Footnotes, September-October 2004, Vol. 28, no. 9-10

Monthly newsletter of the State Library

Footnotes, July/August 2004, Vol. 28, no. 7-9

Monthly newsletter of the State Library

Report of Recommendations to the Iowa Department of Workforce Development on the Review of Selected General Controls, May 10, 2004 to May 28, 2004

State Agency Audit Report

Footnotes, November-December 2004, Vol. 28, no. 11-12

Monthly newsletter of the State Library

Combining palaeodistribution modelling and phylogeographical approaches for identifying glacial refugia in Alpine Primula

Aim We investigated the late Quaternary history of two closely related and partly sympatric species of Primula from the south-western European Alps, P. latifolia Lapeyr. and P. marginata Curtis, by combining phylogeographical and palaeodistribution modelling approaches. In particular, we were interested in whether the two approaches were congruent and identified the same glacial refugia. Location South-western European Alps. Methods For the phylogeographical analysis we included 353 individuals from 28 populations of P. marginata and 172 individuals from 15 populations of P. latifolia and used amplified fragment length polymorphisms (AFLPs). For palaeodistribution modelling, species distribution models (SDMs) were based on extant species occurrences and then projected to climate models (CCSM, MIROC) of the Last Glacial Maximum (LGM), approximately 21 ka. Results The locations of the modelled LGM refugia were confirmed by various indices of genetic variation. The refugia of the two species were largely geographically isolated, overlapping only 6% to 11% of the species' total LGM distribution. This overlap decreased when the position of the glacial ice sheet and the differential elevational and edaphic distributions of the two species were considered. Main conclusions The combination of phylogeography and palaeodistribution modelling proved useful in locating putative glacial refugia of two alpine species of Primula. The phylogeographical data allowed us to identify those parts of the modelled LGM refugial area that were likely source areas for recolonization. The use of SDMs predicted LGM refugial areas substantially larger and geographically more divergent than could have been predicted by phylogeographical data alone

ABCB1 and cytochrome P450 polymorphisms : clinical pharmacogenetics of clozapine

Résumé : Dans le but d'examiner les facteurs génétiques qui influencent la pharmacocinétique de la clozapine in vivo, 75 patients traités avec ce médicament antipsychotique ont été genotypés pour les polymorphismes CYP et ABCB1, et phénotypés pour l'activité de CYP1A2 et CYP3A. L'activité de CYP1A2 et les taux plasmatiques de clozapine en steady-state corrèlent d'une manière significative (r=0.61; p=1x10), sans influence du génotype de CYP1A2*1F (p=0.38). Les métaboliseurs déficients CYP2C19 (génotype *2/*2 genotype) avaient des concentrations de clozapine 2,3 fois (p=0.036) plus élevées que les métaboliseurs rapides (non*2/*2). Chez les patients comédiqués avec la fluvoxamine, un fort inhibiteur de CYP1A2, les concentrations de clozapine et de norclozapine corrèlent significativement avec l'activité de CYP3A (r=0.44, p=0.075; r=0.63, p=0.007, respectivement). Les porteurs du génotype ABC81 3435TT avaient des concentrations plasmatiques de clozapine 1,6 fois plus élevées que ceux qui ne présentaient pas ce génotype (p=0.046). En conclusion, cette étude montre pour la première fois, in vivo, le rôle significatif de CYP2C19 et celui du transporteur P-gp dans la pharmacocinétique de la clozapine. Le CYP1A2 est la forme principale de CYP impliquée dans le métabolisme de clozapine, tandis que le CYP2C19 joue un rôle modéré et que le CYP3A4 n'y contribue que chez les patients qui présentent une activité de CYP1A2 réduite. De plus, le polymorphisme de ABC81, mais pas ceux de CYP2B6, CYP2C9, CYP2D6, CYP3A5 et CYP3A7, influence la pharmacocinétique de la clozapine. Abstract : To examine the genetic factors influencing clozapine kinetics in vivo, 75 patients treated with clozapine were gcnotyped for CYPs and ABCBI polymorphisms and phenotyped for CYPIA2 and CYP3A activity. CYPIA2 activity and dose-corrected trough stéady-state plasma concentrations of clozapine correlated significantly (r = -0.61; P = 1 x 10 pow(-6), with no influence of the CYPIA2*IF genotype (P = 0.38). CYP2C 19 poor metabolizers (*2/*2 genotype) had 2.3-fold higher (P = 0.036) clozapine concentrations than the extensive metabolizers (non-*2/*2). In patients comedicated with fluvoxamine, a strong CYPlA2 inhibitor, clozapine and norclozapine concentrations correlate with CYP3A activity (r = 0.44, P = 0.075; r = 0.63, P = 0.007, respectively). Carriers of the ABCB1 3435TT genotype had a 1.6-fold higher clozapine plasma concentrations than noncarriers (P = 0.046). In conclusion, this study has shown for the first time a significant in vivo role of CYP2C19 and the P-gp transporter in the pharmacokinetics of clozapine. CYPlA2 is the main CYP isoform involved in clozapine metabolism, with CYP2C19 contributing moderately, and CYP3A4 contributing only in patients with reduced CYPIA2 activity. In addition, ABCBI, but not CYP1B6, CYP1C9, CYP1D6, CYP3A5, nor CYP3A7 polymorphisms, influence clozapine pharmacokinetics.

