Avian genomes: different karyotypes but a similar distribution of the GC-richest chromosome regions at interphase

Background & Aims: Previous genome-wide association studies showed that genetic polymorphisms in toll-like receptor 1 (TLR1) and protein kinase AMP-activated alpha 1 catalytic subunit (PRKAA1) genes were associated with gastric cancer (GC) or increased Helicobacter pylori (H. pylori) infection susceptibility. The aim of this study was to evaluate the association between TLR1 and PRKAA1 genes polymorphisms and H.pylori infection, atrophic gastritis (AG) or GC in the European population.Methods: Single-nucleotide polymorphisms (SNPs) were analysed in 511 controls, 340 AG patients and 327 GC patients. TLR1 C>T (rs4833095) and PRKAA1 C>T (rs13361707) were genotyped by the real-time polymerase chain reaction. H. pylori status was determined by testing for anti-H. pylori IgG antibodies in the serum.Results: The study included 697 (59.2%) H. pylori positive and 481 (40.8%) H. pylori negative cases. We observed similar distribution of TLR1 and PRKAA1 alleles and genotypes in H. pylori positive and negative cases. TLR1 and PRKAA1 SNPs were not linked with the risk of AG. TC genotype of TLR1 gene was more prevalent in GC patients compared to the control group (29.7% and 22.3% respectively, p=0.002). Carriers of TC genotype had a higher risk of GC (aOR=1.89, 95% CI: 1.26–2.83, p=0.002). A similar association was observed in a dominant inheritance model for TLR1 gene SNP, where comparison of CC+TC vs. TT genotypes showed an increased risk of GC (aOR=1.86, 95% CI: 1.26–2.75, p=0.002). No association between genetic polymorphism in PRKAA1 gene and GC was observed.Conclusions: TLR1 rs4833095 SNP was associated with an increased risk of GC in a European population, while PRKAA1 rs13361707 genetic variant was not linked with GC. Both genetic polymorphisms were not associated with H. pylori infection susceptibility or the risk of AG.

Download Full-text

Restriction Fragment Length Polymorphism and Divergence in the Genomic Regions of High and Low Recombination in Self-Fertilizing and Cross-Fertilizing Aegilops Species

Genetics ◽

10.1093/genetics/148.1.423 ◽

1998 ◽

Vol 148 (1) ◽

pp. 423-434

Author(s):

Jan Dvorřák ◽

Ming-Cheng Luo ◽

Zu-Li Yang

Keyword(s):

Related Species ◽

Gene Diversity ◽

Single Copy ◽

Species Variation ◽

Recombination Rates ◽

Distal Chromosome ◽

Phylogenetic Status ◽

Average Gene ◽

Genomic Regions ◽

Chromosome Regions

Abstract RFLP was investigated at 52 single-copy gene loci among six species of Aegilops, including both cross-fertilizing and self-fertilizing species. Average gene diversity (H) was found to correlate with the level of outcrossing. No relationship was found between H and the phylogenetic status of a species. In all six species, the level of RFLP at a locus was a function of the position of the locus on the chromosome and the recombination rate in the neighborhood of the locus. Loci in the proximal chromosome regions, which show greatly reduced recombination rates relative to the distal regions, were significantly less variable than loci in the distal chromosome regions in all six species. Variation in recombination rates was also reflected in the haplotype divergence between closely related species; loci in the chromosome regions with low recombination rates were found to be diverged less than those in the chromosome regions with high recombination rates. This relationship was not found among the more distantly related species.

Download Full-text

Comparison of Novelty Detection Methods for Detection of Various Rotary Machinery Faults

Sensors ◽

10.3390/s21103536 ◽

2021 ◽

Vol 21 (10) ◽

pp. 3536

Author(s):

Jakub Górski ◽

Adam Jabłoński ◽

Mateusz Heesch ◽

Michał Dziendzikowski ◽

Ziemowit Dworakowski

Keyword(s):

