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PubMed2006

Mutations and polymorphisms of Hirschsprung disease candidate genes in Thai patients.

Mutation and polymorphism data for Hirschsprung disease (HSCR) varies among ethnic groups. Single nucleotide polymorphisms (SNP) of RET proto-oncogene (RET) were recently shown to be associated with the disease, and with disease severity, in different populations. In this study, comprehensive analysis of RET, GDNF, EDNRB, ET-3, and SOX-10 genes among sporadic HSCR in Thailand was conducted by standard PCR-SSCP, RFLP, and sequencing methods. Of 41 patients, 30 cases had rectosigmoid disease (RSD) and 11 cases were assigned to the long-segment disease (LSD) group. Four missense mutations of RET, S100M, R231H, T278N, and G533S, were identified in three patients. One novel missense mutation, V111Q, was detected in EDNRB. For ET-3, two novel missense mutations, D166E and C173R, occurred concomitantly in a patient. The incidence of missense mutation was significantly higher in our female HSCR patient than in the male counterpart. Statistical analysis of the SNPs revealed a significant difference between allele distribution of RET L769L in patients in the LSD and RSD groups. The predominant genotype construct of RET A45A/L769L in our HSCR was GG/GG, which is obviously different from results from all previous studies. The GG/GG genotype construct was associated with RSD and with males. The study also detected a variant allele of RET S836S which has never been reported in Asian cohorts.

Alleles↗

PubMed2006

The NR4A nuclear receptor family in eosinophils.

It is well-known that many members of the family of nuclear receptors have been implicated in human diseases, and metabolic disorders in particular. The NR4A nuclear receptor family consists of three members, Nur77, Nurr1, and NOR1. All of these are orphan receptors, and Nur77 and NOR1 exert possible pathological roles in immune diseases through the modulation of leukocyte functions. CD30 stimulation, which induces eosinophil-specific apoptosis, markedly enhances expression of Nur77 and NOR1 in eosinophils. This suggests the possibility of pharmacological modulation of Nur77- or NOR1-specific apoptotic pathways via receptor-dependent transactivation. In this review, we discuss treatment of allergic diseases by low molecular weight compounds acting through the NR4A receptor family to cause eosinophil apoptosis. NR4A nuclear receptor genes were selected following comprehensive analysis of differentially expressed genes in eosinophils of atopic dermatitis patients compared with healthy volunteers.

Animals↗

PubMed2006

TCR variable gene involvement in chromosome inversion between 14q11 and 14q24 in adult T-cell leukemia.

Chromosomal translocations in T-cell malignancies frequently involve the T-cell receptor (TCR)alpha/delta locus at chromosome 14q11. Although 14q11 abnormalities are found in about 10% of adult T-cell leukemia (ATL) cases, until now there has been no direct evidence showing involvement of the TCR locus in ATL-a malignancy closely associated with HTLV-1 infection. The breakpoints of T-cell malignancies most commonly occur within the Jalpha or Jdelta region of the TCR locus. In ATL, however, despite extensive searching no breakpoint has yet been found in that region. Using fluorescence in situ hybridization with a panel of cosmid and bacterial artificial chromosome probes derived from chromosome 14, including the variable region of the TCRalpha locus, comprehensive analysis of an ATL patient carrying inv(14)(q11q32) revealed that the TCR locus was indeed involved in this inversion. Molecular cloning of the breakpoint revealed the juxtaposition of TCR Valpha to the 14q24 region as a result of two consecutive inversions: inv(14)(q11q32) and inv(14)(q11q24). We also found a gene near the breakpoint at the 14q24 region that is downregulated in this ATL patient and is assigned in the database as a pseudogene of ADAM21 (a disintegrin and metalloproteinase domain 21). Our expression analysis, however, showed that this pseudogene was actually expressed and was capable of encoding a protein similar to ADAM21; thus we have named this gene ADAM21-like (ADAM21-L).

ADAM Proteins↗

PubMed2004

Are survival rates different for young and older patients with rectal cancer?

