bluuebunny/crossref_metadata_2025 huggingface dataset:
Substance P promotes expansion of human mesenteric preadipocytes through proliferative and antiapoptotic pathways
Authors: Gross Kara , Karagiannides Iordanes , Thomou Thomas , Koon Hon Wai , Bowe Collin , Kim Ho , Giorgadze Nino , Tchkonia Tamara , Pirtskhalava Tamara , Kirkland James L. , Pothoulakis Charalabos
Published: March 2009

White adipose tissue is intimately involved in the regulation of immunity and inflammation. We reported that human mesenteric preadipocytes express the substance P (SP)-mediated neurokinin-1 receptor (NK-1R), which signals proinflammatory responses. Here we tested the hypothesis that SP promotes proliferation and survival of human mesenteric preadipocytes and investigated responsible mechanism(s). Preadipocytes were isolated from mesenteric fat biopsies during gastric bypass surgery. Proliferative and antiapoptotic responses were delineated in 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2 H-tetrazolium (MTS), bromodeoxyuridine (BrdU), caspase-3, and TUNEL assays, as well as Western immunoanalysis. SP (10−7M) increased MTS and proliferation (BrdU) and time dependently (15–30 min) induced Akt, EGF receptor, IGF receptor, integrin αVβ3, phosphatidylinositol 3-kinase, and PKC-θ phosphorylation. Furthermore, pharmacological antagonism of Akt and PKC-θ activation significantly attenuated SP-induced preadipocyte proliferation. Exposure of preadipocytes to the proapoptotic Fas ligand (FasL, 100 μM) resulted in nuclear DNA fragmentation (TUNEL assay), as well as increased cleaved poly (ADP-ribose) polymerase, cleaved caspase-7, and caspase-3 expression. Cotreatment with SP almost completely abolished these responses in a NK-1R-dependent fashion. SP (10−7M) also time dependently stimulated expression 4E binding protein 1 and phosphorylation of p70 S6 kinase, which increased protein translation efficiency. SP increases preadipocyte viability, reduces apoptosis, and stimulates proliferation, possibly via cell cycle upregulation and increased protein translation efficiency. SP-induced proliferative and antiapoptotic pathways in fat depots may contribute to development of the creeping fat and inflammation characteristic of Crohn's disease.
Nelfinavir/ritonavir reduces acinar injury but not inflammation during mouse caerulein pancreatitis
Authors: Singh Vijay P. , Bren Gary D. , Algeciras-Schimnich Alicia , Schnepple David , Navina Sarah , Rizza Stacey A. , Dawra Rajinder K. , Saluja Ashok K. , Chari Suresh T. , Vege Santhi S. , Badley Andrew D.
Published: March 2009

There is no clinical treatment that reduces acinar injury during pancreatitis. Human immunodeficiency virus (HIV) protease inhibitors (PI), including nelfinavir (NFV) and ritonavir (RTV), may reduce the rate of pancreatitis in HIV-infected patients. Since permeability transition pore (PTPC)-mediated mitochondrial dysfunction occurs during pancreatitis, and we have shown that PI prevents PTPC opening, we studied its effects in a model of pancreatitis. The effect of NFV plus RTV (NFV/RTV) or vehicle on caerulein-induced pancreatitis in mice was compared by measuring changes in mitochondrial membrane potential in vitro and cytochrome c leakage in vivo. Histological and inflammatory makers were also compared. NFV/RTV improved DiOC6 retention in acini exposed to caerulein in vitro. In vivo NFV prevented cytosolic leakage of cytochrome c and reduced pancreatic acinar injury, active caspase-3 staining, TUNEL-positive acinar cells, and serum amylase ( P < 0.05). Conversely, trypsin activity, serum cytokine levels, and pancreatic and lung inflammation were unaffected. NFV/RTV reduces pancreatic injury and acinar cell death in experimental mouse caerulein-induced pancreatitis but does not impact inflammation.
Partial downregulation of junctin enhances cardiac calcium cycling without eliciting ventricular arrhythmias in mice
Authors: Yuan Qunying , Han Peidong , Dong Min , Ren Xiaoping , Zhou Xiaoyang , Chen Shan , Jones W. Keith , Chu Guoxiang , Wang Hong-Sheng , Kranias Evangelia G.
Published: March 2009

Human failing hearts exhibit significant decreases in junctin expression levels with almost nondetectable levels, which may be associated with premature death, induced by lethal cardiac arrhythmias, based on mouse models. However, the specific contribution of junctin to the delayed afterdepolarizations has been difficult to delineate in the phase of increased Na+-Ca2+ exchanger activity accompanying junctin ablation. Thus we characterized the heterozygous junctin-deficient hearts, which expressed 54% of junctin levels and similar increases in Na+-Ca2+ exchanger activity, as the null model. Cardiac contractile parameters, Ca2+ transients, and sarcoplasmic reticulum Ca2+ content were significantly increased in junctin heterozygous hearts, although they did not reach the levels of null hearts. However, Ca2+ spark properties were not altered in heterozygous cardiomyocytes, compared with wild-types, and there were no aftercontractions elicited by the increased frequency of stimulation in the presence of isoproterenol, unlike the junctin-deficient cells. Furthermore, heterozygous mice did not exhibit an increased susceptibility to arrhythmia upon catecholamine challenge in vivo, and there were no premature deaths up to 1 yr of age. These findings suggest that a partial downregulation of junctin enhances sarcoplasmic reticulum Ca2+ cycling but does not elicit cardiac arrhythmias even in the context of increased Na+-Ca2+ exchanger activity.
Systemic injection of planktonic forms of mammalian-derived nanoparticles alters arterial response to injury in rabbits
Authors: Schwartz Maria K , Lieske John C , Hunter Larry W. , Miller Virginia M
Published: March 2009