Novelty Detection ◽

Feature Space ◽

Detection Methods ◽

Data Sets ◽

Similar Distribution ◽

Detection Algorithms ◽

Rotary Machinery ◽

Detection Approach ◽

Input Reconstruction ◽

Quantitative Indicators

Condition monitoring is an indispensable element related to the operation of rotating machinery. In this article, the monitoring system for the parallel gearbox was proposed. The novelty detection approach is used to develop the condition assessment support system, which requires data collection for a healthy structure. The measured signals were processed to extract quantitative indicators sensitive to the type of damage occurring in this type of structure. The indicator’s values were used for the development of four different novelty detection algorithms. Presented novelty detection models operate on three principles: feature space distance, probability distribution, and input reconstruction. One of the distance-based models is adaptive, adjusting to new data flowing in the form of a stream. The authors test the developed algorithms on experimental and simulation data with a similar distribution, using the training set consisting mainly of samples generated by the simulator. Presented in the article results demonstrate the effectiveness of the trained models on both data sets.

Download Full-text

Dramatic nucleolar dispersion in the salivary gland of Schwenkfeldina sp. (Diptera: Sciaridae)

Scientific Reports ◽

10.1038/s41598-021-87012-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

José Mariano Amabis ◽

Eduardo Gorab

Keyword(s):

Salivary Gland ◽

Transcriptional Activity ◽

Relative Proportion ◽

Extreme Case ◽

Cell Types ◽

Chromosome Length ◽

Chromosomal Distribution ◽

Dna And Rna ◽

Polytene Nuclei ◽

Chromosome Regions

AbstractMicronucleoli are among the structures composing the peculiar scenario of the nucleolus in salivary gland nuclei of dipterans representative of Sciaridae. Micronucleolar bodies contain ribosomal DNA and RNA, are transcriptionally active and may appear free in the nucleoplasm or associated with specific chromosome regions in salivary gland nuclei. This report deals with an extreme case of nucleolar fragmentation/dispersion detected in the salivary gland of Schwenkfeldina sp. Such a phenomenon in this species was found to be restricted to cell types undergoing polyteny and seems to be differentially controlled according to the cell type. Furthermore, transcriptional activity was detected in virtually all the micronucleolar bodies generated in the salivary gland. The relative proportion of the rDNA in polytene and diploid tissues showed that rDNA under-replication did not occur in polytene nuclei suggesting that the nucleolar and concomitant rDNA dispersion in Schwenkfeldina sp. may reflect a previously hypothesised process in order to counterbalance the rDNA loss due to the under-replication. The chromosomal distribution of epigenetic markers for the heterochromatin agreed with early cytological observations in this species suggesting that heterochromatin is spread throughout the chromosome length of Schwenkfeldina sp. A comparison made with results from another sciarid species argues for a role played by the heterochromatin in the establishment of the rDNA topology in polytene nuclei of Sciaridae.

Download Full-text

Comparison of Risk Factors in Patients with Normal Arteries and Coronary Disease After Infarction

10.1055/s-0039-1680773 ◽

1977 ◽

Author(s):

S. K. Durairaj ◽

A. H. Khan ◽

L. J. Haywood

Keyword(s):

Risk Factors ◽

Coronary Artery Disease ◽

At Risk ◽

Coronary Artery ◽

Mexican American ◽

Acute Attack ◽

Similar Distribution ◽

Laboratory Findings ◽

High Prevalence ◽

Artery Disease

Risk factors were compared in 42 patients (pts) with coronary artery disease (CAD) and 18 with radiographically patent arteries (RPA) on angiography performed three weeks to six months after documented myocardial infarction (Ml). All pts had typical clinical and laboratory findings during the acute attack. All pts were below age 50 and both groups had a similar distribution of racial background (Caucasian, black and Mexican-American). Psychiatric problems were not more frequent in either group. The data demonstrated a high prevalence of standard risk factors in the CAD group for hypertension (28 of 42 = 67%), hypercholesterolemia (25 of 42 = 60%) and smoking (17 of 42 = 64%), and similarly high prevalence of smoking (16 of 18 = 89%), heavy labor (12 of 18 = 61%) and obesity (9 of 18 = 50%) in the RPA group. Factors significantly more common in the CAD group as compared to the RPA group by the Chi Square test were:Hypertension (P < 0.001), hypercholesterolemia (P < 0.001), diabetes (P < 0.001), and family history (P < 0.05). Factors more common in the RPA group were heavy alcohol consumption (P < 0.001), smoking (P < 0.05), heavy laborer occupation (P < 0.001) and obesity (P < 0.001). The data suggest that risk factor screening would identify individuals at risk from coronary artery disease but would be unreliable in identifying individuals at risk for MI with RPA. Further study is indicated to determine what factors operate to produce ischemia and infarction in the RPA group of pts.

