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Results for “Heterogeneity Mapping”

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PubMed2006

Regional variation in mRNA transcript abundance within the ventricular wall.

Previous studies have shown that regional variation in ion channel gene expression contributes to electrical heterogeneity within the walls of the cardiac ventricles. To map the extent of regional variation in gene expression in the ventricular walls and to begin to understand its genesis we have performed a microarray analysis of gene expression in the epicardial and endocardial tissues of the rat adult left ventricle. While the vast majority of the genes are expressed at uniform levels across the ventricular wall, a total of 36 transcripts (representing less than 0.1% of the genes expressed in the ventricle) are expressed more abundantly in either epicardium or endocardium. One of these differentially expressed genes is the sodium channel gene Scn5a, which is expressed at higher levels in the endocardium than in the epicardium of rat heart. The transcription factor genes Irx3, Irx5 and Etv1 were found to be expressed in transmural gradients across the ventricular wall of rat heart and also of canine heart. The Irx3 and Irx5 genes were expressed in an inverse pattern to that of the Kcnd2 (Kv4.2) gene in rat heart, suggesting that these transcription factors may act as negative regulators of Kcnd2 expression in vivo.

Animals↗

PubMed1987

Brain glucose metabolism in children with the autistic syndrome: positron tomography analysis.

Brain glucose metabolism was measured in 18 autistic children, using high resolution positron emission tomography. Global brain glucose utilization in the autistic population was slightly more elevated than in young adult volunteers but did not differ significantly from that of control children. Regional metabolic maps were also normal, although there was evidence for heterogeneities, particularly at the level of prefrontal and parieto-temporo-occipital association areas: 6 children showed a relative hyperfrontality whilst hypofrontality was found in 2 cases; these heterogeneities were not correlated with clinical symptoms. These data suggest that both the rate and the regional distribution of brain glucose metabolism are normal in autistic children. Variations in terms of relative metabolic rates in association cortex remains to be investigated further.

Adolescent↗

PubMed1997

Molecular genetic analysis of familial neuroblastoma.

Neuroblastoma has several clinical and molecular genetic parallels with the other paediatric embryonal tumours, such as retinoblastoma, including a hereditary form of the disease. We hypothesised that neuroblastoma susceptibility is due to germline mutations in a tumour suppressor gene and that this predisposition gene may be involved in sporadic neuroblastoma tumorigenesis as well. We therefore aimed to localise the familial neuroblastoma predisposition gene by linkage analysis in neuroblastoma kindreds. Eighteen families segregating for neuroblastoma were ascertained for candidate locus linkage analysis. Although many of the 49 affected individuals in these families were diagnosed as infants with multifocal primary tumours, there was marked clinical heterogeneity. We originally hypothesised that familial neuroblastoma predisposition would map to the telomeric portion of chromosome band 1p36, a genomic region likely to contain a sporadic neuroblastoma suppressor gene. However, neuroblastoma predisposition did not map to any of eight polymorphic markers spanning 1p36.2-.3 in three large kindreds. In addition, there was strong evidence against linkage to two Hirschsprung disease susceptibility genes (RET and EDNRB), a condition that can cosegregate with neuroblastoma as in one of the kindreds tested here. We conclude that the neuroblastoma susceptibility gene is distinct from the 1p36 neuroblastoma suppressor and two of the currently identified Hirschsprung disease susceptibility genes.

Adult↗

PubMedDate not supplied

Blood-brain barrier permeation models: discriminating between potential CNS and non-CNS drugs including P-glycoprotein substrates.

The aim of this article is to present the design of a large heterogeneous CNS library (approximately 1700 compounds) from WDI and mapping CNS drugs using QSAR models of blood-brain barrier (BBB) permeation and P-gp substrates. The CNS library finally includes 1336 BBB-crossing drugs (BBB+), 259 molecules non-BBB-crossing (BBB-), and 91 P-gp substrates (either BBB+ or BBB-). Discriminant analysis and PLS-DA have been used to model the passive diffusion component of BBB permeation and potential physicochemical requirement of P-gp substrates. Three categories of explanatory variables (Cdiff, BBBpred, PGPpred) have been suggested to express the level of permeation within a continuous scale, starting from two classes data (BBB+/BBB-), allowing that the degree to which each compound belongs to an activity class is given using a membership score. Finally, statistical data analyses have shown that some very simple descriptors are sufficient to evaluate BBB permeation in most cases, with a high rate of well-classified drugs. Moreover, a "CNS drugs" map, including P-gp substrates and accurately reflecting the in vivo behavior of drugs, is proposed as a tool for CNS drug virtual screening.

