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PubMed2003

Use of pulsed-field gel electrophoresis to characterize the heterogeneity and clonality of salmonella isolates obtained from the carcasses and feces of swine at slaughter.

Salmonella enterica isolates were recovered from swine at a collaborating processing plant over a 2-month period in the spring of 2000. In the present study, molecular subtyping by pulsed-field gel electrophoresis (PFGE) was performed on the 581 confirmed Salmonella isolates from the 84 Salmonella-positive samples obtained from the previous study. A total of 32 different PFGE pulsotypes were observed visually, and a BioNumerics software analysis clustered those pulsotypes into 12 PFGE groups. The B, F, and G groups predominated throughout the sampling period and were isolated from 39, 22, and 13% of the swine, respectively. In addition, multiple isolates were obtained from 67 of the 84 Salmonella-positive samples, and subtyping revealed multiple PFGE profiles in 35 of these 67 (62%) samples. Both carcass and fecal isolates of Salmonella were recovered from 13 swine, resulting in "matched" samples. Molecular typing of the 252 isolates recovered from the matched samples revealed that 7 (54%) of the 13 carcasses were contaminated with Salmonella pulsotypes that were not isolated from the feces of the same animal. Conversely, from 6 of the 13 (46%) matched animals, Salmonella clonal types were isolated from the feces that were not isolated from the carcass of the same animal. These data establish that each lot of swine introduces new contaminants into the plant environment and that swine feces from one animal can contaminate many carcasses. In addition, these results indicate that the examination of multiple Salmonella isolates from positive samples is necessary to determine the variety of potential contaminants of swine carcasses during slaughter and processing.

Abattoirs↗
PubMed2005

Genetic characterization of the lobster pathogen Aerococcus viridans var. homari by 16S rRNA gene sequence and RAPD.

A combination of 16S rRNA sequencing and random amplified polymorphic DNA (RAPD) analysis was used to evaluate the genetic diversity within Aerococcus viridans var. homari, the causative agent of gaffkemia in lobsters. A collection of 7 A. viridans var. homari strains and 2 avirulent A. viridans-like cocci isolated from homarid lobsters harvested from different regions on the Atlantic Coast of North America were analyzed. The isolates are separated geographically and temporally between the years 1947 and 2000. Sequencing of 16S rRNA genes confirmed the inclusion of all 9 isolates in the monophyletic A. viridans clade (99.8 to 100% similarity). RAPD analysis revealed that the 9 A. viridans var. homari isolates could be separated into 2 distinct subtypes. Subtype 1 included the 7 pathogenic lobster isolates and constituted a homogeneous group regardless of their geographical, temporal or virulence differences. Subtype 2 contained the 2 avirulent A. viridans-like cocci that had distinct RAPD patterns and clustered separately with the non-marine A. viridans. RAPD analysis represented a useful method for determining molecular subtyping for the intraspecific classification and epidemiological investigations of A. viridans var. homari.

Animals↗
PubMed1988

Muscarinic receptor subtypes and the selectivity of agonists and antagonists.

Receptors may be grouped into superfamilies, according to their mechanism. Muscarinic receptors belong to one such superfamily, that of the G-protein coupled receptors. Subtypes of muscarinic receptors may be defined according to their primary amino acid sequence, their mechanism and their pharmacology. However, there is as yet no consistent scheme to explain the pharmacology and function of each molecular subtype. The pharmacological tools which distinguish between muscarinic receptor subtypes are described and the emerging evidence for the location of the ligand binding site is discussed.

(4-(m-Chlorophenylcarbamoyloxy)-2-butynyl)trimethy↗
PubMed2001

PulseNet standardized protocol for subtyping Listeria monocytogenes by macrorestriction and pulsed-field gel electrophoresis.

