PCA and K-Means decipher genome

In this paper, we aim to give a tutorial for undergraduate students studying statistical methods and/or bioinformatics. The students will learn how data visualization can help in genomic sequence analysis. Students start with a fragment of genetic text of a bacterial genome and analyze its structure. By means of principal component analysis they ``discover'' that the information in the genome is encoded by non-overlapping triplets. Next, they learn how to find gene positions. This exercise on PCA and K-Means clustering enables active study of the basic bioinformatics notions. Appendix 1 contains program listings that go along with this exercise. Appendix 2 includes 2D PCA plots of triplet usage in moving frame for a series of bacterial genomes from GC-poor to GC-rich ones. Animated 3D PCA plots are attached as separate gif files. Topology (cluster structure) and geometry (mutual positions of clusters) of these plots depends clearly on GC-content.Comment: 18 pages, with program listings for MatLab, PCA analysis of genomes and additional animated 3D PCA plot

Oidium longipes, a new powdery mildew fungus on petunia in the USA: A potential threat to ornamental and vegetable solanaceous crops

This is the first North American report of Oidium longipes, an anamorphic powdery mildew species described recently in Europe. It was found on vegetatively propagated petunia grown in a commercial greenhouse in New Jersey, USA, where it caused a rapidly spreading disease. The pathogen might have originated offshore and may have already been distributed in the United States through horticultural trade. During field surveys in Europe, it was found on petunia in Hungary and Austria as well; this is the first report of O. longipes from these two countries. A detailed light microscopy study of American and European specimens of O. longipes, including freshly collected samples and authentic herbarium specimens, revealed that its conidiophore morphology is more variable than illustrated in the original species description or in subsequent works. Microcycle conidiation, a process not yet known to occur in powdery mildews, was repeatedly observed in O. longipes. The rDNA internal transcribed spacer (ITS) sequences were identical in colonies containing different conidiophore types as well as in a total of five specimens collected from petunia in the United States, Austria, Hungary, Germany, and Switzerland. A phylogenetic analysis of the ITS sequences revealed that the closest known relative of O. longipes is O. lycopersici, known to infect tomato only in Australia. Cross-inoculation tests showed that O. longipes from petunia heavily infected tobacco cv. Xanthi, while the tomato and eggplant cultivars tested were moderately susceptible to this pathogen. These results indicate that its spread represents a potential danger to a number of solanaceous crops. Our ad hoc field surveys conducted in 2006 and 2007 did not detect it outside New Jersey in the United States; all the other powdery mildew–infected petunias, collected in New York and Indiana, were infected by Podosphaera xanthii. In Europe, most of the powdery mildew–infected petunias examined in this study were infected by P. xanthii or Golovinomyces orontii. Our multiple inoculation tests revealed that the same petunia plants and even the same leaves can be infected concomitantly by O. longipes, O. neolycopersici, G. orontii, and P. xanthii. Thus, it is at present unclear to what extent O. longipes contributes to the powdery mildew epidemics that develop year after year on solanaceous plants in many parts of the world

Oidium neolycopersici: Intra-specific variability inferred from AFLP analysis and relationship with closely related powdery mildew fungi infecting various plant species

Previous works indicated a considerable variation in the pathogenicity, virulence, and host range of Oidium neolycopersici isolates causing tomato powdery mildew epidemics in many parts of the world. In this study, rDNA internal transcribed spacer (ITS) sequences, and amplified fragment length polymorphism (AFLP) patterns were analyzed in 17 O. neolycopersici samples collected in Europe, North America, and Japan, including those which overcame some of the tomato major resistance genes. The ITS sequences were identical in all 10 samples tested and were also identical to ITS sequences of eight previously studied O. neolycopersici specimens. The AFLP analysis revealed a high genetic diversity in O. neolycopersici and indicated that all 17 samples represented different genotypes. This might suggest the existence of either a yet unrevealed sexual reproduction or other genetic mechanisms that maintain a high genetic variability in O. neolycopersici. No clear correlation was found between the virulence and the AFLP patterns of the O. neolycopersici isolates studied. The relationship between O. neolycopersici and powdery mildew anamorphs infecting Aquilegia vulgaris, Chelidonium majus, Passiflora caerulea, and Sedum alboroseum was also investigated. These anamorphs are morphologically indistinguishable from and phylogenetically closely related to O. neolycopersici. The cross-inoculation tests and the analyses of ITS sequences and AFLP patterns jointly indicated that the powdery mildew anamorphs collected from the above mentioned plant species all represent distinct, but closely related species according to the phylogenetic species recognition. All these species were pathogenic only to their original host plant species, except O. neolycopersici which infected S. alboroseum, tobacco, petunia, and Arabidopsis thaliana, in addition to tomato, in cross-inoculation tests. This is the first genome-wide study that investigates the relationships among powdery mildews that are closely related based on ITS sequences and morphology. The results indicate that morphologically indistinguishable powdery mildews that differed in only one to five single nucleotide positions in their ITS region are to be considered as different taxa with distinct host ranges

Stress Distribution in Mandible Regulated by Bone and Dental Implant Parameters: Part I - Methodology

