Context based mixture model for cell phase identification in automated fluorescence microscopy

Background  

Automated identification of cell cycle phases of individual live cells in a large population captured via automated fluorescence microscopy technique is important for cancer drug discovery and cell cycle studies. Time-lapse fluorescence microscopy images provide an important method to study the cell cycle process under different conditions of perturbation. Existing methods are limited in dealing with such time-lapse data sets while manual analysis is not feasible. This paper presents statistical data analysis and statistical pattern recognition to perform this task.     

Phenotype ontologies: the bridge between genomics and evolution

Understanding the developmental and genetic underpinnings of particular evolutionary changes has been hindered by inadequate databases of evolutionary anatomy and by the lack of a computational approach to identify underlying candidate genes and regulators. By contrast, model organism studies have been enhanced by ontologies shared among genomic databases. Here, we suggest that evolutionary and genomics databases can be developed to exchange and use information through shared phenotype and anatomy ontologies. This would facilitate computing on evolutionary questions pertaining to the genetic basis of evolutionary change, the genetic and developmental bases of correlated characters and independent evolution, biomedical parallels to evolutionary change, and the ecological and paleontological correlates of particular types of change in genes, gene networks and developmental pathways.     

Meristem fate and bulbil formation in Titanotrichum (Gesneriaceae)

Titanotrichum oldhamii (a monotypic genus from Taiwan, Okinawa, and adjacent regions of China) has inflorescences bearing either showy yellow flowers or asexual bulbils. Asexual reproduction by bulbils is important in natural populations, and bulbil production increases in August and September at the end of the flowering season (which runs from June to the end of September). The bulbils are small (～1-2.5 mm long) and numerous. They consist of a small portion of stem (bract-stem) topped by opposite storage bracts that enclose a minute apical meristem. A secondary root develops from the side of the bract-stem. The floral meristem of T. oldhamii has three possible fates: (1) bulbil formation, (2) flower formation, or (3) bracteose proliferation. Bracteose proliferation rarely occurs and appears to be a developmental transition between the bulbiliferous and racemose inflorescence forms. It is strongly reminiscent of the floricaula and squamosa mutants of Antirrhinum. In the bulbiliferous form a single floral primordium, which would normally produce one flower, gives rise to ～50-70 bulbils by repeated subdivision of the meristem. This form of bulbil production appears to be unique to Titanotrichum. Occasionally a floral meristem divides, but the subdivision forms multiflowered units of up to four flowers rather than bulbils, suggesting that meristem fate is reversible up to the first or second meristem subdivision. In Titanotrichum, therefore, primordium fate is apparently not determined at inception but becomes irreversibly determined shortly after the appearance of developmental characteristics of the floral or bulbil pathway.     

Food choice and feeding on carrion in two African mongoose species in an urban environment

Urbanisation negatively affects many species, yet small carnivores may flourish in urban spaces because of accessible resources and a reduction of predators. Food choices of urban carnivores might be influenced by the availability and abundance of anthropogenic food resources and the co-existence of competing species. We studied the food selection and feeding on carrion of the yellow mongoose (Cynictis penicillata) and slender mongoose (Galerella sanguinea) in a small urban reserve in South Africa. In cafeteria-style food choice tests, both species preferred meat and insects over bread, dog kibble, chicken eggs, and plants; however, yellow mongoose in a more urbanised area preferred bread to insects. Yellow mongoose had a shorter latency to approach and consume provided food compared to slender mongoose. At carrion-baited stations, slender mongoose were more prevalent at carcasses and displayed aggression and competitive exclusion of yellow mongoose. Slender mongoose fed more on carcasses during the colder months than warmer months when they fed on available insects around and on carcasses. The greater consumption of anthropogenic items by yellow mongoose and the preference by slender mongoose for feeding on carcasses provide evidence of possible resource partitioning, which may aid in the co-existence of these sympatric herpestids in urban areas.     