ATP Binding Cassette Transporter, Subfamily B↗

PubMed2003

Buffed energy landscapes: another solution to the kinetic paradoxes of protein folding.

The energy landscapes of proteins have evolved to be different from most random heteropolymers. Many studies have concluded that evolutionary selection for rapid and reliable folding to a given structure that is stable at biological temperatures leads to energy landscapes having a single dominant basin and an overall funnel topography. We show here that, although such a landscape topography is indeed a sufficient condition for folding, another possibility also exists, giving a previously undescribed class of foldable sequences. These sequences have landscapes that are only weakly funneled in the conventional thermodynamic sense but have unusually low kinetic barriers for reconfigurational motion. Traps have been specifically removed by selection. Here we examine the possibility of folding on these "buffed" landscapes by mapping the determination of statistics of pathways for the heterogeneous nucleation processes involved in escaping from traps to the solution of an imaginary time Schroedinger equation. This equation is solved analytically in adiabatic and "soft-wall" approximations, and numerical results are shown for the general case. The fraction of funneled vs. buffed proteins in sequence space is estimated, suggesting the statistical dominance of the funneling mechanism for achieving foldability.

Biophysical Phenomena↗

PubMed1982

Molecular comparison of delta beta-thalassemia and hereditary persistence of fetal hemoglobin DNAs: evidence of a regulatory area?

The hematological phenotypes of several Mediterranean patients with delta beta-thalassemia and hereditary persistence of fetal hemoglobin have been characterized. Although clinical and hematological characteristics are essentially superimposable in all heterozygous delta beta-thalassemics, these patients show typical G gamma/A gamma ratios in their Hb F, ranging from approximately 0.07 in Sardinian to approximately 0.15 in Sicilian and approximately 0.35 in Spanish patients. A gamma Sardinian-(isoleucine-75 leads to threonine) is found in Spanish patients and accounts for all of the A gamma production in heterozygotes, indicating that persistent production of gamma chains occurs cis to the delta beta-thalassemia gene. The molecular heterogeneity of these conditions is demonstrated by restriction enzyme mapping of DNA; Sicilian and Calabrian patients show a deletion starting from the delta-globin intron and extending several kilobases 3' to the beta-globin gene; in Spanish patients the deletion starts approximately 2-3 kilobases 5' to the delta-globin gene and extends well beyond the beta-globin gene. Comparison of these deletions with previously described ones in Negro and in a new Southern Italian case of hereditary persistence of fetal hemoglobin suggests that the deletion of a region centered at a cluster of repetitive sequences approximately 3.5 kilobases 5' to the delta-globin gene may be critical for the persistent expression of high levels of gamma-globin in hereditary persistence of fetal hemoglobin compared to delta beta-thalassemia. The concept that the deletion or mutation of specific areas (rather than nonspecific changes brought about by large deletions in the globin cluster) is important in determining the persistent expression of gamma-globin genes is supported by the finding of a nondeletion type of delta beta-thalassemia in Sardinians.

Chromosome Deletion↗

PubMed2002

Mapping spatial pattern in biodiversity for regional conservation planning: where to from here?

Vast gaps in available information on the spatial distribution of biodiversity pose a major challenge for regional conservation planning in many parts of the world. This problem is often addressed by basing such planning on various biodiversity surrogates. In some situations, distributional data for selected taxa may be used as surrogates for biodiversity as a whole. However, this approach is less effective in data-poor regions, where there may be little choice but to base conservation planning on some form of remote environmental mapping, derived, for example, from interpretation of satellite imagery or from numerical classification of abiotic environmental layers. Although this alternative approach confers obvious benefits in terms of cost-effectiveness and rapidity of application, problems may arise if congruence is poor between mapped land-classes and actual biological distributions. I propose three strategies for making more effective use of available biological data and knowledge to alleviate such problems by (1) more closely integrating biological and environmental data through predictive modeling, with increased emphasis on modeling collective properties of biodiversity rather than individual entities; (2) making more rigorous use of remotely mapped surrogates in conservation planning by incorporating knowledge of heterogeneity within land-classes, and of varying levels of distinctiveness between classes, into measures of conservation priority and achievement; and (3) using relatively data-rich regions as test-beds for evaluating the performance of surrogates that can be readily applied across data-poor regions.

