Reference gene alternatives to <Emphasis Type="Italic">Gapdh</Emphasis> in rodent and human heart failure gene expression studies

Background  

Quantitative real-time RT-PCR (RT-qPCR) is a highly sensitive method for mRNA quantification, but requires invariant expression of the chosen reference gene(s). In pathological myocardium, there is limited information on suitable reference genes other than the commonly used Gapdh mRNA and 18S ribosomal RNA. Our aim was to evaluate and identify suitable reference genes in human failing myocardium, in rat and mouse post-myocardial infarction (post-MI) heart failure and across developmental stages in fetal and neonatal rat myocardium.     

Characterization and expression patterns of <Emphasis Type="Italic">let-7</Emphasis> microRNA in the silkworm (<Emphasis Type="Italic">Bombyx mori</Emphasis>)

Background  

lin-4 and let-7, the two founding members of heterochronic microRNA genes, are firstly confirmed in Caenorhabditis elegans to control the proper timing of developmental programs in a heterochronic pathway. let-7 has been thought to trigger the onset of adulthood across animal phyla. Ecdysone and Broad-Complex are required for the temporal expression of let-7 in Drosophila melanogaster. For a better understanding of the conservation and functions of let-7, we seek to explore how it is expressed in the silkworm (Bombyx mori).     

Genetics and geometry of canalization and developmental stability in <Emphasis Type="Italic">Drosophila subobscura</Emphasis>

Background  

Many properties of organisms show great robustness against genetic and environmental perturbations. The terms canalization and developmental stability were originally proposed to describe the ability of an organism to resist perturbations and to produce a predictable target phenotype regardless of random developmental noise. However, the extent to which canalization and developmental stability are controlled by the same set of genes and share underlying regulatory mechanisms is largely unresolved.     

The use of reference gene selection programs to study the silvering transformation in a freshwater eel <Emphasis Type="Italic">Anguilla australis</Emphasis>: a cautionary tale

Background  

Quantitative real-time PCR (qPCR) has been the method of choice for the quantification of mRNA. Due to the various artifactual factors that may affect the accuracy of qPCR, internal reference genes are most often used to normalize qPCR data. Recently, many studies have employed computer programs such as GeNorm, BestKeeper and NormFinder in selecting reference genes, but very few statistically validate the outcomes of these programs. Thus, in this study, we selected reference genes for qPCR of liver and ovary samples of yellow (juvenile), migratory (silver) and 11-KT treated juveniles of New Zealand shortfinned eels (Anguilla australis) using the three computer programs and validate the selected genes statistically using REST 2009 software and the Mann-Whitney test. We also tested for the repeatability of use for the best reference genes by applying them to a data set obtained in a similar experiment conducted the previous year.     

The origin of bmp16, a novel Bmp2/4 relative, retained in teleost fish genomes

Background  

Whole genome sequences have allowed us to have an overview of the evolution of gene repertoires. The target of the present study, the TGFβ superfamily, contains many genes involved in vertebrate development, and provides an ideal system to explore the relationships between evolution of gene repertoires and that of developmental programs.     

Large impact of the apoplast on somatic embryogenesis in <Emphasis Type="Italic">Cyclamen persicum</Emphasis> offers possibilities for improved developmental control <Emphasis Type="Italic">in vitro</Emphasis>

Background  

Clonal propagation is highly desired especially for valuable horticultural crops. The method with the potentially highest multiplication rate is regeneration via somatic embryogenesis. However, this mode of propagation is often hampered by the occurrence of developmental aberrations and non-embryogenic callus. Therefore, the developmental process of somatic embryogenesis was analysed in the ornamental crop Cyclamen persicum by expression profiling, comparing different developmental stages of embryogenic cell cultures, zygotic vs. somatic embryos and embryogenic vs. non-embryogenic cell cultures.     

Identifying candidate genes affecting developmental time in <Emphasis Type="Italic">Drosophila melanogaster</Emphasis>: pervasive pleiotropy and gene-by-environment interaction

Background  

Understanding the genetic architecture of ecologically relevant adaptive traits requires the contribution of developmental and evolutionary biology. The time to reach the age of reproduction is a complex life history trait commonly known as developmental time. In particular, in holometabolous insects that occupy ephemeral habitats, like fruit flies, the impact of developmental time on fitness is further exaggerated. The present work is one of the first systematic studies of the genetic basis of developmental time, in which we also evaluate the impact of environmental variation on the expression of the trait.     

Identification of a <Emphasis Type="Italic">Rice stripe necrosis virus</Emphasis> resistance locus and yield component QTLs using <Emphasis Type="Italic">Oryza sativa</Emphasis> × <Emphasis Type="Italic">O. glaberrima</Emphasis> introgression lines

Background  

Developing new population types based on interspecific introgressions has been suggested by several authors to facilitate the discovery of novel allelic sources for traits of agronomic importance. Chromosome segment substitution lines from interspecific crosses represent a powerful and useful genetic resource for QTL detection and breeding programs.     

Diapause in the pea aphid (<Emphasis Type="Italic">Acyrthosiphon pisum</Emphasis>) is a slowing but not a cessation of development

Background  

Many insects undergo a period of arrested development, called diapause, to avoid seasonally recurring adverse conditions. Whilst the phenology and endocrinology of insect diapause have been well studied, there has been comparatively little research into the developmental details of diapause. We investigated developmental aspects of diapause in sexually-produced embryos of the pea aphid, Acyrthosiphon pisum.     

Studies on <Emphasis Type="Italic">Xenopus laevis</Emphasis>intestine reveal biological pathways underlying vertebrate gut adaptation from embryo to adult

Background  

To adapt to its changing dietary environment, the digestive tract is extensively remodeled from the embryo to the adult during vertebrate development. Xenopus laevis metamorphosis is an excellent model system for studying mammalian gastrointestinal development and is used to determine the genes and signaling programs essential for intestinal development and maturation.     

Riboswitches as hormone receptors: hypothetical cytokinin-binding riboswitches in <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>

Background  

Riboswitches are mRNA elements that change conformation when bound to small molecules. They are known to be key regulators of biosynthetic pathways in both prokaryotes and eukaryotes.     

Identification,cloning and characterization of <Emphasis Type="Italic">sis7</Emphasis> and <Emphasis Type="Italic">sis10</Emphasis> sugar-insensitive mutants of <Emphasis Type="Italic">Arabidopsis</Emphasis>

Background  

The levels of soluble sugars, such as glucose and sucrose, help regulate many plant metabolic, physiological and developmental processes. Genetic screens are helping identify some of the loci involved in plant sugar response and reveal extensive cross-talk between sugar and phytohormone response pathways.     

<Emphasis Type="Italic">ClustalXeed</Emphasis>: a GUI-based grid computation version for high performance and terabyte size multiple sequence alignment

Background  

There is an increasing demand to assemble and align large-scale biological sequence data sets. The commonly used multiple sequence alignment programs are still limited in their ability to handle very large amounts of sequences because the system lacks a scalable high-performance computing (HPC) environment with a greatly extended data storage capacity.     

Parasexual genetics of <Emphasis Type="Italic">Dictyostelium</Emphasis> gene disruptions: identification of a ras pathway using diploids

Background  

The relative ease of targeted gene disruption in the social amoeba Dictyostelium has stimulated its widespread use as an experimental organism for cell and developmental biology. However, the field has been hamstrung by the lack of techniques to recombine disrupted genes.