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No evidence for oncogenic mutations in guanine nucleotide-binding proteins of human adrenocortical neoplasms.

G-Proteins are membrane-bound heterotrimeric polypeptides that couple receptor signals to second messenger systems such as cAMP. Recently, point mutations at 2 codons of the highly preserved alpha-chain of Gs, the adenyl cyclase-stimulating G-protein, were found in GH-secreting pituitary tumors. These mutations resulted in constitutively activated Gs alpha and high intracellular cAMP levels. In addition, point mutations at similar codons of a different G-protein, G(i) alpha 2, were reported in adrenocortical neoplasms, suggesting a potential role of this isoform in the genesis of these tumors. We reevaluated the frequency of constitutively activating point mutations in the alpha-chain of the stimulatory (Gs alpha) and inhibitory (G(i) alpha 2) G-proteins in human adrenocortical tumors. Seven adrenocortical carcinomas, 2 human adrenocortical tumor cell lines, and 11 adrenocortical adenomas were studied. Genomic DNA was purified from either frozen tumor tissue or paraffin-embedded sections. Using specific primers and the polymerase chain reaction, DNA fragments surrounding codons 201 and 227 (Gs alpha) and 179 and 205 (G(i) alpha 2) were amplified and visualized on a 2% agarose gel. In a second asymmetric polymerase chain reaction, using nested primers, single stranded DNA was generated using 1-10 microL of the initial amplification mixture and directly sequenced using the dideoxy chain termination method of Sanger. We found no mutations at codons 201, 227 and 179, 205 of Gs alpha and G(i) alpha 2, respectively, in the tumors studied. We conclude that previously identified oncogenic point mutations in the stimulatory and inhibitory alpha-chain of G-proteins do not appear to be present at high frequency in adrenal neoplasms. Thus, the mechanism(s) of tumorigenesis in these tumors is different from that in GH-secreting adenomas and may involve oncogenic mutations of other cell constituents.

Adolescent↗

Non-radioactive hybridization probes prepared using M13 phage vector and the universal sequencing primer.

Non-radioactive hybridization probes were prepared using the M13 phage vector and the universal sequencing primer. The probe sequence to be used was first cloned into the M13 vector, and the minus strand of the template DNA was then synthesized with the Klenow fragment of E. coli DNA polymerase I in the presence of the biotinylated nucleotide, biotin-11-dUTP, as a label. Resultant DNA was heavily biotinylated, and made up of the entire minus strand of the template DNA. The long tag sequence derived from the M13 vector may increase the sensitivity of the detection. The biotinylated hybrids were visualized with the streptavidin-alkaline phosphatase conjugate and chromogenic substrates. As shown by Southern hybridization, the probe prepared in this way could be used to detect less than 1 pg of target sequence and a single copy gene sequence in human genomic DNA within several hours of signal development.

Bacteriophages↗

Scintigraphic imaging of gene expression and gene transfer.

Assessment of gene function following the completion of human genome sequencing can be performed with nuclear medicine procedures. These techniques may be applied for the determination of gene function and regulation using established and new tracers or using in vivo reporter genes such as genes encoding enzymes, receptors, antigens, or transporters. Visualization of in vivo reporter gene expression can be done using radiolabeled substrates, antibodies, or ligands. Combinations of specific promoters and in vivo reporter genes may deliver information about the regulation of the corresponding genes. The role of radiolabeled antisense molecules for the analysis of mRNA content has to be investigated. However, possible applications are therapeutic interventions using triplex oligonucleotides with therapeutic isotopes, which can be brought near to specific DNA sequences to induce DNA strand breaks at selected loci. Imaging of labeled siRNA's makes sense if these are used for therapeutic purposes in order to assess the delivery of these new drugs to their target tissue. Pharmacogenomics will identify new surrogate markers for therapy monitoring which may represent potential new tracers for imaging.

Animals↗

[Spinocerebellar ataxia type VII (AEC 7). Report of a Spanish family with the disease].