Algorithms↗

PubMed2001

Quantitative architecture distinguishes prefrontal cortical systems in the rhesus monkey.

The prefrontal cortex encompasses a large and heterogeneous set of areas, whose borders have been variously mapped in different architectonic studies. Differences in cortical maps present a formidable problem in comparing data across studies and in constructing databanks on the connections and functional attributes of cortical areas. Here we used quantitative approaches to cortical mapping to investigate (i) if architectonic areas of the prefrontal cortex in adult rhesus monkeys have unique profiles and (ii) if groups of architectonic areas belonging to distinct cortical types, ranging from agranular to eulaminate, have similar features. In addition, we used multidimensional analyses to see if, and how, prefrontal areas form clusters when multiple features are considered simultaneously. We used quantitative unbiased sampling procedures to estimate the areal and laminar density of neurons, glia and neurons positive for the calcium binding proteins parvalbumin (PV), calbindin (CB) and calretinin (CR) among 21 prefrontal areas or subdivisions of areas. Neuronal density varied among the prefrontal cortices (range: 38 569 +/- 4078 to 58 708 +/- 2327 neurons/mm(3)); it was lowest in caudal orbitofrontal and medial areas (OPAll, OPro, 13, 24a, 32, M25) and highest in lateral prefrontal areas (subdivisions of areas 46 and 8). Neurons positive for PV were most prevalent in lateral prefrontal areas and least prevalent in caudal orbitofrontal and medial pre-frontal areas, whereas the opposite trend was noted for neurons that expressed CB. Neurons positive for CR did not show regional differences, and the density of glia showed small variations among prefrontal cortices. The differences among areas, along with differences in the thickness of individual areas and layers, were used to establish a quantitative profile for each area. The results showed that differences in the density of neurons, and the preponderance of neurons positive for PV and CB, were related to different architectonic types of areas found within the prefrontal cortex. Conventional as well as multiparameter statistical analyses distinguished at one extreme the agranular and dysgranular (limbic) cortices, which were characterized by prominent deep layers (V-VI), the lowest neuronal density, the highest ratio of glia/neurons, and the lowest density of PV and the highest for CB. At the other extreme, lateral eulaminate cortices were characterized by the highest density of neurons, a prominent granular layer IV, denser supragranular (II-III) than infragranular (V-VI) layers, and a balanced distribution of neurons positive for PV and CB. The results provide insights into potentially different rates of development or maturation of limbic and eulaminate prefrontal areas, and their differential vulnerability in neurological and psychiatric diseases. The quantitative methods used provide an objective approach to construct maps, address differences in nomenclature across studies, establish homologies in different species and provide a baseline to identify changes in pathologic conditions.

Animals↗

PubMed2000

New approach for dose reconstruction: application to one case of localized irradiation with radiological burns.

When localized accidental irradiation occurs, it is necessary to determine the extent to which tissues and vital organs have been damaged, mainly in the vicinity of the source. At present, biological markers cannot be used to estimate the heterogeneity of the dose distribution. An alternative is to map the absorbed dose in the different regions of the body. Using a Monte Carlo calculation code, it is possible to simulate the accident while taking into account the specific morphology of the irradiated individual and his environment, as well as the source characteristics. The calculated values are matched to the clinical signs of the lesion, particularly around the rim of the radiation-induced necrosis. This technique was applied successfully on two patients who presented very severe lesions due to acute localized irradiation after an accident that occurred at Lilo (Georgia) in 1996-1997; only the most demonstrative case is presented here.

Bone and Bones↗

PubMed2005

Clinical symptoms according to genotype amongst patients with hereditary haemorrhagic telangiectasia.

