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PubMed2001

Clinicopathologic, immunophenotypic, and molecular characterization of primary cutaneous follicular B-cell lymphoma.

OBJECTIVE: To determine the clinicopathologic, immunophenotypic, and molecular characteristics of primary follicular cutaneous B-cell lymphoma (CBCL) as defined by the revised European-American lymphoma classification. DESIGN: A retrospective survey of the medical records, an immunohistochemical study of archival biopsy specimens. and molecular studies of preserved DNA of all patients with follicle center lymphoma-follicular (FCL-F) primary CBCL from 1987 to 1997. SETTING: A single-center outpatient specialty clinic at an academic medical center. PATIENTS: Twenty-one patients (68% of all new primary CBCL cases), including 14 men and 7 women (age range, 33-88 years; mean, 55 years). RESULTS: The head and neck region was the most frequent primary site. Following treatment, recurrences were relatively frequent, but the overall mortality rate during 1.0 to 11.3 years (mean, 6.3 years) of follow-up was 4.8%. Immunohistochemical analysis for B- and T-cell lineages was helpful in enhancing the folliclelike structures. CD10, bcl-2, and CD43 were expressed by the neoplastic cells in 9 (47%) of 19 cases, 4 (21%) of 19 cases, and 2 (13%) of 16 cases, respectively. Immunohistochemical detection of cytoplasmic immunoglobulin light chains, using steaming in EDTA as the antigen-retrieval technique, was successful in 12 (71%) of 17 cases. The Ig heavy-chain gene rearrangements, using the Southern blot technique, detected clonality in 17 (94%) of 18 cases. The bcl-2 gene rearrangements were detected in only 2 (13%) of 15 of the primary cutaneous FCL-F cases, compared with 9 (75%) of 12 of the primary nodal FCL-F cases (P =.002). CONCLUSIONS: Primary cutaneous FCL-F is a relatively common subtype of CBCL, with a relatively indolent course. It has many features in common with primary nodal FCL-F, except for low rates of bcl-2 expression and bcl-2 gene rearrangements.

Adult↗
PubMed1992

A simple, sensitive technique for classification of apolipoprotein(a) isoforms by sodium dodecyl sulphate-polyacrylamide gel electrophoresis.

Lipoprotein(a) (Lp(a)) is a lipoprotein containing a unique glycoprotein, apolipoprotein(a) (apo(a)), which shows considerable heterogeneity of apparent molecular mass on sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE). A unifying classification of isoform has been lacking. A simple sensitive procedure for classifying apo(a) isoforms was developed in which the relative mobility of apo(a) on SDS-PAGE was related to that of apolipoprotein (apo) B-100 (Rf vs B). After Western blotting apo(a) bands were visualised by a sensitive double antibody technique employing commercial polyclonal antibodies (sheep antihuman Lp(a) antibody, alkaline phosphatase-linked donkey antisheep antibody). The technique was sensitive (lower limit of detection 0.02 micrograms apo(a)) and had good reproducibility (coefficient of variation 0.9-6.4%). Ten isoform mobilities are described (less than 0.35, 0.40, 0.50, 0.60, 0.70, 0.80, 1.0, 1.10, greater than 1.15). Individuals may have single or double band phenotypes. This classification is compatible with those previously described and the method is suitable for many laboratories, as it employs standard equipment and commercially available materials.

Apolipoproteins A↗
PubMed1997

Molecular analysis of synchronous uterine and ovarian endometrioid tumors.