INTRODUCTION: The dominant autosomic ataxias are a group of neurodegenerative disorders caused by expansion of a CAG triplet in different genes, found along the genome. The dominant autosomic ataxias present very varied clinical findings. However, genetic studies are being done to establish the genotype-phenotype relationship of the different autosomal dominant ataxias. CLINICAL CASE: A 50 year old man had alterations in gait, dysarthria and visual changes (retinal degeneration). Study of the different genes known to be responsible for the dominant autosomic ataxias have an expansion of the superior CAG of more than 37 repetitions of the gene SCA 7, whilst in the normal control population there are 9-18 repetitions of this gene. Other members of the family had similar clinical findings, although the age of onset varied. One did not have retinal degeneration but did have expansion of the SCA 7 gene. CONCLUSIONS: The non-pathological range of SCA 7 in the Spanish population, according to our study, is between 9-18 repetitions of triplet CAG, whilst in members of the patient's family they were over 37. The clinical findings, which were similar in all patients were found in all patients except for one, who did not have retinal degeneration. We observed the phenomenon of genetic anticipation in the family studied.

Aged↗

DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes.

The identification and study of evolutionarily conserved genomic sequences that surround disease-related genes is a valuable tool to gain insight into the functional role of these genes and to better elucidate the pathogenetic mechanisms of disease. We created the DG-CST (Disease Gene Conserved Sequence Tags) database for the identification and detailed annotation of human-mouse conserved genomic sequences that are localized within or in the vicinity of human disease-related genes. CSTs are defined as sequences that show at least 70% identity between human and mouse over a length of at least 100 bp. The database contains CST data relative to over 1088 genes responsible for monogenetic human genetic diseases or involved in the susceptibility to multifactorial/polygenic diseases. DG-CST is accessible via the internet at http://dgcst.ceinge.unina.it/ and may be searched using both simple and complex queries. A graphic browser allows direct visualization of the CSTs and related annotations within the context of the relative gene and its transcripts.

Animals↗

GELBANK: a database of annotated two-dimensional gel electrophoresis patterns of biological systems with completed genomes.

GELBANK is a publicly available database of two-dimensional gel electrophoresis (2DE) gel patterns of proteomes from organisms with known genome information (available at http://gelbank.anl.gov and ftp://bioinformatics.anl.gov/gelbank/). Currently it includes 131 completed, mostly microbial proteomes available from the National Center for Biotechnology Information. A web interface allows the upload of 2D gel patterns and their annotation for registered users. The images are organized by species, tissue type, separation method, sample type and staining method. The database can be queried based on protein or 2DE-pattern attributes. A web interface allows registered users to assign molecular weight and pH gradient profiles to their own 2D gel patterns as well as to link protein identifications to a given spot on the pattern. The website presents all of the submitted 2D gel patterns where the end-user can dynamically display the images or parts of images along with molecular weight, pH profile information and linked protein identification. A collection of images can be selected for the creation of animations from which the user can select sub-regions of interest and unlimited 2D gel patterns for visualization. The website currently presents 233 identifications for 81 gel patterns for Homo sapiens, Methanococcus jannaschii, Pyro coccus furiosus, Shewanella oneidensis, Escherichia coli and Deinococcus radiodurans.

Databases, Factual↗

[Computerized analysis of inverted repeats in Mycobacterium tuberculosis genome].

Thermodynamic stable inverted repeats, capable of stabilizing nuclease-influenced mRNA, have been determined for M. tuberculosis slowly growing isolates H37Rv and CDC1551 with the completely sequenced genome. The genome of laboratory strain H37Rv may contain 50 pin structures formed by inverted repeats, whose stem varies in length from 11 to 28 nucleotide pairs (n.p.), the loop size being equal to 4-5 nucleotides and free energy deltaG=-15.2 to -56.2 kcal/mol. The genome of strain CDC1551 (clinical isolate) having a high level of virulence contains 47 pins. Each of the two isolates contains 8 long inverted repeats with a length of 48-62 nucleotides and free energy deltaG=-38.9 to -56.2 kcal/mol; of these, 6 pins are completely similar. At the same time in the genome of strain CDC1551, in contrast to that of strain H37Rv, a highly stable pin 58 nucleotides long is localized at 5'-end. The localization of the highly stable pin with deltaG=-53.9 kcal/mol in the area of 5'-end of isolate CDC1551 may lead to a different degree of stabilization of RNA-transcripts in M. tuberculosis CDC1551 in comparison with isolate H37Rv. This may, in its turn, serve as one of the reasons of differences in the virulence of strains. The possibility of the formation of pins with stems of 11 n.p. and longer has been visually cofirmed with the use of atomic power microscopy. The possibility of the participation of the secondary structures formed by pins in the protection of mRNA of slowly growing pathogenic M. tuberculosis from the degrading activity of RNases is discussed.