PURPOSE: Although it is generally believed that young patients with rectal cancer have worse survival rates, no comprehensive analysis has been reported. This study uses a national-level, population-based cancer registry to compare rectal cancer outcomes between young vs. older populations. METHODS: All patients with rectal carcinoma in the Surveillance, Epidemiology, and End Results cancer database from 1991 to 1999 were evaluated. Young (range, 20-40 years; n = 466) and older groups (range, 60-80 years; n = 11,312) were compared for patient and tumor characteristics, treatment patterns, and five-year overall and stage-specific survival. Cox multivariate regression analysis was performed to identify predictors of survival. RESULTS: Mean ages for the groups were 34.1 and 70 years. The young group was comprised of more black and Hispanic patients compared with the older group (P < 0.001). Young patients were more likely to present with late-stage disease (young vs. older: Stage III, 27 vs. 20 percent respectively, P < 0.001; Stage IV, 17.4 vs. 13.6 percent respectively, P < 0.02). The younger group also had worse grade tumors (poorly differentiated 24.3 vs. 14 percent respectively, P < 0.001). Although the majority of both groups received surgery (85 percent for each), significantly more young patients received radiation (P < 0.001). Importantly, overall and stage-specific, five-year survival rates were similar for both groups (P = not significant). CONCLUSIONS: Although previous studies have found young rectal cancer patients to have poorer survival compared with older patients, this population-based study shows that young rectal cancer patients seem to have equivalent overall and stage-specific survival.

Adult↗

PubMed2005

Malignancies of the appendix: beyond case series reports.

PURPOSE: A comprehensive analysis was performed for five histologic types of appendiceal tumors to compare incidence, clinicopathologic features, survival, and appropriateness of surgery. METHODS: All patients diagnosed with mucinous adenocarcinoma (n = 951), adenocarcinoma (n = 646), carcinoid (n = 435), goblet (n = 369), and signet-ring cell (n = 113) in the Surveillance, Epidemiology, and End Results database (1973-2001) were analyzed. Evaluation of incidence, stage, and five-year relative survival were determined for each histology. The appropriateness of the operative procedure (i.e. , appendectomy vs. colectomy) was examined by tumor type and size. RESULTS: Tumor incidence, patient demographics, survival outcomes, and appropriateness of surgery varied significantly among the different appendiceal tumor histologies. The most common appendiceal tumors were mucinous. With regard to patient demographics, carcinoids presented at an earlier mean age of 41 years and 71 percent were female (P < 0.001 for both). Overall five-year survival was highest for carcinoid (83 percent) and lowest for signet ring (18 percent). Although current guidelines specify that a right hemicolectomy (rather than an appendectomy) be performed for all noncarcinoid tumors and carcinoid tumors >2 cm, we found that 30 percent of noncarcinoids underwent appendectomy. Similarly, 28 percent of carcinoids >2 cm under-went appendectomy, which is a lesser resection than is indicated. CONCLUSIONS: This study provides a population-based analysis of epidemiology, tumor characteristics, survival, and quality of care for appendiceal carcinomas. This characterization provides a novel description of the presentation and outcomes for malignancies of the appendix and highlights that a substantial number of patients with appendiceal tumors may not be receiving appropriate surgical resection.

Adenocarcinoma, Mucinous↗

PubMed2005

Biomarker profile and genetic abnormalities in lobular carcinoma in situ.

