Mating system and the hybridization between self-compatible Phlox cuspidata and self-incompatible Phlox drummondii

Mating system can impact the frequency of hybridization and therefore the maintenance of species diversity. I evaluate the effects of weak self-incompatibility (SI) in Phlox cuspidata and SI in Phlox drummondii on mating success within species and on hybridization dynamics between species under controlled conditions. The effects of SI on hybridization frequency were assessed by manipulating the relatedness of conspecific pollen and the relative timing of pollen deposition in mixed-donor interspecific pollinations. Selfing as opposed to outcrossing increased hybridization by 16% in P. cuspidata maternal plants and by 48% in P. drummondii maternal plants because self pollen did not compete as well against heterospecific pollen. The relative timing of conspecific versus heterospecific pollen deposition also impacted hybridization. In self-compatible P. cuspidata, the deposition of self pollen 5 h earlier than heterospecific pollen decreased hybridization by 28%. In self-incompatible P. drummondii, a 5 h delay in the deposition of compatible conspecific pollen increased hybridization by 32%. In this hybrid system, early self-pollination can decrease hybridization (but increase inbreeding) by P. cuspidata maternal plants, and SI may increase hybridization by P. drummondii maternal plants.     

Quantitative trait loci affecting clinical mastitis and somatic cell count in dairy cattle

Norway has a field recording system for dairy cattle that includes recording of all veterinary treatments on an individual animal basis from 1978 onwards. Application of these data in a genome search for quantitative trait loci (QTL) verified genome-wise significant QTL affecting clinical mastitis on Chromosome (Chr) 6. Additional putative QTL for clinical mastitis were localized to Chrs. 3, 4, 14, and 27. The comprehensive field recording system includes information on somatic cell count as well. This trait is often used in selection against mastitis when direct information on clinical mastitis is not available. The absence of common QTL positions for the two traits in our study indicates that the use of somatic cell count data in QTL studies aimed for reducing the incidence of mastitis should be carefully evaluated. Received: 9 May 2001 / Accepted: 6 July 2001     

Anticodon sequence mutants of Escherichia coli initiator tRNA: effects of overproduction of aminoacyl-tRNA synthetases,methionyl-tRNA formyltransferase,and initiation factor 2 on activity in initiation

Anticodon sequence mutants of Escherichia coli initiator tRNA initiate protein synthesis with codons other than AUG and amino acids other than methionine. Because the anticodon sequence is, in many cases, important for recognition of tRNAs by aminoacyl-tRNA synthetases, the mutant tRNAs are aminoacylated in vivo with different amino acids. The activity of a mutant tRNA in initiation in vivo depends on (i) the level of expression of the tRNA, (ii) the extent of aminoacylation of the tRNA, (iii) the extent of formylation of the aminoacyl-tRNA to formylaminoacyl-tRNA (fAA-tRNA), and (iv) the affinity of the fAA-tRNA for the initiation factor IF2 and the ribosome. Previously, using E. coli overproducing aminoacyl-tRNA synthetases, methionyl-tRNA formyltransferase, or IF2, we identified the steps limiting the activity in initiation of mutant tRNAs aminoacylated with glutamine and valine. Here, we have identified the steps limiting the activity of mutant tRNAs aminoacylated with isoleucine and phenylalanine. The combined results of experiments involving a variety of initiation codons (AUG, UAG, CAG, GUC, AUC, and UUC) provide support to the hypothesis that the ribosome.fAA-tRNA complex can act as an intermediate in initiation of protein synthesis. Comparison of binding affinities of various fAA-tRNAs (fMet-, fGln-, fVal-, fIle-, and fPhe-tRNAs) to IF2 using surface plasmon resonance supports the idea that IF2 can act as a carrier of fAA-tRNA to the ribosome. Other results suggest that the C1xA72 base pair mismatch, unique to eubacterial and organellar initiator tRNAs, may also be important for the binding of fAA-tRNA to IF2.     