The presence of simultaneous carcinomas involving both the ovary and uterine corpus presents a diagnostic challenge, particularly if the tumors have a similar histology. The classification of these lesions as either two separate primary tumors, or as a single primary tumor with a metastasis has significant implications with respect to patient prognosis and recommendations for therapy. Although several morphologic criteria have been proposed as guidelines for the classification of these lesions, certain cases remain difficult to confidently classify. The application of current molecular biology techniques to pathological specimens can provide genetic information than can be helpful in establishing the relationship between synchronous neoplasms. Specifically, the use of tissue microdissection and polymerase chain reaction (PCR) amplification of DNA can be helpful. In this study we used polymorphic DNA markers on chromosomes 17q21.3-22 and 11q13 to study loss of heterozygosity (LOH) in 13 patients who presented with endometrioid tumors in both the uterus and ovary. Ten of the 13 cases showed LOH in one or both tumors. In eight of the 13 cases the detected LOH either chromosome 17q21.3-22 or 11q13 occurred selectively in only one of the two tumor sites. The results of this study suggest that the eight cases with LOH selective for one tumor site represent patients with two separate primary tumors. Molecular analysis may be useful in determining the relationship of synchronous uterine and ovarian endometrioid neoplasms.

Carcinoma, Endometrioid↗
PubMed2003

[Classification of Fungi in modern view].

Fungi are a heterogeneous jumble coming together from three kingdoms of organisms. The True Fungi represent a kingdom of its own and are positioned closer to the Animalia than to the Plantae. At present the Fungi are divided into five Divisions. Species pathogenic for humans are found in the Divisions Zygomycota, Ascomycota and Basidiomycota. The Pneumocystidales are now classified in the Ascomycota. The Malasseziales are included in the Class Ustilaginomycetes. Essential characteristics for the classification of Fungi are derived from ultrastructure, chemistry, and more recently also from molecular biology of these organisms. None of these methods can stand for its own, all characteristics must be included.

Classification↗
PubMed2026

Plastid genome evolution and phylogenomics with broad taxon sampling: insights into intrafamilial classification of Hamamelidaceae.

Hamamelidaceae, within the order Saxifragales, comprises 27 genera and approximately 120 species. The family has a pantropical and temperate distribution across the Americas, Asia, Africa, and Australia. Previous molecular investigations, constrained by limited taxon sampling and inadequate genetic markers, supported a five-subfamily classification system. However, these studies predominantly focused on Asian taxa, resulting in poor resolution of the evolutionary relationships among American, African, and Australian genera. To address these sampling gaps, we employed near-complete generic sampling (26 of 27 genera) to investigate plastome architecture, structural variation, and phylogenetic relationships. We newly sequenced and assembled 15 plastid genomes representing geographically and taxonomically underrepresented genera and analyzed them alongside 59 publicly available plastomes retrieved from GenBank. Plastid genomes exhibited conserved quadripartite architecture with sizes ranging from 158, 076 bp to 160, 814 bp, minimal structural variation, consistent GC content (37.7-38.2%), and identical gene order. Inverted repeat (IR) regions had limited size variation (26, 211-26, 429 bp). Simple sequence repeat (SSR) distribution (2, 219 loci) showed no clear correlation with the genus-level phylogenetic relationships. We identified ten hypervariable regions, including coding sequences (accD, ycf1, clpP, ndhF, and rpl22) and intergenic spacers (rpl33-rps18, the trnG-UCC intron, trnH-GUG-psbA, accD-psaI, and petA-psbJ), as promising candidate regions for future applications in species delimitation and phylogenetic studies. Phylogenetic analyses revealed largely congruent topologies across datasets and methods, providing improved resolution and strong support for most subfamilial and tribal relationships compared with previous studies. This study highlights the utility of plastid genome data for resolving deep-level phylogenetic relationships within Hamamelidaceae. The genome architecture reflects the high conservation of plastid genomes, while the identified mutation hotspots represent potential resources for future taxonomic and phylogenetic studies. Our results support the existing subfamily classification while improving geographical coverage and generic representation, providing a robust framework for future taxonomic and evolutionary studies of this globally distributed and taxonomically complex family.

Hamamelidaceae↗
PubMed2002

Molecular biology of anaplastic lymphoma kinase-positive anaplastic large-cell lymphoma.

