The bacterial species definition in the genomic era

The bacterial species definition, despite its eminent practical significance for identification, diagnosis, quarantine and diversity surveys, remains a very difficult issue to advance. Genomics now offers novel insights into intra-species diversity and the potential for emergence of a more soundly based system. Although we share the excitement, we argue that it is premature for a universal change to the definition because current knowledge is based on too few phylogenetic groups and too few samples of natural populations. Our analysis of five important bacterial groups suggests, however, that more stringent standards for species may be justifiable when a solid understanding of gene content and ecological distinctiveness becomes available. Our analysis also reveals what is actually encompassed in a species according to the current standards, in terms of whole-genome sequence and gene-content diversity, and shows that this does not correspond to coherent clusters for the environmental Burkholderia and Shewanella genera examined. In contrast, the obligatory pathogens, which have a very restricted ecological niche, do exhibit clusters. Therefore, the idea of biologically meaningful clusters of diversity that applies to most eukaryotes may not be universally applicable in the microbial world, or if such clusters exist, they may be found at different levels of distinction.     

Measurement of non-randomness in spatial distributions

The measurement of departure from randomness in spatial distributions has widespread application in ecological work. Several “indices of non-randomness” are compared with regard to their dependence on sample number, sample size and density. Criteria for the best choice of index for specific situations are discussed. A new coefficient C_x is proposed for use with positively contagious distributions and tests of significance are given. When C_x and another index (S²/m−1) are used for positive and negative contagion respectively, values ranging from −1 through 0 (random) to +1 are obtained, regardless of sample number, sample size or density.     

Evaluation of the non-randomness of protein compositions

A method is described for assessing the non-randomness of protein compositions, based on the chi-squared statistic for the differences between the observed numbers of residues of each type and the numbers expected for a random distribution of codons. The analysis indicates that changes in at least 30% of the residues in natural proteins are selected against.     

Patterns of non-randomness in the exotic avifauna of Florida

It is now generally recognized that human-mediated biological invasion is a multistage process, successively comprising transport, introduction, establishment, and spread, and that a complete understanding of the causes of invasion requires studies of all stages. However, while many studies address the characteristics that influence establishment, relatively few address the characteristics that influence whether or not a species transits the earlier stages of transport and introduction. Here, we use data on the rich exotic avifauna of Florida to assess non-randomness in the identities of species that have passed through the transport and introduction stages. Bird species transported and introduced to Florida are non-random with respect to their taxonomic affiliations, body mass, native geographical range size, and region of origin: introductions are more likely for widespread, large-bodied species from the Neotropics and belonging to the Anatidae, Psittacidae, Ciconiidae, and Passeridae. Data on the identities of species that have attempted to breed but failed, and on the breeding population size for most established species, also allowed us to assess the extent to which the same variables influenced various aspects of post-introduction establishment. Only native geographical range size and latitudinal range mid-point distinguish between these different classes of exotic species. Geographical range size is the most general correlate of different classes of invaders in our analyses.     

Tracking adaptive evolutionary events in genomic sequences

As more gene and genomic sequences from an increasing assortment of species become available, new pictures of evolution are emerging. Improved methods can pinpoint where positive and negative selection act in individual codons in specific genes on specific branches of phylogenetic trees. Positive selection appears to be important in the interaction between genotype, protein structure, function, and organismal phenotype.     

Changes in non-randomness in the expanding introduced avifauna of the world

The identities of bird species introduced to areas beyond the limits of their native geographic ranges have historically depended on a combination of societal demands for species with certain characteristics, and the availability of species for capture, transport and release. However, both societal demands and availability have changed over time, which should also change the characteristics of species more recently added to the list of introduced birds. Here, we quantify temporal changes in selectivity of introduced bird species by comparing the characteristics of 423 species listed in the seminal catalogue of introduced birds (Long, J. L. 1981 . Introduced birds of the world. – David and Charles, London) with those of 122 species that have been introduced but are not listed in Long (1981) . We demonstrate differences between these two groups of species in the frequencies with which different taxa are represented, in the geographic range sizes of species, and in their biogeographic regions of origin, but not in body mass. Both groups also differ from bird species in general in terms of geographic range sizes, body masses, and taxonomic composition. We relate the observed differences in the characteristics of species listed or unlisted in Long (1981) to changes in the changes in attitudes, legislation and vectors of transport relating to exotic species. We conclude by noting that the utility of published catalogues of introduced bird species is increasingly being eroded by the continued liberation and establishment of bird species.     

