Effects of postfire salvage logging on deadwood-associated beetles.

In Canada and the United States pressure to recoup financial costs of wildfire by harvesting burned timber is increasing, despite insufficient understanding of the ecological consequences of postfire salvage logging. We compared the species richness and composition of deadwood-associated beetle assemblages among undisturbed, recently burned, logged, and salvage-logged, boreal, mixed-wood stands. Species richness was lowest in salvage-logged stands, largely due to a negative effect of harvesting on the occurrence of wood- and bark-boring species. In comparison with undisturbed stands, the combination of wildfire and logging in salvage-logged stands had a greater effect on species composition than either disturbance alone. Strong differences in species composition among stand treatments were linked to differences in quantity and quality (e.g., decay stage) of coarse woody debris. We found that the effects of wildfire and logging on deadwood-associated beetles were synergistic, such that the effects of postfire salvage logging could not be predicted reliably on the basis of data on either disturbance alone. Thus, increases in salvage logging of burned forests may have serious negative consequences for deadwood-associated beetles and their ecological functions in early postfire successional forests.

Pangenomic changes induced by DHEA in the skin of postmenopausal women.

The objective of this study was to explore, for the first time, the changes in the pangenomic profile induced in human skin in women treated with dehydroepiandrosterone (DHEA) applied locally. Sixty postmenopausal women participated in this phase II prospective, randomized, double-blind and placebo-controlled study. Women were randomized to the twice daily local application of 0% (placebo), 0.3%, 1% or 2% DHEA cream. Changes in the pangenomic expression profile were studied using Affymetrix Genechips. Significant changes (p<0.05) in sixty-six DHEA-responsive probe sets corresponding to 52 well-characterized genes and 9 unknown gene sequences were identified. A dose-dependent increase in the expression of several members of the collagen family was observed, namely COL1, COL3 and COL5 as well as the concomitant modulation of SPARC, a gene required for the normal deposition and maturation of collagen fibrils in the dermis. Several genes involved in the proliferation and differentiation of keratinocytes were also modulated. In addition, topical DHEA reduced the expression of genes associated with the terminal differentiation and cornification of keratinocytes. Our results strongly suggest the possibility that DHEA could exert an anti-aging effect in the skin through stimulation of collagen biosynthesis, improved structural organization of the dermis while modulating keratinocyte metabolism.

A genome-wide scan points to a susceptibility locus for bipolar disorder on chromosome 12.

Our previous results pointed to a putative gene for susceptibility to bipolar affective disorder located on the chromosomal region 12q23-q24 that segregated in the Saguenay-Lac-St-Jean population of Quebec. We report here results from a second genome-wide scan based on the analysis of 380 polymorphic microsatellite markers. For the purpose of this analysis, an additional 18 families were recruited from the Saguenay-Lac-St-Jean region and pooled to our previous sample to improve its statistical power, giving a total of 394 sampled individuals. This work confirms the presence of a susceptibility locus for affective disorder on chromosome 12q24 with parametric LOD score value of 3.35 at D12S378 when pedigrees were broken into nuclear families and analysed under a recessive segregation model. This result was supported by neighbouring markers and by a LOD score value of 5.05 at D12S378 under model-free analysis. Other regions of lower interest were indicated on chromosomes 2, 5, 7, 9, 10, 17 and 20.

Effects of dihydrotestosterone on adipose tissue measured by serial analysis of gene expression.

Intra-abdominal fat accumulation is related to several diseases, especially diabetes and heart disease. Molecular mechanisms associated with this independent risk factor are not well established. Through the serial analysis of gene expression (SAGE) strategy, we have studied the transcriptomic effects of castration and dihydrotestosterone (DHT) in retroperitoneal adipose tissue of C57BL6 male mice. Approximately 50,000 SAGE tags were isolated in intact and gonadectomized mice, as well as 3 and 24 h after DHT administration. Transcripts involved in energy metabolism, such as glyceraldehyde-3-phosphate dehydrogenase, malic enzyme supernatant, fatty acid synthase, lipoprotein lipase, hormone-sensitive lipase and monoglyceride lipase, were upregulated by DHT. Transcripts involved in adipogenesis, and cell cycle and cell shape organization, such as DDX5, C/EBPalpha, cyclin I, procollagen types I, III, IV, V and VI, SPARC and matrix metalloproteinase 2, were upregulated by DHT. Cell defense, division and signaling, protein expression and many novel transcripts were regulated by castration and DHT. The present results provide global genomic evidence for a stimulation of glycolysis, fatty acids and triacylglycerol production, lipolysis and cell shape reorganization, as well as cell proliferation and differentiation, by DHT. The novel transcripts regulated by DHT may contribute to identify new mechanisms involved in the action of sex hormones and their potential role in obesity.