PulseNet is a national network of pubic health and food regulatory laboratories established in the US to detect clusters of foodborne disease and respond quickly to foodborne outbreak investigations. PulseNet laboratories currently subtype Escherichia coli O157:H7, non-typhoidal Salmonella, and Shigella isolates by a highly standardized 1-day pulsed-field gel electrophoresis (PFGE), and exchange normalized DNA "fingerprint" patterns via the Internet. We describe a standardized molecular subtyping protocol for subtyping Listeria monocytogenes that was recently added to PulseNet. The subtyping can be completed within 30 h from the time a pure culture of the bacteria is obtained.

Bacterial Typing Techniques↗
PubMed2006

Evaluation of MetriGenix custom 4D arrays applied for detection of breast cancer subtypes.

BACKGROUND: Previously, a total of five breast cancer subtypes have been identified based on variation in gene expression patterns. These expression profiles were also shown to be associated with different prognostic value. In this study tumour samples from 27 breast cancer patients, previously subtyped by expression analysis using DNA microarrays, and four controls from normal breast tissue were included. A new MetriGenix 4D array proposed for diagnostic use was evaluated. METHODS: We applied MetriGenix custom 4D arrays for the detection of previously defined molecular subtypes of breast cancer. MetriGenix 4D arrays have special features including probe immobilization in microchannels with chemiluminescence detection that enable shorter hybridization time. RESULTS: The MetriGenix 4D array platform was evaluated with respect to both the accuracy in classifying the samples as well as the performance of the system itself. In a cross validation analysis using "Nearest Shrunken Centroid classifier" and the PAM software, 77% of the samples were classified correctly according to earlier classification results. CONCLUSION: The system shows potential for fast screening; however, improvements are needed.

Breast Neoplasms↗
PubMed2025

UALCAN Mobile, an app for cancer proteogenomic data analysis.

Cancer is a complex disease affecting various organs and is a major cause of death worldwide. During cancer initiation, disease progression, and tumor metastasis, various genomic and proteomic alterations are observed. Recent technological advances have led to the generation of large amounts of molecular data, including genomics and transcriptomics. These large-scale datasets can be utilized to analyze and identify sub-class-specific cancer biomarkers and targets. However, there is a need for the development of user-friendly tools for large-scale data analysis, disseminating the analyzed data in a visualizable format to cancer researchers with no programming skills. We developed UALCAN, a comprehensive platform that allows users to integrate disparate data to better understand the genes, proteins, and pathways perturbed in cancer and make discoveries of potential biomarkers and targets. In the current study, we describe the development of the UALCAN Mobile application (app) that will provide cancer transcriptomic data obtained from The Cancer Genome Atlas (TCGA) project to evaluate protein-coding gene expression based on various stratifications, including stage, grade, race, gender, and molecular-subtypes across over 30 types of cancers. In addition, the UALCAN mobile provides data analysis options for epigenetic changes due to DNA promoter methylation and Clinical Proteomic Tumor Analysis Consortium (CPTAC) cancer proteomic data. The app provides access to large cancer molecular datasets on the go. To find changes in the expression of causative genes and proteins and to identify biomarkers and therapeutic targets, UALCAN mobile app will be extremely valuable. The "UALCAN Mobile" app is free to use and can be downloaded from both the iOS/Apple and the Android Play Store and has been downloaded over 100 times in each of iOS and android app stores.

app↗
PubMed2005

How to best classify breast cancer: conventional and novel classifications (review).

Breast cancer is a complex disease and different classifications, mostly based on clinical and pathological features, have been used for guiding the management of patients. Most of them fail to reflect breast cancer heterogeneity, which could be the reason why the treatment fails in approximately 30% of cases. Emerging molecular studies based on gene expression profiling using DNA microarrays have defined new molecular subtypes of breast cancer associated with the cell-of-origin distinction. Thus, breast cancer has been divided into five subgroups with distinct biological features and clinical outcomes. We have tried here to confront the conventional existing classifications with this new molecular taxonomy. It is likely that using all types of classification together will help in the management of breast cancer.

Breast Neoplasms↗
PubMed2026

Chinese expert consensus on precision testing and molecular diagnosis of pancreatic cancer (2025).