Anaplastic large-cell lymphoma (ALCL) provides an excellent example of how molecular insights into tumor pathogenesis are influencing and improving tumor classification. ALCL was described initially as a subtype of T-cell/null-cell lymphoma characterized by unusual tumor cell morphology and the expression of CD30. However, it was soon recognized that a subset of ALCLs contained chromosomal translocations involving anaplastic lymphoma kinase (ALK), a novel receptor tyrosine kinase gene. These rearrangements create chimeric genes encoding self-associating, constitutively active ALK fusion proteins that activate a number of downstream effectors, including phospholipase C-gamma, phosphoinositol 3'-kinase, RAS, and signal transducer and activator of transcription proteins, all of which seem potentially important in cellular transformation. Not all tumors classified as ALCLs have ALK rearrangements and, conversely, ALK rearrangements occur in lymphomas of widely varying morphology. Hence, only molecular markers can reliably identify ALK+ ALCL. The importance of doing so is reflected by clinical studies suggesting that ALK+ ALCLs have a significantly better prognosis than other aggressive peripheral T-cell or B-cell lymphomas, including ALK- ALCLs. The unique molecular pathogenesis of ALK+ ALCL is likely to lead to novel therapeutic approaches directed at specific inhibition of ALK or downstream effectors.

Anaplastic Lymphoma Kinase↗
PubMed2004

Tumor taxonomy for the developmental lineage classification of neoplasms.

BACKGROUND: The new "Developmental lineage classification of neoplasms" was described in a prior publication. The classification is simple (the entire hierarchy is described with just 39 classifiers), comprehensive (providing a place for every tumor of man), and consistent with recent attempts to characterize tumors by cytogenetic and molecular features. A taxonomy is a list of the instances that populate a classification. The taxonomy of neoplasia attempts to list every known term for every known tumor of man. METHODS: The taxonomy provides each concept with a unique code and groups synonymous terms under the same concept. A Perl script validated successive drafts of the taxonomy ensuring that: 1) each term occurs only once in the taxonomy; 2) each term occurs in only one tumor class; 3) each concept code occurs in one and only one hierarchical position in the classification; and 4) the file containing the classification and taxonomy is a well-formed XML (eXtensible Markup Language) document. RESULTS: The taxonomy currently contains 122,632 different terms encompassing 5,376 neoplasm concepts. Each concept has, on average, 23 synonyms. The taxonomy populates "The developmental lineage classification of neoplasms," and is available as an XML file, currently 9+ Megabytes in length. A representation of the classification/taxonomy listing each term followed by its code, followed by its full ancestry, is available as a flat-file, 19+ Megabytes in length. The taxonomy is the largest nomenclature of neoplasms, with more than twice the number of neoplasm names found in other medical nomenclatures, including the 2004 version of the Unified Medical Language System, the Systematized Nomenclature of Medicine Clinical Terminology, the National Cancer Institute's Thesaurus, and the International Classification of Diseases Oncolology version. CONCLUSIONS: This manuscript describes a comprehensive taxonomy of neoplasia that collects synonymous terms under a unique code number and assigns each tumor to a single class within the tumor hierarchy. The entire classification and taxonomy are available as open access files (in XML and flat-file formats) with this article.

Cell Lineage↗
PubMed2004

Identification of carboxypeptidase E and gamma-glutamyl hydrolase as biomarkers for pulmonary neuroendocrine tumors by cDNA microarray.

Pulmonary neuroendocrine tumors vary dramatically in their malignant behavior. Their classification, based on histological examination, is often difficult. In search of molecular and prognostic markers for these tumors, we used cDNA microarray analysis of human transcripts against reference RNA from a well-characterized immortalized bronchial epithelial cell line, BEAS-2B. Tumor cells were isolated by laser-capture microdissection from primary tumors of 17 typical carcinoids, small cell lung cancers, and large cell neuroendocrine carcinomas. An unsupervised, hierarchical clustering algorithm resulted in a precise classification of each tumor subtype according to the proposed histological classification. Selection of genes, using supervised analysis, resulted in the identification of 198 statistically significant genes (P <.004) that also accurately discriminated between 3 predefined tumor subtypes. Two-by-two comparisons of these genes identified classifier genes that distinguished each tumor subtype from the others. Changes in expression of selected differentially expressed genes for each tumor subtype were internally validated by real-time reverse-transcription polymerase chain reaction. Expression of 2 potential classifier gene products, carboxypeptidase E (CPE) and gamma-glutamyl hydrolase (GGH), was validated by immunohistochemistry and cross-validated on additional archival samples of pulmonary neuroendocrine tumors. Kaplan-Meier survival analysis revealed that immunostaining for CPE was a statistically significant predictor of good prognosis, whereas GGH expression correlated with poor prognosis. Thus, cDNA microarray analysis led to the identification of 2 novel biomarkers that should facilitate molecular diagnosis and further study of pulmonary neuroendocrine tumors.