Lottery Action, November 15-28, 2004, Vol. 11, no. 12

Iowa Lottery Retailer Newsletter

Validade e confiabilidade do Inventário de Atitudes frente à Dor Crônica (IAD-28 itens) em lingua portuguesa

Trata-se da reavaliação da confiabilidade e validade do Inventário de Atitudes frente à Dor Crônica-versão breve, (IAD-breve) com 183 pacientes com dor crônica não oncológica. O IAD-breve 28 itens avalia as crenças sobre dor crônica relacionadas ao controle, emoção, solicitude, cura médica, dano físico, incapacidade e medicação. A análise mostrou sete domínios e 28 itens. Houve diferenças na alocação de dois itens e, após análises, optou-se por retirá-los. Quatro domínios apresentaram valores de alfa de Cronbach considerados bons (entre 0,74 e 0,85) e em três, foram moderados (entre 0,58 e 0,65). O IAD-breve 28 itens em língua portuguesa é superior à primeira versão.

Nucleotide, cytogenetic and expression impact of the human chromosome 8p23.1 inversion polymorphism

Background: The human chromosome 8p23.1 region contains a 3.8–4.5 Mb segment which can be found in different orientations (defined as genomic inversion) among individuals. The identification of single nucleotide polymorphisms (SNPs) tightly linked to the genomic orientation of a given region should be useful to indirectly evaluate the genotypes of large genomic orientations in the individuals. Results: We have identified 16 SNPs, which are in linkage disequilibrium (LD) with the 8p23.1 inversion as detected by fluorescent in situ hybridization (FISH). The variability of the 8p23.1 orientation in 150 HapMap samples was predicted using this set of SNPs and was verified by FISH in a subset of samples. Four genes (NEIL2, MSRA, CTSB and BLK) were found differentially expressed (p<0.0005) according to the orientation of the 8p23.1 region. Finally, we have found variable levels of mosaicism for the orientation of the 8p23.1 as determined by FISH. Conclusion: By means of dense SNP genotyping of the region, haplotype-based computational analyses and FISH experiments we could infer and verify the orientation status of alleles in the 8p23.1 region by detecting two short haplotype stretches at both ends of the inverted region, which are likely the relic of the chromosome in which the original inversion occurred. Moreover, an impact of 8p23.1 inversion on gene expression levels cannot be ruled out, since four genes from this region have statistically significant different expression levels depending on the inversion status. FISH results in lymphoblastoid cell lines suggest the presence of mosaicism regarding the 8p23.1 inversion.

Improving gene annotation using peptide mass spectrometry

Annotation of protein-coding genes is a key goal of genome sequencing projects. In spite of tremendous recent advances in computational gene finding, comprehensive annotation remains a challenge. Peptide mass spectrometry is a powerful tool for researching the dynamic proteome and suggests an attractive approach to discover and validate protein-coding genes. We present algorithms to construct and efficiently search spectra against a genomic database, with no prior knowledge of encoded proteins. By searching a corpus of 18.5 million tandem mass spectra (MS/MS) from human proteomic samples, we validate 39,000 exons and 11,000 introns at the level of translation. We present translation-level evidence for novel or extended exons in 16 genes, confirm translation of 224 hypothetical proteins, and discover or confirm over 40 alternative splicing events. Polymorphisms are efficiently encoded in our database, allowing us to observe variant alleles for 308 coding SNPs. Finally, we demonstrate the use of mass spectrometry to improve automated gene prediction, adding 800 correct exons to our predictions using a simple rescoring strategy. Our results demonstrate that proteomic profiling should play a role in any genome sequencing project.