This consensus by the CSCO Pancreatic Cancer Expert Committee establishes evidence-based guidelines for molecular testing in pancreatic ductal adenocarcinoma. It details recommendations for biomarkers (e.g., KRAS, BRCA, MSI), liquid biopsy, and precision imaging to direct targeted therapies and immunotherapy, aiming to standardize diagnosis and optimize individualized patient care. Pancreatic ductal adenocarcinoma (PDAC) is the most common pathological type of primary pancreatic malignancy, accounting for ~95% of cases and generally referred to as pancreatic cancer [1]. Its prognosis is extremely poor and its incidence continues to rise [2]. According to the most recent global cancer statistics, the incidence of pancreatic cancer ranks 12th among all cancers, and its mortality ranks 6th, making it one of the deadliest malignancies worldwide [3]. Approximately 57% of patients have metastatic disease at diagnosis and require systemic therapy, for which chemotherapy remains the standard first-line option [1]. However, the overall response rate to currently available systemic regimens is low, and the 5-year survival rate for patients with metastatic disease remains below 5% [3]. Although most pancreatic cancers harbor canonical driver mutations, they exhibit marked heterogeneity at the molecular level. Whole-genome sequencing (WGS) and integrative genomic analyses have identified molecular subtypes of PDAC with potential clinical relevance [4-9]. With the increasing implementation of precision oncology, the Chinese Society of Clinical Oncology (CSCO) Guidelines for the Diagnosis and Treatment of Pancreatic Cancer give a level 1 recommendation to perform genetic and other molecular testing on tissue or cytologic specimens as part of the pathological diagnostic work-up, in order to guide individualized treatment, including targeted therapy and immunotherapy [10]. To further promote the use of genetic and molecular testing in the precision treatment of pancreatic cancer, the CSCO Pancreatic Cancer Expert Committee convened a multidisciplinary panel to develop the present Chinese Expert Consensus on Precision Testing and Molecular Diagnosis of Pancreatic Cancer (2025), aiming to provide clinicians with an authoritative reference for precision diagnostics and treatment decision-making.

Humans↗
PubMed1991

Rearrangements of the RAR-alpha gene in acute promyelocytic leukaemia: correlations with morphology and immunophenotype.

We have used genomic probes which specifically recognize DNA rearrangements of the RAR-alpha locus on chromosome 17q21 in patients with acute promyelocytic leukaemia (APL) and acute myeloid leukaemia (AML) subtypes. Molecular data were examined in comparison with morphological and immunophenotypic characterization at diagnosis in 20 hypergranular FAB M3 cases, five microgranular APL (M3v), 51 non-M3 AML and 12 myeloid CML blast crises. Rearrangements of the RAR-alpha locus were only detected in 23/25 APL cases and in none of the other FAB subtypes analysed. Surface marker characterization showed a consistent immunophenotypic profile--HLADR negative, CD9 and CD13/33 positive--in all M3 and M3v cases. Neither HLADR negativity nor CD9 positivity were associated with RAR-alpha rearrangements in non M3 AML. Our data indicate that RAR-alpha gene rearrangements are relevant diagnostic features of both M3 and M3v, and may prove useful molecular marker for follow-up analysis in APL patients.

Acute Disease↗
PubMed2026

Hierarchical modeling of tumor subtypes in cell lines using large-scale genomic datasets.

Cancer cell lines (CLs) are widely used to study tumor biology and drug response, yet their translational relevance is often limited by inaccurate subtype annotations. Existing CL-tumor matching approaches are frequently constrained by flat classification schemes, weak subtype definitions, and the exclusion of normal tissue references, leading to potential confounding of tumor-specific and tissue-of-origin signals. To address these limitations, a hierarchical classification (HC) framework is presented in which CLs are aligned with patient tumors across biological resolutions, from organ to molecular subtype. Gene expression profiles from 802 CLs, 5,612 tumors from The Cancer Genome Atlas (TCGA) , and 8,939 non-cancerous tissues were integrated to separate oncogenic signals from tissue-specific signals. Node-specific features were selected using maximum relevance minimum redundancy, and balanced accuracies of 89% in cross-validation and 75%, and 80% on external datasets were achieved. Through the framework, 43 CLs were reassigned, and clinically relevant underrepresented subtypes were identified.

cancer cell lines↗
PubMed2007

Cross contamination of turkey carcasses by Salmonella species during defeathering.

