Publications by authors named "Virpi Ahola"

17 Publications

  • Page 1 of 1

Karyotypes versus Genomes: The Nymphalid Butterflies Melitaea cinxia, Danaus plexippus, and D. chrysippus.

Cytogenet Genome Res 2017 2;153(1):46-53. Epub 2017 Nov 2.

Institut für Biologie, Zentrum für medizinische Struktur- und Zellbiologie, Universität zu Lübeck, Lübeck, Germany.

The number of sequenced lepidopteran genomes is increasing rapidly. However, the corresponding assemblies rarely represent whole chromosomes and generally also lack the highly repetitive W sex chromosome. Knowledge of the karyotypes can facilitate genome assembly and further our understanding of sex chromosome evolution in Lepidoptera. Here, we describe the karyotypes of the Glanville fritillary Melitaea cinxia (n = 31), the monarch Danaus plexippus (n = 30), and the African queen D. chrysippus (2n = 60 or 59, depending on the source population). We show by FISH that the telomeres are of the (TTAGG)n type, as found in most insects. M. cinxia and D. plexippus have "conventional" W chromosomes which are heterochromatic in meiotic and somatic cells. In D. chrysippus, the W is inconspicuous. Neither telomeres nor W chromosomes are represented in the published genomes of M. cinxia and D. plexippus. Representation analysis in sequenced female and male D. chrysippus genomes detected an evolutionarily old autosome-Z chromosome fusion in Danaus. Conserved synteny of whole chromosomes, so called "macro synteny", in Lepidoptera permitted us to identify the chromosomes involved in this fusion. An additional and more recent sex chromosome fusion was found in D. chrysippus by karyotype analysis and classical genetics. In a hybrid population between 2 subspecies, D. c. chrysippus and D. c. dorippus, the W chromosome was fused to an autosome that carries a wing colour locus. Thus, cytogenetics and the present state of genome data complement one another to reveal the evolutionary history of the species.
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http://dx.doi.org/10.1159/000484032DOI Listing
January 2018

Ecological and genetic basis of metapopulation persistence of the Glanville fritillary butterfly in fragmented landscapes.

Nat Commun 2017 02 17;8:14504. Epub 2017 Feb 17.

Metapopulation Research Centre, Department of Biosciences, University of Helsinki, PO Box 65, Helsinki FI-00014, Finland.

Ecologists are challenged to construct models of the biological consequences of habitat loss and fragmentation. Here, we use a metapopulation model to predict the distribution of the Glanville fritillary butterfly during 22 years across a large heterogeneous landscape with 4,415 small dry meadows. The majority (74%) of the 125 networks into which the meadows were clustered are below the extinction threshold for long-term persistence. Among the 33 networks above the threshold, spatial configuration and habitat quality rather than the pooled habitat area predict metapopulation size and persistence, but additionally allelic variation in a SNP in the gene Phosphoglucose isomerase (Pgi) explains 30% of variation in metapopulation size. The Pgi genotypes are associated with dispersal rate and hence with colonizations and extinctions. Associations between Pgi genotypes, population turnover and metapopulation size reflect eco-evolutionary dynamics, which may be a common feature in species inhabiting patch networks with unstable local dynamics.
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http://dx.doi.org/10.1038/ncomms14504DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5321745PMC
February 2017

RNA sequencing reveals differential thermal regulation mechanisms between sexes of Glanville fritillary butterfly in the Tianshan Mountains, China.

Mol Biol Rep 2016 Dec 20;43(12):1423-1433. Epub 2016 Sep 20.

College of Life Sciences, Peking University, Beijing, 100871, People's Republic of China.

The Glanville fritillary butterfly (Melitaea cinxia; Nymphalidae) has been extensively studied as a model species in metapopulation ecology. We investigated in the earlier studies that female butterflies exhibit higher thermal tolerance than males in the Tianshan Mountains of China. We aim to understand the molecular mechanism of differences of thermal responses between sexes. We used RNA-seq approach and performed de novo assembly of transcriptome to compare the gene expression patterns between two sexes after heat stress. All the reads were assembled into 84,376 transcripts and 72,701 unigenes. The number of differential expressed genes (DEGs) between control and heat shock samples was 175 and 268 for males and females, respectively. Heat shock proteins genes (hsps) were up-regulated in response to heat stress in both males and females. Most of the up-regulated hsps showed higher fold changes in males than in females. Females expressed more ribosomal subunit protein genes, transcriptional elongation factor genes, and methionine-rich storage protein genes, participating in protein synthesis. It indicated that protein synthesis is needed for females to replace the damaged proteins due to heat shock. In addition, aspartate decarboxylase might contribute to thermal tolerance in females. These differences in gene expression may at least partly explain the response to high temperature stress, and the fact that females exhibit higher thermal tolerance.
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http://dx.doi.org/10.1007/s11033-016-4076-xDOI Listing
December 2016

Flight-induced changes in gene expression in the Glanville fritillary butterfly.