BACKGROUND: Hereditary haemorrhagic telangiectasia (HHT) is a dominantly inherited disease, characterized by a wide variety of clinical manifestations, including epistaxis, gastrointestinal (GI) bleeding, pulmonary arteriovenous malformations (PAVMs) and neurological symptoms. HHT is a genetically heterogeneous disorder involving at least two loci; HHT 1 mapping to chromosome 9 q 34.1 (ENG) and HHT 2 mapping to chromosome 12 q 31 (ALK-1). OBJECTIVE: To evaluate and describe the diversity of clinical manifestations in a Danish population of HHT patients with known HHT 1 or HHT 2 subtype. DESIGN: Prospective clinical examination with genetic evaluation and follow-up. SETTING: Investigation centre was Odense University Hospital. All HHT patients in the County of Fyn were included. METHODS: HHT family members were invited to a clinical examination including registration of HHT manifestations, screening for PAVM and neurological evaluation. Blood tests were performed for analysis of disease-causing mutation, and clinical manifestations in the HHT subtypes were compared. The survival of the patients was studied in the follow-up period. RESULTS: Included in the study were 73 HHT patients representing 18 families. In 14 of the families we identified a disease-causing mutation. Thirty-nine patients (from 10 families) had HHT1 and 16 HHT patients from four families had HHT2. CONCLUSION: Amongst patients with HHT1 genotype the prevalence of PAVM was higher than amongst HHT patients with HHT2 genotype. HHT1 patients had experienced more severe GI bleeding than HHT2 patients. There was no significant difference in severity of epistaxis or age at debut. Finally the mortality over a 90-month observation period was not significantly increased.

Activin Receptors, Type I↗

PubMedDate not supplied

Linear response range characterization and in vivo application of laser speckle imaging of blood flow dynamics.

Noninvasive blood flow imaging can provide critical information on the state of biological tissue and the efficacy of approaches to treat disease. With laser speckle imaging (LSI), relative changes in blood flow are typically reported, with the assumption that the measured values are on a linear scale. A linear relationship between the measured and actual flow rate values has been suggested. The actual flow rate range, over which this linear relationship is valid, is unknown. Herein we report the linear response range and velocity dynamic range (VDR) of our LSI instrument at two relevant camera integration times. For integration times of 1 and 10 ms, the best case VDR was 80 and 60 dB, respectively, and the worst case VDR was 20 and 50 dB. The best case VDR values were similar to those reported in the literature for optical Doppler tomography. We also demonstrate the potential of LSI for monitoring blood flow dynamics in the rodent dorsal skinfold chamber model. These findings imply that LSI can provide accurate wide-field maps of microvascular blood flow rate dynamics and highlight heterogeneities in flow response to the application of exogenous agents.

Animals↗

PubMed2005

Towards biologically conformal radiation therapy (BCRT): selective IMRT dose escalation under the guidance of spatial biology distribution.

It is well known that the spatial biology distribution (e.g., clonogen density, radiosensitivity, tumor proliferation rate, functional importance) in most tumors and sensitive structures is heterogeneous. Recent progress in biological imaging is making the mapping of this distribution increasingly possible. The purpose of this work is to establish a theoretical framework to quantitatively incorporate the spatial biology data into intensity modulated radiation therapy (IMRT) inverse planning. In order to implement this, we first derive a general formula for determining the desired dose to each tumor voxel for a known biology distribution of the tumor based on a linear-quadratic model. The desired target dose distribution is then used as the prescription for inverse planning. An objective function with the voxel-dependent prescription is constructed with incorporation of the nonuniform dose prescription. The functional unit density distribution in a sensitive structure is also considered phenomenologically when constructing the objective function. Two cases with different hypothetical biology distributions are used to illustrate the new inverse planning formalism. For comparison, treatments with a few uniform dose prescriptions and a simultaneous integrated boost are also planned. The biological indices, tumor control probability (TCP) and normal tissue complication probability (NTCP), are calculated for both types of plans and the superiority of the proposed technique over the conventional dose escalation scheme is demonstrated. Our calculations revealed that it is technically feasible to produce deliberately nonuniform dose distributions with consideration of biological information. Compared with the conventional dose escalation schemes, the new technique is capable of generating biologically conformal IMRT plans that significantly improve the TCP while reducing or keeping the NTCPs at their current levels. Biologically conformal radiation therapy (BCRT) incorporates patient-specific biological information and provides an outstanding opportunity for us to truly individualize radiation treatment. The proposed formalism lays a technical foundation for BCRT and allows us to maximally exploit the technical capacity of IMRT to more intelligently escalate the radiation dose.