Transcriptome of mouse uterus by serial analysis of gene expression (SAGE): comparison with skeletal muscle.

The aim of this study was to identify the transcriptome of the normal mouse uterus by Serial Analysis of Gene Expression method. mRNA was extracted from the uterus and also from the gastrocnemius muscle of mice. Short sequences (tags), each one usually corresponding to a distinct transcript, were isolated and concatemerized into long DNA molecules which were cloned and sequenced. We detected 44,484 tags for the uterus and 42,518 tags for the muscle, representing 14,543 and 14,958 potential transcript species, respectively. Seventy-five and sixty-nine genes were expressed at more than 0.1%, thus corresponding to 37 and 34% of the mRNA population detected in the respective tissues. In both cases, the most highly expressed genes are especially involved in muscle contraction, energy metabolism, and protein synthesis. Compared to skeletal muscle, some differentially expressed genes in the uterus are likely to correspond to its specific reproductive functions. The majority of these genes remain to be characterized. More than 70% of the different tags detected in the uterus did not match any sequence in the public databases and can represent novel or poorly identified genes. This study is the first quantitative description of the transcriptome of the uterus.

Genome scan meta-analysis of schizophrenia and bipolar disorder, part III: Bipolar disorder.

Genome scans of bipolar disorder (BPD) have not produced consistent evidence for linkage. The rank-based genome scan meta-analysis (GSMA) method was applied to 18 BPD genome scan data sets in an effort to identify regions with significant support for linkage in the combined data. The two primary analyses considered available linkage data for "very narrow" (i.e., BP-I and schizoaffective disorder-BP) and "narrow" (i.e., adding BP-II disorder) disease models, with the ranks weighted for sample size. A "broad" model (i.e., adding recurrent major depression) and unweighted analyses were also performed. No region achieved genomewide statistical significance by several simulation-based criteria. The most significant P values (<.01) were observed on chromosomes 9p22.3-21.1 (very narrow), 10q11.21-22.1 (very narrow), and 14q24.1-32.12 (narrow). Nominally significant P values were observed in adjacent bins on chromosomes 9p and 18p-q, across all three disease models on chromosomes 14q and 18p-q, and across two models on chromosome 8q. Relatively few BPD pedigrees have been studied under narrow disease models relative to the schizophrenia GSMA data set, which produced more significant results. There was no overlap of the highest-ranked regions for the two disorders. The present results for the very narrow model are promising but suggest that more and larger data sets are needed. Alternatively, linkage might be detected in certain populations or subsets of pedigrees. The narrow and broad data sets had considerable power, according to simulation studies, but did not produce more highly significant evidence for linkage. We note that meta-analysis can sometimes provide support for linkage but cannot disprove linkage in any candidate region.

Genetic heterogeneity in a very large bipolar affective disorder pedigree from Quebec.

We previously reported a genome-wide scan for bipolar affective disorder based on a multigenerational family sampled from a relatively homogeneous population derived from founding families that migrated to an isolated area of Quebec from the early 1830s onwards. For the genome scan, the pedigree was split into five branches to facilitate calculation and a second family was added to more specifically analyze chromosome 12 results. In the present study, we reanalyzed the undivided pedigree after genealogical links were reconstructed over ten generations to investigate a founder effect using an algorithm in the SIMWALK2 package. Our results do not lend support to the presence of a common haplotype shared among affected individuals.

Osteogenesis imperfecta type VII maps to the short arm of chromosome 3.