Download Full-text

Biochemical Systematics, Biogeography and Evolutionary Rates in Species of the Mediterranean Genus Tyrrhenoleuctra (Plecoptera, Leuctridae)

Insect Systematics & Evolution ◽

10.1163/187631204788920211 ◽

2004 ◽

Vol 35 (3) ◽

pp. 299-306 ◽

Cited By ~ 7

Author(s):

◽

J. M. Tierno de Figueroa ◽

◽

Keyword(s):

North Africa ◽

Evolutionary Rate ◽

Taxonomic Status ◽

Morphological Characters ◽

Genetic Distances ◽

Western Mediterranean ◽

Similar Distribution ◽

Undescribed Species ◽

Vicariance Event ◽

Definition Of

AbstractThe western Mediterranean stonefly genus Tyrrhenoleuctra traditionally includes 3 species: T. minuta (Spain, North Africa, Balearic Islands), T. tangerina (Spain, North Africa), T. zavattarii (Corsica and Sardinia). Since the traditional morphological characters display great and overlapping variation, allozyme electrophoresis was used to clarify taxonomic and phylogenetic relationships within the genus and to discuss biogeographical implications. The results clearly discriminate at least four entities: the Corso-Sardinian unit, for which the name T. zavattarii can be used; the Balearic population, representing an undescribed species; at least two Iberian peninsular species. However, more data on topotypic populations are needed to define the taxonomic status of the Iberian species (including definition of the currently used names T. minuta and T. tangerina). The presence of Tyrrhenoleuctra in Sardinia and Corsica is likely due to an old vicariance event following separation of the Sardinia-Corsica microplate from the Iberian Peninsula. Calibration of the molecular clock (genetic distances vs. Corso-Sardinian plate split from Iberia) resulted in a very low evolutionary rate (0.008 D/my), lower than those found in taxonomically distant groups (including stoneflies) with similar distribution.

Download Full-text

Integrated Genomic Analysis of Sézary Syndrome

Genetics Research International ◽

10.4061/2011/980150 ◽

2011 ◽

Vol 2011 ◽

pp. 1-13 ◽

Cited By ~ 1

Author(s):

Xin Mao ◽

Tracy Chaplin ◽

Bryan D. Young

Keyword(s):

Copy Number ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Genomic Analysis ◽

Gene Clusters ◽

Sézary Syndrome ◽

Sezary Syndrome ◽

Snp Microarray ◽

The Impact ◽

Chromosome Regions

Sézary syndrome (SS) is a rare variant of primary cutaneous T-cell lymphoma. Little is known about the underlying pathogenesis of S. To address this issue, we used Affymetrix 10K SNP microarray to analyse 13 DNA samples isolated from 8 SS patients and qPCR with ABI TaqMan SNP genotyping assays for the validation of the SNP microarray results. In addition, we tested the impact of SNP loss of heterozygosity (LOH) identified in SS cases on the gene expression profiles of SS cases detected with Affymetrix GeneChip U133A. The results showed: (1) frequent SNP copy number change and LOH involving 1, 2p, 3, 4q, 5q, 6, 7p, 8, 9, 10, 11, 12q, 13, 14, 16q, 17, and 20, (2) reduced SNP copy number at FAT gene (4q35) in 75% of SS cases, and (3) the separation of all SS cases from normal control samples by SNP LOH gene clusters at chromosome regions of 9q31q34, 10p11q26, and 13q11q12. These findings provide some intriguing information for our current understanding of the molecular pathogenesis of this tumour and suggest the possibility of presence of functional SNP LOH in SS tumour cells.

Download Full-text

Fluorescent antibodies and lectins stain intracellular structures in fixed cells treated with nonionic detergent.