DNA, Bacterial↗

Bioinformatics Analysis and Experimental Validation of Key Genes Associated With Hypoxia and Ischemia in Myocardial Infarction.

BACKGROUND: This study aimed to screen and identify core hypoxia-ischemia-related genes associated with myocardial infarction (MI). METHOD: Two transcriptomic datasets, GSE97320 and GSE48060, were retrieved from the Gene Expression Omnibus (GEO) database. After data integration and batch effect elimination, differential expression analysis was performed to screen differentially expressed genes (DEGs), and the corresponding visualization analysis was conducted. Hypoxia-ischemia-related genes were acquired from the GeneCards database; hypoxia-ischemia related genes (HIRGs) were subsequently identified by intersecting the retrieved genes with screened DEGs. Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were implemented to explore the biological functions and underlying signaling pathways of HIRGs. A combination of protein-protein interaction (PPI) network analysis and random forest (RF) algorithm was applied to screen hub genes from HIRGs. The external GEO dataset GSE66360 was utilized to validate the expression patterns of candidate hub genes. Furthermore, an acute myocardial infarction (AMI) mouse model was established, and quantitative real-time polymerase chain reaction (qPCR) was performed to detect the mRNA expression levels of hub genes in myocardial tissues for in&#xa0;vivo validation. RESULTS: A total of 633 DEGs and 308 hypoxia-ischemia-related genes were screened in the present study, among which 21 overlapping HIRGs were obtained. PLAUR and IL1B were finally identified as two hub genes from HIRGs based on PPI network and random forest algorithm. The qPCR results revealed that the expression levels of PLAUR and IL1B were significantly upregulated in the AMI group compared with the sham operation group (p&#x2009;<&#x2009;0.05). CONCLUSION: The present findings demonstrated that PLAUR and IL1B serve as pivotal genes involved in the pathological hypoxia-ischemia process of AMI. These two genes may act as novel biomarkers and promising therapeutic targets for the recognition and clinical intervention of hypoxia-ischemia injury following AMI.

Myocardial Infarction↗

Detection by northern analysis of alpha 1-adrenergic receptor gene transcripts in the rat.

In Northern blots of total cellular and poly(A+) RNA isolated from rat liver, renal cortex, spleen, and brain probed with a full-length cDNA encoding the hamster alpha 1-adrenergic receptor, hybridization was observed to two distinct mRNAs, at approximately 3.3 kb and approximately 2.7 kb. Only the approximately 2.7 kb mRNA species was visualized in Northern blots of total cellular and poly(A+) RNA isolated from cardiac ventricular muscle. From screening a rat heart cDNA library with the full-length hamster alpha 1-adrenergic receptor cDNA, a 632 base pair cDNA was isolated. Based upon its high degree of identity, 86% at the nucleotide level, with the hamster alpha 1-adrenergic receptor cDNA, this cDNA was considered to include the 3' end of the rat alpha 1-adrenergic receptor. When used as a probe in Northern blots of liver RNA, both the approximately 3.3 kb and approximately 2.7 kb mRNAs were visualized. Both mRNA species were expressed in fetal as well as adult liver, but steady-state levels of each gene transcript were approximately 3-fold higher in adult compared to fetal liver. Finally, results from Southern analysis of restriction enzyme fragments of genomic DNA suggest that the two gene transcripts may be products of a single gene.

Animals↗

Effect of flanking matrix attachment regions on the expression of microinjected transgenes during preimplantation development of mouse embryos.