Prominent use of distal 5’ transcription start sites and discovery of a large number of additional exons in ENCODE regions

This report presents systematic empirical annotation of transcript products from 399 annotated protein-coding loci across the 1% of the human genome targeted by the Encyclopedia of DNA elements (ENCODE) pilot project using a combination of 5' rapid amplification of cDNA ends (RACE) and high-density resolution tiling arrays. We identified previously unannotated and often tissue- or cell-line-specific transcribed fragments (RACEfrags), both 5' distal to the annotated 5' terminus and internal to the annotated gene bounds for the vast majority (81.5%) of the tested genes. Half of the distal RACEfrags span large segments of genomic sequences away from the main portion of the coding transcript and often overlap with the upstream-annotated gene(s). Notably, at least 20% of the resultant novel transcripts have changes in their open reading frames (ORFs), most of them fusing ORFs of adjacent transcripts. A significant fraction of distal RACEfrags show expression levels comparable to those of known exons of the same locus, suggesting that they are not part of very minority splice forms. These results have significant implications concerning (1) our current understanding of the architecture of protein-coding genes; (2) our views on locations of regulatory regions in the genome; and (3) the interpretation of sequence polymorphisms mapping to regions hitherto considered to be "noncoding," ultimately relating to the identification of disease-related sequence alterations.

Signatures of selection in the human olfactory receptor OR5I1 gene

The human olfactory receptor repertoire is reduced in comparison to other mammalsand to other non-human primates. Nonetheless, this olfactory decline opens an opportunity forevolutionary innovation and improvement. In the present study, we focus on an olfactoryreceptor gene, OR5I1, which had previously been shown to present an excess of amino acidreplacement substitutions between humans and chimpanzees. We analyze the geneticvariation in OR5I1 in a large worldwide human panel and find an excess of derived allelessegregating at relatively high frequencies in all populations. Additional evidence for selectionincludes departures from neutrality in allele frequency spectra tests but no unusually extendedhaplotype structure. Moreover, molecular structural inference suggests that one of thenonsynonymous polymorphisms defining the presumably adaptive protein form of OR5I1may alter the functional binding properties of the olfactory receptor. These results arecompatible with positive selection having modeled the pattern of variation found in the OR5I1gene and with a relatively ancient, mild selective sweep predating the “Out of Africa”expansion of modern humans.

Design and evaluation of a panel os single-nucleotide polymorphisms in microRNA genomic regions for association studies in human disease

MicroRNAs (miRNA) are recognized posttranscriptional gene repressors involved in the control of almost every biological process. Allelic variants in these regions may be an important source of phenotypic diversity and contribute to disease susceptibility. We analyzed the genomic organization of 325 human miRNAs (release 7.1, miRBase) to construct a panel of 768 single-nucleotide polymorphisms (SNPs) covering approximately 1 Mb of genomic DNA, including 131 isolated miRNAs (40%) and 194 miRNAs arranged in 48 miRNA clusters, as well as their 5-kb flanking regions. Of these miRNAs, 37% were inside known protein-coding genes, which were significantly associated with biological functions regarding neurological, psychological or nutritional disorders. SNP coverage analysis revealed a lower SNP density in miRNAs compared with the average of the genome, with only 24 SNPs located in the 325 miRNAs studied. Further genotyping of 340 unrelated Spanish individuals showed that more than half of the SNPs in miRNAs were either rare or monomorphic, in agreement with the reported selective constraint on human miRNAs. A comparison of the minor allele frequencies between Spanish and HapMap population samples confirmed the applicability of this SNP panel to the study of complex disorders among the Spanish population, and revealed two miRNA regions, hsa-mir-26a-2 in the CTDSP2 gene and hsa-mir-128-1 in the R3HDM1 gene, showing geographical allelic frequency variation among the four HapMap populations, probably because of differences in natural selection. The designed miRNA SNP panel could help to identify still hidden links between miRNAs and human disease.