Journal of Histochemistry & Cytochemistry ◽

10.1177/26.4.207770 ◽

1978 ◽

Vol 26 (4) ◽

pp. 251-257 ◽

Cited By ~ 58

Author(s):

P Laurila ◽

I Virtanen ◽

J Wartiovaara ◽

S Stenman

Keyword(s):

Binding Sites ◽

Human Fibroblasts ◽

T Antigen ◽

Similar Distribution ◽

Sv40 T Antigen ◽

Con A ◽

Acetone Treatment ◽

Nonionic Detergent ◽

Detergent Treatment ◽

Scanning Electron

Nonionic detergent (NP40) treatment of paraformaldehyde-fixed normal and SV40-transformed human fibroblasts resulted in intracellular penetration of two chosen fluorescent antibodies and Concanavalin A (Con A). After the detergent treatment nuclear SV40 T antigen, cytoplasmic fibronectin glycoprotein and Con A binding sites could be visualized in fluorescence microscopy. The lowest NP40 concentration which made fixed cells permeable was 0.05%. The morphology of cells was preserved better by this new method than by conventional fixation methods, such as acetone treatment. In scanning electron microscopy the surface of the fixed NP40-treated cells had only small rugosities and fine pores. The subsurface cytoskeleton especially was well preserved and had a more distinct fine structure. The improved morphology made it possible to detect a similar distribution of fibronectin and Con A binding sites in the perinuclear endoplasmic reticulum regions.

Download Full-text

Close Encounters: RIDGEs, Hyperacetylated Chromatin, Radiation Breakpoints and Genes Differentially Expressed in Tumors Cluster at Specific Human Chromosome Regions

Cytogenetic and Genome Research ◽

10.1159/000296072 ◽

2010 ◽

Vol 128 (1-3) ◽

pp. 17-27 ◽

Cited By ~ 5

Author(s):

G.A. Folle ◽

P. Liddle ◽

L. Lafon-Hughes ◽

M.V. Di Tomaso

Keyword(s):

Human Chromosome ◽

Differentially Expressed ◽

Close Encounters ◽

Chromosome Regions

Download Full-text

BRAF/NRAS Mutation Frequencies Among Primary Tumors and Metastases in Patients With Melanoma

Journal of Clinical Oncology ◽

10.1200/jco.2011.41.2452 ◽

2012 ◽

Vol 30 (20) ◽

pp. 2522-2529 ◽

Cited By ~ 295

Author(s):

Maria Colombino ◽

Mariaelena Capone ◽

Amelia Lissia ◽

Antonio Cossu ◽

Corrado Rubino ◽

...

Keyword(s):

Lymph Nodes ◽

Primary Melanoma ◽

Similar Distribution ◽

Nras Mutation ◽

Tissue Samples ◽

Primary Tumors ◽

Paired Samples ◽

Automated Dna Sequencing ◽

Tumor Tissues ◽

Visceral Metastases

Purpose The prevalence of BRAF, NRAS, and p16CDKN2A mutations during melanoma progression remains inconclusive. We investigated the prevalence and distribution of mutations in these genes in different melanoma tissues. Patients and Methods In all, 291 tumor tissues from 132 patients with melanoma were screened. Paired samples of primary melanomas (n = 102) and synchronous or asynchronous metastases from the same patients (n = 165) were included. Tissue samples underwent mutation analysis (automated DNA sequencing). Secondary lesions included lymph nodes (n = 84), and skin (n = 36), visceral (n = 25), and brain (n = 44) sites. Results BRAF/NRAS mutations were identified in 58% of primary melanomas (43% BRAF; 15% NRAS); 62% in lymph nodes, 61% subcutaneous, 56% visceral, and 70% in brain sites. Mutations were observed in 63% of metastases (48% BRAF; 15% NRAS), a nonsignificant increase in mutation frequency after progression from primary melanoma. Of the paired samples, lymph nodes (93% consistency) and visceral metastases (96% consistency) presented a highly similar distribution of BRAF/NRAS mutations versus primary melanomas, with a significantly less consistent pattern in brain (80%) and skin metastases (75%). This suggests that independent subclones are generated in some patients. p16CDKN2A mutations were identified in 7% and 14% of primary melanomas and metastases, with a low consistency (31%) between secondary and primary tumor samples. Conclusion In the era of targeted therapies, assessment of the spectrum and distribution of alterations in molecular targets among patients with melanoma is needed. Our findings about the prevalence of BRAF/NRAS/p16CDKN2A mutations in paired tumor lesions from patients with melanoma may be useful in the management of this disease.

Download Full-text