The predisposition of patients with lobular carcinoma in situ (LCIS) to develop invasive breast cancer (IBC) is well known. However, relatively little is known about the biologic characteristics, which may be involved in the development and progression of LCIS. This study evaluated 59 cases of LCIS (29 pure, 30 with synchronous IBC) for five biomarkers known to be important in IBC (ER, PgR, c-erbB-2, p53 and Ki-67 proliferation rate) by immunohistochemistry. A comprehensive analysis of loss-of-heterozygosity (LOH) was performed in 12 cases (10 pure, 2 with synchronous IBC) at 15 genetic loci on 9 chromosomes. LCIS demonstrated a low grade/favorable biophenotype that was not significantly different in cases with and without synchronous IBC (ER 98%, PgR 84%, c-erbB-24%, p53 19% and proliferation rate 2%). LOH was present in 80% of pure LCIS and the highest rates of LOH were at loci on 9p (30%), 16q (63%), 17p (33%) and 17q (50%). The clustering of LOH at these four foci suggests that inactivated tumor suppressor genes in these regions may be particularly important. LOH was present in both cases of LCIS with synchronous IBC and the LOH phenotype was shared by LCIS and IBC. Our findings suggest that five known prognostic factors in IBC do not have prognostic utility in LCIS. Multiple genetic mechanisms may be involved in the development of LCIS.

Biomarkers, Tumor↗

PubMed2006

WWOX protein expression in normal human tissues.

WWOX is a putative tumor suppressor gene that spans approximately a 1 Mb genomic region and is the site for the second most common chromosomal fragile site, FRA16D at 16q23. Various studies have focused on the expression of WWOX in human cancer mostly at the RNA level, but little is known about the normal pattern of WWOX protein expression in non-neoplastic tissues. In this study, a comprehensive analysis of WWOX protein expression in normal tissues was performed by means of immunohistochemistry utilizing a very specific anti-WWOX polyclonal antibody. We analyzed tissue cores of human samples representing more than 30 organs, using various tissue microarray (TMA) slides. Due to the potential role of WWOX in sex-steroid metabolism, whole sections from hormonally regulated organs like breast, ovaries, testes and prostate were also analyzed. The results from our study indicate that WWOX is preferentially highly expressed in secretory epithelial cells of reproductive, endocrine and exocrine organs, as well as in ductal epithelial cells from specific segments of the urinary system. Interestingly, we also observed significant WWOX protein expression in various cell types of neural origin including neurons, ependymal cells and astrocytes. No expression of WWOX was detected in adipose, connective, and lymphoid tissues, myelinized structures and blood vessels. By better defining the topographic distribution of WWOX in normal tissues this study provides some insight on the potential physiological role of this novel protein.

Humans↗

PubMed2006

Distribution of soluble epoxide hydrolase, cytochrome P450 2C8, 2C9 and 2J2 in human malignant neoplasms.

Soluble epoxide hydrolase (sEH) is a bifunctional enzyme with a C-terminal epoxide hydrolase activity and an N-terminal phosphatase activity. Arachidonic acid epoxides, previously suggested to be involved in apoptosis, oncogenesis and cell proliferation, are generated by cytochrome P450 epoxygenases and are good substrates of the sEH C-terminal domain. In addition, the N-terminal phosphatase domain hydrolyzes isoprenoid mono- and pyrophosphates, which are involved in cell signaling and apoptosis. Here we provide a comprehensive analysis of the distribution of sEH, CYP2C8, 2C9 and 2J2 in human neoplastic tissues using tissue micro-arrays. The human neoplastic tissue micro-arrays provide a well-controlled side by side analysis of a wide array of neoplastic tissues and their surrounding normal tissue controls. Many of the neoplastic tissues showed altered expression of these enzymes as compared to normal tissues. Altered expression was not limited to the neoplastic tissues but also found in the surrounding non-neoplastic tissues. For example, sEH expression in renal and hepatic malignant neoplasms and surrounding non-neoplastic tissues was found to be significantly decreased, whereas expression was found to be increased in seminoma as compared to normal tissues. Our study warrants further investigation of the role of altered expression of these enzymes in neoplastic tissues.

Aryl Hydrocarbon Hydroxylases↗

PubMed2006

Trends in gambling studies research: quantifying, categorizing, and describing citations.