Salmonella present on the feathers of live birds could be a source of contamination to carcass skin during defeathering. In this study, the possibility of transfer of Salmonella from the feathers of live turkeys to carcass tissue during the defeathering process at a commercial turkey processing plant was investigated. The contribution of scald water and the fingers of the picker machines to cross contamination were also examined. Over 4 visits, swab samples were collected from 174 randomly selected tagged birds before and after defeathering. Two swab samples from the fingers of the picker machines and a sample of scald water were also collected during each visit. Detection of Salmonella was carried out following standard cultural and identification methods. The DNA fingerprints obtained from pulsed field gel electrophoresis of Salmonella serotypes isolated before and after defeathering, from scald water, and from the fingers of the picker machines were compared to trace cross contamination routes. Salmonella prevalence was similar before and after defeathering during visits 2 and 3 and significantly increased after defeathering during visits 1 and 4. Over the 4 visits, all Salmonella subtypes obtained after defeathering were also isolated before defeathering. The results of this study suggest that Salmonella was transferred from the feathers to carcass skin during each visit. On each visit, the Salmonella subtypes isolated from the fingers of the picker machines were similar to subtypes isolated before and after defeathering, indicating that the fingers facilitate carcass cross contamination during defeathering. Salmonella isolated from scald water during visit 4 was related to isolates obtained before and after defeathering, suggesting that scald water is also a vehicle for cross contamination during defeathering. By using molecular subtyping, this study demonstrated the relationship between Salmonella present on the feathers of live turkeys and carcass skin after defeathering, suggesting that decontamination procedures applied to the external surfaces of live turkeys could reduce Salmonella cross contamination during defeathering.

Abattoirs↗
PubMed2007

Classification of colorectal cancer based on correlation of clinical, morphological and molecular features.

Over the last 20 years it has become clear that colorectal cancer (CRC) evolves through multiple pathways. These pathways may be defined on the basis of two molecular features: (i) DNA microsatellite instability (MSI) status stratified as MSI-high (MSI-H), MSI-low (MSI-L) and MS stable (MSS), and (ii) CpG island methylator phenotype (CIMP) stratified as CIMP-high, CIMP-low and CIMP-negative (CIMP-neg). In this review the morphological correlates of five molecular subtypes are outlined: Type 1 (CIMP-high/MSI-H/BRAF mutation), Type 2 (CIMP-high/MSI-L or MSS/BRAF mutation), Type 3 (CIMP-low/MSS or MSI-L/KRAS mutation), Type 4 (CIMP-neg/MSS) and Type 5 or Lynch syndrome (CIMP-neg/MSI-H). The molecular pathways are determined at an early evolutionary stage and are fully established within precancerous lesions. Serrated polyps are the precursors of Types 1 and 2 CRC, whereas Types 4 and 5 evolve through the adenoma-carcinoma sequence. Type 3 CRC may arise within either type of polyp. Types 1 and 4 are conceived as having few, if any, molecular overlaps with each other, whereas Types 2, 3 and 5 combine the molecular features of Types 1 and 4 in different ways. This approach to the classification of CRC should accelerate understanding of causation and will impact on clinical management in the areas of both prevention and treatment.

Adenocarcinoma↗
PubMed2004

Phenotypic and genotypic analyses of enterohemorrhagic Escherichia coli O145 strains from patients in Germany.