Experiments were designed to test the hypothesis that the systemic delivery of planktonic forms of nanoparticles (NPs) derived from calcified, diseased human tissue or bovine blood are transmissible particles that exacerbate arterial response to injury. New Zealand White rabbits in which the endothelium was mechanically removed from one carotid artery were injected intravenously with either saline (control), lipopolysaccharide (LPS; surrogate for subclinical infection), hydroxyapatite crystals (HA; surrogate for NP shell), HA crystals exposed to culture media, or planktonic forms of bovine- or human-derived NPs. Carotid arteries were monitored by ultrasonography for 5 wk and then removed for histological examination. Uninjured arteries from all animals in each group remained patent with a normal anatomy. Injured arteries from 6 of 11 animals injected with human-derived NPs occluded and/or calcified; none of the injured arteries from animals in the other groups occluded ( n = 28; P ≤ 0.05). Injured arteries of rabbits injected with LPS or HA crystals developed eccentric hyperplasia. Discontinuous internal elastic laminae and thinning media characterized arteries from animals injected with bovine-derived NPs or cultured HA crystals. In conclusion, the systemic administration of planktonic forms of human-derived NPs exacerbated arterial response to injury distinct from that of bovine-derived NPs and other inflammatory agents.
Endurance exercise is protective for mice with mitochondrial myopathy
Authors: Wenz Tina , Diaz Francisca , Hernandez Dayami , Moraes Carlos T.
Published: March 2009

Defects in the mitochondrial ATP-generating system are one of the most commonly inherited neurological disorders, but they remain without treatment. We have recently shown that modulation of the peroxisome proliferator-activated receptor-γ coactivator-1α (PGC-1α) level in skeletal muscle of a mitochondrial myopathy mouse model offers a therapeutic approach. Here we analyzed if endurance exercise, which is known to be associated with an increased PGC-1α level in muscle, offers the same beneficial effect. We subjected male and female mice that develop a severe mitochondrial myopathy due to a cytochrome- c oxidase deficiency at 3 mo of age to endurance exercise training and monitored phenotypical and metabolic changes. Sedentary myopathy and wild-type mice were used as controls. Exercise increased PGC-1α in muscle, resulting in increased mitochondrial biogenesis, and successfully stimulated residual respiratory capacity in muscle tissue. As a consequence, ATP levels were increased in exercised mice compared with sedentary myopathy animals, which resulted in a delayed onset of the myopathy and a prolonged lifespan of the exercised mice. As an added benefit, endurance exercise induced antioxidant enzymes. The overall protective effect of endurance exercise delayed the onset of the mitochondrial myopathy and increased life expectancy in the mouse model. Thus stimulating residual oxidative phosphorylation function in the affected muscle by inducing mitochondrial biogenesis through endurance exercise might offer a valuable therapeutic intervention for mitochondrial myopathy patients.
CNVs and genetic medicine (excitement and consequences of a rediscovery)
Authors: Beckmann J.S. , Sharp A.J. , Antonarakis S.E.
Published: March 2009

The extensive variability of individual human genomes contributes to phenotypic variability. Structural genomic variants, and copy number variants (CNVs) in particular, have recently been rediscovered as contributors to the genomic plasticity and evolution and as pathoetiologic elements for both monogenic and complex traits. Herein we review some of the consequences of CNVs in the context of human inherited diseases.
Human genes involved in copy number variation: mechanisms of origin, functional effects and implications for disease
Authors: de Smith A.J. , Walters R.G. , Froguel P. , Blakemore A.I.
Published: March 2009

Copy number variants (CNVs) overlap over 7000 genes, many of which are pivotal in biological pathways. The implications of this are profound, with consequences for evolutionary studies, population genetics, gene function and human phenotype, including elucidation of genetic susceptibility to major common diseases, the heritability of which has thus far defied full explanation. Even though this research is still in its infancy, CNVs have already been associated with a number of monogenic, syndromic and complex diseases: the development of high throughput and high resolution techniques for CNV screening is likely to bring further new insights into the contribution of copy number variation to common diseases. Amongst genes overlapped by CNVs, significant enrichments for certain gene ontology categories have been identified, including those related to immune responses and interactions with the environment. Genes in both of these categories are thought to be important in evolutionary adaptation and to be particular targets of natural selection. Thus, a full appreciation of copy number variation may be important for our understanding of human evolution.
Detection and validation of copy number variation in X-linked mental retardation
Authors: Bauters M. , Weuts A. , Vandewalle J. , Nevelsteen J. , Marynen P. , Van Esch H. , Froyen G.
Published: March 2009

