Comparative floral biology of Penstemon eatonii and Penstemon cyananthus in central Utah: a preliminary study

A comparison of the floral visitors of two closely related plant species, Penstemon cyananthus and P. eatonii suggests that flower shape and color may affect the number and type of pollinators, and the ability of the plant to set fruit. Penstemon cyananthus, which is most attractive to hymenopteran visitors, has a blue flower, large in diameter, that is positioned as a convenient “landing pad.” Although many types of insects visit the flower, the transport of pollen directly to flowers of another individual of the same species is somewhat inefficient, since fruiting success is low (66.7 percent). The tubular red flowers of P. eatonii are narrow and droop downward from the stem. The nectar is accessible to a specific and well-adapted visitor, the hummingbird. This less promiscuous, bird-pollinated species sets fruit more successfully (82.4 percent) than P. cyananthus.     

The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism

Here we present a draft genome sequence of the nematode Pristionchus pacificus, a species that is associated with beetles and is used as a model system in evolutionary biology. With 169 Mb and 23,500 predicted protein-coding genes, the P. pacificus genome is larger than those of Caenorhabditis elegans and the human parasite Brugia malayi. Compared to C. elegans, the P. pacificus genome has more genes encoding cytochrome P450 enzymes, glucosyltransferases, sulfotransferases and ABC transporters, many of which were experimentally validated. The P. pacificus genome contains genes encoding cellulase and diapausin, and cellulase activity is found in P. pacificus secretions, indicating that cellulases can be found in nematodes beyond plant parasites. The relatively higher number of detoxification and degradation enzymes in P. pacificus is consistent with its necromenic lifestyle and might represent a preadaptation for parasitism. Thus, comparative genomics analysis of three ecologically distinct nematodes offers a unique opportunity to investigate the association between genome structure and lifestyle.     

Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2)

Streptomyces coelicolor is a representative of the group of soil-dwelling, filamentous bacteria responsible for producing most natural antibiotics used in human and veterinary medicine. Here we report the 8,667,507 base pair linear chromosome of this organism, containing the largest number of genes so far discovered in a bacterium. The 7,825 predicted genes include more than 20 clusters coding for known or predicted secondary metabolites. The genome contains an unprecedented proportion of regulatory genes, predominantly those likely to be involved in responses to external stimuli and stresses, and many duplicated gene sets that may represent 'tissue-specific' isoforms operating in different phases of colonial development, a unique situation for a bacterium. An ancient synteny was revealed between the central 'core' of the chromosome and the whole chromosome of pathogens Mycobacterium tuberculosis and Corynebacterium diphtheriae. The genome sequence will greatly increase our understanding of microbial life in the soil as well as aiding the generation of new drug candidates by genetic engineering.     

Generation and annotation of the DNA sequences of human chromosomes 2 and 4

Human chromosome 2 is unique to the human lineage in being the product of a head-to-head fusion of two intermediate-sized ancestral chromosomes. Chromosome 4 has received attention primarily related to the search for the Huntington's disease gene, but also for genes associated with Wolf-Hirschhorn syndrome, polycystic kidney disease and a form of muscular dystrophy. Here we present approximately 237 million base pairs of sequence for chromosome 2, and 186 million base pairs for chromosome 4, representing more than 99.6% of their euchromatic sequences. Our initial analyses have identified 1,346 protein-coding genes and 1,239 pseudogenes on chromosome 2, and 796 protein-coding genes and 778 pseudogenes on chromosome 4. Extensive analyses confirm the underlying construction of the sequence, and expand our understanding of the structure and evolution of mammalian chromosomes, including gene deserts, segmental duplications and highly variant regions.     