Biomarkers, Tumor↗
PubMed2002

New approach to polycystic ovary syndrome and other forms of anovulatory infertility.

UNLABELLED: Anovulation can be classified in the clinic on the basis of serum hormone assays. Low gonadotropins along with low estrogen concentrations are suggestive of a central origin of the disease, whereas low estrogen levels along with elevated gonadotropins indicate a primary defect at the ovarian level. Most anovulatory patients (approximately 80%) present with serum FSH and estradiol levels within the normal range (World Health Organization class II). Polycystic ovary syndrome (PCOS) is a common but poorly defined heterogeneous clinical entity. Historically, characteristic ovarian abnormalities represented a hallmark of the syndrome. Because several etiological factors may lead to a similar end point (i.e., polycystic ovaries), the development of a clinically applicable classification of the syndrome has proven difficult. Clinical, morphological, biochemical, endocrine, and, more recently, molecular studies have identified an array of underlying abnormalities and added to the confusion concerning the pathophysiology of the disease. Despite the vast literature regarding the etiology and classification of PCOS, no consensus has been reached regarding the validity of criteria used to diagnose the syndrome. For instance, the significance of elevated serum luteinizing hormone (LH) concentrations, insulin resistance or polycystic-appearing ovaries assessed by ultrasound for PCOS diagnosis remains uncertain. In contrast, hyperandrogenism and chronic anovulation generally are believed to be mandatory diagnostic features. Patients with PCOS might visit a dermatologist for hirsutism, a generalist, or internist for complaints related to obesity or a gynecologist for irregular or absent bleeding. However, most patients seek the care of a gynecologist because of cycle abnormalities (oligomenorrhea) and infertility. In PCOS, serum FSH and estradiol (E2) levels are usually found to be within the (broad) normal ranges, whereas LH may either be normal or elevated. Because PCOS with normal or high LH does not seem to represent different clinical entities, it seems justifiable to consider this syndrome as a subgroup of WHO-II patients, although estrogen levels may be tonically elevated in these patients. This review will focus on characteristics of the heterogeneous group of WHO-II patients in an attempt to identify factors involved in the etiology and possible ovulation induction outcome of PCOS. TARGET AUDIENCE: Obstetricians & Gynecologists, Family Physicians. LEARNING OBJECTIVES: After completion of this article, the reader will be able to outline the current classification of anovulatory infertility and to explain the characteristics and features used for classification.

Adult↗
PubMed1996

[Traditional and future criteria for progression in renal cell carcinoma. Molecular biology and clinical aspects].

In addition to the commonly used pathologic staging systems such as the TNM classification, the grading and demographic features have been reported to affect survival following surgical extirpation of renal cell carcinoma (RCC). These features, especially the pathologic stage, are well established as prognostic factors. However, several cellular and molecular variables, although potentially important in the ultimate outcome, are not taken into consideration by these criteria. Thus patients with different prognoses may be classified as belonging to the same stages. Attempts are now made to use cytogenetic and molecular findings to predict long-term survival of RCC patients. Chromosome 16 q and 14 q aberrations may play an important role in the future by identifying the high-risk groups of patients with papillary and nonpapillary RCC, resp. In nonpapillary RCC, mutations of the von Hippel-Lindau gene have been implicated as the initial step of carcinogenesis. However, the subsequent steps remain to be elucidated and the search for genetic markers associated with tumor progression is under way. The distinction between patients with high and low risk of progression will become increasingly important as more effective adjuvant therapies are available.

Carcinoma, Renal Cell↗
PubMed2005

A comparative review of classification systems in myelodysplastic syndromes (MDS).

