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Luteinizing hormone (LH/hCG) responsiveness of normal and pathological human adrenal glands as well as the possibility of constitutive expressions of luteinizing hormone receptor (LHR) in adrenal cortex has been reported. Some recent studies showed a correlation between the LHR and abundant GATA-4 expression in both metastasizing and non-metastasizing human adrenocortical tumors, but not in normal adrenals, implicating the putative relevance of LHR and GATA-4 for adrenocortical pathophysiology. However, the physio- and pathophysiological significance of LHR and GATA-4 in the mechanism of adrenocortical tumorigenesis remains unclear. The paucity of suitable models for adrenal tumorigenesis makes the establishment of proper animal models highly important. LHR expression in the murine adrenal gland is an exception and not found in wild-type (WT) animal. We have previously shown that ectopic LHR expression in the murine adrenal gland can be induced by chronically elevated LH levels. We have generated a gonadotropin-responsive adrenal tumor model in gonadectomized transgenic (TG) mice expressing the inhibin alpha promoter/Simian Virus 40 T antigen transgene (inhalpha/Tag). Given the induction of expression and regulation of GATA-4 and GATA-6 zinc finger transcription factors in the gonads by gonadotropins, this review will explore their relationship to LHR expression and their role in adrenocortical tumorigenesis. A functional link between LHR and GATA-4 actions in the adrenal pathophysiology is proposed.
Mol Cell Endocrinol 2007 Apr 15
PMID:Adrenocortical tumorigenesis, luteinizing hormone receptor and transcription factors GATA-4 and GATA-6. 1733 16

We have designed, tested, and validated synthetic DNA molecules that may be used as reference standard controls in the simultaneous detection of mutations in one or more genes. These controls consist of a mixture of oligonucleotides (100 to 120 bases long) each designed for the detection of one or more disease-causing mutation(s), depending on the proximity of the mutations to one another. Each control molecule is identical to 80 to 100 bases that span the targeted mutations. In addition, each oligonucleotide is tagged at the 5' and 3' ends with distinct nucleic acid sequences that allow for the design of complementary primers for polymerase chain reaction amplification. We designed the tags to amplify control molecules comprising 32 CFTR mutations, including the American College of Medical Genetics minimum carrier screening panel of 23, with one pair of primers in a single tube. We tested the performance of these controls on many platforms including the Applied Biosystems/Celera oligonucleotide ligation assay and the Tm Bioscience Tag-It platforms. All 32 mutations were detected consistently. This simple methodology allows for maximum flexibility and rapid implementation. It has not escaped our notice that the design of these molecules makes possible the production of similar controls for virtually any mutation or sequence of interest.
J Mol Diagn 2007 Jul
PMID:Design, development, validation, and use of synthetic nucleic acid controls for diagnostic purposes and application to cystic fibrosis testing. 1759 30

Multiple cystic fibrosis (CF) testing platforms, using diverse and rapidly evolving technologies, are available to clinical laboratories commercially or for evaluation. Considerations when choosing a CF platform may include: sensitivity, specificity, accuracy, signal discrimination, ability to genotype, ability to reflex test, no calls/repeat rate, composition of mutation panel, hands-on time, start-to-finish time, integration into laboratory workflow, data analysis methods, flexibility regarding custom test design, and required instrumentation. Mindful of these considerations, we evaluated five technologically diverse CF platforms: 1) eSensor, an electronic detection assay system; 2) InPlex, a signal amplification methodology using a microfluidics card; 3) oligonucleotide ligation assay, an electrophoretic-based separation of amplicon-derived ligation-generated products; and two liquid bead arrays; 4) Signature, a direct hybridization assay using allele-specific capture probes; and 5) Tag-It, an assay using allele-specific primer extension and a universal microarray. A core of 150 samples, focusing on mutations in the American College of Medical Genetics/American College of Obstetricians and Gynecologists mutation panel, was tested throughout several runs for each platform. All of the platforms performed comparably in respect to sensitivity, specificity, and no-call rate. As our results indicate, consideration of all of the parameters evaluated may be useful when selecting the most appropriate platform for the specific setting.
J Mol Diagn 2007 Jul
PMID:A comparative study of five technologically diverse CFTR testing platforms. 1759 40