A new species of Phrynobatrachus (Amphibia: Anura: Phrynobatrachidae) from the Northern Mountains of Tanzania

ABSTRACT

Using integrative approaches, a new large-bodied species of Phrynobatrachus is described from a series of 48 specimens from the montane forests of the West Usambara and North Pare Mountains of Tanzania. The most distinguishing morphological feature separating Phrynobatrachus ambanguluensis sp. nov from similar species is the markedly overhanging and pointed upper jaw and snout. Mitochondrial 16S rRNA indicates that the new species differs from all other species with published sequence data by a minimum distance of 4.75% and is sister to P. krefftii, with which it has been confused in the past. The new species is known from two forest reserves and is of high conservation concern given these areas are highly impacted by anthropogenic change.

http://www.zoobank.org/urn:lsid:zoobank.org:pub:E0C82A87-47A5-426B-978D-96D27FA7A3B7     

Perinatal lethal osteogenesis imperfecta in transgenic mice bearing an engineered mutant pro-alpha 1(I) collagen gene

Substitutions of single glycine residues of alpha 1(I) collagen have previously been associated with the inherited disease osteogenesis imperfecta type II. Transgenic mice bearing a mutant alpha 1(I) collagen gene into which specific glycine substitutions have been engineered show a dominant lethal phenotype characteristic of the human disease, and demonstrate that as little as 10% mutant gene expression can disrupt normal collagen function.     

A novel retinoblastoma therapy from genomic and epigenetic analyses

Retinoblastoma is an aggressive childhood cancer of the developing retina that is initiated by the biallelic loss of RB1. Tumours progress very quickly following RB1 inactivation but the underlying mechanism is not known. Here we show that the retinoblastoma genome is stable, but that multiple cancer pathways can be epigenetically deregulated. To identify the mutations that cooperate with RB1 loss, we performed whole-genome sequencing of retinoblastomas. The overall mutational rate was very low; RB1 was the only known cancer gene mutated. We then evaluated the role of RB1 in genome stability and considered non-genetic mechanisms of cancer pathway deregulation. For example, the proto-oncogene SYK is upregulated in retinoblastoma and is required for tumour cell survival. Targeting SYK with a small-molecule inhibitor induced retinoblastoma tumour cell death in vitro and in vivo. Thus, retinoblastomas may develop quickly as a result of the epigenetic deregulation of key cancer pathways as a direct or indirect result of RB1 loss.     

Whole-genome analysis informs breast cancer response to aromatase inhibition

To correlate the variable clinical features of oestrogen-receptor-positive breast cancer with somatic alterations, we studied pretreatment tumour biopsies accrued from patients in two studies of neoadjuvant aromatase inhibitor therapy by massively parallel sequencing and analysis. Eighteen significantly mutated genes were identified, including five genes (RUNX1, CBFB, MYH9, MLL3 and SF3B1) previously linked to haematopoietic disorders. Mutant MAP3K1 was associated with luminal A status, low-grade histology and low proliferation rates, whereas mutant TP53 was associated with the opposite pattern. Moreover, mutant GATA3 correlated with suppression of proliferation upon aromatase inhibitor treatment. Pathway analysis demonstrated that mutations in MAP2K4, a MAP3K1 substrate, produced similar perturbations as MAP3K1 loss. Distinct phenotypes in oestrogen-receptor-positive breast cancer are associated with specific patterns of somatic mutations that map into cellular pathways linked to tumour biology, but most recurrent mutations are relatively infrequent. Prospective clinical trials based on these findings will require comprehensive genome sequencing.     

Stability and change in ethnic groups in England and Wales

The Office for National Statistics (ONS) Longitudinal Study (LS) is an exceptional resource for exploring dynamic processes in individuals' lives for a representative sample of the population of England and Wales and across a thirty year period, including how those processes vary by ethnic group. However, analyses tend to assume a certain stability in the meaning of the ethnic group being studied: the insights into ethnic group differentiation are premised on the fact that the group has the same meaning over time. Here we show how the LS allows us to challenge such notions of group stability. This has practical implications for the ways we measure and conceive of Britain's minority ethnic groups. We illustrate this point with two examples: one exploring the change in ethnic group identification by the same individuals between 1991 and 2001, and the second exploring how loss to follow up is differentially experienced according to ethnic group. We provide some suggestions on the implications of this ethnic group instability for other research.