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PubMed2004

Linkage analysis of diabetes status among hypertensive families: the Hypertension Genetic Epidemiology Network study.

Type 2 diabetes susceptibility is determined by multiple genetic and environmental factors. Genome-wide linkage scans have localized common regions, possibly harboring susceptibility genes on chromosomes 1, 2, 12, and 20. Variability in linkage findings underscores the probable genetic heterogeneity of type 2 diabetes. Thus, we conducted a genome scan of diabetes status using maximum likelihood methods that model affection status by a liability threshold model. Hypertensive sibships and their offspring and/or parents in the Hypertension Genetic Epidemiology Network study were recruited from five field centers. The diabetes phenotype was derived using the World Health Organization criteria and adjusted for race/study center, age, age2, sex, and with and without percent body fat. In total, 567 diabetic participants were identified in 437 families. Variance component linkage analysis was performed among 1,545 Caucasians and 1,608 African Americans using race-specific marker allele frequencies. We detected a quantitative trait loci (QTLs) influencing diabetes variance (logarithm of odds = 3.4) on chromosome 22, which overlaps a positive type 2 diabetes finding among Canadian Oji-Cree Indians. We also observed suggestive evidence for linkage on chromosomes 1, 2, 5, 8, 14, 17, and 19. The identification and replication of type 2 diabetes QTLs will bring us closer to the detection of functional genes that influence diabetes susceptibility.

Chromosome Mapping↗
PubMed1999

Update on hereditary optic neuropathy.

Although no treatment is available for hereditary optic neuropathies, recent localization and identification of some of the genetic loci have helped the evaluation and management of patients with these disorders. This article discusses the clinical features and known genetic information regarding Leber's hereditary optic neuropathy, dominant optic atrophy, recessive optic atrophy, and Wolfram syndrome.

Audiovisual Aids↗
PubMed2002

Plant genomics: an overview.

Recent technological advancements have substantially expanded our ability to analyze and understand plant genomes and to reduce the gap existing between genotype and phenotype. The fast evolving field of genomics allows scientists to analyze thousand of genes in parallel, to understand the genetic architecture of plant genomes and also to isolate the genes responsible for mutations. Furthermore, whole genomes can now be sequenced. This review addresses these issues and also discusses ways to extract biological meaning from DNA data. Although genomic issuesare addressed from a plant perspective, this review provides insights into the genomic analyses of other organisms.

Arabidopsis↗
PubMed1997

Biomarkers of squamous cell carcinoma of the head and neck.

Despite the remarkable advances in cancer treatment, the 5-year survival rate for head and neck squamous cell carcinoma (HNSCC) has improved only marginally over the past 20 years. Investigators have attempted to develop new therapeutic methods to improve the survival rate from these tumors. Another approach, chemoprevention, has recently been tried to reduce cancer incidence. Biological understanding of tumorigenesis is critically important to provide risk assessment and intermediate end points during chemoprevention trials. Based on the fact that HNSCC develops through a multistep process by the accumulation of genetic and phenotypic changes in the field exposed to carcinogens, the investigation of specific biomarkers that represent each step must be valuable, since these biomarkers could be used to inhibit and/or to reverse the pathway of carcinogenesis. The potential biomarkers are classified as nonspecific and specific genetic biomarkers, proliferation markers, and differentiation markers in this review. Their usefulness in predicting tumors' biological behavior and responses to treatment and in monitoring the preventive effects of chemoprevention trials is also discussed.

Biomarkers, Tumor↗
PubMed2006

Expression of Integrin beta3 is correlated to the properties of quiescent hemopoietic stem cells possessing the side population phenotype.