Reliable classification and prognostic scoring systems for myelodysplastic syndromes (MDS) are needed to facilitate medically appropriate treatment and management decisions. The French-American-British (FAB) classification scheme for MDS was described in 1982 and has become the reference standard for subsequent MDS classification schemes. The FAB classification system divides MDS into five subgroups, based mainly on morphologic criteria and the percentage of myeloblasts in bone marrow (BM). More recently, the increasing availability of BM cytogenetics, immunologic markers, and molecular genetics has provided important information for staging, prognosis, and treatment of MDS. A World Health Organization panel incorporated this new diagnostic information into a revised classification system that modified the FAB criteria while retaining most of its basic features. The major changes included the creation of additional categories (eg, 5q- syndrome), distinction of unilineage from multilineage dysplasias in the refractory anemias, and subdivision of the heterogeneous refractory anemias with excess blasts into two categories based on BM blast percentage. Additionally, some MDS subtypes were removed or merged with other myeloid disorders into newly created categories. In independent validations, the World Health Organization revisions were shown to provide more-homogeneous subgroups of patients and greater prognostic power compared with the FAB system, although controversies remain. The International Prognostic Scoring System combines blast percentage, karyotype, and number of cytopenias to generate a scoring system that reliably estimates survival and risk of transformation to acute myeloid leukemia for patients with MDS. This universally accepted scoring system is often combined with FAB or World Health Organization morphologic criteria to provide a more complete clinical picture and the most accurate prognostic assessment possible. As more is learned about the pathogenesis of MDS at the molecular level, it is anticipated that these classification and scoring systems will continue to evolve to incorporate the new information.

Bone Marrow↗
PubMed2003

Effective dimension reduction methods for tumor classification using gene expression data.

MOTIVATION: One particular application of microarray data, is to uncover the molecular variation among cancers. One feature of microarray studies is the fact that the number n of samples collected is relatively small compared to the number p of genes per sample which are usually in the thousands. In statistical terms this very large number of predictors compared to a small number of samples or observations makes the classification problem difficult. An efficient way to solve this problem is by using dimension reduction statistical techniques in conjunction with nonparametric discriminant procedures. RESULTS: We view the classification problem as a regression problem with few observations and many predictor variables. We use an adaptive dimension reduction method for generalized semi-parametric regression models that allows us to solve the 'curse of dimensionality problem' arising in the context of expression data. The predictive performance of the resulting classification rule is illustrated on two well know data sets in the microarray literature: the leukemia data that is known to contain classes that are easy 'separable' and the colon data set.

Algorithms↗
PubMed2004

Distances that perfectly mislead.

Given a collection of discrete characters (e.g., aligned DNA sites, gene adjacencies), a common measure of distance between taxa is the proportion of characters for which taxa have different character states. Tree reconstruction based on these (uncorrected) distances can be statistically inconsistent and can lead to trees different from those obtained using character-based methods such as maximum likelihood or maximum parsimony. However, in these cases the distance data often reveal their unreliability by some deviation from additivity, as indicated by conflicting support for more than one tree. We describe two results that show how uncorrected (and miscorrected) distance data can be simultaneously perfectly additive and misleading. First, multistate character data can be perfectly compatible and define one tree, and yet the uncorrected distances derived from these characters are perfectly treelike (and obey a molecular clock), only for a completely different tree. Second, under a Markov model of character evolution a similar phenomenon can occur; not only is there statistical inconsistency using uncorrected distances, but there is no evidence of this inconsistency because the distances look perfectly treelike (this does not occur in the classic two-parameter Felsenstein zone). We characterize precisely when uncorrected distances are additive on the true (and on a false) tree for four taxa. We also extend this result to a more general setting that applies to distances corrected according to an incorrect model.

Classification↗
PubMed1999

Functional and structural diversities of C-reactive proteins present in horseshoe crab hemolymph plasma.