WormBase: a cross-species database for comparative genomics

WormBase (http://www.wormbase.org/) is a web-accessible central data repository for information about Caenorhabditis elegans and related nematodes. The past two years have seen a significant expansion in the biological scope of WormBase, including the integration of large-scale, genome-wide data sets, the inclusion of genome sequence and gene predictions from related species and active literature curation. This expansion of data has also driven the development and refinement of user interfaces and operability, including a new Genome Browser, new searches and facilities for data access and the inclusion of extensive documentation. These advances have expanded WormBase beyond the obvious target audience of C. elegans researchers, to include researchers wishing to explore problems in functional and comparative genomics within the context of a powerful genetic system.     

Textpresso: an ontology-based information retrieval and extraction system for biological literature

We have developed Textpresso, a new text-mining system for scientific literature whose capabilities go far beyond those of a simple keyword search engine. Textpresso's two major elements are a collection of the full text of scientific articles split into individual sentences, and the implementation of categories of terms for which a database of articles and individual sentences can be searched. The categories are classes of biological concepts (e.g., gene, allele, cell or cell group, phenotype, etc.) and classes that relate two objects (e.g., association, regulation, etc.) or describe one (e.g., biological process, etc.). Together they form a catalog of types of objects and concepts called an ontology. After this ontology is populated with terms, the whole corpus of articles and abstracts is marked up to identify terms of these categories. The current ontology comprises 33 categories of terms. A search engine enables the user to search for one or a combination of these tags and/or keywords within a sentence or document, and as the ontology allows word meaning to be queried, it is possible to formulate semantic queries. Full text access increases recall of biological data types from 45% to 95%. Extraction of particular biological facts, such as gene-gene interactions, can be accelerated significantly by ontologies, with Textpresso automatically performing nearly as well as expert curators to identify sentences; in searches for two uniquely named genes and an interaction term, the ontology confers a 3-fold increase of search efficiency. Textpresso currently focuses on Caenorhabditis elegans literature, with 3,800 full text articles and 16,000 abstracts. The lexicon of the ontology contains 14,500 entries, each of which includes all versions of a specific word or phrase, and it includes all categories of the Gene Ontology database. Textpresso is a useful curation tool, as well as search engine for researchers, and can readily be extended to other organism-specific corpora of text. Textpresso can be accessed at http://www.textpresso.org or via WormBase at http://www.wormbase.org.     

Towards a working list of all known plant species

A complete listing of the world's known plant species has long been considered desirable but has remained an elusive target for generations of botanists. The adoption of the Global Strategy for Plant Conservation has reinforced the urgent need for a global plant checklist to support, facilitate and monitor the conservation and sustainable use of plant diversity worldwide. The increasing availability of large databases of biological information over the Internet has demonstrated that many of the obstacles to the collation and dissemination of vast, shared datasets can be overcome. We examine the challenges that still remain to be addressed if the botanical community is to achieve its ambitious objective of delivering a working list of all known plant species by 2010.     

Use of the radiation-inducible WAF1 promoter to drive iNOS gene therapy as a novel anti-cancer treatment

BACKGROUND: Inducible nitric oxide synthase (iNOS) gene therapy has been identified as a potential anti-tumour strategy. A major problem common to most gene therapy strategies is targeting of treatment to the tumour volume. In this study we report on the use of the X-ray-inducible WAF1 promoter to achieve targeting of iNOS expression to the tumour volume. METHODS: A WAF1/iNOS/liposome complex was injected directly into RIF-1 and HT29 tumours in mice. A 4 Gy dose of X-rays was applied to induce the WAF1 promoter followed, 8 h later, by treatment doses of 10 or 20 Gy. Tumour volume was measured, and growth curves plotted. RESULTS: Intra-tumoural injection of WAF1/iNOS combined with a priming dose of X-rays to induce the WAF1 promoter, followed by a treatment dose, resulted in sensitiser enhancement ratios of 2.0 and 1.3 in RIF-1 and HT29 tumours, respectively, compared with radiation treatment alone. PCR analysis of organ tissue after intra-tumoural injection of WAF1/iNOS showed that vector sequences were detected in all tissue tested; however, Western blot analysis revealed that iNOS protein levels were significantly increased only in tumour and the surrounding dermal tissue that had been exposed to the 4 Gy inducing dose. CONCLUSIONS: iNOS gene therapy in combination with an inducible promoter results in significant tumour cell radiosensitisation. The WAF1 promoter may be a good candidate for a gene therapy as it is silent in normal tissue yet can be induced by the tumour environment.     