With significant attention paid to the field of tissue-specific stem cells, the identification of stem cell-specific markers is of considerable importance. Previously, the side population (SP) phenotype, with the capacity to efflux the DNA-binding dye Hoechst 33342, has been recognized as a common feature of adult tissue-specific stem cells. In this study, we show that high expression of integrin beta(3) (CD61) is an attribute of SP cells isolated from mouse bone marrow. Additionally, we confirmed that the expression of integrin beta(3) is correlated with properties of quiescent hemopoietic stem cells (HSCs) including the strength of the SP phenotype, cell cycle arrest, expression of HSC markers, and long-term hemopoiesis. Importantly, Lineage(-) (Lin(-))/integrin beta(3)(high) (beta(3)(high)) SP cells have as strong a capacity for long-term hemopoiesis as c-Kit(+)/Sca-1(+)/Lin(-) SP cells, which are regarded as one of the most highly enriched HSC populations. Finally, the integrin beta(3) subunit that is present in SP cells having the properties of HSCs, is associated with integrin alpha(v) (CD51). Therefore, our results demonstrate that high expression of integrin beta(3) is correlated to the properties of quiescent HSCs and suggest that the integrin beta(3) subunit is available as a common surface marker of tissue-specific stem cells.

Animals↗
PubMed1998

A cluster of meningococcal disease in western Sydney, Australia initially associated with a nightclub.

Fourteen cases of meningococcal disease (MD) occurred in August September 1996 in western Sydney, Australia. Seven of the 10 young adults affected had a direct or indirect link with a local nightclub. Ten of 11 systemic meningococcal isolates had the phenotype C:2a:P1.5 and showed close genetic relationship by pulsed-field gel electrophoresis (PFGE). Organisms of this phenotype have not previously caused outbreaks in Australia, but have been associated with outbreaks and hyperendemic serogroup C MD in Europe, Canada, and the United States. This is the largest cluster of serogroup C MD reported in urban Australia, and the first involving a nightclub. The strain differentiation results were available rapidly enough to augment epidemiological investigations on a daily basis. Public health staff could thus establish links between cases quickly, follow the spread of new cases in the community, give accurate information to health officials and the press, and utilize existing knowledge about the characteristics of this phenotype to predict likely developments during the outbreak and afterwards. The strain differentiation data was also very helpful when the role of vaccination was considered, and existing guidelines on the management of outbreaks of MD could be used effectively for the first time in western Sydney.

Adolescent↗
PubMed2026

Deep soil layers show the most pronounced genetic variation in wheat root length.

Wheat is one of the most important cereals worldwide, yet significant gaps remain in our understanding of genetic variability in root traits, especially those associated with deeper rooting that support resource acquisition in challenging environments. Root traits are typically controlled by many genes with small effects and often display low heritability. Our aim was to develop a statistical approach to analyse root variation across soil depth and to determine where genetic differences in root intensity are most detectable. An experiment was conducted at the RadiMax semi-field facility, which is designed to measure deep root systems. Five years of phenotypic data recorded each June produced observations from 1500 rows. Each row captured root intensity across the soil profile from 0.6 m to 2.6 m, enabling detailed analysis of vertical root distribution. Across the five years, 513 winter wheat cultivars were grown in the facility, and among those 409 were genotyped with SNP chips. Depth-resolved regression models with random coefficients were used to quantify genetic and non-genetic variation in root intensity across soil depths, while accounting for spatial variation between rows. Random variation within rows was found to be constant across depths. The models showed that genetic variance for cumulative root intensity increased substantially below 1.1 m, with the deepest layers exhibiting the largest differences between wheat lines. Narrow-sense heritability of point measurements peaked at approximately 1.5 m ([Formula: see text]).

Genetic variability↗
PubMed1997

Ocular findings in patients with autosomal dominant retinitis pigmentosa and Cys110Phe, Arg135Gly, and Gln344stop mutations of rhodopsin.