Introduction and synthesis: Plant phylogeny and the origin of major biomes

Phylogenetic trees based upon DNA sequence data, when calibrated with a dimension of time, allow inference of: (i) the pattern of accumulation of lineages through time; (ii) the time of origin of monophyletic groups; (iii) when lineages arrived in different geographical areas; (iv) the time of origin of biome-specific morphologies. This gives a powerful new view of the history of biomes that in many cases is not provided by the incomplete plant fossil record. Dated plant phylogenies for angiosperm families such as Leguminoaceae (Fabaceae), Melastomataceae sensu stricto, Annonaceae and Rhamnaceae indicate that long-distance, transoceanic dispersal has played an important role in shaping their distributions, and that this can obscure any effect of tectonic history, previously assumed to have been the major cause of their biogeographic patterns. Dispersal from other continents has also been important in the assembly of the Amazonian rainforest flora and the Australian flora. Comparison of dated biogeographic patterns of plants and animals suggests that recent long-distance dispersal might be more prevalent in plants, which has major implications for community assembly and coevolution. Dated plant phylogenies also reveal the role of past environmental changes on the evolution of lineages in species-rich biomes, and show that recent Plio-Pleistocene diversification has contributed substantially to their current species richness. Because of the critical role of fossils and morphological characters in assigning ages to nodes in phylogenetic trees, future studies must include careful morphological consideration of fossils and their extant relatives in a phylogenetic context. Ideal study systems will be based upon DNA sequence data from multiple loci and multiple fossil calibrations. This allows cross-validation both of age estimates from different loci, and from different fossil calibrations. For a more complete view of biome history, future studies should emphasize full taxon sampling in ecologically important groups, and should focus on geographical areas for which few species-level phylogenies are available, such as tropical Africa and Asia. These studies are urgent because understanding the history of biomes can both inform conservation decisions, and help predict the effects of future environmental changes at a time when biodiversity is being impacted on an unprecedented scale.     

3D cell nuclei segmentation based on gradient flow tracking

Background  

Reliable segmentation of cell nuclei from three dimensional (3D) microscopic images is an important task in many biological studies. We present a novel, fully automated method for the segmentation of cell nuclei from 3D microscopic images. It was designed specifically to segment nuclei in images where the nuclei are closely juxtaposed or touching each other. The segmentation approach has three stages: 1) a gradient diffusion procedure, 2) gradient flow tracking and grouping, and 3) local adaptive thresholding.     

Phylogeny and disjunct distribution: evolution of Saintpaulia (Gesneriaceae).

The molecular phylogeny of African violets (Saintpaulia H. Wendl.), based on ribosomal DNA internal transcribed spacer (ITS) sequences, follows the disjunct biogeography of the genus. Sequence analysis by parsimony of 19 accessions, representing 17 currently recognized Saintpaulia species, resulted in four trees of 182 steps. The first major division is between S. goetzeana, from the Uluguru Mts, Tanzania, and the rest of the genus. The basal position of S. goetzeana, and its putative primitive characters, may indicate an Uluguru origin for Saintpaulia and subsequent colonization of the more northerly mountains. Of the remainder, S. teitensis, from the Teita Hills of Kenya, is sister taxon to the other species (which occur mainly in the Usambara Mts of north-east Tanzania). A group of nine Usambaran species that we call the ''ionantha complex'' show minimal ITS genetic differentiation and are also taxonomically critical. Species diversity in the Usambara Mts appears to be the result of rapid, recent (possibly Pleistocene) radiation. This study reveals the limitations of ITS sequences for elucidating the radiation of poorly differentiated species (the ionantha complex). However, the molecular data strongly suggest that conservation of the Uluguru and Teita populations is essential for the protection of the full range of diversity within the genus.     

Fetal growth as measured by ultrasound

Until the last decade, investigation of fetal growth has been based on data from premature births and abortuses. Advances in ultrasound scanning have expanded the precision and uses of this technology in studies of fetal growth. Most ultrasound studies of fetal growth are based on clinical populations and are reported in clinical journals. The present paper reviews features of ultrasound technology relating to fetal measurement. The most commonly measured dimensions and their associated measurement errors, distributions and uses are detailed. Ultrasound studies of intrauterine growth retardation and in utero fetal weight estimation are critically reviewed. Finally, a comparison between the fetal growth curve based on ultrasound measurement and on data from preterm or aborted fetuses is compared. Critical comments on sample design and statistical treatment of the data from ultrasound studies is included in each of the areas discussed.