Studies to identify the genetic defects associated with X-linked mental retardation (XLMR) in males have revealed tens of genes important for normal brain development and cognitive functioning in men. Despite extensive efforts in breakpoint cloning of chromosomal rearrangements and mutation screening of candidate genes on the X chromosome, still many XLMR families and sporadic cases remain unsolved. It is now clear that submicroscopic copy number changes on the X chromosome can explain about 5% of these idiopathic cases. Interestingly, beside gene deletions, an increase in gene dosage due to genomic duplications seems to contribute to causality more often than expected. Since larger duplications on the X chromosome are tolerated compared to deletions, they often harbour more than one gene hampering the identification of the causal gene. In contrast to copy number variations (CNVs) on autosomes, most disease-associated CNVs on the X chromosome in males are inherited from their mothers who normally do not present with any clinical symptoms due to non-random X inactivation. Here, we review the different methods applied to study copy number alterations on the X chromosome in patients with cognitive impairment, discuss those CNVs that are associated with disease and elaborate on the genes and mechanisms involved. At the end, we will resume in vivo assays to study the relation of CNVs on the X chromosome and mental disability.
Benign copy number changes in clinical cytogenetic diagnostics by array CGH
Authors: Whitby H. , Tsalenko A. , Aston E. , Tsang P. , Mitchell S. , Bayrak-Toydemir P. , Hopkins C. , Peters G. , Bailey D.K. , Bruhn L. , Brothman A.R.
Published: March 2009

A database of apparently benign copy number variants (bCNVs) detected by a Spectral Genomics Inc./PerkinElmer BAC array platform has been maintained through the University of Utah Comparative Genomic Hybridization laboratory since 2005. The target population for this database represents 1,275 patients with abnormal phenotypes, primarily children referred for developmental delay and mental retardation. These bCNVs are independent of any identified copy number abnormality detected. The most common 35 bCNVs observed and their frequencies are reported here, and a subset of ten of the patients studied was evaluated on a new oligonucleotide CNV array set designed by Agilent Technologies. There was a 76% concordance of calls for these 35 bCNVs detected by both array platforms in the same patients. The higher resolution of the Agilent oligonucleotide array compared to the BAC array allowed determination of the precise breakpoints of the observed CNVs, in addition to documentation of additional CNVs of smaller sizes. As expected, observed CNVs and their frequencies were generally consistent with those of other previously published and available databases, including the Database of Genomic Variants (http://projects.tcag.ca/variation/). The availability of these data should assist other clinical laboratories in the evaluation of CNVs of unknown clinical significance.
Copy number variations in chronic pancreatitis
Authors: Chen J.M. , Masson E. , Le Maréchal C. , Férec C.
Published: March 2009

In 1996, shortly after a locus for hereditary pancreatitis had been mapped to chromosome 7q35, an apparent gain-of-function missense mutation, p.R122H, in the cationic trypsinogen gene (PRSS1) was identified. Thereafter, the search for chronic pancreatitis-associated genetic factors has been largely focused on one form of genetic variation, namely, single nucleotide substitutions (SNSs). Only very recently has another type of genetic variation – copy number variations (CNVs) – been found to cause the disease. First, we identified duplication and triplication of an ∼605 kb segment on chromosome 7q35 in French white patients with hereditary or idiopathic chronic pancreatitis. These alterations increased the copy number of PRSS1 as well as PRSS2, which encodes anionic trypsinogen. Second, we characterized a hybrid trypsinogen gene, in which exons 1 and 2 were derived from PRSS2 and exons 3 to 5 from PRSS1. Interestingly, this hybrid gene had two independent gain-of-function effects: increased trypsinogen gene copy number and it contained the p.N29I pancreatitis-causing missense mutation. Lastly, we identified two loss-of-function copy number mutations (deletions) in the SPINK1 gene, which encodes pancreatic secretory trypsin inhibitor (PSTI). Particularly, in one family with chronic pancreatitis, deletion of the complete SPINK1 gene was co-inherited with a CFTR missense mutation (p.L997F), revealing another layer of complexity between CNV and SNS interactions in the determination of a given disease phenotype. These findings represent a further demonstration of how studies of CNVs have altered the landscape of genetic research in the past few years and offer a fresh glimpse into the exciting realm of human CNVs.
The emerging role of structural variations in common disorders: initial findings and discovery challenges
Authors: Armengol L. , Rabionet R. , Estivill X.
Published: March 2009

After the successful discoveries of genetic associations for common disorders using single nucleotide polymorphisms (SNPs) in genome-wide association scans (GWAS), new efforts are ongoing to evaluate the contribution of structural variations to disease, mainly in the form of copy number variants (CNVs). These are mainly motivated after the identification of consistent relationships between CNVs and disease, and the recognition that there is not a unique human genome sequence at the structural level. The current knowledge reflects that few regions of the genome are free of structural rearrangements and that genes with a role in response to environment are particularly prone to contain CNVs with phenotypic consequences. In the following years many individuals will be sequenced, defining the variability of the genome at the sequence and structural levels. The characterization of regions of the genome that are variable in the orientation and order of genes and genomic segments between individuals is a major challenge, which can only be reliably tackled by high-throughput sequencing technologies and bioinformatics designs. The goal is to explore the whole set of genome diversity to extract the molecular basis of disorders that could affect any individual in the population and that is inherent to the adaptation of human groups to environmental conditions.
Phenotypes, genotypes and disease susceptibility associated with gene copy number variations: complement C4 CNVs in European American healthy subjects and those with systemic lupus erythematosus
Authors: Wu Y.L. , Yang Y. , Chung E.K. , Zhou B. , Kitzmiller K.J. , Savelli S.L. , Nagaraja H.N. , Birmingham D.J. , Tsao B.P. , Rovin B.H. , Hebert L.A. , Yu C.Y.
Published: March 2009