This report describes ocular findings obtained in four patients from three families with autosomal dominant retinitis pigmentosa (adRP) due to missense mutations in the rhodopsin gene. Phenotypes were characterized by standard ophthalmologic examinations, visual fields, electroretinography (ERG), dark adaptation, and two-color dark-adapted threshold perimetry. Two patients aged 38 and 45 years, respectively, from a family with the Cys110Phe mutation showed mild fundus changes without bone spicules as well as small arcuate scotomas in the inferior quadrants of their visual fields but displayed severe functional loss of rods and cones in the ERG. Two-color dark-adapted threshold perimetry revealed a regional type of degeneration. A 48-year-old patient with an Arg135Gly mutation had typical RP with concentrically narrowed visual fields and nondetectable ERG responses. Central visual functions were well preserved for a long time. Two-color dark-adapted threshold perimetry indicated a diffuse type of retinal degeneration. An 18-year-old patient with a Gln344stop mutation has been followed for 13 years. His ERG was clearly reduced at the age of 5 years; since that time, disease progression has been very slow. Currently, there are relatively mild alterations in visual acuity, rod sensitivity, and visual fields. Our findings confirm that there is a large phenotypic variety among patients with adRP and different rhodopsin mutations.

Adolescent↗
PubMed1989

Genetic markers and inflammatory bowel disease: immunoglobulin allotypes (GM, KM) and protease inhibitor.

We have studied immunoglobulin allotypes (GM and KM) in 101 patients with Crohn's disease, 51 patients with ulcerative colitis, and 99 healthy local blood donor controls. In addition, protease inhibitor (PI) types were examined in a random subset of patients and in all controls. No significant differences were found between Crohn's disease patients and controls, or between ulcerative colitis patients and controls, in the frequencies of GM phenotypes, GM haplotypes, KM phenotypes, or PI phenotypes.

Colitis, Ulcerative↗
PubMed2001

Statistical aspects of quantitative image analysis of beta-amyloid in the APP(V717F) transgenic mouse model of Alzheimer's disease.

Cerebral beta-amyloidosis is a central part of the neuropathology of Alzheimer's disease (AD). Quantitation of beta-amyloid plaques in the human AD brain, and in animal models of AD, is an important study endpoint in AD research. Methodologic approaches to the measurement of beta-amyloid in the brain vary between investigators, and these differences affect outcome measures. Here, one quantitative approach to the measurement of beta-amyloid plaques in brain sections was analyzed for sources of variability due to sampling. Brain tissue was from homozygous APP(V717F) transgenic male mice. Sampling variables were at the mouse and microscopic slide and field levels. Results indicated that phenotypic variability in the mouse sample population was the largest contributor to the standard error of the analyses. Within each mouse, variability between slides or between fields within slides had smaller effects on the error of the analyses. Therefore, when designing studies of adequate power, in this and in other similar models of cerebral beta-amyloidosis, sufficient numbers of mice per group must be included in order for change in mean plaque burden attributable to an experimental variable to outweigh phenotypic variability.

Alzheimer Disease↗
PubMed2005

Characterization of Clostridium botulinum strains associated with an infant botulism case in the United Kingdom.

The sixth case of infant botulism in the United Kingdom was reported in 2001. The case was caused by a type B strain of Clostridium botulinum. Strains of C. botulinum were isolated from the baby's feces and from foodstuffs in the household in an attempt to document transmission. The aims of this study were to characterize the strains of C. botulinum associated with the botulism case. This was performed using a variety of techniques, including C. botulinum culture phenotypic properties, neurotoxin characterization, and pulsed-field gel electrophoresis (PFGE) banding patterns. Cultures associated with this case as well as isolates from stored and historical samples were analyzed and compared. C. botulinum type B PFGE patterns from the infant and from an opened container of infant formula were indistinguishable, while the PFGE profile of a strain presumably isolated from an unopened archival container was unique. The results suggest that the unopened brand of formula was not the source for transmission of spores to the infant and that the strain was distinct from previous botulism cases in the United Kingdom. Since environmental testing was not performed, it is not possible to deduce other sources of transmission.

Botulinum Toxins↗
PubMed2003

The mapping of quantitative trait loci underlying strain differences in locomotor activity between 129S6 and C57BL/6J mice.

