Biomedical subjects

Virpi Ahola

Publications and source records attributed to Virpi Ahola.

6 recordsLinked to original sources

PubMed2006

A statistical score for assessing the quality of multiple sequence alignments.

BACKGROUND: Multiple sequence alignment is the foundation of many important applications in bioinformatics that aim at detecting functionally important regions, predicting protein structures, building phylogenetic trees etc. Although the automatic construction of a multiple sequence alignment for a set of remotely related sequences cause a very challenging and error-prone task, many downstream analyses still rely heavily on the accuracy of the alignments. RESULTS: To address the need for an objective evaluation framework, we introduce a statistical score that assesses the quality of a given multiple sequence alignment. The quality assessment is based on counting the number of significantly conserved positions in the alignment using importance sampling method in conjunction with statistical profile analysis framework. We first evaluate a novel objective function used in the alignment quality score for measuring the positional conservation. The results for the Src homology 2 (SH2) domain, Ras-like proteins, peptidase M13, subtilase and beta-lactamase families demonstrate that the score can distinguish sequence patterns with different degrees of conservation. Secondly, we evaluate the quality of the alignments produced by several widely used multiple sequence alignment programs using a novel alignment quality score and a commonly used sum of pairs method. According to these results, the Mafft strategy L-INS-i outperforms the other methods, although the difference between the Probcons, TCoffee and Muscle is mostly insignificant. The novel alignment quality score provides similar results than the sum of pairs method. CONCLUSION: The results indicate that the proposed statistical score is useful in assessing the quality of multiple sequence alignments.

Algorithms↗

PubMed2006

An intronic insertion in KPL2 results in aberrant splicing and causes the immotile short-tail sperm defect in the pig.

The immotile short-tail sperm defect is an autosomal recessive disease within the Finnish Yorkshire pig population. This disease specifically affects the axoneme structure of sperm flagella, whereas cilia in other tissues appear unaffected. Recently, the disease locus was mapped to a 3-cM region on porcine chromosome 16. To facilitate identification of candidate genes, we constructed a porcine-human comparative map, which anchored the disease locus to a region on human chromosome 5p13.2 containing eight annotated genes. Sequence analysis of a candidate gene KPL2 revealed the presence of an inserted retrotransposon within an intron. The insertion affects splicing of the KPL2 transcript in two ways; it either causes skipping of the upstream exon, or causes the inclusion of an intronic sequence as well as part of the insertion in the transcript. Both changes alter the reading frame leading to premature termination of translation. Further work revealed that the aberrantly spliced exon is expressed predominantly in testicular tissue, which explains the tissue-specificity of the immotile short-tail sperm defect. These findings show that the KPL2 gene is important for correct axoneme development and provide insight into abnormal sperm development and infertility disorders.

Alternative Splicing↗

PubMed2005

Endophthalmitis following cataract surgery in southwest Finland from 1987 to 2000.

PURPOSE: To investigate the incidence, causes, prevention, treatment and outcome of postoperative endophthalmitis (POE) following cataract surgery in southwest Finland from 1987 to 2000. METHODS: We reviewed the medical records of all patients with POE following cataract surgery treated in the hospital district of Southwest Finland from 1 January 1987 to 31 December 2000. Population-based annual incidence rates of cataract extractions and POE were calculated using the corrected population statistics of the hospital district. RESULTS: There were 29,350 cataract procedures during the 14-year period. POE developed in 47 patients. The annual incidence of cataract operations increased more than fivefold from 1987 (155 per 100,000 population) to the maximum in 1999 (930 per 100,000 population), whereas the annual incidence of postcataract endophthalmitis decreased from the maximum of 11.1 per 1,000 cataract extractions (1.91 per 100,000 population) in 1988 to the minimum of 0-0.6 per 1,000 cataract extractions in 1999 and 2000. POE occurred statistically significantly more frequently after extracapsular cataract extraction (ECCE) than after phacoemulsification (Phaco) (P=0.0006). Gram-positive bacteria were the most frequent cause of acute POE and Propionibacterium acnes was the most frequent reason for delayed-onset POE. The complications of POE after cataract surgery included visual loss to below 0.05 (25.5% of affected eyes), opacification of the cornea (21.3%), secondary cataract (40.4%), increase in intraocular pressure (29.8%), vitreous clouding (63.8%), and retinal detachment (6.4%). Nearly one half of the eyes achieved final visual acuity of 0.5 or better. CONCLUSIONS: During the 14-year study period there was a shift from ECCE to Phaco, a fivefold increase in cataract extractions, and a decrease in the annual incidence of POE from 5.5-11.1 to 0-0.6 per 1,000 operations. Phaco was associated with a lower risk of POE than ECCE.