A new paradigm in human genetics is high frequencies of inter-individual variations in copy numbers of specific genomic DNA segments. Such common copy number variation (CNV) loci often contain genes engaged in host-environment interaction including those involved in immune effector functions. DNA sequences within a CNV locus often share a high degree of identity but beneficial or deleterious polymorphic variants are present among different individuals. Thus, common gene CNVs can contribute, both qualitatively and quantitatively, to a spectrum of phenotypic variants. In this review we describe the phenotypic and genotypic diversities of complement C4 created by copy number variations of RCCX modules (RP-C4-CYP21-TNX) and size dichotomy of C4 genes. A direct outcome of C4 CNV is the generation of two classes of polymorphic proteins, C4A and C4B, with differential chemical reactivities towards peptide or carbohydrate antigens, and a range of C4 plasma protein concentrations (from 15 to 70 mg/dl) among healthy subjects. Deliberate molecular genetic studies enabled development of definitive techniques to determine exact patterns of RCCX modular variations, copy numbers of long and short C4A and C4B genes by Southern blot analyses or by real-time quantitative PCR. It is found that in healthy European Americans, the total C4 gene copy number per diploid genome ranges from 2 to 6: 60.8% of people with four copies of C4 genes, 27.2% with less than four copies, and 12% with more than four copies. Such a distribution is skewed towards the low copy number side in patients with systemic lupus erythematosus (SLE), a prototypic autoimmune disease with complex etiology. In SLE, the frequency of individuals with less than four copies of C4 is significantly increased (42.2%), while the frequency of those with more than four copies is decreased (6%). This decrease in total C4 gene copy number in SLE is due to increases in homozygous and heterozygous deficiencies of C4A but not C4B. Therefore, it is concluded that lower copy number of C4 is a risk factor for and higher gene copy number of C4 is a protective factor against SLE disease susceptibility.
Copy number variation of beta-defensins and relevance to disease
Authors: Hollox E.J.
Published: March 2009

Beta-defensins are multifunctional proteins that have an important role in the innate immune system. A cluster of beta-defensin genes shows common and extensive variation in copy number in humans. This copy number has been associated with differing susceptibility to Crohn’s disease and psoriasis. In this review, I summarise what is currently known about copy number variation (CNV) of beta-defensins, and discuss practical considerations when studying these genes, and copy number variation in general. I also suggest future directions for research, with an emphasis on improvement of methods for accurately typing CNV.
HIV-1/AIDS susceptibility and copy number variation in CCL3L1, a gene encoding a natural ligand for HIV-1 co-receptor CCR5
Authors: Nakajima T. , Kaur G. , Mehra N. , Kimura A.
Published: March 2009

Variations of gene copy number in the human genome are increasingly recognized as a genetic factor in phenotypic variation. Human CC chemokine ligand 3-like 1 gene (CCL3L1), which is located on human chromosome 17q11.2, is highly variable in copy number owing to having a hot spot for segmental duplications. CCL3L1, a natural ligand for HIV-1 co-receptor CCR5, is a potent HIV-1–suppressive chemokine. CCL3L1 copy number variation (CNV) is tightly linked to HIV-1/AIDS susceptibility, and a lower copy number is associated with an enhanced risk for acquiring HIV-1 and also progressing more rapidly to AIDS and death. In this article we review recent studies to evaluate the association between the CCL3L1 copy number and HIV-1/AIDS susceptibility.
Copy number variation in metabolic phenotypes
Authors: Lanktree M. , Hegele R.A.
Published: March 2009

Despite successes in identifying genetic contributors to common metabolic phenotypes, only part of the heritable component of these traits has thus far been explained. Copy number variation (CNV) is likely to be responsible for some of the unexplained variation. As observed with single nucleotide changes, it is probable that both rare and common CNVs will contribute to susceptibility to metabolic disease. For instance, CNVs in the LDLR gene underlie a substantial portion of disease in patients with heterozygous familial hypercholesterolemia. As well, a common CNV in LPA encoding apolipoprotein(a) is the primary determinant of plasma lipoprotein(a) concentrations, a risk factor for atherosclerosis. Recent efforts to map CNVs in control populations have defined their size, frequency and distribution. Many of the identified CNVs overlap genes with important functions in metabolic pathways. The overlap of CNVs that were found in control datasets with functional candidate genes or genes with previous evidence of association with metabolic syndrome presents an important subset for future CNV association studies. Finally, we describe an approach to search for CNVs in a rare high-penetrance metabolic disorder, namely lipodystrophy. As methods to identify CNVs increase in precision and accuracy, the prospect of identifying their role in both rare Mendelian and common complex metabolic phenotypes will become a reality.
Germline copy number variation in control populations
Authors: Al-Sukhni W. , Gallinger S.
Published: March 2009