Performance in the open field and rotarod paradigms, two common assessments of locomotor function, have been demonstrated to be strain dependent in mice. In this study, eight significant quantitative trait loci (QTL) for behavior phenotypes in either the open field or rotarod paradigms were identified between the 129S6 (129/SvEvTac) and C57BL/6J strains. These strains were chosen for comparison because of their frequent use in the generation of mutant mice from gene-targeted, embryonic stem cells. Two of the QTLs for horizontal distance traveled are located on Chromosomes (Chrs) 1 and 12 and closely replicate the findings of other groups using different strains of mice. Rotarod performance was influenced in an oppositional manner by two separate QTLs on Chr 1 and 2. Additionally, examination of several different aspects of behavior in the open field revealed significant QTLs for average speed (Chr 12), duration (Chrs 2, 16, and 18), time spent in motion (Chr 16), vertical movements (rearing) (Chrs 6 and 12), and vertical time (rearing time) (Chrs 6 and 12). Our finding of independent QTLs for these topographic components of open field activity supports the idea that they are separate and distinct from total horizontal distance traveled and should be studied independently. The QTLs described in this study, in combination with our panel of polymorphic chromosomal markers for 129S6 and C57BL/6J strains, will be useful in assessing the potential epistatic effects of parental strain background on the phenotypes of genetically modified mice.

Animals↗
PubMed1985

Modulation of collagen production in cultured fibroblasts by a low-frequency, pulsed magnetic field.

Primary cultures of chicken tendon fibroblasts have been exposed for various periods to a low-frequency, pulsed magnetic field, and the effects on protein and collagen synthesis have been examined by radioisotopic incorporation. Total protein synthesis was increased in confluent cells treated with a pulsed magnetic field for the last 24 h of culture as well as in cells treated for a total of 6 days. However, in 6 day-treated cultures, collagen accumulation was specifically enhanced as compared to total protein, whereas after short-term exposure, collagen production was increased only to the same extent as total protein. Levels of cyclic AMP were significantly decreased after 6-day pulsed magnetic field treatment, probably as a consequence of diminished adenylate cyclase activity. Exposure to pulsed magnetic field had no effect on cell proliferation or collagen phenotype. These results indicate that a pulsed magnetic field can specifically increase production of collagen, the major differentiated function of fibroblasts, possibly by altering cyclic-AMP metabolism.

Animals↗
PubMed1997

Enterotoxin and toxic shock syndrome toxin-1 production of methicillin resistant and methicillin sensitive Staphylococcus aureus strains.

In this study the production of enterotoxin A-D and toxic shock syndrome toxin-1 (TSST-1) of 181 methicillin resistant (MRSA) and 100 methicillin sensitive (MSSA) Staphylococcus aureus first isolates from different patients was investigated. All the MRSA- and MSSA isolates in the study were collected in a period between 1993 and 1995 from specimens sent from 11 different acute care hospitals in the greater Düsseldorf area. As far as possible the isolates were matched according to ward and hospital. The isolates were collected in the same time period and matched for specimen from which isolated. Furthermore, only first isolates were analysed in both groups. No significant difference in the production of toxin of any type between MRSA and MSSA could be detected (51 and 40% respectively). When the individual toxins were analysed, again no significant difference between MRSA and MSSA was demonstrable (enterotoxin production by MRSA 40% and MSSA 36%, and TSST-1 16% and 8% respectively). Despite this, a slight tendency for MRSA to produce enterotoxin A and B and for MSSA to produce enterotoxin C was observed. In addition, generation of TSST-1 by both groups was independent of enterotoxin A-D production. Interestingly, no increase in the proportion of TSST-1- or enterotoxin-producing MRSA and MSSA isolates was observed in strains isolated from blood cultures from patients with a clinical diagnosis of sepsis. Genotypical pulsed-field-gel-electrophoresis (PFGE) and phenotypical (bacteriophage typing, lysotyping) characterization of the 181 MRSA isolates resulted in 28 different PFGE patterns (of which 19 were toxin producers) and 22 lysotyping groups (18 of which produced toxin). In summary, the investigated clinical S. aureus isolates showed no difference in their ability to produce toxin and this was independent of their sensitivity to methicillin.

Bacterial Toxins↗
PubMed2003

Genetic evidence for cognitive reserve: variations in memory and related cognitive functions.