Mol Ecol 2015 Oct;24(19):4886-900

Department of Biosciences, University of Helsinki, P.O. Box 65 (Viikinkaari 1), Helsinki, FI-00014, Finland.

Insect flight is one of the most energetically demanding activities in the animal kingdom, yet for many insects flight is necessary for reproduction and foraging. Moreover, dispersal by flight is essential for the viability of species living in fragmented landscapes. Here, working on the Glanville fritillary butterfly (Melitaea cinxia), we use transcriptome sequencing to investigate gene expression changes caused by 15 min of flight in two contrasting populations and the two sexes. Male butterflies and individuals from a large metapopulation had significantly higher peak flight metabolic rate (FMR) than female butterflies and those from a small inbred population. In the pooled data, FMR was significantly positively correlated with genome-wide heterozygosity, a surrogate of individual inbreeding. The flight experiment changed the expression level of 1513 genes, including genes related to major energy metabolism pathways, ribosome biogenesis and RNA processing, and stress and immune responses. Males and butterflies from the population with high FMR had higher basal expression of genes related to energy metabolism, whereas females and butterflies from the small population with low FMR had higher expression of genes related to ribosome/RNA processing and immune response. Following the flight treatment, genes related to energy metabolism were generally down-regulated, while genes related to ribosome/RNA processing and immune response were up-regulated. These results suggest that common molecular mechanisms respond to flight and can influence differences in flight metabolic capacity between populations and sexes.
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http://dx.doi.org/10.1111/mec.13359DOI Listing
October 2015

Heat shock protein 70 gene family in the Glanville fritillary butterfly and their response to thermal stress.

Gene 2015 Feb 27;556(2):132-41. Epub 2014 Nov 27.

College of Life Science, Peking University, Beijing 100871, PR China. Electronic address:

Temperature variation in the environment is a great challenge to organisms. Induction of heat shock protein 70 (HSP70) is a common genetic mechanism to cope with thermal stress. The Glanville fritillary butterfly (Melitaea cinxia) is a model species in population and evolutionary biology, and its behavior and life history are greatly influenced by ambient temperature. We cloned and sequenced the full coding sequences of seven hsp70 genes from the Glanville fritillary. Of those genes, McHsc70-1 and McHsc70-2 were identified as heat shock cognate 70 (hsc70), of which the latter located in endoplasmic reticulum. We analyzed the expression patterns of different hsp70s under various thermal stresses using quantitative PCR. Heat shock at 40°C for 2h induced high expression of McHsp70-1, McHsp70-2 and McHsc70-2. Only McHsc70-2 had a small increase after cold shock at 0°C for 2h. Acclimation at 35°C for three days before heat shock reduced expression of McHsp70 after heat shock. The maximum mRNA level of McHsp70s was reached in the first 2h after the heat shock. This study uncovers the complexity of the hsp70 system, and provides the valuable information for further temperature-related research in the Glanville fritillary butterfly.
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http://dx.doi.org/10.1016/j.gene.2014.11.043DOI Listing
February 2015

The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera.

Nat Commun 2014 Sep 5;5:4737. Epub 2014 Sep 5.

1] European Bioinformatics Institute, Hinxton CB10 1SD, UK [2] Baylor College of Medicine, Human Genome Sequencing Center, Houston, Texas 77030-3411, USA.

Previous studies have reported that chromosome synteny in Lepidoptera has been well conserved, yet the number of haploid chromosomes varies widely from 5 to 223. Here we report the genome (393 Mb) of the Glanville fritillary butterfly (Melitaea cinxia; Nymphalidae), a widely recognized model species in metapopulation biology and eco-evolutionary research, which has the putative ancestral karyotype of n=31. Using a phylogenetic analyses of Nymphalidae and of other Lepidoptera, combined with orthologue-level comparisons of chromosomes, we conclude that the ancestral lepidopteran karyotype has been n=31 for at least 140 My. We show that fusion chromosomes have retained the ancestral chromosome segments and very few rearrangements have occurred across the fusion sites. The same, shortest ancestral chromosomes have independently participated in fusion events in species with smaller karyotypes. The short chromosomes have higher rearrangement rate than long ones. These characteristics highlight distinctive features of the evolutionary dynamics of butterflies and moths.
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http://dx.doi.org/10.1038/ncomms5737DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4164777PMC
September 2014

Transcriptome analysis reveals signature of adaptation to landscape fragmentation.