As opportunities to gamble have increased during the 20th century, so has gambling research. This study used new strategies, methods, and technology to examine citation trends and the growth of knowledge in the field of gambling studies. The sample included 2,246 citations that were published between 1903 and 2003. By using multiple keywords to classify each citation into distinct topic areas, this study yielded a more comprehensive analysis than was previously available. The results reveal that gambling-related research has grown at an exponential rate. The most prevalent topics explored within gambling studies citations have been pathology, risk-taking, decision-making and addiction. Between 1999 and 2003, studies addressing epidemiology, drug abuse, comorbidity and neuroscience have become increasingly prevalent. Based on these trends and their implications, this paper provides several recommendations for both future areas of inquiry within the field of gambling studies and better classification techniques for citations within all fields of psychology.

Abstracting and Indexing↗

PubMed2025

Bacteriophages as a modern diagnostic tool: innovations, applications and challenges.

Bacteriophages, viruses that specifically infect bacteria, have emerged as a valuable tool in diagnostics due to their unique specificity and adaptability. This review explores the diverse applications of bacteriophages in diagnostic methods, from traditional phage typing to advanced molecular techniques such as phage display and PCR-based diagnostics. It highlights their use in identifying bacterial strains, monitoring fermentation processes, and diagnosing critical conditions like tuberculosis, MRSA infections, and cancer. Innovations such as phage-based biosensors and reporter phages enhance the speed and precision of diagnostics, offering significant advantages over traditional methods. Challenges, including bacterial resistance and immune responses to phages, are also discussed alongside strategies for mitigation, such as phage cocktails and engineering. Integrating phage technology with modern bioscience holds promise for addressing antibiotic resistance and revolutionizing clinical and industrial diagnostics. This comprehensive analysis underscores the potential of bacteriophages to transform the diagnostic landscape while identifying areas requiring further research and development.

Bacteriophages↗

PubMed2026

The application of the CRISPR-Cas system in Pseudomonas aeruginosa infections.

Due to the extensive drug resistance of Pseudomonas aeruginosa (P. aeruginosa), it is still a great clinical challenge. The clustered regularly interspaced short palindromic repeats and associated proteins (CRISPR-Cas) system has become a promising strategy against this pathogen. This review critically evaluates the multifaceted applications of CRISPR-Cas technology in P. aeruginosa, including its role in antimicrobial resistance, diagnostics, genome editing, and emerging therapeutic and vaccine strategies. In addition to conducting a comprehensive analysis of various studies, we also compared the performance and limitations of various CRISPR platforms, and discussed the main technologies and transformation obstacles in this field. Finally, we look forward to the direction of applying these experimental tools to clinical research in the future.

Pseudomonas aeruginosa↗

PubMed2006

Molecular control of nuclear and subnuclear targeting of the plant CDK inhibitor ICK1 and ICK1-mediated nuclear transport of CDKA.

ICK1 is the first member of a family of plant cyclin-dependent kinase (CDK) inhibitors. It has been shown that ICK1 is localized in the nuclei of transgenic Arabidopsis plants. Since cellular localization is important for the functions of cell cycle regulators, a comprehensive analysis was undertaken to identify specific sequences regulating the cellular localization of ICK1. Deletion and site-specific mutants fused to the green fluorescent protein (GFP) were used in transgenic Arabidopsis plants and transfected tobacco cells. Surprisingly, three separate sequences in the N-terminal, central and C-terminal regions of ICK1 could independently confer nuclear localization of the GFP fusion proteins. The central nuclear localization signal NLS(ICK1) could transport the much larger GUS (beta-glucuronidase)-GFP fusion protein into nuclei, while the other two sequences were unable to. These results suggest that NLS(ICK1) is a strong NLS that actively transports the fusion protein into nuclei, while the other two sequences are either a weaker NLS or confer the nuclear localization of GFP indirectly. It was further observed that the N-terminal sequence specifies a punctate pattern of subnuclear localization, while the C-terminal sequence suppresses it. Furthermore, co-expression of ICK1 and Arabidopsis CDKA, tagged with different GFP variants, showed that ICK1 could mediate the transport of CDKA into nuclei while a mutant ICK1(1-162) that does not interact with CDKA lost this ability. These results illustrate how the nuclear localization of ICK1 is regulated and also suggest a possible role of ICK1 in regulating the cellular distribution of CDKA.