Dose-Response Relationship, Radiation↗

PubMed1990

Molecular cloning and physical and functional characterization of the Salmonella typhimurium and Salmonella typhi galactose utilization operons.

The chromosomally encoded galactose utilization (gal) operons of Salmonella typhimurium and S. typhi were each cloned on similar 5.5-kilobase HindIII fragments into pBR322 and were identified by complementation of Gal- Escherichia coli strains. Restriction endonuclease analyses indicated that these Salmonellae operons share considerable homology, but some heterogeneities in restriction sites were observed. Subcloning and exonuclease mapping experiments showed that both operons have the same genetic organization as that established for the E. coli gal operon (i.e., 5' end, promoter, epimerase, transferase, kinase, and 3' end). Two gal operator regions (oE and oI) of S. typhimurium, identified by repressor titration in an E. coli superrepressor [galR(Sup)] mutant, were sequenced and found to flank the promoter region. This promoter region is identical to the -10 and -35 regions of the E. coli gal operon. Minicell studies demonstrated that the three gal structural genes of S. typhimurium encode separate polypeptides of 39 kilodaltons (kDa) (epimerase, 337 amino acids [aa's]), 41 kDa (transferase, 348 aa's), and 43 kDa (kinase, 380 aa's). Despite functional and organizational similarities, DNA sequence analysis revealed that the S. typhimurium gal genes show less than 70% homology to the E. coli gal operon. Because of codon degeneracy, the deduced amino acid sequences of these polypeptides are highly conserved (greater than 90% homology) as compared with those of the E. coli gal enzymes. These studies have defined basic genetic parameters of the gal genes of two medically important Salmonella species, and our findings support the hypothesized divergent evolution of E. coli and Salmonella spp. from a common ancestral parent bacterium.

Amino Acid Sequence↗

PubMed1976

Structure of Herpesvirus saimiri genomes: arrangement of heavy and light sequences in the M genome.

Herpesvirus saimiri contains two species of DNA molecules. (i) The M genome is composed of 70% light (L) DNA (36% cytosine plus guanine; density in CsCl, 1.695 g/ml), which consists of unique sequences, and 30% heavy (H) DNA (71% cytosine plus guanine; density, 1.729 g/ml). (ii) The H genome contains heavy sequences exclusively. H sequences in M and H genomes cross-hybridize completely and are cleaved identically by restriction endonuclease R-Sma I into four classes of fragments with molecular weights of about 360,000, 300,000, 130,000 and 40,000, respectively. H sequences are chains of identical repeat units in tandem arrangement. The molecular weight of each repeat unit is about 830,000. L sequences have no cleavage site for endo R-Sma I H sequences are terminally arranged at both ends of the M genome, as seen by electron microscopy after partial denaturation. The length of the individual heavy ends varies between 21 mum and less than 1 mum, whereas the light region is uniform in size (35.3+/-0.35 mum). As a rule, molecules with a long heavy end at one side have a short heavy end at the other side, thus giving rise to a limited size heterogeneity. Orientation of M DNA molecules by the denaturation map of the light region shows that the longer heavy end may be located at the left or at the right side of the M genome.

Base Sequence↗

PubMed2003

Diagnostic criteria, clinical characteristics, and natural history of Cohen syndrome.

Cohen syndrome is a rare, recessively inherited condition associated with facial dysmorphism, developmental delay, and visual disability. A delay in making the diagnosis commonly occurs, contributed to by the lack of a definitive molecular test and the clinical variability of published case reports. A specific clinical phenotype has been delineated in a homogeneous cohort of Finnish Cohen syndrome patients, but the applicability of their diagnostic criteria to non-Finnish patients has been debated. Detailed delineation of Cohen syndrome in patients from outside Finland is therefore warranted. We report on the clinical features of 33 non-Finnish Cohen syndrome patients. Variability within the clinical spectrum is identified and the natural history of Cohen syndrome described. Diagnostic guidelines for facilitating accurate and early diagnosis are discussed. Results from molecular genetic analysis using markers located within the previously mapped COH1 critical region support allelic but not genetic heterogeneity in this UK cohort.

Abnormalities, Multiple↗

PubMed2002

Significance of carbohydrate epitopes in a latex allergen with beta-1,3-glucanase activity.