Copy number variation (CNV) is an important source of genomic variation. Characterizing CNVs in phenotypically normal individuals is important for understanding the functional significance of these variants. Many studies have reported CNVs in control populations, but wide variability is observed in their design and outcome. Importantly, medical and phenotypic information for control populations must be carefully documented, and accurate genotyping will be necessary to determine the population genetics of CNVs. Despite existing challenges in studying this class of variants, it is evident that CNVs are ubiquitous in human genomes, with non-random distribution, and they affect thousands of coding regions, potentially contributing to human disease and phenotypic variability. Higher-resolution detection platforms and improved algorithms will further define our understanding of CNVs in control populations, leading to development of effective disease-association studies.
Large-scale copy number variants (CNVs) detected in different ethnic human populations
Authors: Takahashi N. , Satoh Y. , Kodaira M. , Katayama H.
Published: March 2009

The large-scale copy-number variations (CNVs) in the human genome are associated with developmental disorders and susceptibility to diseases. More importantly, CNVs may represent a major genetic component of our phenotypic diversity. Following the development of methodologies and introduction of new research platforms, accumulation of the nature and pattern of CNVs from normal populations has progressed. The examination of relatively large numbers of specific ethnic groups has recently started. Although the results are not always consistent, it is likely that different human populations bear different CNVs, as is the case for single-nucleotide polymorphisms (SNPs) and insertion-deletion (indel) polymorphisms. We review recent publications about the nature of inter-population, especially inter-ethnic group, differences of CNVs.
Genomic drift and copy number variation of chemosensory receptor genes in humans and mice
Authors: Nozawa M. , Nei M.
Published: March 2009

Recent studies about the structural variation of genomic sequences have shown that there is a large amount of copy number variations (CNVs) of genes within species. Analyzing Redon et al.’s (2006) crude data on copy number variable regions (CNVRs), we previously showed that CNVs are particularly high for chemosensory receptor genes in human populations. In this paper, we reanalyzed the CNVs of these genes using more refined data by Perry et al. (2008). The results showed that the extent of CNVs is somewhat lower in this dataset than in the previous one, but that the extent is still substantial for olfactory receptor (OR), vomeronasal receptor (VR), and taste receptor (TR) genes. We also studied the CNVs for chemosensory receptor genes in mice, using CNVR data obtained from inbred strains. It was found that the extent of CNVs is quite substantial but is lower than that for human populations. However, because the mouse data came from inbred strains and might be biased, this conclusion should be regarded as tentative. Despite this reservation, the distribution of gene copy number for the OR gene family was approximately normal in both humans and mice, suggesting that genomic drift caused by random duplication and deletion of genes plays important roles in determining the evolutionary change of chemosensation.
Copy number variation and mosaicism
Authors: Notini A.J. , Craig J.M. , White S.J.
Published: March 2009

Mosaicism is the presence of cells within an organism that have a different genetic composition despite deriving from a single zygote. The consequence of this depends on the number and type of cells that are affected as well as the specific DNA involved. There are several diseases where mosaicism is known to occur, but the currently observed frequency is presumably an underestimation due to the difficulty of detecting changes in only a percentage of cells. Recent advances in technology have provided a greater insight into the frequency and mechanisms of mosaicism in all forms. This review will cover the different techniques that can be used for detecting copy number variation (CNV) in mosaic form, and describe some of the insights that different diseases have given on the true frequencies and mechanisms responsible for somatic rearrangements. It will conclude with a discussion of the implications of the recent description of CNV in identical twins, and what remains to be elucidated in the world of mosaic CNV.
The evolutionary significance of copy number variation in the human genome
Authors: Perry G.H.
Published: March 2009

Copy number variation provides the raw material for gene family expansion and diversification, which is an important evolutionary force. Moreover, copy number variants (CNVs) can influence gene transcriptional and translational levels and have been associated with complex disease susceptibility. Therefore, natural selection may have affected at least some of the greater than one thousand CNVs thus far discovered among the genomes of phenotypically normal humans. While identifying and understanding particular instances of natural selection may shed light on important aspects of human evolutionary history, our ability to analyze CNVs in traditional population genetic frameworks has been limited. However, progress has been made by adapting some of these frameworks for use with copy number data. Moving forward, these efforts will be aided by non-human organism studies of the population genetics of copy number variation, and by more direct comparisons of within-species copy number variation and between-species copy number fixation.
Comparative analysis of copy number variation in primate genomes
Authors: Kehrer-Sawatzki H. , Cooper D.N.
Published: March 2009

Copy number differences between human and chimpanzee genomic sequences often overlap with regions of intraspecies copy number variation. Copy number variations (CNVs) that occur at orthologous sites in both humans and chimpanzees (‘shared’ CNVs) are likely to represent unstable genomic regions that have been prone to recurrent rearrangements during primate evolution. Lineage-specific CNVs are also important because they may have been subject to positive selection in specific primate lineages and hence could have contributed both to intra- and interspecies phenotypic diversity. In this study, we reinvestigated the data originally obtained by Perry et al. (2006) relating to chimpanzee CNVs and identified 24 genomic regions with the potential to be chimpanzee-specific CNVs. Since every putative chimpanzee-specific CNV was found in at least two of the 20 chimpanzees originally studied, it would appear as if these 24 CNVs are fairly frequent in chimpanzees. A combination of new mutation, genetic drift, and directional or balancing selection is likely to have influenced the maintenance of these CNVs in the chimpanzee population. Several genes map to the regions encompassed by the chimpanzee-specific CNVs. Some of their human orthologues are already known either to influence the phenotype (e.g., SLC24A4) or to be associated with inherited diseases (e.g., PAK3 and DTNBP1). Although the relatively small number of chimpanzee-specific CNVs (N = 24) among the 355 CNVs originally identified may be in part due to the use of a human BAC array to detect them, we nevertheless surmise that lineage-specific CNVs are not abundant in the chimpanzee. The thorough characterization of CNVs in the great ape genomes is a sine qua non for identifying the human-specific CNVs that may constitute genomic regions which have experienced either positive or negative selection during human evolution.
Copy number variation in the mouse genome: implications for the mouse as a model organism for human disease
Authors: Cutler G. , Kassner P.D.
Published: March 2009