Arabidopsis↗

PubMed2006

The grapevine polygalacturonase-inhibiting protein (VvPGIP1) reduces Botrytis cinerea susceptibility in transgenic tobacco and differentially inhibits fungal polygalacturonases.

Polygalacturonase-inhibiting proteins (PGIPs) selectively inhibit polygalacturonases (PGs) secreted by invading plant pathogenic fungi. PGIPs display differential inhibition towards PGs from different fungi, also towards different isoforms of PGs originating from a specific pathogen. Recently, a PGIP-encoding gene from Vitis vinifera (Vvpgip1) was isolated and characterised. PGIP purified from grapevine was shown to inhibit crude polygalacturonase extracts from Botrytis cinerea, but this inhibitory activity has not yet been linked conclusively to the activity of the Vvpgip1 gene product. Here we use a transgenic over-expression approach to show that the PGIP encoded by the Vvpgip1 gene is active against PGs of B. cinerea and that over-expression of this gene in transgenic tobacco confers a reduced susceptibility to infection by this pathogen. A calculated reduction in disease susceptibility of 47-69% was observed for a homogeneous group of transgenic lines that was statistically clearly separated from untransformed control plants following infection with Botrytis over a 15-day-period. VvPGIP1 was subsequently purified from transgenic tobacco and used to study the specific inhibition profile of individual PGs from Botrytis and Aspergillus. The heterologously expressed and purified VvPGIP1 selectively inhibited PGs from both A. niger and B. cinerea, including BcPG1, a PG from B. cinerea that has previously been shown to be essential for virulence and symptom development. Altogether our data confirm the antifungal nature of the VvPGIP1, and the in vitro inhibition data suggest at least in part, that the VvPGIP1 contributed to the observed reduction in disease symptoms by inhibiting the macerating action of certain Botrytis PGs in planta. The ability to correlate inhibition profiles to individual PGs provides a more comprehensive analysis of PGIPs as antifungal genes with biotechnological potential, and adds to our understanding of the importance of PGIP:PG interactions during disease and symptom development in plants.

Botrytis↗

PubMed2026

Genome-wide identification of CHY zinc finger and RING finger (CHYR) genes in pepper and functional characterization of CaCHYR5 in response to Phytophthora capsici infection.

CHY zinc finger and RING finger (CHYR) proteins play crucial roles in the growth and development, as well as stress response. To date, no systematic or comprehensive analysis of the CHYR gene family has been performed in pepper (Capsicum annuum L.). In this study, we identified 8 CaCHYR genes (CaCHYR1-CaCHYR8), which were classified into 3 groups based on phylogenetic relationships. CaCHYR members within the same group exhibited similar distributions of conserved motifs and exon-intron structures. Chromosomal localization analysis showed that 8 CaCHYR genes were unevenly distributed on 6 chromosomes. Segmental duplication, rather than tandem duplication, was found to be the major contributor to the expansion of this gene family. CaCHYR genes feature a variety of cis-elements involved in developmental processes, phytohormone responses, and stress adaptation. Expression analysis based on RNA-seq data revealed that CaCHYR genes exhibited distinct spatial expression patterns across different tissues and in response to Phytophthora capsici infection (PCI), and quantitative real-time PCR (qRT-PCR) further confirmed that three of them (CaCHYR2, CaCHYR3, and CaCHYR5) exhibited altered expression under PCI. Furthermore, transient overexpression of CaCHYR5 in pepper leaves increased susceptibility to PCI, suggesting its potential negative regulatory role in pepper defense against P. capsici. Collectively, these findings reveal the expression patterns and regulatory functions of pepper CHYR genes in growth and development, laying a groundwork for breeding pepper cultivars tolerant to PCI.

Phytophthora capsici infection (PCI)↗

PubMed1975

Mechanical performance of surgical sutures.