We have identified a novel form of autosomal recessive osteogenesis imperfecta (OI) in a small First Nations community from northern Quebec. Mutation screening of the COL1A1/COL1A2 genes revealed no detectable mutations, and type I collagen protein analyses were also normal. By linkage analysis, we mapped this unique autosomal recessive variant of osteogenesis imperfecta to chromosome 3p22-24.1. Based on the assumption of a founder effect, genome-wide screening was performed on a DNA sample pooled from seven affected individuals. Familial as well as historical recombinations identified within an extended haplotype of 19 markers localized the disease between markers D3S2324 and D3S1561, separated by <5 cM. Based on chromosomal localization to 3p22-24.1, the transforming growth factor-beta receptor 2 gene and the parathyroid hormone/parathyroid hormone-related peptide receptor were tested, but were excluded as being associated with the phenotype. This study excludes type I collagen mutations in the pathogenesis of the disease and assigns this form of OI to a locus other than the ones containing the type I collagen genes.

Criterion validity study of lumbar goniometers BROM II and EDI-320 for range of motion of lumbar flexion of low back pain patients.

PURPOSE: The purpose was to estimate the criterion validity of the Back Range of Motion (BROM II) and Electronic Digital Inclinometer (EDI-320) devices. METHODS. This study compared the range of motion measurements of low back pain (LBP) patients taken with the BROM II and EDI-320 with measurements using the double inclinometer (DI) method as the gold standard. Forty subjects with LBP volunteered for the study. The subjects were asked to do three forward flexion movements. A measurement was taken with each of the three different devices for each movement. RESULTS: The BROM II demonstrated good linear relationship (Pearson r = 0.78; 95% CI: 0.78-0.94) and the EDI-320 very good linear relationship (Pearson r = 0.88; 95% CI: 0.62-0.89) with the gold standard, the DI. CONCLUSIONS: The Pearson correlation value indicates good validity of the EDI-320 in our sample of LBP patients. Although a good correlation was established for the BROM II, the significant difference of the mean ROM reported for this instrument compared to the gold standard data suggests that the BROM II actually measures ROM differently. Our results suggest that the EDI 320 is clinically useful in providing objective and valid data for outcome measures in a population with LBP. More research is needed on the BROM II before we can make final conclusion on its use in clinical settings as an outcome measure.

A radiation hybrid transcript map of the mouse genome.

Expressed-sequence tag (EST) maps are an adjunct to sequence-based analytical methods of gene detection and localization for those species for which such data are available, and provide anchors for high-density homology and orthology mapping in species for which large-scale sequencing has yet to be done. Species for which radiation hybrid-based transcript maps have been established include human, rat, mouse, dog, cat and zebrafish. We have established a comprehensive first-generation-placement radiation hybrid map of the mouse consisting of 5,904 mapped markers (3,993 ESTs and 1,911 sequence-tagged sites (STSs)). The mapped ESTs, which often originate from small-EST clusters, are enriched for genes expressed during early mouse embryogenesis and are probably different from those localized in humans. We have confirmed by in situ hybridization that even singleton ESTs, which are usually not retained for mapping studies, may represent bona fide transcribed sequences. Our studies on mouse chromosomes 12 and 14 orthologous to human chromosome 14 show the power of our radiation hybrid map as a predictive tool for orthology mapping in humans.

Paget disease of bone: mapping of two loci at 5q35-qter and 5q31.