The complicated inter-relationships between mandibular bone components and dental implants have attracted the attention of many a structural mechanics researcher as well as many a dental practitioner. This paper describes the methodology and analysis techniques employed to enable accurate evaluation of a vast range of the implant and bone parameters. The complex material and geometric properties of the bone and implant are modelled using two-dimensional (2D) triangular and quadrilateral plane strain elements. Assumptions made in the analysis include: (a) 50% osseointegration between bone and implant; (b) linear relationships exist between the stress value and the Young’s moduli of the cancellous and cortical bone at any specific point. In the companion paper (Part II) various bone, implant and loading parameters are evaluated for their influence on the stress distribution within the bone, in particular in the mandible

Cerulean: A hybrid assembly using high throughput short and long reads

Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking regions. The emergence of third generation sequencing (Pacific Biosciences) with long reads enables the opportunity to resolve complicated repeats that could not be resolved by the short read data. However, these long reads have high error rate and it is an uphill task to assemble the genome without using additional high quality short reads. Recently, Koren et al. 2012 proposed an approach to use high quality short reads data to correct these long reads and, thus, make the assembly from long reads possible. However, due to the large size of both dataset (short and long reads), error-correction of these long reads requires excessively high computational resources, even on small bacterial genomes. In this work, instead of error correction of long reads, we first assemble the short reads and later map these long reads on the assembly graph to resolve repeats. Contribution: We present a hybrid assembly approach that is both computationally effective and produces high quality assemblies. Our algorithm first operates with a simplified version of the assembly graph consisting only of long contigs and gradually improves the assembly by adding smaller contigs in each iteration. In contrast to the state-of-the-art long reads error correction technique, which requires high computational resources and long running time on a supercomputer even for bacterial genome datasets, our software can produce comparable assembly using only a standard desktop in a short running time.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Bacterial community dynamics and activity in relation to dissolved organic matter availability during sea-ice formation in a mesocosm experiment

Peer reviewe

Potential medicinal value of some South African seaweeds

Eleven macroalgae were collected from the KwaZulu-Natal coast and nineteen species from the cooler Western Cape coast in March and April 2000. Ethanolic and aqueous extracts were made and tested for biological activity in the Cox-1 anti-inflammatory assay, in a nematode mortality bioassay for anthelminthic activity, an IC50 anticancer assay and a MIC antimicrobial assay. The ethanolic extracts were very active in the Cox-1 anti-inflammatory assay for almost all of the species tested. The aqueous extracts were not active. No anthelminthic mortality was detected in extracts from any of the species tested. Many of the extracts had cytotoxic activity against three cancer cell lines tested, with those from representative species of the Chlorophyta and Rhodophyta being the most effective. The extracts had much lower cytotoxic activity when tested on normal mouse fibroblasts (NIH3T3). Extracts from only a few species had antimicrobial activity with those of the Chlorophyta tested being the most effective against both the Gram-positive and Gram-negative bacteria

Natural organic matter in drinking water sources: its characterisation and treatability

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Characteristics of matrix structures, and their effects on project success

This paper investigates the characteristics of matrix structures and their relationships with drivers of project success, such as communication, collaboration, and trust between project team members. Matrix characteristics that were expected to correlate positively with project success mostly did correlate with the success drivers. However, characteristics expected to impact negatively on project success did not show such significant correlations; some even correlated positively with success drivers. The success drivers investigated, in turn, correlated positively with perceived project success. A proposed model illustrates the effects of matrix characteristics on the drivers of success and their ultimate effect on project performance.Eienskappe van matriks strukture en hul effek op drywers van projeksukses – naamlik kommunikasie, samewerking, en vertroue tussen projek-spanlede – is ondersoek. Eienskappe wat verwag was om positief met projeksukses te korreleer het meestal wel positief gekorreleer met die drywers van sukses. Eienskappe wat verwag was om negatief met projeksukses te korreleer het egter nie sulke beduidende korrelasies getoon nie; sommige het selfs positief gekorreleer met projeksukses. Drywers van sukses het ook positief gekorreleer met waargenome projeksukses. ’n Voorgestelde model illustreer die verwantskappe tussen matriks-eienskappe op kommunikasie, samewerking, en vertroue tussen spanlede, en die uit eindelike effek op projekprestasie.http://sajie.journals.ac.za/pubam201

CHARACTERISTICS OF MATRIX STRUCTURES, AND THEIR EFFECTS ON PROJECT SUCCESS

This paper investigates the characteristics of matrix structures and their relationships with drivers of project success, such as communication, collaboration, and trust between project team members. Matrix characteristics that were expected to correlate positively with project success mostly did correlate with the success drivers. However, characteristics expected to impact negatively on project success did not show such significant correlations; some even correlated positively with success drivers. The success drivers investigated, in turn, correlated positively with perceived project success. A proposed model illustrates the effects of matrix characteristics on the drivers of success and their ultimate effect on project performance.Eienskappe van matriks strukture en hul effek op drywers van projeksukses – naamlik kommunikasie, samewerking, en vertroue tussen projek-spanlede – is ondersoek. Eienskappe wat verwag was om positief met projeksukses te korreleer het meestal wel positief gekorreleer met die drywers van sukses. Eienskappe wat verwag was om negatief met projeksukses te korreleer het egter nie sulke beduidende korrelasies getoon nie; sommige het selfs positief gekorreleer met projeksukses. Drywers van sukses het ook positief gekorreleer met waargenome projeksukses. ’n Voorgestelde model illustreer die verwantskappe tussen matriks-eienskappe op kommunikasie, samewerking, en vertroue tussen spanlede, en die uit eindelike effek op projekprestasie.http://sajie.journals.ac.za/pubam201