFingerprinter, to unambiguously produce a set of three-dimensional coordinates from a sequence, followed by one three-dimensional plot and six two-dimensional trajectory projections, to illustrate the genome fingerprint of a given genome sequence. Second, we develop a set of concepts and tools, and thereby establish a method called the universal genome fingerprint analysis (UGFA). Particularly, we define the total genetic component configuration (TGCC) (including chromosome, plasmid, and phage) for describing a strain as a systematic unit, the universal genome fingerprint map (UGFM) of TGCC for differentiating strains as a universal system, and the systematic comparative genomics (SCG) for comparing a set of genomes crossing genetic components and biological categories. Third, we construct a method of quantitative analysis to compare two genomes by using the outcome dataset of genome fingerprint analysis. Specifically, we define the geometric center and its geometric mean for a given genome fingerprint map, followed by the Euclidean distance, the differentiate rate, and the weighted differentiate rate to quantitatively describe the difference between two genomes of comparison. Moreover, we demonstrate the applications through case studies on various genome sequences, giving tremendous insights into the critical issues in microbial genomics and taxonomy.

Conclusions

We have created a method, GenomeFingerprinter, for rapidly computing, geometrically visualizing, intuitively comparing a set of genomes at genome fingerprint level, and hence established a method called the universal genome fingerprint analysis, as well as developed a method of quantitative analysis of the outcome dataset. These have set up the methodology of systematic comparative genomics based on the genome fingerprint analysis.