The efficiency of transgenic animal production would increase if microinjected embryos with a successfully integrated transgene could be identified prior to transfer. It is possible to detect microinjected DNA in embryos. However, no reliable system is able to distinguish between transgenes merely present as extrachromosomal DNA and those that have been integrated into chromatin. The experiments reported here were designed to determine if the inclusion of matrix attachment regions (MARs) would enhance the efficiency of transgenic embryos identification using a selection scheme based on the expression of green fluorescent protein (GFP). Pronuclei of mouse embryos were microinjected with GFP reporter gene under the control of three different promoters and flanked or not by three different MAR elements. Transgene expression profiles were followed by direct visualization of GFP in cultured microinjected embryos. Embryos at different developmental stages were classified according to their GFP expression and groups with the same expression pattern were transferred into oviducts of pseudopregnant female mice. Fetuses were collected between days 12-15, and their genomic DNA was purified and analyzed to detect transgene integration. We did not find any statistically significant difference between the percentage of transgenic fetuses produced from GFP-positive or GFP-negative embryos transferred at 4-cell, morula, or blastocyst stage. However, when MAR elements were included in the construct, we found that GFP-positive embryos transferred at the 2-cell stage produced a significantly higher percentage of transgenic fetuses than GFP-negative embryos, but MAR sequences did not completely eliminate false positives.

Animals↗

Chimeric amplicons containing the c-myc gene in HL60 cells.

The major amplicon present in HL60 cells is chimeric in nature being composed of 70 kb of DNA sequence derived from the MYC locus linked to 80 kb of novel DNA sequence derived from a non contiguous region located telomeric to the c-myc gene at 8q24 (Feo et al., 1996). Here we show by fluorescence in situ hybridization (FISH) that these coamplified sequences, MCR (Myc Coamplified Region), are derived from a locus located 3-4 Mb telomeric to the c-myc gene in the q24.2-24.3 region of chromosome 8. Genomic cloning and Southern blot analysis indicate the arrangement of chimeric amplicons are in tandem arrays. Analysis of the DNA sequences at the juncture of the MYC locus and the MCR suggest that these non syntenic regions were joined by nonhomologous recombination events. Visualization of the organization of the amplified DNA by fiber-FISH analysis illustrates we have cloned the complete amplicon. This is the first complete mammalian amplicon to be cloned and have its structure visualized. In addition to the major class of tandemly repeated amplicons, a second class of amplicons was detected by fiber-FISH in which the extent of the MCR component is about twice the size of the MCR component in the major amplicon. These longer amplicons most likely contain inverted repeats of MCR and MYC region sequences. Whether the amplicons contain mixtures of these two types of structures or separate amplicons only contain one type of structure has not yet been resolved. Properties of the MCR sequences responsible for retention in the chimeric HL60 amplicons upon long term passage are discussed.

Base Sequence↗

[FRAP, FLIP, FRET, BRET, FLIM, PRIM...new techniques for a colourful life].

Cell and tissue imaging provides scientists with wonderful tools, thanks to a fruitful dialog between chemistry, optical, mechanical, computational sciences and biology. Confocal microscopy, videomicroscopy together with a new generation of fluorochromes (especially those derived from green fluorescent protein, GFP) and image analysis software allow to visualize life in all its dimensions (space and time). Cell imaging also allows to quantify biological processes at the cellular level, to analyse both stoechiometry and dynamics of molecular interactions involved in cell and tissue regulations. Entering the new era of post-genomics requires a better knowledge of advantages and limitations of these new approaches.

Cell Physiological Phenomena↗

Phylogenetic relationships in the genus Oryza based on mitochondrial RFLPs.

Restriction fragment length polymorphism (RFLP) of mitochondrial DNA in the genus Oryza was surveyed using 20 accessions including 11 species and a single endonuclease, EcoRI. RFLPs were visualized by Southern hybridization with eight rice mitochondrial DNA probes labeled non-radioactively with digoxigenin-dUTP. A total of 66 bands were obtained from all of the accessions. The total number of fragments per plant was higher in diploid A-genome species (an average of 35.3) than that in diploid B- and C-genome species and allotetraploid BC- and CD-genome species (an average of 28.2). The extent of the polymorphism in the RFLP patterns was various depending on the probes used. A diverse polymorphism was observed with most of the probes used, i.e. the cob, cox I, atp6, rrn18, rrn26 and atp9 regions, whereas, no polymorphic band was observed with a probe for the coxII region. The genus Oryza was separated into two large clusters. One cluster was comprised of A-genome species and the other cluster was comprised of B-, BC-, C-, and CD- genome species. Within A-genome species, the genetic variation was relatively high. Even in O. sativa species, the RFLP patterns of japonica and indica subspecies were clearly different from each other when three probes were used. However, there was no polymorphism between O. glaberrima and O. barthii. Within the genomes of B, BC, C, and CD, RFLP patterns were similar to each other and they showed a closer affinity except for O. minuta (BBCC). Within the BC genome species, the patterns of O. punctata and O. minuta were largely different from each other and separated into two different subclusters. Thus, the mitochondrial genomes of the two BC species (O. punctata and O. minuta) apparently evolved independently. Among CD genome species (O. latifolia and O. alta), the patterns of one accession, O. alta W0017 were largely different from those of the other accessions of CD genome species.