Individuals within a species have genetic differences which ultimately result in the spectrum of phenotypic variation that we observe. Genetic variation exists at the nucleotide level in the form of single nucleotide polymorphisms (SNPs), and at a structural level as inversions, deletions and amplifications of larger stretches of nucleotides. Profiling of human and mouse genomes has identified numerous genomic segmental copy number variations (CNVs) throughout these genomes. Since inbred mice are widely used laboratory models for the study of both normal and disease biology, it is crucial that we understand the full scope of genetic variation, including CNVs, within these animals. These genetic differences can inform us about the history of a population or species, enlighten us on gene function, and guide our selection of a model system for the study of human disease.
Methods to detect CNVs in the human genome
Authors: Aten E. , White S.J. , Kalf M.E. , Vossen R.H.A.M. , Thygesen H.H. , Ruivenkamp C.A. , Kriek M. , Breuning M.H.B. , den Dunnen J.T.
Published: March 2009

The detection of quantitative changes in genomic DNA, i.e. deletions and duplications or Copy Number Variants (CNVs), has recently gained considerable interest. First, detailed analysis of the human genome showed a surprising amount of CNVs, involving thousands of genes. Second, it was realised that the detection of CNVs as a cause of genetic disease was often neglected, but should be an essential part of a complete screening strategy. In both cases new efficient CNV screening methods, covering the entire range from specific loci to genome-wide, were behind these developments. This paper will briefly review the methods that are available to detect CNVs, discuss their strong and weak points, show some new developments and look ahead. Methods covered include microscopy, fluorescence in situ hybridization (including fiber-FISH), Southern blotting, PCR-based methods (including MLPA), array technology and massive parallel sequencing. In addition, we will show some new developments, including a 1400-plex CNV bead assay, fast-MLPA (from DNA to result in ∼6 h) and a simple Melting Curve Analysis assay to confirm potential CNVs. Using the 1400-plex CNV bead assay, targeting selected chromosomal regions only, we detected confirmed rearrangements in 9% of 320 mental retardation patients studied.
Detection, breakpoint identification and detailed characterisation of a CNV at the FRA16D site using SNP assays
Authors: Winchester L. , Newbury D.F. , Monaco A.P. , Ragoussis J.
Published: March 2009

Copy Number Variants (CNV) and other submicroscopic structural changes are now recognised to be widespread across the human genome. We show that SNP data generated for association study can be utilised for the identification of deletion CNVs. During analysis of data for an SNP association study for Specific Language Impairment (SLI) a deletion was identified. SLI adversely affects the language development of children in the absence of any obvious cause. Previous studies have found linkage to a region on chromosome 16. The deletion was located in a known fragile site FRA16D in intron 5–6 of the WWOX gene (also known as FOR). Changes in the FRA16D site have been previously linked to cancer and are often characterised in cell lines. A long-range PCR assay was used to confirm the existence of the deletion. We also show the breakpoint identification and large-scale characterisation of this CNV in a normal human sample set.
Recent Racial/Ethnic Disparities in Stroke Hospitalizations and Outcomes for Young Adults in Florida, 2001–2006
Authors: Pathak Elizabeth Barnett , Sloan Michael A.
Published: March 2009

Background: Black-white disparities in stroke mortality are well documented, but few recent studies have examined racial/ethnic disparities in stroke hospitalizations among young adults. We analyzed recent (2001–2006) trends in stroke hospitalizations and hospital case-fatality for black, Hispanic, and white adults aged 25–49 years in Florida. Methods: Hospitalization rates were calculated using population estimates from the census, and hospital discharges with a primary diagnosis of stroke (ICD-9-CM 430, 431, 434, 436) (n = 16,317). Multivariate logistic regression modeling was used to examine racial/ethnic disparities in stroke mortality prior to discharge, after adjustment for patient sociodemographics, stroke subtype, risk factors, and comorbidities. Results: Age-adjusted stroke hospitalization rates for blacks were over 3 times higher than rates for whites, while rates for Hispanics were slightly higher than rates for whites. Hemorrhagic strokes were proportionally greater among Hispanics compared with blacks and whites (p < 0.0001). Blacks were most likely to have diagnosed hypertension (62.3%), morbid obesity (10.9%) or drug abuse (13.6%). Whites were most likely to have diagnosed hyperlipidemia (21.0%), alcohol abuse (9.5%), and to be smokers (30.6%). The in-hospital fatality rate for all strokes was highest among blacks (10.0%) compared with whites (9.0%) and Hispanics (8.2%). After adjustment for age, gender, insurance status, and all diagnosed risk factors and comorbidities, the black excess was no longer observed [odds ratio (OR) 1.01, 95% confidence interval (CI) 0.88–1.15, p = 0.93]. However, the Hispanic advantage in case-fatality was strengthened (OR 0.66, 95% CI 0.55–0.79, p < 0.0001). Separate case-fatality analyses for ischemic versus hemorrhagic strokes yielded similar results. Conclusions: Our study found a strong and persistent black-white disparity in stroke hospitalization rates for young adults. In contrast, rates were similar for Hispanics and whites. Multivariate adjustment explained the 15% excess case-fatality for blacks; the short-term mortality advantage among Hispanics was strengthened after adjustment.
The Effect of Rate Control on Speech Rate and Intelligibility of Dysarthric Speech
Authors: van Nuffelen Gwen , De Bodt Marc , Wuyts Floris , Van de Heyning Paul
Published: March 2009

