Algorithms and software for support of gene identification experiments

MOTIVATION: Gene annotation is the final goal of gene prediction algorithms. However, these algorithms frequently make mistakes and therefore the use of gene predictions for sequence annotation is hardly possible. As a result, biologists are forced to conduct time-consuming gene identification experiments by designing appropriate PCR primers to test cDNA libraries or applying RT-PCR, exon trapping/amplification, or other techniques. This process frequently amounts to 'guessing' PCR primers on top of unreliable gene predictions and frequently leads to wasting of experimental efforts. RESULTS: The present paper proposes a simple and reliable algorithm for experimental gene identification which bypasses the unreliable gene prediction step. Studies of the performance of the algorithm on a sample of human genes indicate that an experimental protocol based on the algorithm's predictions achieves an accurate gene identification with relatively few PCR primers. Predictions of PCR primers may be used for exon amplification in preliminary mutation analysis during an attempt to identify a gene responsible for a disease. We propose a simple approach to find a short region from a genomic sequence that with high probability overlaps with some exon of the gene. The algorithm is enhanced to find one or more segments that are probably contained in the translated region of the gene and can be used as PCR primers to select appropriate clones in cDNA libraries by selective amplification. The algorithm is further extended to locate a set of PCR primers that uniformly cover all translated regions and can be used for RT-PCR and further sequencing of (unknown) mRNA.      

Recent evolutionary history of American Onchocerca volvulus, based on analysis of a tandemly repeated DNA sequence family

Polymerase chain reaction (PCR) products were characterized for a repeated sequence family (designated "O-150") of the human filarial parasite Onchocerca volvulus. In phylogenetic inferences, the O-150 sequences clustered into closely related groups, suggesting that concerted evolution maintains sequence homology in this family. Using a novel mathematical model based on a nested application of an analysis of variance, we demonstrated that African rainforest and savannah strain parasite populations are significantly different. In contrast, parasites collected in the New World are indistinguishable from African savannah strains of O. volvulus. This finding supports the hypothesis that onchocerciasis was recently introduced into the New World, possibly as a result of the slave trade.      

Systematics of the Platyrrhinus helleri species complex (Chiroptera: Phyllostomidae), with descriptions of two new species

Platyrrhinus is a diverse genus of small to large phyllostomid bats characterized by a comparatively narrow uropatagium thickly fringed with hair, a white dorsal stripe, comparatively large inner upper incisors that are convergent at the tips, and three upper and three lower molars. Eighteen species are currently recognized, the majority occurring in the Andes. Molecular, morphological, and morphometric analyses of specimens formerly identified as Platyrrhinus helleri support recognition of Platyrrhinus incarum as a separate species and reveal the presence of two species from western and northern South America that we describe herein as new ( Platyrrhinus angustirostris sp. nov. from eastern Colombia and Ecuador, north‐eastern Peru, and Venezuela and Platyrrhinus fusciventris sp. nov. from Guyana, Suriname, French Guiana, Trinidad and Tobago, northern Brazil, eastern Ecuador, and southern Venezuela). These two new species are sister taxa and, in turn, sister to Platyrrhinus incarum. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 159 , 785–812.     

SIMPROT: Using an empirically determined indel distribution in simulations of protein evolution

Background  

General protein evolution models help determine the baseline expectations for the evolution of sequences, and they have been extensively useful in sequence analysis and for the computer simulation of artificial sequence data sets.     

Effect of phytase supplementation on phosphorus digestibility in low-phytate barley fed to finishing pigs

Forty crossbred barrows (Camborough 15 Line female×Canabred sire) weighing an average of 79.6±8.0?kg were used in a factorial design experiment (5 barleys×2 enzyme levels) conducted to determine the effects of phytase supplementation on nutrient digestibility in low-phytate barleys fed to finishing pigs. The pigs were assigned to one of 10 dietary treatments comprised of a normal 2-rowed, hulled variety of barley (CDC Fleet, 0.26% phytate) or 2 low-phytate hulled genotypes designated as LP422 (0.14% phytate) and LP635 (0.09% phytate). A normal, hulless barley (CDC Dawn, 0.26% phytate) and a hulless genotype designated as LP422H (0.14% phytate) were also included. All barleys were fed with and without phytase (Natuphos 5000 FTU/kg). The diets fed contained 98% barley, 0.5% vitamin premix, 0.5% trace mineral premix, 0.5% NaCl and 0.5% chromic oxide but no supplemental phosphorus. The marked feed was provided for a 7-day acclimatization period, followed by a 3-day faecal collection. In the absence of phytase, phosphorus digestibility increased substantially (P<0.05) as the level of phytate in the barley declined. For the hulled varieties, phosphorus digestibility increased from 12.9% for the normal barley (0.26% phytate) to 35.3 and 39.8% for the two low-phytate genotypes (0.14 and 0.09% phytate respectively). For the hulless varieties, phosphorus digestibility increased from 9.2% for the normal barley (0.26% phytate) to 34.7% for the hulless variety with 54% of the normal level of phytate (0.14% phytate). In contrast, when phytase was added to the diet, there was little difference in phosphorus digestibility between pigs fed normal barley and those fed the low-phytate genotypes (significant barley×enzyme interaction, P=0.01). For the hulled varieties, phosphorus digestibility was 50.1% for the barley with the normal level of phytate (0.26% phytate) compared with 51.1 and 52.4% for the varieties with 54 and 35% of the normal level of phytate (0.14 and 0.09% phytate respectively). For the hulless varieties, phosphorus digestibility increased from 47.1% for the normal barley (0.26% phytate) to 54.4% for the hulless variety with 54% of the normal level of phytate (0.14% phytate). In conclusion, both supplementation with phytase and selection for low-phytate genotypes of barley were successful in increasing the digestibility of phosphorus for pigs. Unfortunately, the effects did not appear to be additive. Whether or not swine producers will choose low-phytate barley or supplementation with phytase as a means to improve phosphorus utilization, will likely depend on the yield potential of low-phytate barley and the additional costs associated with supplementation with phytase.     

Reproductive traits of the freshwater oyster Etheria elliptica (Bivalvia: Etheriidae) in the Pendjari River,Benin: implications for conservation

The African freshwater oyster Etheria elliptica, which is of great economic importance throughout the continent, is facing overharvesting in many fisheries in West Africa. Its reproductive traits (sex ratio, size at sexual maturity, oocyte diameter and fecundity) were studied at four stations located along the Pendjari River, northern Benin, in April 2013. Histological techniques were implemented to identify sex and gonad development stages. Oocyte sizes were measured based on the histological images and mean oocyte diameter was 38 µm. Fecundity, estimated by counting the developing eggs, averaged 106 724 eggs and increased significantly with shell size. The average sex ratio was approximately 1:1. Hermaphrodites were rare. Males reached sexual maturity at 57.6 mm dorsoventral height, earlier than females at 64.7 mm. The majority of the oyster specimens were in ripe-spawning stages, indicating that reproductive activities partly took place towards the end of the dry season. Both mature and immature individuals were subjected to harvesting at all the investigated fishing sites. The mean size of exploited oysters was 60.6 mm, lower than the size of females at maturity. Management strategies must enforce the minimum size of 65 mm required for harvesting, particularly in open access sites where juveniles are mostly harvested.