Phosphorylase kinase (PhK), the key enzyme that regulates glycogenolysis, has traditionally been thought to be expressed predominantly in muscle and liver. In this study, we show by two different database searches (Expressed Sequence Tag and UniGene) that PhK gene expression occurs in at least 28-36 different tissues, and that the genes encoding the alpha, beta, and gamma subunits of PhK undergo extensive transcriptional processing. In particular, we have identified exon 6 of PHKG1 as a 3' composite terminal exon due to the presence of a weak polyadenylation and cleavage site in intron 6. We have verified biochemically that transcriptional processing of PHKG1 does occur in vivo; mRNA corresponding to the alternate variant is expressed in skeletal muscle, brain, heart, and tongue. In silico translation of this mRNA yields a PhK gamma subunit that contains the first 181 residues of the protein, followed by an additional 21 amino acids. The implication of this alternate processing is discussed within the context of gamma catalysis and regulation.
Mol Genet Metab 2007 Nov
PMID:In Silico characterization of phosphorylase kinase: evidence for an alternate intronic polyadenylation site in PHKG1. 1769 48

We characterized the insertion sites of newly transposed copies of the tissue-culture-induced ty1-copia retrotransposon Tos17 in the Oryza Tag Line (OTL) T-DNA mutant library of rice cv. Nipponbare. While Nipponbare contains two native copies of Tos17 the number of additional copies, deduced from Southern blot analyses in a subset of 384 T-DNA lines and using a reverse transcriptase probe specific to the element, ranged from 1 to 8 and averaged 3.37. These copies were shown to be stably inherited and to segregate independently in the progenies of insertion lines. We took advantage of the absence of EcoRV restriction sites in the immediate vicinity of the 3' LTR of the native copies of Tos17 in the genome sequence of cv. Nipponbare, thereby preventing amplification of corresponding PCR fragments, to efficiently and selectively amplify and sequence flanking regions of newly transposed Tos17 inserts. From 25,286 T-DNA plants, we recovered 19,252 PCR products (76.1%), which were sequenced yielding 14,513 FSTs anchored on the rice pseudomolecules. Following elimination of redundant sequences due to the presence of T-DNA plants deriving from the same cell lineage, these FSTs corresponded to 11,689 unique insertion sites. These unique insertions exhibited higher densities in subtelomeric regions of the chromosomes and hot spots for integration, following a distribution that remarkably paralleled that of Tos17 sites in the National Institute for Agrobiological Sciences (NIAS) library. The insertion sites were mostly found in genic regions (77.5%) and preferably in coding sequences (68.8%) compared to unique T-DNA insertion sites in the same materials (49.1% and 28.3%, respectively). Predicted non- transposable element (TE) genes prone to a high frequency of Tos17 integration (i.e. from 5 to 121 inserts) in the OTL T-DNA collection were generally found to be also hot spots for integration in the NIAS library. The 9,060 Tos17 inserts inserted into non TE genes were found to disrupt a total of 2,773 genes with an average of 3.27 inserts per gene, similar to that in the NIAS library (3.28 inserts per gene on average) whereas the 4,472 T-DNA inserted into genes in the same materials disrupted a total of 3,911 genes (1.14 inserts per gene on average). Interestingly, genes disrupted by both Tos17 and T-DNA inserts in the library represented only 14.9% and 10.6% of the complement of genes interrupted by Tos17 and T-DNA inserts respectively while 52.1% of the genes tagged by Tos17 inserts in the OTL library were found to be tagged also in the NIAS Tos17 library. We concluded that the first advantage in characterizing Tos17 inserts in a rice T-DNA collection lies in a complementary tagging of novel genes and secondarily in finding other alleles in a same genetic background, thereby greatly enhancing the library genome coverage and its overall value for implementing forward and reverse genetics strategies.
Plant Mol Biol 2007 Nov
PMID:Large-scale characterization of Tos17 insertion sites in a rice T-DNA mutant library. 1787 25

Mass spectrometry-based tissue profiling and imaging are technologies that allow identification and visualization of protein signals directly on thin sections cut from fresh frozen tissue specimens. These technologies were utilized to evaluate protein expression profiles in the normal mouse prostate during development (1-5 weeks of age), at sexual maturation (6 weeks of age), and in adult prostate (at 10, 15, or 40 weeks of age). The evolution of protein expression during normal prostate development and maturation were subsequently compared with 15-week prostate tumors derived from genetically engineered mice carrying the Large T antigen gene under regulation of the prostate-specific probasin promoter (LPB-Tag mouse model for prostate cancer). This approach identified proteins differentially expressed at specific time points during prostate development. Furthermore expression of some of these proteins, for example probasin and spermine-binding protein, were associated with prostate maturation, and prostate tumor formation resulted in their loss of expression. Cyclophilin A, a protein found in other cancers, was differentially alpha-acetylated on the N terminus, and both isoforms appeared during normal prostate and prostate tumor development. Imaging mass spectrometry localized the protein signals to specific prostatic lobes or regions. Thus, tissue profiling and imaging can be utilized to analyze the ontogeny of protein expression during prostate morphogenesis and tumorigenesis and identify proteins that could potentially serve as biomarkers for prostate cancer.
Mol Cell Proteomics 2008 Feb
PMID:Monitoring mouse prostate development by profiling and imaging mass spectrometry. 1799 18