PLoS One 2014 2;9(7):e101467. Epub 2014 Jul 2.

Department of Biosciences, University of Helsinki, Helsinki, Finland.

We characterize allelic and gene expression variation between populations of the Glanville fritillary butterfly (Melitaea cinxia) from two fragmented and two continuous landscapes in northern Europe. The populations exhibit significant differences in their life history traits, e.g. butterflies from fragmented landscapes have higher flight metabolic rate and dispersal rate in the field, and higher larval growth rate, than butterflies from continuous landscapes. In fragmented landscapes, local populations are small and have a high risk of local extinction, and hence the long-term persistence at the landscape level is based on frequent re-colonization of vacant habitat patches, which is predicted to select for increased dispersal rate. Using RNA-seq data and a common garden experiment, we found that a large number of genes (1,841) were differentially expressed between the landscape types. Hexamerin genes, the expression of which has previously been shown to have high heritability and which correlate strongly with larval development time in the Glanville fritillary, had higher expression in fragmented than continuous landscapes. Genes that were more highly expressed in butterflies from newly-established than old local populations within a fragmented landscape were also more highly expressed, at the landscape level, in fragmented than continuous landscapes. This result suggests that recurrent extinctions and re-colonizations in fragmented landscapes select a for specific expression profile. Genes that were significantly up-regulated following an experimental flight treatment had higher basal expression in fragmented landscapes, indicating that these butterflies are genetically primed for frequent flight. Active flight causes oxidative stress, but butterflies from fragmented landscapes were more tolerant of hypoxia. We conclude that differences in gene expression between the landscape types reflect genomic adaptations to landscape fragmentation.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0101467PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4079591PMC
October 2015

In vitro maturation supplements affect developmental competence of bovine cumulus-oocyte complexes and embryo quality after vitrification.

Cryobiology 2011 Dec 1;63(3):245-55. Epub 2011 Oct 1.

MTT Agrifood Research Finland, Biotechnology and Food Research, Jokioinen, Finland.

Oocyte quality affects subsequent embryo development and quality. We examined the impact of bovine oocyte in vitro maturation (IVM) conditions on subsequent embryo yield, quality and cryosurvival. Cumulus-oocyte complexes (COCs) were sampled for cytological and gene expression analysis after IVM in TCM199 supplemented with 10% fetal bovine serum (FBS), 4 mg/ml of fatty-acid-free bovine serum albumin (FAFBSA), 4 mg/ml of polyvinylpyrrolidone (PVP), FAFBSA with epidermal growth factor (EGF, 100 ng/ml) and insulin-like growth factor 1 (IGF-I, 100 ng/ml) (FAFBSAGF), PVP with EGF and IGF-I (PVPGF) or PVP with single strength BME and MEM amino acids (PVPAA). The remaining COCs were fertilized. On day 7 (IVF=day 0) quality 1 blastocysts were vitrified or analyzed for glucose transporter 1 (Glut-1) expression levels. The remaining blastocysts (days 7-9) were evaluated for morphology and total cell counts. After warming, survival and hatching rates were evaluated followed by total cell counts and Glut-1 expression levels. Only PVPGF IVM resulted in embryo production rates comparable to those recorded with FBS IVM. Growth factors with FAFBSA and amino acids with PVP reduced embryo production rates whereas the effect of the growth factors with PVP was negligible. Insulin-like growth factor 2 binding protein 3 (IGF2BP3) and beta cell translocation gene 4 (BTG4) were revealed as potential candidates for oocyte developmental competence, and secreted protein, acidic and rich in cysteine (SPARC) for cumulus cell expansion. There were no differences among treatments in hatching rates of vitrified embryos after warming. However, total cell numbers and Glut-1 expression levels at 72 h were affected.
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http://dx.doi.org/10.1016/j.cryobiol.2011.09.134DOI Listing
December 2011

Mapping of QTL affecting incidence of blood and meat inclusions in egg layers.

BMC Genet 2011 Jun 13;12:55. Epub 2011 Jun 13.

Biotechnology and Food Research, MTT, Jokioinen, 31600, Finland.

Background: Occurrence of blood and meat inclusions is an internal egg quality defect. Mass candling reveals most of the spots, but because brown eggshell hampers selection in brown chicken lines it has not been possible to eliminate the defect by selection. Estimated frequency of blood and meat inclusions in brown layers is about 18% whereas it is 0.5% in white egg layers. Several factors are known to increase the incidence of this fault: genetic background, low level of vitamin A and/or D, stress or infections, for instance. To study the genetic background of the defect, a mapping population of 1599 F2 hens from a cross of White Rock and Rhode Island Red lines was set up.