DNA Probes↗

Changes in neuronal acetylcholinesterase gene expression and division of labor in honey bee colonies.

Division of labor in honey bee colonies is highlighted by adult bees making a transition at 2-3 wk of age from working in the hive to foraging for nectar and pollen outside. This behavioral development involves acquisition of new tasks that may require advanced learning capabilities. Because acetylcholinesterase (AChE) hydrolyzes acetylcholine, a major neurotransmitter associated with learning in the insect brain, we searched for changes in AChE expression in the brain during bee behavioral development. Biochemical aspects of the AChE protein were similar in foragers and "nurse" bees that work in the hive tending brood. However, catalytic AChE activity was significantly lower in foragers. Cloning of bee AChE cDNA enabled mRNA analysis, which demonstrated that the forager-related decrease in AChE activity was associated with decreased AChE mRNA levels. This was particularly apparent in the mushroom bodies, a brain region known to be involved with olfactory and visual learning and memory. In addition, treatment with the AChE-inhibitor metrifonate improved performance in an olfactory-learning assay. These findings demonstrate long-term, naturally occurring developmental downregulation of AChE gene expression in the bee brain, and suggest that this genomic plasticity can contribute to facilitated learning capabilities in forager bees.

Acetylcholinesterase↗

Nuclear structure, gene expression and development.

This article considers the extent to which features of nuclear structure are involved in the regulation of genome function. The recent renaissance in imaging technology has inspired a new determination to assign specific functions to nuclear domains or structures, many of which have been described as "factories" to express the idea that they coordinate nuclear processes in an efficient way. Visual data have been combined with genetic and biochemical information to support the idea that nuclear organization has functional significance. Particular DNA sequences or chromatin structures may nucleate domains that are permissive or restrictive of transcription, to which active or inactive loci could be recruited. Associations within the nucleus, as well as many nuclear structures, are transient and change dynamically during cell cycle progression and development. Despite this complexity, elucidation of the possible structural basis of epigenetic phenomena, such as the inheritance of a "cellular memory" of gene expression status, is an important goal for cell biology. Topics for discussion include the regulatory effect of chromatin structure on gene expression, putative "nuclear addresses" for genes and proteins, the functional significance of nuclear bodies, and the role of the nuclear matrix in nuclear compartmentalization.

Animals↗

A Practical Workflow for Spatial Transcriptomics Data Analysis: From Data Acquisition to Advanced Analyses.

Spatial transcriptomics (ST) profiles genome-wide gene expression while preserving the two-dimensional spatial context of mRNA molecules within tissue sections, enabling studies of tissue architecture and microenvironment-associated biology. However, ST analysis remains challenging because data import, quality control, integration, deconvolution, spatial statistics, and visualization often require multiple software environments and reproducible parameter choices. This protocol presents a practical computational workflow for public ST datasets in R, beginning with data acquisition and software setup and proceeding through Seurat-based data loading, quality control, normalization, multi-sample integration, clustering, and spatially variable gene analysis. The workflow then applies complementary deconvolution strategies, including reference-guided SPOTlight analysis and unsupervised STdeconvolve topic modeling, followed by Giotto-based spatial cell-cell communication analysis and interactive region-of-interest (ROI) selection using a custom Python Dash application. By emphasizing script-based execution, explicit parameter rationales, expected outputs, and troubleshooting checkpoints, the protocol provides an adaptable framework for standard array-based ST datasets and related platforms after dataset- and platform-specific parameter evaluation.