Limulin, a sialic-acid-binding and phosphorylethanolamine-binding hemagglutinin in the hemolymph plasma of the American horseshoe crab (Limulus polyphemus), is a hemolytic C-reactive protein [Armstrong, P.B., Swarnakar, S., Srimal, S., Misquith, S., Hahn, E.A., Aimes, R. T. & Quigley, J.P. (1996) J. Biol. Chem. 271, 14717-14721]. We have now identified three types of C-reactive protein in the plasma of the Japanese horseshoe crab (Tachypleus tridentatus), based on different affinities against fetuin-agarose and phosphorylethanolamine-agarose determined by quantitative precipitin assays using fetuin and an artificial phosphorylethanolamine-protein conjugate. Partial amino acid sequences of the isolated C-reactive proteins identified homologous proteins which were named Tachypleus tridentatus CRP-1 (tCRP-1), tCRP-2 and tCRP-3, each of which possibly constitute isoprotein mixtures. tCRP-2 and tCRP-3, but not tCRP-1, agglutinated mammalian erythrocytes. tCRP-1, the most abundant C-reative protein in the plasma, exhibited the highest affinity to the phosphorylethanolamine-protein conjugate but lacked both sialic-acid-binding and hemolytic activities. tCRP-2 bound to both fetuin-agarose and phosphorylethanolamine-agarose, and exhibited Ca2+-dependent hemolytic and sialic-acid-binding activities, suggestive of limulin-like properties. Furthermore, tCRP-2 exhibited a higher affinity to colominic acid, a bacterial polysialic acid. By contrast, tCRP-3 shows stronger hemolytic, sialic-acid-binding and hemagglutinating activities than tCRP-2. tCRP-3 has no affinity to phosphorylethanolamine-agarose, phosphorylethanolamine-protein conjugate and colominic acid. This suggests tCRP-3 is a novel hemolytic C-reactive protein lacking a common characteristic of phosphorylethanolamine-agarose binding affinity. Twenty-two clones of tCRPs with different deduced amino acid sequences were obtained by PCR using oligonucleotide primers based on the N-terminal and C-terminal sequences of tCRPs and with templates including genomic DNA and cDNA of hemocytes or hepatopancreas derived from one individual. The translation products of the tCRP clones possess high molecular diversity which falls into three related groups, consistent with classification based on their biological activities. Only tCRP-3 contained a unique hydrophobic nonapeptide sequence that appears in the transmembrane domain of a major histocompatibility complex class I heavy chain of rainbow trout, suggesting the importance of the hydrophobic patch to the hemolytic activity of tCRP-3. The structural and functional diversities of tCRPs provide a good model for studying the properties of innate immunity in invertebrates, which survive without the benefit of acquired immunity.

Amino Acid Sequence↗
PubMed2002

Antigen expression patterns reflecting genotype of acute leukemias.

Multi-parameter flow cytometry, molecular genetics, and cytogenetic studies have all contributed to new classification of leukemia. In this review we discuss immunophenotypic characteristics of major genotypic leukemia categories. We describe immunophenotype of: B-lineage ALL with MLL rearrangements, TEL/AML1, BCR/ABL, E2A/PBX1 translocations, hyperdiploidy, and myc fusion genes; T-ALL with SCL gene aberrations and t(5;14) translocation; and AML with AML1/ETO, PML/RARalpha, OTT/MAL and CBFbeta/MYH11 translocations, trisomies 8 or 11 and aberrations of chromosomes 7 and 5. Whereas some genotypes associate with certain immunophenotypic features, others can present with variable immunophenotype. Single molecules (as NG2, CBFbeta/SMMHC and PML/RARalpha proteins) associated with or derived from specific translocations have been described. More often, complex immunophenotype patterns have been related to the genotype categories. Most known associations between immunophenotype and genotype have been defined empirically. Therefore, these associations should be validated in independent patient cohorts before they can be widely used for prescreening of leukemia. Progress in our knowledge on leukemia will show how the molecular-genetic changes modulate the immunophenotype as well as how the expressed protein molecules further modulate cell behavior.

Acute Disease↗
PubMed2006

Aetiology-specific patterns in end-stage heart failure patients identified by functional annotation and classification of microarray data.