An investigation of genomic base distribution

While veritable oceans of ink have been spilled over the base distributions within genes, the literature is virtually silent on large scale intra genomic base distribution. To address this issue, we have examined approximately 3400 chromosomal sequences from approximately 2000 entire genomes-including DNA and RNA, single- and double-stranded, coding and non-coding genomes. For each sequence the mean, variance, skewness, and kurtosis for each base were computed along with the genome base composition. The main findings are: (1) there is no simple relationship between these statistics and the base composition of the genome, (2) in non-viral genomes, base distribution is non-uniform, (3) base distribution in non-eukaryotic genomes obeys a number of simple rules, (4) these rules are not dependent on the presence of coding sequences, (5) bacterial genomes in particular are unusually compliant with these rules, and (6) eukaryotes have a unique pattern of base distribution.     

The distribution of events in the human menstrual cycle

Daily reports of 85 married couples concerning their sexual behaviour for about 3 menstrual cycles per couple were organized according to menstrual events by using six techniques of aggregation. While there were some similarities among the different displays, including an apparent peak about 6 days before mid-cycle, different methods of aggregation produce widely different frequency curves. It is concluded that there is no single method of display of events of the menstrual cycle which will fit all investigations.     

Factors contributing to non-randomness in species Co-occurrences on Islands

Summary There has been dispute whether patterns of species co-occurrence on islands are largely random. We present a new method for testing this question; this method lets one not only examine whether a whole fauna is non-randomly structured, but also identify in which direction and by how much each particular species combination deviates from expectations based on randomness. Application of this method to the whole Bismarck and New Hebridean avifaunas, and to two particular guilds, shows that some pairs of species have more exclusive distributions than expected for random placement of species, because of competition, differing distributional strategies, or different geographical orgins. Other pairs of species have more coincident distributions than expected, because of shared habitat, single-island endemism, shared distributional strategies, or shared geographical origins. Much of the information about non-random co-occurrence is contained in the incidence graphs for occurrence of individual species. Finally, our present understanding of assembly rules is summarized.     

Patterns of non-randomness in the composition and characteristics of the Taiwanese bird trade

The invasion pathway is composed of a sequential series of stages that need to be quantified separately in order properly to understand the invasion process. Here, we examine the composition and characteristics of bird species being sold in the pet bird market in Taiwan. The bird trade in Taiwan is of high volume and financially lucrative. The identity of species in this trade is vital for informing later stages (introduction, establishment, spread) of the invasion pathway. We conducted interviews and surveys of 72 outlets selling pet birds from seven cities across Taiwan, from which we identified 247 bird species (within 34 families) for sale. Of these, 170 bird species (from 27 families) are exotic to Taiwan. Using randomization tests, we show that nine families are significantly over-represented in the pet trade (Psittacidae, Muscicapidae, Timaliidae, Sturnidae, Turdidae, Estrildidae, Chloropseidae, Zosteropidae and Fringillidae), and three after sequential Bonferroni correction (Psittacidae, Muscicapidae and Sturnidae). Species that have been identified in Taiwanese pet shops tend to have a larger native geographic range, originate further from the equator, are smaller-bodied, and have more aesthetically-pleasing songs than expected by chance. The native ranges of pet shop species are more likely to be situated in the Indo-Malay and Palearctic biogeographic realms, while fewer species than expected derive from the Neotropic, Afrotropic and Nearctic realms. Our results show that bird species for sale in Taiwan are determined by the interaction of species availability and societal demands.     

Elucidating genomic patterns and recombination events in plant cybrid mitochondria

Plant Molecular Biology - Cybrid plant mitochondria undergo homologous recombination, mainly BIR, keep a single allele for each gene, and maintain exclusive sequences of each parent and a single...     

A generalization of Pielou's index of non-randomness.

Pielou's index of non-randomness a measuring the distribution of point spatial patterns on a plane generalizes to an index in n-dimensional Euclidean space Eⁿ. This defines an index of non-randomness measuring the extent of regularity, randomness, or aggregation in distributions of point spatial patterns in Eⁿ.     

Real-time dynamic imaging of virus distribution in vivo

The distribution of viruses and gene therapy vectors is difficult to assess in a living organism. For instance, trafficking in murine models can usually only be assessed after sacrificing the animal for tissue sectioning or extraction. These assays are laborious requiring whole animal sectioning to ascertain tissue localization. They also obviate the ability to perform longitudinal or kinetic studies in one animal. To track viruses after systemic infection, we have labeled adenoviruses with a near-infrared (NIR) fluorophore and imaged these after intravenous injection in mice. Imaging was able to track and quantitate virus particles entering the jugular vein simultaneous with injection, appearing in the heart within 500 milliseconds, distributing in the bloodstream and throughout the animal within 7 seconds, and that the bulk of virus distribution was essentially complete within 3 minutes. These data provide the first in vivo real-time tracking of the rapid initial events of systemic virus infection.     