Spatial Transcriptomics↗

Molecular cloning, expression and purification of protein 2A of hepatitis A virus.

Expression of the protein 2A of Hepatitis A virus (HAV), spanning amino acids 764 through 981 of the viral polyprotein results in a strong inhibition of cap-dependent translation (Maltese et al., 2000). However, the molecular mechanism responsible has remained unclear, in part because the HAV 2A protein was not available in amounts large enough to allow biological or structural studies. To address this issue, a cDNA representation of the sequences encoding HAV 2A was generated by PCR, using primers that introduced an AUG triplet, and a sequence coding for 6 histidine residues at the 5'- and 3'-termini of the genomic sequence, respectively. The cDNA fragment was introduced by cassette exchange in the inducible expression vector pQE-60, and the construct was propagated in bacteria E. coli M15 which constitutively expresses the lac repressor. Upon induction with IPTG (1 mM), HAV 2A was visualized by SDS-PAGE of bacterial lysates as a prominent band M(r) = 21 kDa. The identity of the polypeptide was confirmed by both MALDI-TOF peptide mapping and direct amino acid sequencing. The His-tagged HAV 2A was extracted from bacterial pellets under totally denaturing conditions (6 M urea), subjected to Ni(++)-Sepharose affinity chromatography, allowed to refold while still attached to the matrix, and eluted with 250 mM Imidazole. Contaminant material was partly removed by differential ammonium sulfate precipitation. The protein was further concentrated (Vivaspin centrifugal concentrator), the insoluble material (if present) was discarded, and the homogeneity of the dispersion was ascertained by light scattering. SDS-PAGE revealed that in addition to the main protein (Mr = 21 kDa), a second one of apparent Mr = 14 kDa was always present in variable amounts. The proportion of the latter tended to increase with aging of the preparation. Edman degradation analysis proved that the 14 kDa protein resulted from the cleavage of HAV 2A at a so far undetected scissile bond Gly856/Val857 of the viral polyprotein. A first attempt to crystallize the protein by the hanging drop procedure yielded only small crystals containing exclusively the 14 kDa derivative of HAV 2A. Western blot analysis of HeLa cell extracts that had been incubated with the His-tagged HAV 2A so purified failed to reveal any change in the electrophoretic mobility of the eukaryotic initiation factor (eIF) 4G I.

Amino Acid Sequence↗

[Cytogenetic aberrations of esthesioneuroblastoma studied by comparative genomic hybridization].

OBJECTIVE: To characterize the cytogenetic alterations of esthesioneuroblastoma (ENB). METHODS: Comparative genomic hybridization (CGH) was performed on genomic DNA extracted from 12 patients with primary ENB, 4 patients with tumor recurrence and 7 with metastasis. Equal amounts of biotin-labeled tumor DNA and digoxigenin-labeled normal reference DNA were hybridized to normal meta phase chromosomes. Tumor DNA was visualized by fluorescein (FITC) and normal DNA by rhodamin (TRITC ) and detected by fluorescence microscopy. The signal intensities of the different fluorochromes were quantitated as gray levels along the single chromosomes. The over-and under-represented DNA segments were determined by computation of FITC/TRITC ratio images and average ratio profiles. RESULTS: Consensus deletion regions were most frequently observed on chromosomes 1p, 2q, 3p/q, 4p/q, 5p/q, 6q, 8p/q, 9p, 10p/q, 11p, 12q, 13q, 18q, and 21q. DNA over-representations were identified on chromosomes 1p, 7q, 9q, 11q, 14q, 16p/q, 17p/q, 19p/q, 20p/q and 22p/q. The genetic pattern of ENB was distinct from that of other small round-cell tumor types and neuroblastomas. The deletion on chromosome band 1p21-p31 was associated with bad prognosis. In particular, all patients died whose tumors had combined 1p21-p31 deletion, with tumors in clinical stage C or D, and of low differentiation (grade III or IV). Clonality analysis revealed a high concordance between pairs of primaries and metastases. CONCLUSION: CGH analysis identifies characteristic cytogenetic aberrations of esthesioneuroblastoma associated with its malignant phenotype.

Adolescent↗