Enterohemorrhagic Escherichia coli (EHEC) strains of serogroup O145 are emerging as causes of diarrhea and the hemolytic-uremic syndrome. However, there have been few genetic analyses of this EHEC group. We investigated the serotypes, virulence genes, plasmid profiles, pulsed-field gel electrophoresis (PFGE) patterns, and genetic variability of the fliC and eae genes in 120 EHEC O145 strains isolated from cases of hemolytic-uremic syndrome (n = 24) or diarrhea (n = 96) in Germany between 1996 and 2002. Three isolates belonged to serotype O145:H28, one to serotype O145:H25, and 116 were nonmotile (O145:H(-)). One hundred fourteen of the nonmotile strains shared fliC restriction fragment length polymorphism (RFLP) patterns identical to that of the O145:H28 strains. The remaining two nonmotile strains displayed a fliC-RFLP pattern identical to that of the O145:H25 strain. Each of the 117 strains with the fliC-RFLP(H28) pattern harbored eae gamma, whereas the three strains with the fliC-RFLP(H25) pattern possessed eae beta. Five different stx genotypes, six combinations of plasmid-encoded putative virulence genes, 29 plasmid profiles, and 47 PFGE types were identified. Strains within some of the PFGE types could be further subtyped by means of distinct plasmid profiles. These data demonstrate that the EHEC O145 serogroup is comprised of two different serotypes that possess distinct eae types. The heterogeneity of EHEC O145 strains at the chromosomal and plasmid level, in particular the high diversity in PFGE patterns, provides a basis for molecular subtyping of these pathogens.

Electrophoresis, Gel, Pulsed-Field↗
PubMed1995

A new HTLV type II subtype A isolate in an HIV type 1-infected prostitute from Cameroon, Central Africa.

Among 332 female sex workers in Douala, Cameroon, 113 were HIV-1 seropositive, 3 were HTLV-I seropositive, and only 1 had specific anti-HTLV-II antibodies. By cocultivation with BJAB cells, an HTLV-II was isolated from the peripheral blood mononuclear cells of this 32-year-old woman coinfected by HIV-1. This new African HTLV-II isolate (PH230PCAM) belongs to the molecular subtype A, exhibiting, however, a nucleotide variability of 2.4% and 0.8%, vis-à-vis the MO prototype, in the LTR and in the gp21 env gene, respectively. These data, as well as the previous findings of another HTLV-II subtype A in a Ghanean prostitute, suggest that this viral subtype had been imported into Africa, while the HTLV-II subtype B, described in remote areas of Zaire, Gabon, and Cameroon, could be a genuine African HTLV-II, present in this continent for a long period of time.

Adult↗
PubMed1993

[Molecular characterization of human T-cell lymphotrophic virus type II].

Human T-cell leukemia (or lymphotrophic) virus type II (HTLV-II) was isolated from eight HTLV seropositive patients. Restriction endonuclease mapping of the proviruses demonstrated consistent differences among isolates, and two distinct physical map patterns were observed. These studies have provided evidence for existence of two related, but distinct molecular subtype of HTLV-II, which are designated HTLV-II a and HTLV-II b. Between the two subtypes, the gag region encoding the p19 protein of HTLV-II b isolates contained a 66bp deletion in addition to single nucleotide differences. Immunoblotting methods employing sera from infected patients with each subtype failed to demonstrate any antigenic differences when recombinant gag p19 protein of each subtype was used as antigen. However, similar assays using recombinant HTLV-I and HTLV-II p19 proteins were able to differentiate the two viruses. ELISA using the synthetic peptides corresponding the deleted region gave the negative results for HTLV-II b (0/6) in contrast to the high positivity for HTLV-II a (6/10), which would provide an initial screening method for differentiation of the HTLV-II subtypes.

Acquired Immunodeficiency Syndrome↗
PubMed2000

Dopamine D(5) receptor immunolocalization in rat and monkey brain.