Real-time cross-correlation image analysis of early events in IgE receptor signaling

Signaling in mast cells and basophils is mediated through IgE and its high affinity cell surface receptor, FcepsilonRI. Crosslinking of the receptors by a cognate multivalent antigen leads to degranulation and release of mediators of the allergic immune response. Using multicolor fluorescence confocal microscopy, we probed the spatio-temporal dynamics of early events in the IgE receptor signal cascade. We monitored the recruitment of GFP-/CFP-labeled signaling proteins by acquiring sequential images with time resolution of 3 s during stimulation of RBL-2H3 mast cells with multivalent antigen. A fluorescent tag on the antigen allowed us to visualize the plasma membrane localization of crosslinked receptors, and fluorescent cholera toxin B served as a plasma membrane marker. We developed an automated image analysis scheme to quantify the recruitment of fluorescent intracellular proteins to the plasma membrane and to assess the time-dependent colocalization of these and other membrane-associated proteins with crosslinked receptors as measured by cross-correlation between the plasma membrane distributions of the two fluorophores. This automated method permits analysis of thousands of individual images from multiple experiments for each cross-correlation pair. We systematically applied this analysis to characterize stimulated interactions of IgE receptors with several signaling proteins, including the tyrosine kinases Lyn and Syk, and the adaptor protein LAT. Notably, for Syk-CFP we observed a rapid stimulated translocation to the plasma membrane but very little colocalization with aggregated receptors. Our results demonstrate the utility of this simple, automated method to monitor protein interactions quantitatively during cell signaling.     

Real-time measurement of RFR energy distribution in the macaca mulatta head

Temperature increases due to absorption of 1.2 GHz, CW, 70 mW/cm², radio frequency (RF) energy, were measured in 3.3-cm-radius homogeneous muscle-equivalent spheres, M. mulatta cadaver heads (both detached from and attached to the body) and living, anesthetized M. mulatta heads. Temperatures were measured with a Vitek, Model 101 Electrothermia Monitor and temperature distributions were compared to theoretical predictions from a thermal-response model of a simulated cranial structure. The results show that the thermal response model accurately predicts the temperature distribution in muscle-equivalent spheres, the distribution of temperature in detached M. mulatta heads when exposed from the back of the head, and the distribution of temperature in attached M. mulatta cadaver heads for animals oriented with body parallel to the H-field. The temperature distribution in the detached M. mulatta heads varies markedly with exposure orientation, ie, facing forward, backward, or to the side. The orientation of the M. mulatta cadaver body significantly affects the temperature distribution in the head - with H-field orientation showing high, nonuniform values, and E-field orientation showing low, uniform values. In live animals blood flow produces a significant short-term effect on the temperature distribution in the midbrain, but not the cortex. Midbrain temperatures are both significantly higher and lower than the comparable cadaver measurements, depending on location.     

Complex polyandry in the Magnoliatae: definition, distribution and systematic value

A revised definition of complex polyandry is presented for the Magnoliatae. The differences between primary polyandry and secondary (complex) polyandry are clarified. Fascicled stamens are probably not primitive in Magnoliatae. Complex polyandry finds its origin by an increase of stamens in an oligandrous framework. Multiplications of stamens occur either on primary complex primordia, which follow the regular phyllotactic sequence in the flower, either on a girdling primordium (ringwall). The primary primordia may be fully developed before a secondary proliferation of stamens takes place or provide room for more stamens by a continuing growth process. This happens by the development of a staminal tube (e.g. Malvales) or by the growth of a hypanthium (e.g. Myrtales). A typical floral vasculature is developed concomitantly with complex polyandry. Stamen trunk bundles (stamen fascicle traces) are correlated with preformed complex primordia and the absence of a hypanthium. The inception of a ringwall is responsible for a higher complexity in vasculature and for obscuring the identity of the trunk bundles. The presence of a hypanthium does not permit trunk bundle formation because stamens develop on a limited section of the hypanthial slope. In that case the vasculature is characteristically represented by few large bundles linked with the perianth and the androecium. The distribution of complex polyandry is plotted on a Dahlgrenogram and presented in a table. The systematic relevance of complex polyandry is limited to the lower taxonomic (e.g. familial) levels.     

Neural network schemes for detecting rare events in human genomic DNA

MOTIVATION: Many problems in molecular biology as well as other areas involve detection of rare events in unbalanced data. We develop two sample stratification schemes in conjunction with neural networks for rare event detection in such databases. Sample stratification is a technique for making each class in a sample have equal influence on decision making. The first scheme proposed stratifies a sample by adding up the weighted sum of the derivatives during the backward pass of training. The second scheme proposed uses a technique of modified bootstrap aggregating. After training neural networks with multiple sets of bootstrapped examples of the rare event classes and subsampled examples of common event classes, multiple voting for classification is performed. RESULTS: These two schemes make rare event classes have a better chance of being included in the sample used for training neural networks and thus improve the classification accuracy for rare event detection. The experimental performance of the two schemes using two sets of human DNA sequences as well as another set of Gaussian data indicates that proposed schemes have the potential of significantly improving accuracy of neural networks to recognize rare events.