Sequence Tag Analysis of Genomic Enrichment (STAGE) is a method for experimentally identifying the in vivo chromosomal targets of DNA-binding proteins in any sequenced genome. STAGE generates 21-bp tags derived from DNA isolated by chromatin immunoprecipitation (ChIP; UNIT 21.3). Concatamers of tags are cloned and sequenced to yield a STAGE library. Tags in the library represent DNA fragments that were occupied by the DNA-binding protein, and mapping these tag sequences to the genome identifies the binding loci of the DNA-binding protein in vivo. STAGE can be applied to any sequenced genome to identify targets of DNA-binding proteins without requiring extensive microarray resources.
Curr Protoc Mol Biol 2005 Nov
PMID:Identifying chromosomal targets of DNA-binding proteins by Sequence Tag Analysis of Genomic Enrichment (STAGE). 1826 57

In recent years, genome-wide detection of alternative splicing based on Expressed Sequence Tag (EST) sequence alignments with mRNA and genomic sequences has dramatically expanded our understanding of the role of alternative splicing in functional regulation. This chapter reviews the data, methodology, and technical challenges of these genome-wide analyses of alternative splicing, and briefly surveys some of the uses to which such alternative splicing databases have been put. For example, with proper alternative splicing database schema design, it is possible to query genome-wide for alternative splicing patterns that are specific to particular tissues, disease states (e.g., cancer), gender, or developmental stages. EST alignments can be used to estimate exon inclusion or exclusion level of alternatively spliced exons and evolutionary changes for various species can be inferred from exon inclusion level. Such databases can also help automate design of probes for RT-PCR and microarrays, enabling high throughput experimental measurement of alternative splicing.
Methods Mol Biol 2008
PMID:Bioinformatics detection of alternative splicing. 1856 65

The cell adhesion molecule TAG-1 is expressed by neurons and glial cells and plays a role in axon outgrowth, migration and fasciculation during development. TAG-1 is also required for the clustering of Kv1.1/1.2 potassium channels and Caspr2 at the juxtaparanodes of myelinated fibers. Behavioral examination of TAG-1 deficient mice (Tag-1(-/-)) showed cognitive impairments in the Morris water maze and novel object recognition tests, reduced spontaneous motor activity, abnormal gait coordination and increased response latency to noxious stimulation. Investigation at the molecular level revealed impaired juxtaparanodal clustering of Caspr2 and Kv1.1/1.2 in the hippocampus, entorhinal cortex, cerebellum and olfactory bulb, with diffusion into the internode. Caspr2 and Kv1.1 levels were reduced in the cerebellum and olfactory bulb. Moreover, Tag-1(-/-) mice had shorter internodes in the cerebral and cerebellar white matter. The detected molecular alterations may account for the behavioural deficits and hyperexcitability in these animals.
Mol Cell Neurosci 2008 Nov
PMID:Impairment of learning and memory in TAG-1 deficient mice associated with shorter CNS internodes and disrupted juxtaparanodes. 1876 Mar 66

Expression of calcitonin (CT) and its receptor (CTR) is elevated in advanced prostate cancer, and activated CT-CTR autocrine axis plays a pivotal role in tumorigenicity and metastatic potential of multiple prostate cancer cell lines. Recent studies suggest that CT promotes prostate cancer metastasis by reducing cell-cell adhesion through the disassembly of tight and adherens junctions and activation of beta-catenin signaling. We attempted to identify a class of molecules that enhances cell-cell adhesion of prostate cells and reverses the disruptive actions of CT on tight and adherens junctions. Screening several compounds led to the emergence of phenyl-methylene hydantoin (PMH) as a lead candidate that can augment cell-cell adhesion and abolish disruptive actions of CT on junctional complexes. PMH reduced invasiveness of PC-3M cells and abolished proinvasive actions of CT. Importantly, PMH did not display significant cytotoxicity on PC-3M cells at the tested doses. I.p. administered PMH and its S-ethyl derivative remarkably decreased orthotopic tumor growth and inhibited the formation of tumor micrometastases in distant organs of nude mice. PMH treatment also reduced the growth of spontaneous tumors in LPB-Tag mice to a significant extent without any obvious cytotoxic effects. By virtue of its ability to stabilize cell junctions, PMH could reverse the effect of CT on junctional disruption and metastasis, which strengthens the possibility of using PMH as a potential drug candidate for CT-positive androgen-independent prostate cancers.
Mol Cancer Ther 2009 Mar
PMID:Identification of a small molecule class to enhance cell-cell adhesion and attenuate prostate tumor growth and metastasis. 1927 66


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