Facilitating functional annotation of chicken microarray data

<p>Abstract</p> <p>Background</p> <p>Modeling results from chicken microarray studies is challenging for researchers due to little functional annotation associated with these arrays. The Affymetrix GenChip chicken genome array, one of the biggest arrays that serve as a key research tool for the study of chicken functional genomics, is among the few arrays that link gene products to Gene Ontology (GO). However the GO annotation data presented by Affymetrix is incomplete, for example, they do not show references linked to manually annotated functions. In addition, there is no tool that facilitates microarray researchers to directly retrieve functional annotations for their datasets from the annotated arrays. This costs researchers amount of time in searching multiple GO databases for functional information.</p> <p>Results</p> <p>We have improved the breadth of functional annotations of the gene products associated with probesets on the Affymetrix chicken genome array by 45% and the quality of annotation by 14%. We have also identified the most significant diseases and disorders, different types of genes, and known drug targets represented on Affymetrix chicken genome array. To facilitate functional annotation of other arrays and microarray experimental datasets we developed an Array GO Mapper (<it>AGOM</it>) tool to help researchers to quickly retrieve corresponding functional information for their dataset.</p> <p>Conclusion</p> <p>Results from this study will directly facilitate annotation of other chicken arrays and microarray experimental datasets. Researchers will be able to quickly model their microarray dataset into more reliable biological functional information by using <it>AGOM </it>tool. The disease, disorders, gene types and drug targets revealed in the study will allow researchers to learn more about how genes function in complex biological systems and may lead to new drug discovery and development of therapies. The GO annotation data generated will be available for public use via AgBase website and will be updated on regular basis.</p

Mutation Screening of Multiple Genes in Spanish Patients with Autosomal Recessive Retinitis Pigmentosa by Targeted Resequencing

Retinitis Pigmentosa (RP) is a heterogeneous group of inherited retinal dystrophies characterised ultimately by the loss of photoreceptor cells. RP is the leading cause of visual loss in individuals younger than 60 years, with a prevalence of about 1 in 4000. The molecular genetic diagnosis of autosomal recessive RP (arRP) is challenging due to the large genetic and clinical heterogeneity. Traditional methods for sequencing arRP genes are often laborious and not easily available and a screening technique that enables the rapid detection of the genetic cause would be very helpful in the clinical practice. The goal of this study was to develop and apply microarray-based resequencing technology capable of detecting both known and novel mutations on a single high-throughput platform. Hence, the coding regions and exon/intron boundaries of 16 arRP genes were resequenced using microarrays in 102 Spanish patients with clinical diagnosis of arRP. All the detected variations were confirmed by direct sequencing and potential pathogenicity was assessed by functional predictions and frequency in controls. For validation purposes 4 positive controls for variants consisting of previously identified changes were hybridized on the array. As a result of the screening, we detected 44 variants, of which 15 are very likely pathogenic detected in 14 arRP families (14%). Finally, the design of this array can easily be transformed in an equivalent diagnostic system based on targeted enrichment followed by next generation sequencing

Prebiotic effects of a wheat germ preparation in human healthy subjects

A double-blind placebo-controlled study was performed to investigate the behaviour of different intestinal bacterial groups in 32 healthy subjects during treatment with the prebiotic wheat germ preparation Viogerm\uaePB1. Microbiological methods and fluorescent in situ hybridization technique were used to identify the following bacterial groups: coliforms, clostridia, bacteroides, lactobacilli and bifidobacteria. After 20 days of supplementation of the product, the coliform population and pH decreased significantly. The number of lactobacilli and bifidobacteria increased significantly only in subjects with low basal levels. No significant changes were observed for the other bacterial groups and total bacteria did not increase. Treatment with placebo did not induce any variation. These results showed that the product Viogerm\uaePB1 possesses a prebiotic effect and has a potential to improve host's health

Prebiotic effects of a wheat germ preparation in human healthy subjects

A double-blind placebo-controlled study was performed to investigate the behaviour of different intestinal bacterial groups in 32 healthy subjects during treatment with the prebiotic wheat germ preparation ViogermsPB1. Microbiological methods and fluorescent in situ hybridization technique were used to identify the following bacterial groups: coliforms, clostridia, bacteroides, lactobacilli and bifidobacteria. After 20 days of supplementation of the product, the coliform population and pH decreased significantly. The number of lactobacilli and bifidobacteria increased significantly only in subjects with low basal levels. No significant changes were observed for the other bacterial groups and total bacteria did not increase. Treatment with placebo did not induce any variation. These results showed that the product ViogermsPB1 possesses a prebiotic effect and has a potential to improve host\u2019s healt