Paget disease of bone is characterized by focal increases of the bone-remodeling process. It is the second most common metabolic bone disease after osteoporosis. Genetic factors play a major role in the etiology of Paget disease of bone, and two loci have been mapped for the disorder: PDB1 and PDB2. The gene(s) causing the typical form of the disorder remains to be characterized. To decipher the molecular basis of Paget disease of bone, we performed genetic linkage analysis in 24 large French Canadian families (479 individuals) in which the disorder was segregating as an autosomal dominant trait. After exclusion of PDB2, a genomewide scan was performed on the three most informative family nuclei. LOD scores >1.0 were observed at seven locations. The 24 families were then used to detect strong evidence for linkage to chromosome 5q35-qter. Under heterogeneity, a maximum LOD score of 8.58 was obtained at D5S2073, at straight theta= .1. The same characteristic haplotype was carried by all patients in eight families, suggesting a founder effect. A recombination event in a key family confined the disease region within a 6-cM interval between D5S469 and the telomere. The 16 other families, with very low conditional probability of linkage to 5q35-qter, were further used, to map a second locus at 5q31. Under heterogeneity, a maximum LOD score of 3.70 was detected at D5S500 with straight theta=.00. Recombination events refined the 5q31 region within 12.2 cM, between D5S642 and D5S1972. These observations demonstrate the mapping of two novel loci for Paget disease of bone and provide further evidence for genetic heterogeneity of this highly prevalent disorder. It is proposed that the 5q35-qter and 5q31 loci be named "PDB3" and "PDB4," respectively.

Isolated four-chamber working swine heart model.

BACKGROUND: Isolated heart models separate cardiac characteristics from systemic characteristics with subsequent findings used in cardiac research, including responses to pharmacologic, mechanical, and electrical components. The model objective was to develop the ability to represent in situ physiologic cardiac function ex vivo. METHODS: Swine hearts were chosen over rat or guinea pig models due to their notably greater anatomical and physiologic similarities to humans. An in vitro apparatus was designed to work all four chambers under simulated in situ physiologic conditions. Using standard cardiac surgical techniques, 12 porcine hearts (mean weight 331 +/- 18 g) were explanted into the apparatus. Preload and afterload resistances simulated in situ input and output physiologic conditions. Hemodynamic characterizations, including cardiac output, max +/- dP/dt, and heart rate, were used to determine in situ function leading to explantation (prethoracic operation, postmedial sternotomy, and postperidectomy) and during in vitro function (t = 0, 60, 120, and 240 minutes). RESULTS: In vitro performance decayed with time, with statistical differences from base line (t = 0) function at t = 240 minutes (p > 0.05). CONCLUSIONS: An isolation and in vitro explantation protocol has been improved to aid in the study of isolated cardiac responses, and to determine cardiac hemodynamic function during open chest operation, transplantation, and in vitro reanimation with a crystalloid perfusate. The resulting model offers similar working physiologic function, with real-time imaging capabilities. The resulting model is advantageous in representing human cardiac function with regard to anatomic and physiologic functions, and can account for atrial and ventricular interactions.

Evidence for association and linkage between atopy, airway hyper-responsiveness, and the beta subunit Glu237Gly variant of the high-affinity receptor for immunoglobulin E in the French-Canadian population.

Following detection of linkage between atopy and chromosome 11q13 markers, association between this disorder and variants of the beta subunit of the high-affinity receptor for immunoglobulin E (FcepsilonRI-beta, a candidate gene for asthma-related conditions co-localizing within the same region) was reported in Australian, British and Japanese populations. Investigations in several other ethnic groups failed to replicate these observations. Due to the complexity of defining intermediate phenotypes related to asthma, detection of such associations may have been hampered by clinical misclassifications. To assess whether the FcepsilonRI-beta gene was involved in atopy and/or airway hyperresponsiveness (AHR) in the French-Canadian population, we conducted a case-control study in 200 subjects using strict criteria for asthma and related conditions. The Ile181Leu and Glu237Gly FcepsilonRI-beta sequence variants were tested exploiting two amplification refractory mutation systems. No association was detected between atopy or AHR and the Ile181Leu FcepsilonRI-beta variant. However, a strong association was observed between atopy and the Glu237Gly FcepsilonRI-beta variant (odds ratio=12.25). Four large Eastern Québec families (n=106 subjects) were also recruited to perform a genetic linkage study. We observed suggestive evidence of linkage between atopy and the Glu237Gly FcepsilonRI-beta variant (Zmax=2.30). This study is the first to detect the presence of an association between atopy and the Glu237Gly FcepsilonRI-beta variant in French-Canadians. Our data suggest that a susceptibility locus for atopy is located on chromosome 11q13 in this population.