Dopamine D(5) receptor localization has been difficult because even the most specific ligands cannot distinguish between molecular subtypes of the D(1)-like receptor subfamily. Antifusion protein rabbit polyclonal antibodies directed against the C-terminus of human D(5) receptor were therefore developed for immunolocalization of the D(5) receptor protein in brain. The antibodies were characterized by immunoblot analysis and immunoprecipitation and used for light microscopic immunocytochemistry in rat and monkey brain. Affinity purified D(5) antibodies were specific for D(5) fusion protein as well as cloned and native D(5) receptor on Western blots, and D(5) antisera specifically immunoprecipitated solubilized, cloned D(5) receptor. Regional distribution of D(5) receptor immunoreactivity was consistent across species and correlated well with D(5) mRNA distribution previously reported in monkey brain. Immunoreactivity was widespread and tended to label perikarya and proximal dendrites of neurons in cerebral cortex, basal ganglia, basal forebrain, hippocampus, diencephalon, brainstem, and cerebellum. Neuropil was immunoreactive in olfactory bulb, islands of Calleja, cerebral cortex, superior colliculus, and molecular layer of cerebellum. The distribution of D(5) in brain was clearly different from that of other dopamine receptor subtypes, including D(1), the other member of the D(1)-like receptor subfamily. This unique distribution corroborates the idea that the D(5) receptor subtype has a distinct role in dopamine neurotransmission.

Animals↗
PubMed2000

[Epidemiology, origin and genetic diversity of HTLV-1 retrovirus and STLV-1 simian affiliated retrovirus].

Human T Cell leukemia/lymphoma virus type I, the first human oncogenic retrovirus, is the aetiological factor of Adult T cell leukemia (ATL), a CD4+ malignant lymphoproliferative disease and of a chronic neuromyelopathy, the tropical spastic paraparesis or HTLV-1 associated myelopathy (TSP/HAM). HTLV-1, which infects from 15 to 25 million individuals world-wide, is highly endemic in certain areas such as south-western Japan, Central Africa, the Caribbean basin and some regions of South America, Melanesia and of the middle East (for example the Mashhad area of Iran). The three major modes of transmission for HTLV-1 infection are perinatal, sexual and by blood transfusion. Recent molecular studies on HTLV-1 have shown the existence of several molecular subtypes (genotypes). These are related to the geographical origin of the infected populations and not to the associated diseases. The virus has a very high genetic stability. Viral amplification via clonal expansion of infected cells, rather than by use of reverse transcription could explain this remarkable phenomenon which can be used as a molecular tool for gaining new insights into the origin, evolution and modes of dissemination of HTLV-1. Analyses of HTLV-1 and STLV-1 (the simian counterpart) viral strains from throughout the world suggest that four events are responsible for this pattern of dissemination: 1) the transmission in the wild of STLV-1 between simian species, 2) the transmission of STLV-1 to humans as exemplified by the high percentage of identity between STLV-1 strains from chimpanzees or from mandrills with some HTLV-1 strains present in inhabitants of Central Africa, 3) persistence of HTLV-1 over a long period of time (by sexual and perinatal transmissions) in remote populations, as seen in the Australo-Melanesian region and 4) a global distribution of HTLV-1 via large scale human migrations, e.g., the slave trade from Africa to the New World.

Animals↗
PubMed2002

K-ras mutations in sporadic colorectal tumors in Israel: unusual high frequency of codon 13 mutations and evidence for nonhomogeneous representation of mutation subtypes.

Colorectal cancer is one of the most common malignancies in the western world, including Israel. An important step in progression includes induction of activating mutations in the protooncogene K-ras. This event is very frequent and is detected in about 40% of colorectal carcinomas. Previous studies of a variety of genetic disorders revealed unique gene mutation prevalence in Jewish populations, attributed both to differences in genetic background and to variability in environmental exposure. To determine the incidence and molecular subtypes of K-ras mutations in colorectal cancer in Israel, compared with other countries, DNA was isolated from a random collection of 105 colorectal carcinoma samples, and K-ras mutations were detected by an improved designed RFLP and direct sequencing. K-ras sporadic mutations in colorectal cancer in Israel are relatively frequent, with a higher fraction in codon 13 than reported thus far. Comparison with other countries shows a vast heterogeneity in terms of the relative abundance of the affected K-ras codon and in type and representation of specific mutations. The heterogeneous distribution found may be due to a variable genetic background and different environmental factors involved in the initiation and propagation of sporadic colorectal cancer.

Adult↗