Adult↗

PubMed2005

Comparison of topical 0.7% dexamethasone-cyclodextrin with 0.1% dexamethasone sodium phosphate for postcataract inflammation.

BACKGROUND: To compare 0.7% dexamethasone-cyclodextrin aqueous eye drop solution applied once daily with 0.1% dexamethasone sodium phosphate eye drops applied three times a day for the control of postoperative inflammation after cataract surgery. METHODS: Twenty cataract patients who underwent phacoemulsification and intraocular lens implantation were randomly divided into two postoperative treatment groups. Postoperative medication in group I included 0.1% dexamethasone sodium phosphate eye drops three times daily and in group II 0.7% dexamethasone-cyclodextrin eye drop solution once daily. Testing of visual acuity, biomicroscopic examination, applanation tonometry and laser flare cell meter (LFCM) examination were carried out before operation and days 1, 3, 7 and 21 after surgery. RESULTS: Preoperative and postoperative visual acuity, aqueous flare and cells in biomicroscopic examination, and the mean intraocular pressure did not show any statistically significant differences between the treatment groups. LFCM examination showed that the mean postoperative photon count values (P=0.032) and the median cell count values on the 1st (P=0.014), 3rd (P=0.031), 7th (P=0.034), and 21st (P=0.0097) postoperative days in group I were more elevated than in group II. CONCLUSIONS: 0.7% dexamethasone-cyclodextrin eye drops applied once daily is a more effective postoperative anti-inflammatory medication than 0.1% dexamethasone sodium phosphate applied three times a day. In both groups, 3 weeks after the operation the mean visual acuity was normal and intraocular pressure significantly lower than before operation. The use of 0.7% dexamethasone-cyclodextrin eye drops may be useful especially in elderly people who cannot apply themselves the eye drops onto the eye.

Administration, Topical↗

PubMed2004

Statistical methods for identifying conserved residues in multiple sequence alignment.

The assessment of residue conservation in a multiple sequence alignment is a central issue in bioinformatics. Conserved residues and regions are used to determine structural and functional motifs or evolutionary relationships between the sequences of a multiple sequence alignment. For this reason, residue conservation is a valuable measure for database and motif search or for estimating the quality of alignments. In this paper, we present statistical methods for identifying conserved residues in multiple sequence alignments. While most earlier studies examine the positional conservation of the alignment, we focus on the detection of individual conserved residues at a position. The major advantages of multiple comparison methods originate from their ability to select conserved residues simultaneously and to consider the variability of the residue estimates. Large-scale simulations were used for the comparative analysis of the methods. Practical performance was studied by comparing the structurally and functionally important residues of Src homology 2 (SH2) domains to the assignments of the conservation indices. The applicability of the indices was also compared in three additional protein families comprising different degrees of entropy and variability in alignment positions. The results indicate that statistical multiple comparison methods are sensitive and reliable in identifying conserved residues.

Journal Article↗

PubMed2003

Efficient estimation of emission probabilities in profile hidden Markov models.

MOTIVATION: Profile hidden Markov models provide a sensitive method for performing sequence database search and aligning multiple sequences. One of the drawbacks of the hidden Markov model is that the conserved amino acids are not emphasized, but signal and noise are treated equally. For this reason, the number of estimated emission parameters is often enormous. Focusing the analysis on conserved residues only should increase the accuracy of sequence database search. RESULTS: We address this issue with a new method for efficient emission probability (EEP) estimation, in which amino acids are divided into effective and ineffective residues at each conserved alignment position. A practical study with 20 protein families demonstrated that the EEP method is capable of detecting family members from other proteins with sensitivity of 98% and specificity of 99% on the average, even if the number of free emission parameters was decreased to 15% of the original. In the database search for TIM barrel sequences, EEP recognizes the family members nearly as accurately as HMMER or Blast, but the number of false positive sequences was significantly less than that obtained with the other methods. AVAILABILITY: The algorithms written in C language are available on request from the authors.

Algorithms↗