Results: Our histopathological analyses show that blood spots consist of mainly erythrocytes and that meat spots are accumulations of necrotic material. Linkage analysis of 27 chromosomes with 162 microsatellite markers revealed one significant quantitative trait locus (QTL) affecting blood spot and meat spot frequency. We sequenced a fragment of a candidate gene within the region, ZO-2, coding for a tight junction protein. Nine polymorphisms were detected and two of them were included in fine-mapping and association analysis. Fine-mapping defined the QTL result. To further verify the QTL, association analyses were carried out in two independent commercial breeding lines with the marker MCW241 and surrounding SNPs. Association was found mainly in a 0.8 Mb-wide chromosomal area on GGAZ.

Conclusions: There was good agreement between the location of the QTL region on chromosome Z and the association results in the commercial breeds analyzed. Variations found in tight junction protein ZO-2 and microRNA gga-mir-1556 may predispose egg layers to blood and meat spot defects. This paper describes the first results of detailed QTL analyses of the blood and meat spots trait(s) in chickens.
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http://dx.doi.org/10.1186/1471-2156-12-55DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3145579PMC
June 2011

The genome sequence of taurine cattle: a window to ruminant biology and evolution.

Science 2009 Apr;324(5926):522-8

To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
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http://dx.doi.org/10.1126/science.1169588DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2943200PMC
April 2009

Model-based prediction of sequence alignment quality.

Bioinformatics 2008 Oct 4;24(19):2165-71. Epub 2008 Aug 4.

Biotechnology and Food Research, MTT Agrifood Research Finland, FI-31600 Jokioinen, Finland.

Motivation: Multiple sequence alignment (MSA) is an essential prerequisite for many sequence analysis methods and valuable tool itself for describing relationships between protein sequences. Since the success of the sequence analysis is highly dependent on the reliability of alignments, measures for assessing the quality of alignments are highly requisite.

Results: We present a statistical model-based alignment quality score. Unlike other quality scores, it does not require several parallel alignments for the same set of sequences or additional structural information. Our quality score is based on measuring the conservation level of reference alignments in Homstrad. Reference sequences were realigned with the Mafft, Muscle and Probcons alignment programs, and a sum-of-pairs (SP) score was used to measure the quality of the realignments. Statistical modelling of the SP score as a function of conservation level and other alignment characteristics makes it possible to predict the SP score for any global MSA. The predicted SP scores are highly correlated with the correct SP scores, when tested on the Homstrad and SABmark databases. The results are comparable to that of multiple overlap score (MOS) and better than those of normalized mean distance (NorMD) and normalized iRMSD (NiRMSD) alignment quality criteria. Furthermore, the predicted SP score is able to detect alignments with badly aligned or unrelated sequences.

Availability: The method is freely available at http://www.mtt.fi/AlignmentQuality/.
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http://dx.doi.org/10.1093/bioinformatics/btn414DOI Listing
October 2008

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

BMC Bioinformatics 2006 Nov 3;7:484. Epub 2006 Nov 3.

Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, Finland.

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.
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http://dx.doi.org/10.1186/1471-2105-7-484DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1687212PMC
November 2006

Statistical methods for identifying conserved residues in multiple sequence alignment.

Stat Appl Genet Mol Biol 2004 30;3:Article28. Epub 2004 Oct 30.

University of Turku.

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.
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http://dx.doi.org/10.2202/1544-6115.1074DOI Listing
May 2006

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

Proc Natl Acad Sci U S A 2006 Mar 20;103(13):5006-11. Epub 2006 Mar 20.

MTT Agrifood Research Finland, Animal Production Research, Animal Breeding, FIN-31600, Jokioinen, Finland.

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.
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http://dx.doi.org/10.1073/pnas.0506318103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1458785PMC
March 2006

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

Graefes Arch Clin Exp Ophthalmol 2006 May 11;244(5):620-6. Epub 2005 Oct 11.

Department of Ophthalmology, University of Turku, Kiinamyllynkatu 4-8, 20520, Turku, Finland.

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.
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http://dx.doi.org/10.1007/s00417-005-0124-2DOI Listing
May 2006

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

Graefes Arch Clin Exp Ophthalmol 2005 Oct 20;243(10):1010-7. Epub 2005 Oct 20.

Department of Ophthalmology, University of Turku, 20520, Turku, Finland.

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.
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http://dx.doi.org/10.1007/s00417-005-1190-1DOI Listing
October 2005

Efficient estimation of emission probabilities in profile hidden Markov models.

Bioinformatics 2003 Dec;19(18):2359-68

Department of Statistics, FIN-20014 University of Turku, Finland.

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.
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http://dx.doi.org/10.1093/bioinformatics/btg328DOI Listing
December 2003
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