Purpose: This study investigated the effect of rate control methods (RCMs) on speaking rate (SR), articulation rate (AR), and intelligibility in dysarthric speakers. Method: Nineteen dysarthric patients (7 unilateral upper motor neuron dysarthria, 6 hypokinetic, 3 flaccid, 3 ataxic) participated. SR, AR and intelligibility ratings were determined on the basis of 1-min recorded reading passages. Seven RCMs were applied: voluntary rate control, hand tapping, alphabet board, pacing board and delayed auditory feedback with a delay of 50, 100 and 150 ms. Results: Almost all methods resulted in lower mean SRs and ARs (p < 0.05). Rate control did not improve overall intelligibility of the dysarthric population. However, a meaningful increase of intelligibility was found in 5 participants. This study indicates that the effect of rate control on intelligibility is independent of habitual speech rate and type of dysarthria. Degree of intelligibility may be an influencing factor. The most effective methods are: voluntary rate control, alphabet board, hand tapping and pacing board. Conclusion: RCMs do result in lower speech rates. Some dysarthric individuals do benefit from one or more RCMs, but rate control may also have an inverse effect on intelligibility.
Voice Handicap and Health-Related Quality of Life in Laryngectomees: Assessments with the Use of VHI and EORTC Questionnaires
Authors: Lundström Elisabet , Hammarberg Britta , Munck-Wikland Eva
Published: March 2009

Aims: To investigate the Voice Handicap Index (VHI), the health-related quality of life (HRQL), and the correlations between VHI and HRQL in laryngectomees. Methods: Forty-three laryngectomized persons participated (mean age 68;6 years, time since laryngectomy between 0;6 and 12 years). Evaluation of voice handicap was done with the VHI. HRQL was evaluated with questionnaires from the European Organization for Research and Treatment of Cancer, EORTC QLQ-C30 and EORTC QLQ-H&N35. Results: VHI for the whole group demonstrated a moderate voice handicap, with a mean score of 48/120. The functional scales of EORTC QLQ-C30 resulted in scores on the same level as the normal population with the exception of a lower global quality of life scale (Global QOL). EORTC QLQ-H&N35 revealed problems with smell and taste, speech, coughing, xerostomia, and sexuality. VHI correlated significantly with the Global QOL, the functional scales, dyspnea, pain, nausea and financial difficulties (EORTC QLQ-C30). Significant correlations were also found between VHI and speech problems, social contact, pain from the head and neck area, sense problems, sexuality and social eating (EORTC QLQ-H&N35). Conclusion: The EORTC questionnaires in combination with the VHI questionnaire seem to capture most of the problems following laryngectomy, including voice problems.
Hemojuvelin: The Hepcidin Story Continues
Authors: Malyszko Jolanta
Published: March 2009

Hemojuvelin (HJV) is a membrane protein that is responsible for the iron overload condition known as juvenile hemochromatosis. HJV, highly expressed in the liver, skeletal muscle and heart, seems to play a role in iron absorption and release from cells and has anti-inflammatory properties. HJV is a bone morphogenetic protein (BMP) co-receptor and signals via the SMAD (human homolog of Drosophila mad – mother against decapentaplegic) pathway to regulate hepcidin expression. HJV acts as a BMP co-receptor. Moreover, HJV plays an essential role in the regulation of hepcidin expression, specifically in the iron-sensing pathway, although through unknown mechanisms. Dietary iron sensing and inflammatory pathways converge in the regulation of the key regulator hepcidin, but how these two pathways intersect remains unclear. Inflammation, through downregulation of hepatic HJV, might induce temporary elimination of iron sensing. Despite enormous scientific achievements in explaining the pathogenetic mechanisms of iron metabolism, many questions still remain unanswered: What is the functional role of HJV in iron metabolism? How it is related to hepcidin expression in different settings? How do iron-sensing and inflammatory pathways cooperate in hepcidin gene expression?
Serum Neutrophil Gelatinase-Associated Lipocalin as a Marker of Renal Function in Patients with Chronic Heart Failure and Coronary Artery Disease
Authors: Poniatowski Boguslaw , Malyszko Jolanta , Bachorzewska-Gajewska Hanna , Malyszko Jacek S. , Dobrzycki Slawomir
Published: March 2009