Plasticity in cerebellar tactile maps in the adult rat.

We previously demonstrated that the fractured tactile cerebellar map within the crus IIa folia of the cerebellar hemispheres reorganizes after deafferentation of the upper lip in neonatal rats (postnatal day [PND] 1-30). The present study examined the capacity of this map to reorganize after deafferentation in adults and animals late in development (PND 30-89). Several months after cauterization of the infraorbital branch of the trigeminal nerve, the tactile map in the granule cell layer of crus IIa reorganized, with representations of intact structures expanding into the denervated area. The pattern of reorganization was similar to reorganization after neonatal lesions in that (1) all representations were from perioral structures, (2) the reorganized map maintained a fractured somatotopy, and (3) the denervated area was predominantly and consistently invaded by the upper incisor representation. We conclude that the spatial pattern of reorganization is essentially the same regardless of the age of deafferentation. However, we also observed developmental differences in reorganization. First, more areas of crus IIa were nonresponsive in animals lesioned later in development (PND 30-89). Second, we found a surprising degree of variability in the pattern of tactilely evoked cerebellar field potentials of PND 30-40 animals compared with neonates and adults, suggesting that this time period differs from other stages. The pattern of evoked potentials reflects the two primary inputs to the map. Our data show that, although both afferent pathways are capable of reorganization throughout development, their relative contribution to the map appears to differ, depending on the age at which lesion occurs.

Genome-wide search for linkage of bipolar affective disorders in a very large pedigree derived from a homogeneous population in quebec points to a locus of major effect on chromosome 12q23-q24.

We completed a genome-wide scan for susceptibility loci for bipolar affective disorders in families derived from a rather homogeneous population in the Province of Québec. The genetic homogeneity of this population stems from the migration of founding families into this relatively isolated area of Québec in the 1830s. A possible founder effect, combined with a prevalence of very large families, makes this population ideal for linkage studies. Genealogies for probands can be readily constructed from a population database of acts of baptism and marriage from the early 1830s up to the present time (the BALSAC register). We chose probands with a DSM III diagnosis of bipolar affective disorder and who may be grouped within large families having genealogical origins with the founding population of the Saguenay-Lac-St-Jean area. Living members (n approximately 120) of a very large pedigree were interviewed using the Structured Clinical Interview for DSM III (SCID I), SCID II, and with a family history questionnaire. A diagnostic panel evaluated multisource information (interview, medical records, family history) and pronounced best-estimate consensus diagnoses on all family members. Linkage, SimAPM, SimIBD, and sib-pair analyses have been performed with 332 microsatellite probes covering the entire genome at an average spacing of 11 cM. GENEHUNTER and haplotype analyses were performed on regions of interest. Analysis of a second large pedigree in the same regions of interest permitted confirmation of presumed linkages found in the region of chromosome 12q23-q24.

Chromosome 13 workshop report.

Evidence was presented that provided support for linkage in a relatively broad telomeric region of chromosome 13. A significant overlap for positive markers linked to both bipolar disorder and schizophrenia occurred in this area.

Fine mapping of low-density lipoprotein receptor gene by genetic linkage on chromosome 19p13.1-p13.3 and study of the founder effect of four French Canadian low-density lipoprotein receptor gene mutations.

Familial hypercholesterolemia (FH) is one of the most common autosomal codominant diseases. FH is caused by mutations in the low-density lipoprotein receptor (LDLR) gene and is characterized by raised plasma LDL-cholesterol, tendon xanthomas, and premature coronary heart disease. The frequency of FH among French Canadians in northeastern Quebec is higher than in most other populations, 1:154 vs. 1:500 due to high prevalence of few recurrent mutations in the LDLR gene. In the French Canadian population, 11 mutations in the LDLR gene have been found to occur in geographically diverse areas and account for > 90% of cases. We have first constructed a high-resolution genetic map to locate several highly polymorphic markers close to LDLR locus, thus providing the necessary tools to study the origin of the four most common mutations which account for approximately 80% of our FH patients. We have then genotyped five markers (D19S413, D19S865, D19S221, D19S914, D19S586) in 102 heterozygotes (38 del > 15kb; 36 W66G; 16 C646Y; 12 E207K), two compound heterozygotes (del > 15kb/W66G; del > 15kb/C646Y) and seven homozygotes (three del > 15 kb; three W66G: one E207K) with FH unrelated to the first and second degree. We have found that patients bearing the same LDLR gene mutation carry a common haplotype at the LDLR locus although there is evidence for the early occurrence of a recombinational event between the LDLR and the D19S221 locus in the French Canadian patients bearing the W66G mutation. The fine mapping of LDLR gene close to several highly informative microsatellite markers provide fine mapping details of the LDLR region and additional tools for studies of association between plasma lipoprotein levels and LDLR gene.