BACKGROUND: The objective of the present study was to use gene expression profiling, functional annotations and classification to identify aetiology-specific biological processes and potential molecular markers for different aetiologies of end-stage heart failure. METHODS AND RESULTS: Individual left ventricular myocardial samples from eleven coronary artery disease and nine dilated cardiomyopathy transplant patients were co-hybridized with pooled RNA from four non-failing hearts on custom-made arrays of 7000 human genes. Significance analysis identified differential expression of 153 and 147 genes, respectively, in coronary artery disease or dilated cardiomyopathy versus non-failing hearts. Analysis of Gene Ontology biological process annotations indicated aetiology-specific patterns, primarily related to genes involved in catabolism and in regulation of protein kinase activity. Gene expression classifiers were obtained and used for class prediction of random samples of coronary artery diseased and dilated cardiomyopathic hearts. Best classifiers frequently included matrix metalloproteinase 3, fibulin 1, ATP-binding cassette, sub-family B member 1 and iroquois homeobox protein 5. CONCLUSION: Combining functional annotation from microarray data and classification analysis constitutes a potent strategy to identify disease-specific biological processes and gene expression markers in e.g. end-stage coronary artery disease and dilated cardiomyopathy.

Adult↗
PubMed2002

Annotated expressed sequence tags and cDNA microarrays for studies of brain and behavior in the honey bee.

To accelerate the molecular analysis of behavior in the honey bee (Apis mellifera), we created expressed sequence tag (EST) and cDNA microarray resources for the bee brain. Over 20,000 cDNA clones were partially sequenced from a normalized (and subsequently subtracted) library generated from adult A. mellifera brains. These sequences were processed to identify 15,311 high-quality ESTs representing 8912 putative transcripts. Putative transcripts were functionally annotated (using the Gene Ontology classification system) based on matching gene sequences in Drosophila melanogaster. The brain ESTs represent a broad range of molecular functions and biological processes, with neurobiological classifications particularly well represented. Roughly half of Drosophila genes currently implicated in synaptic transmission and/or behavior are represented in the Apis EST set. Of Apis sequences with open reading frames of at least 450 bp, 24% are highly diverged with no matches to known protein sequences. Additionally, over 100 Apis transcript sequences conserved with other organisms appear to have been lost from the Drosophila genome. DNA microarrays were fabricated with over 7000 EST cDNA clones putatively representing different transcripts. Using probe derived from single bee brain mRNA, microarrays detected gene expression for 90% of Apis cDNAs two standard deviations greater than exogenous control cDNAs. [The sequence data described in this paper have been submitted to Genbank data library under accession nos. BI502708-BI517278. The sequences are also available at http://titan.biotec.uiuc.edu/bee/honeybee_project.htm.]

Animals↗
PubMed1998

Molecular methods for detecting t(11;14) translocations in mantle-cell lymphomas.

The t(11;14)(q13;q32) and its molecular counterpart, bcl1/JH, are characteristic of mantle-cell lymphomas (MCL). Molecular detection of the translocation is useful in diagnosis and classification, and also shows promise in detecting minimal residual disease. The purpose of this study was to determine the frequency of detecting bcl1/JH by polymerase chain reaction (PCR) compared with Southern blot analysis in cases proven by cytogenetic analysis to harbor t(11;14). Southern blot analysis using two probes targeting the major translocation cluster (MTC) and a third probe targeting the p94 region was performed, along with PCR using two different bcl1 MTC primers, on 18 cases of MCL known to have t(11;14). Southern blot analysis revealed bcl1 rearrangement in 13 of 18 cases (72%), 12 with MTC breakpoints and 1 with a p94 breakpoint. The 2.1-kb MTC probe "b" was superior to the smaller 700-bp probe "a" in detecting these rearrangements. The MTC translocation was identified by PCR in 10 of 12 cases, and both primer sets that were tested performed equally well. This study illustrates the frequency with which molecular methods detect known t(11;14) translocations in MCLs. These results may help clinical laboratory scientists optimize their procedure for detecting bcl1 translocations by molecular methods at initial diagnosis and for purposes of detecting minimal residual disease.

Blotting, Southern↗