Heart failure and chronic kidney disease share a number of risk factors and pathophysiological pathways. Renal insufficiency is common in patients with chronic heart failure (CHF). The aim of the study was to assess whether neutrophil gelatinase-associated lipocalin (NGAL) could represent a novel, sensitive marker of kidney function in adult patients with chronic heart failure and normal serum creatinine. The study was performed on 150 patients with chronic heart failure due to coronary artery disease. Serum and urinary NGAL as well as serum cystatin C were measured using commercially available kits. Serum NGAL was related, in univariate analysis, to serum creatinine, urinary NGAL, hemoglobin, hematocrit, leukocyte count, eGFR, cystatin C. Urinary NGAL correlated with age, hemoglobin, hematocrit, serum creatinine, eGFR. In multiple regression analysis predictors of serum NGAL were NYHA class, cystatin C, and eGFR. Taking into consideration the fact that the recent DOQI states that individuals with a reduced GFR is at greater risk for cardiovascular disease and cardiac deaths, precise evaluation of renal function is important in order to select the appropriate strategy to reduce the cardiovascular risk. NGAL should be investigated as a potential early and sensitive marker of kidney impairment/injury.
Statins Do Not Affect Mineral Metabolism in Chronic Kidney Disease: A Retrospective Analysis
Authors: Ashman Neil , Banerjee Anindya , Yaqoob Muhammad M.
Published: March 2009

It has recently been proposed that statins act as vitamin D analogs in binding the ubiquitously expressed vitamin D receptor, accounting for the perceived pleiotropic effects of statins (a reduction in cancer risk, prevention of organ transplant rejection and autoimmune disease). Chronic kidney disease (CKD) offers a useful test of this hypothesis: serum 25-hydroxyvitamin D levels are insufficient (<75 nmol/l) in as many as 76% of patients with advanced CKD, associated with secondary hyperparathyroidism and reduced bone mineralization. Vitamin D suppresses parathyroid hormone (PTH) secretion in part through its action on the vitamin D receptor. If statins act as vitamin D analogs, they may then be able to suppress PTH secretion in CKD. We examined data on 714 vitamin D analog naïve patients with stage 3–4 CKD. 404 patients were treated with a statin indicated almost exclusively for primary prevention of coronary heart disease, and 310 patients were not. Both groups were similar in characteristics. Statins had no effect on the intact PTH concentration, the percentage of patients achieving K/DOQI™ PTH targets, or on calcium or phosphate concentrations. In patients with stage 3–4 CKD, statins had no effect on secondary hyperparathyroidism. If the hypothesis contending that statins act as vitamin D analogs to exert pleiotropic effects is true, this is of no clinical benefit in the prevention of secondary hyperparathyroidism in CKD.
Effect of Second Pregnancy on Maternal Carriage and Outcome of High-Risk Human Papillomavirus (HPV)
Authors: Sarkola Marja E. , Grénman Seija E. , Rintala Marjut A.M. , Syrjänen Kari J. , Syrjänen Stina M.
Published: March 2009

Objectives: The effect of second pregnancy on human papillomavirus (HPV) carriage and outcome is modelled in longitudinal setting covering two subsequent pregnancies. Study Design: Among 329 (baseline pregnant) women prospectively followed up inthe Finnish Family HPV Study, two subcohorts were compiled: (i) 78 women (Group B) who became pregnant for the second time during the follow-up, and (ii) 100 women (Group A) who did not develop 2nd pregnancy. The effect of pregnancy on high-risk HPV (HR-HPV) carriage and outcome was analysed using Kaplan-Meier and Cox survival analyses and generalized estimating equation (GEE) modelling of the longitudinal data. Results: Women in the two groups were similar in their baseline HR-HPV status but significantly different in several known risk factors of HR-HPV infection. Group A women showed higher point prevalence of cervical and oral HR-HPV at the 36-month (p = 0.015) and 6-month (p = 0.024) follow-up visit, respectively. Among Group B women, prevalence of both cervical and oral HR-HPV significantly decreased during 2nd pregnancy (p = 0.005 and p = 0.002) as compared with inter-pregnancy period, but increased again after 2nd pregnancy. There was no difference in acquisition or clearance of cervical or oral HR-HPV between the two groups in univariate (Kaplan-Meier) or multivariate (Cox) survival analysis. In the GEE approach, 2nd pregnancy was not significantly associated with cervical or oral HR-HPV carriage or persistence when adjusted for all other covariates. Conclusions: Second pregnancy is of little impact on carriage and persistence of oral and cervical HR-HPV infections in a longitudinal setting over time.
Flow Cytometric Immunophenotyping of Peripheral T Cell Neoplasms Using CD3 Gating
Authors: Hara Satoshi , Yokote Taiji , Akioka Toshikazu , Miyoshi Takuji , Ikemoto Toshiyuki , Tanaka Hidema , Takubo Takayuki , Tsuji Motomu , Hanafusa Toshiaki
Published: March 2009

Peripheral T cell neoplasms (PTCNs) such as peripheral T cell lymphoma, adult T cell leukemia/lymphoma, and mycosis fungoides are associated with poorer prognoses compared to B cell neoplasms. Hence, an accurate and early diagnosis is necessary for the successful treatment of PTCNs; however, this can be difficult to achieve. In this study, flow cytometric immunophenotyping using CD3 gating was performed retrospectively on 56 samples from 52 patients diagnosed with PTCNs, and the analytical data were compared with the immunohistochemical findings. Abnormal CD3 T cell populations were distinguishable from the normal T cell population, using this CD3 gating strategy.