Type I protein C deficiency in French Canadians: evidence of a founder effect and association of specific protein C gene mutations with plasma protein C levels.

Protein C (PROC) deficiency is one of the most common autosomal codominant diseases. Although more than 150 germline mutations in the PROC gene have been described around the world, the spectrum of mutations among French Canadians is unknown. We have identified one frameshift (3363 ins C) and two missense mutations (R178Q and T298M) in 7 French Canadian families with type I PROC deficiency. In order to demonstrate a possible founder effect for the 3363 ins C mutation, we have constructed a high-resolution genetic map to locate several highly polymorphic markers close to PROC locus. We have then genotyped five markers in 36 heterozygotes for the 3363 ins C mutation. Our data suggest that these patients carry a common haplotype at the PROC locus. Immunologic plasma PROC levels of heterozygotes and genetically normal relatives were also correlated with the nature of the mutation in the coding sequence and with the genotype of three polymorphisms in the PROC promoter. We found that the mean immunologic plasma PROC levels were lower in heterozygotes for the frameshift mutation 3363 ins C compared to heterozygotes for one of the two missense mutations R178Q and T298M (0.46 vs 0.61; P = 0.0004). Moreover, this difference cannot be explained by the genetic variation of the three polymorphisms in the PROC promoter which accounts for only 10.4% of the variation of immunologic PROC levels in non-deficient subjects. These results suggest that the nature of the mutation in the coding sequence of PROC gene may modulate immunologic plasma PROC levels.

Mutations of the forkhead/winged-helix gene, FKHL7, in patients with Axenfeld-Rieger anomaly.

Genetic linkage, genome mismatch scanning, and analysis of patients with alterations of chromosome 6 have indicated that a major locus for development of the anterior segment of the eye, IRID1, is located at 6p25. Abnormalities of this locus lead to glaucoma. FKHL7 (also called "FREAC3"), a member of the forkhead/winged-helix transcription-factor family, has also been mapped to 6p25. DNA sequencing of FKHL7 in five IRID1 families and 16 sporadic patients with anterior-segment defects revealed three mutations: a 10-bp deletion predicted to cause a frameshift and premature protein truncation prior to the FKHL7 forkhead DNA-binding domain, as well as two missense mutations of conserved amino acids within the FKHL7 forkhead domain. Mf1, the murine homologue of FKHL7, is expressed in the developing brain, skeletal system, and eye, consistent with FKHL7 having a role in ocular development. However, mutational screening and genetic-linkage analyses excluded FKHL7 from underlying the anterior-segment disorders in two IRID1 families with linkage to 6p25. Our findings demonstrate that, although mutations of FKHL7 result in anterior-segment defects and glaucoma in some patients, it is probable that at least one more locus involved in the regulation of eye development is also located at 6p25.

A physical map of 30,000 human genes.

A map of 30,181 human gene-based markers was assembled and integrated with the current genetic map by radiation hybrid mapping. The new gene map contains nearly twice as many genes as the previous release, includes most genes that encode proteins of known function, and is twofold to threefold more accurate than the previous version. A redesigned, more informative and functional World Wide Web site (www.ncbi.nlm.nih.gov/genemap) provides the mapping information and associated data and annotations. This resource constitutes an important infrastructure and tool for the study of complex genetic traits, the positional cloning of disease genes, the cross-referencing of mammalian genomes, and validated human transcribed sequences for large-scale studies of gene expression.