RFMix: A Discriminative Modeling Approach for Rapid and Robust Local-Ancestry Inference

Local-ancestry inference is an important step in the genetic analysis of fully sequenced human genomes. Current methods can only detect continental-level ancestry (i.e., European versus African versus Asian) accurately even when using millions of markers. Here, we present RFMix, a powerful discriminative modeling approach that is faster (∼30×) and more accurate than existing methods. We accomplish this by using a conditional random field parameterized by random forests trained on reference panels. RFMix is capable of learning from the admixed samples themselves to boost performance and autocorrect phasing errors. RFMix shows high sensitivity and specificity in simulated Hispanics/Latinos and African Americans and admixed Europeans, Africans, and Asians. Finally, we demonstrate that African Americans in HapMap contain modest (but nonzero) levels of Native American ancestry (∼0.4%).     

Environmental effects on pollen-pistil compatibility between Phlox cuspidata and P. drummondii (Polemoniaceae): implications for hybridization dynamics

Postpollination mechanisms of reproductive isolation can critically influence the amount of gene flow between hybridizing species. While much evidence exists for genetically based pollen-pistil incompatibility, we show that environmental variation also influences the postpollination performance of heterospecific pollen in the annual Phlox hybrid system. Thus, the environmental segregation of species can influence hybridization dynamics. We found that P. cuspidata was restricted to soils of low Ca concentrations in the field and performed better under experimentally low Ca; P. drummondii was able to inhabit high-Ca soils and sometimes performed better in this environment. To determine whether soil Ca influenced pollen-pistil compatibility in a manner that alters pollen siring success, single-donor pollinations were performed in a completely factorial crossing design between species, maternal Ca environments, and paternal Ca environments. Maternal and paternal environments interacted in their effects on pollen-pistil compatibility for both inter- and intraspecific crosses, such that pollen performance was highest when mothers and fathers were grown in different soil Ca environments. These results suggest that when Phlox species predictably inhabit different environments, environmental heterogeneity can impede the processes of speciation and local adaptation by enhancing the performance of pollen dispersed across species and environments.     

Adult vascular smooth muscle cells in culture express neural stem cell markers typical of resident multipotent vascular stem cells

Differentiation of resident multipotent vascular stem cells (MVSCs) or de-differentiation of vascular smooth muscle cells (vSMCs) might be responsible for the SMC phenotype that plays a major role in vascular diseases such as arteriosclerosis and restenosis. We examined vSMCs from three different species (rat, murine and bovine) to establish whether they exhibit neural stem cell characteristics typical of MVSCs. We determined their SMC differentiation, neural stem cell marker expression and multipotency following induction in vitro by using immunocytochemistry, confocal microscopy, fluorescence-activated cell sorting analysis and quantitative real-time polymerase chain reaction. MVSCs isolated from rat aortic explants, enzymatically dispersed rat SMCs and rat bone-marrow-derived mesenchymal stem cells served as controls. Murine carotid artery lysates and primary rat aortic vSMCs were both myosin-heavy-chain-positive but weakly expressed the neural crest stem cell marker, Sox10. Each vSMC line examined expressed SMC differentiation markers (smooth muscle α–actin, myosin heavy chain and calponin), neural crest stem cell markers (Sox10⁺, Sox17⁺) and a glia marker (S100β⁺). Serum deprivation significantly increased calponin and myosin heavy chain expression and decreased stem cell marker expression, when compared with serum-rich conditions. vSMCs did not differentiate to adipocytes or osteoblasts following adipogenic or osteogenic inductive stimulation, respectively, or respond to transforming growth factor-β1 or Notch following γ-secretase inhibition. Thus, vascular SMCs in culture express neural stem cell markers typical of MVSCs, concomitant with SMC differentiation markers, but do not retain their multipotency. The ultimate origin of these cells might have important implications for their use in investigations of vascular proliferative disease in vitro.