A comprehensive analysis of the mechanical performance of sutures has been made to provide information concerning the reliability and security of knotted sutures. The tests utilized in this analysis were designed to be easily reproduced by other investigators. The construction of the knot and the knot performance analysis were undertaken utilizing an Instron Tensile Tester. The mechanical reliability of each knotted suture was determined by measuring the number of throws to reach knot break, the expected slippage of the knot when it reaches knot break, and the maximal holding force at knot break. On the basis of these measurements, recommendations are made for the use of a suture at operation.

Biomechanical Phenomena↗

PubMed1990

Induction of haptotactic migration of melanoma cells by neutrophil activating protein/interleukin-8.

Natural or recombinant neutrophil activating cytokine (IL-8) induced migration across polycarbonate filters of human A 2058 melanoma cells. Anti-IL-8 antibodies blocked IL-8 induced melanoma cell migration. Checkerboard experiments revealed a gradient-dependent response of A2058 melanoma cells to IL-8. Filters exposed to IL-8 and washed supported melanoma cell migration, thus implying a haptotactic component in the response. The homologous polypeptide platelet factor 4 was inactive. The observation that IL-8 affects melanoma cells emphasizes the need for a comprehensive analysis of the spectrum of action of platelet factor 4-related peptides. The effect of the inflammatory cytokine IL-8 on melanoma cells may be relevant to augmented secondary localization of tumors at sites of inflammation.

Chemotactic Factors↗

PubMed1988

Mapping and sequencing of mutations in the Escherichia coli rpoB gene that lead to rifampicin resistance.

Rifampicin is an antibiotic that inhibits the function of RNA polymerase in eubacteria. Mutations affecting the beta subunit of RNA polymerase can confer resistance to rifampicin. A large number of rifampicin-resistant (hereafter called Rifr) mutants have been isolated in Escherichia coli to probe the involvement of RNA polymerase in a variety of physiological processes. We have undertaken a comprehensive analysis of Rifr mutations to identify their structural and functional effects on RNA polymerase. Forty-two Rifr isolates with a variety of phenotypes were mapped to defined intervals within the rpoB gene using a set of deletions of the rpoB gene. The mutations were sequenced. Seventeen mutational alterations affecting 14 amino acid residues were identified. These alleles are located in three distinct clusters in the center of the rpoB gene. We discuss the implications of our results with regards to the structure of the rifampicin binding site.

Base Sequence↗

PubMed1990

High-resolution three-dimensional structure of horse heart cytochrome c.

The 1.94 A resolution three-dimensional structure of oxidized horse heart cytochrome c has been elucidated and refined to a final R-factor of 0.17. This has allowed for a detailed assessment of the structural features of this protein, including the presence of secondary structure, hydrogen-bonding patterns and heme geometry. A comprehensive analysis of the structural differences between horse heart cytochrome c and those other eukaryotic cytochromes c for which high-resolution structures are available (yeast iso-1, tuna, rice) has also been completed. Significant conformational differences between these proteins occur in three regions and primarily involve residues 22 to 27, 41 to 43 and 56 to 57. The first of these variable regions is part of a surface beta-loop, whilst the latter two are located together adjacent to the heme group. This study also demonstrates that, in horse cytochrome c, the side-chain of Phe82 is positioned in a co-planar fashion next to the heme in a conformation comparable to that found in other cytochromes c. The positioning of this residue does not therefore appear to be oxidation-state-dependent. In total, five water molecules occupy conserved positions in the structures of horse heart, yeast iso-1, tuna and rice cytochromes c. Three of these are on the surface of the protein, serving to stabilize local polypeptide chain conformations. The remaining two are internally located. One of these mediates a charged interaction between the invariant residue Arg38 and a nearby heme propionate. The other is more centrally buried near the heme iron atom and is hydrogen bonded to the conserved residues Asn52, Tyr67 and Thr78. It is shown that this latter water molecule shifts in a consistent manner upon change in oxidation state if cytochrome c structures from various sources are compared. The conservation of this structural feature and its close proximity to the heme iron atom strongly implicate this internal water molecule as having a functional role in the mechanism of action of cytochrome c.

Amino Acid Sequence↗