Variations in cognitive functions across individuals are observed universally, and such observations serve as the basis of cognitive reserve (CR). Broadly, cognitive reserve refers to the inconsistency between neuropathology and clinical severity. The causes of such individual variations are likely to be multi-factorial. In this review, I present studies which suggest that genes are likely to be the contributing causes, and these genes interact with environmental factors to produce even greater variations in cognitive functions. A number of animal and human studies are beginning to reveal the role of genetic contributions to cognitive functions like memory, memory decline, general intelligence, and language. Twin studies suggest that there is a substantial heritable component for memory and related cognitive functions, such as general intelligence and language, but not for others. Thus, heritability estimates vary by cognitive domain. Animal studies and some human studies have identified genes or candidate loci that contribute to memory as well as other related cognitive phenotypes. Yet, our current understanding is limited. It will require interdisciplinary efforts from a number of different fields to better define the neuropsychological phenotype. At the same time, it is necessary to take into account both genetic and environmental factors to understand the complex network underlying CR.

Adaptation, Physiological↗
PubMed2000

Development of sensory neurons in the absence of NGF/TrkA signaling in vivo.

The neurotrophin survival dependence of peripheral neurons in vitro is regulated by the proapoptotic BCL-2 homolog BAX. To study peripheral neuron development in the absence of neurotrophin signaling, we have generated mice that are double null for BAX and nerve growth factor (NGF), and BAX and the NGF receptor TrkA. All dorsal root ganglion (DRG) neurons that normally die in the absence of NGF/TrkA signaling survive if BAX is also eliminated. These neurons extend axons through the dorsal roots and collateral branches into the dorsal horn. In contrast, superficial cutaneous innervation is absent. Furthermore, rescued sensory neurons fail to express biochemical markers characteristic of the nociceptive phenotype. These findings establish that NGF/TrkA signaling regulates peripheral target field innervation and is required for the full phenotypic differentiation of sensory neurons.

Animals↗
PubMed2003

The phenotype of normal tension glaucoma patients with and without OPA1 polymorphisms.

AIM: Polymorphisms in OPA1, the gene responsible for autosomal dominant optic atrophy, were recently found to be strongly associated with normal tension glaucoma (NTG). The aim of this study was to determine whether OPA1 polymorphisms affect the phenotype of NTG patients. METHODS: A retrospective analysis was performed of 108 well characterised NTG patients who had been genotyped for OPA1 variations, and who had previously undergone automated perimetry and Heidelberg retina tomography (HRT). 25 NTG patients had the at-risk OPA1 genotype (IVS 8 +4 C/T; +32 T/C) and 83 NTG patients did not. Differences between groups were sought in a wide range of structural, psychophysical, and demographic factors. These included sex, age at diagnosis, family history of glaucoma, history of ischaemic risk factors and vasospasm, laterality of glaucoma, presenting and highest diurnal intraocular pressure (IOP), initial cup-disc (CD) ratio, baseline visual field global indices, and optic disc parameters as measured by HRT. For a subgroup of patients with at least 5 years of follow up and 10 visual field tests, pointwise linear regression analysis (PROGRESSOR for Windows software) was applied to the visual field series. RESULTS: There was no significant difference in the two groups with respect to sex, age at diagnosis, family history of glaucoma, history of ischaemic risk factors and vasospasm, or laterality of glaucoma. The comparison of IOP, CD ratio and visual field global indices, MD and CPSD in the two groups showed no significant difference. There were no differences in the mean values for any of the HRT parameters analysed. For the subgroup of patients with at least 5 years of follow up, there was also no significant difference in the number of patients with progressing locations, the mean number of progressing locations per subject, the mean slope of the progressing locations or the mean slope for whole visual field. CONCLUSIONS: The absence of phenotypic differences in normal tension glaucoma patients with and without the OPA1 polymorphisms IVS 8 +4 C/T; +32 T/C suggest that these OPA1 polymorphisms do not underlie any major phenotypic diversity in these patients.

Age of Onset↗