BACKGROUND: One of the latex allergens, Hev b 2, has beta-1,3-glucanase activity. The entire sequence of this allergen is already known. There is one potential N-glycosylation site in this molecule ((27)Asn). Heterogeneous glycosylation of this Asn residue could be a source of the multiplicity of natural Hev b 2. Possible participation of the carbohydrate epitopes of latex beta-1,3-glucanase isoenzymes in their IgE-binding capacity and cross-reactivity was investigated in this study. METHODS: beta-1,3-Glucanase isoenzymes were separated based on their affinities for concanavalin A. IgE-binding capacity and cross-reactivity were examined by immunoblotting and enzyme-linked immunosorbent assay (ELISA). Sequence heterogeneity among the isoenzymes was probed by peptide mass mapping after lysyl endopeptidase digestion. To clarify the relation to Hev b 2, N-terminal sequencing was performed on a fragmented peptide common to the separated isoenzymes. RESULTS: Basic beta-1,3-glucanase was subdivided into two glycosylated isoenzymes (GI and GII) and one non-glycosylated isoenzyme (GIII). IgE antibodies in latex-positive sera chiefly recognized the glycosylated isoenzymes. Inhibition ELISA supported the significance of the carbohydrate epitopes for the IgE recognition and cross-reactivity. However, non-glycosylated GIII, as well as GI and GII, produced positive results in a skin prick test. The three beta-1,3-glucanase isoenzymes shared a partial sequence in common with Hev b 2. CONCLUSIONS: Our results suggest that the carbohydrate epitopes in Hev b 2 homologues are relevant to an in vitro diagnosis of latex allergy and the accompanying cross-reactivity. Carbohydrate epitopes do not necessarily provoke allergic symptoms. Therefore, the actual allergenicity of Hev b 2 and its homologues should be carefully evaluated not only by in vitro IgE tests but also by in vivo tests.

Adult↗

PubMed2006

Confirmation of the adult-onset primary open angle glaucoma locus GLC1B at 2cen-q13 in an Australian family.

Primary open-angle glaucoma (POAG) is genetically heterogeneous, with 6 named POAG loci GLC1A-F mapped and genes myocilin (MYOC) and optineurin (OPTN) identified at 2 of the loci. Using penetrance-model-free methods, we screened the POAG loci GLC1A-F in an extended Australian pedigree, using 3-5 markers within each locus. p values of less than 0.05 were obtained empirically using SimWalk2 and exactly using Genehunter for 2 markers within the GLC1B region on chromosome 2. Fine mapping of this region produced p values of 0.01 or less at 5 markers flanked by D2S1897 and D2S2269. The 9 cM haplotype of interest overlaps the original GLC1B region. These results provide supportive evidence for the GLC1B locus on chromosome 2cen-q13 and verify the existence of POAG susceptibility gene in this region, increasing the likelihood of gene identification.

Adult↗

PubMed2002

Clinical and genetic heterogeneity in benign hereditary chorea.

BACKGROUND: Benign hereditary chorea (BHC) is an autosomal dominant disorder that can be distinguished from Huntington disease by its early onset, stable or only slightly progressive course, and absence of mental deterioration. The variation in clinical features is such that its very existence has been doubted. The authors recently described the localization of a gene responsible for BHC on chromosome 14q in a large Dutch family. OBJECTIVE: To report results of extensive clinical and linkage analyses for this Dutch family and six other families with BHC. RESULTS: Three of the seven families had linkage to a region on chromosome 14q13.1-q21.1. HOMOG analysis showed odds of 10 x 10(11) in favor of locus heterogeneity. Haplotype analyses for the linked families resulted in a reduction of the critical interval for the BHC gene to 8.4 cM between marker D14S49 and marker D14S278. Clinically, these three families had a homogeneous picture with early-onset chorea, sometimes accompanied by slight ataxia in walking, but without dystonia, myoclonic jerks, or dysarthria. The severity of the choreatic movements tended to abate in adolescence or early adulthood. In the unlinked families, symptoms and signs were more heterogeneous as to age at onset and the occurrence of myoclonic jerks or dystonia. CONCLUSIONS: BHC is a clinically and genetically heterogeneous disorder, with one well-defined clinical syndrome mapping to chromosome 14q.

Adolescent↗