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At least 955 records · Page 53Linked to original sources
PubMed2005

A kissing-loop interaction in a hammerhead viroid RNA critical for its in vitro folding and in vivo viability.

Chrysanthemum chlorotic mottle viroid (CChMVd) RNA (398-401 nucleotides) can form hammerhead ribozymes that play a functional role in its replication through a rolling-circle mechanism. In contrast to most other viroids, which adopt rod-like or quasi-rod-like secondary structures of minimal free energy, the computer-predicted conformations of CChMVd and Peach latent mosaic viroid (PLMVd) RNAs are branched. Moreover, the covariations found in a number of natural CChMVd variants support that the same or a closely related conformation exists in vivo. Here we report that the CChMVd natural variability also supports that the branched conformation is additionally stabilized by a kissing-loop interaction resembling another one proposed in PLMVd from in vitro assays. Moreover, site-directed mutagenesis combined with bioassays and progeny analysis showed that: (1) single CChMVd mutants affecting the kissing loops had low or no infectivity at all, whereas infectivity was recovered in double mutants restoring the interaction; (2) mutations affecting the structure of the regions adjacent to the kissing loops reverted to wild type or led to rearranged stems, also supporting their interaction; and (3) the interchange between 4 nucleotides of each of the two kissing loops generated a viable CChMVd variant with eight mutations. PAGE analysis under denaturing and nondenaturing conditions revealed that the kissing-loop interaction determines proper in vitro folding of CChMVd RNA. Preservation of a similar kissing-loop interaction in two hammerhead viroids with an overall low sequence similarity suggests that it facilitates in vivo the adoption and stabilization of a compact folding critical for viroid viability.

Asteraceae↗
PubMed2004

Integrative analysis of the mitochondrial proteome in yeast.

In this study yeast mitochondria were used as a model system to apply, evaluate, and integrate different genomic approaches to define the proteins of an organelle. Liquid chromatography mass spectrometry applied to purified mitochondria identified 546 proteins. By expression analysis and comparison to other proteome studies, we demonstrate that the proteomic approach identifies primarily highly abundant proteins. By expanding our evaluation to other types of genomic approaches, including systematic deletion phenotype screening, expression profiling, subcellular localization studies, protein interaction analyses, and computational predictions, we show that an integration of approaches moves beyond the limitations of any single approach. We report the success of each approach by benchmarking it against a reference set of known mitochondrial proteins, and predict approximately 700 proteins associated with the mitochondrial organelle from the integration of 22 datasets. We show that a combination of complementary approaches like deletion phenotype screening and mass spectrometry can identify over 75% of the known mitochondrial proteome. These findings have implications for choosing optimal genome-wide approaches for the study of other cellular systems, including organelles and pathways in various species. Furthermore, our systematic identification of genes involved in mitochondrial function and biogenesis in yeast expands the candidate genes available for mapping Mendelian and complex mitochondrial disorders in humans.

Chemical Fractionation↗
PubMed2006

Immunoinformatics comes of age.

With the burgeoning immunological data in the scientific literature, scientists must increasingly rely on Internet resources to inform and enhance their work. Here we provide a brief overview of the adaptive immune response and summaries of immunoinformatics resources, emphasizing those with Web interfaces. These resources include searchable databases of epitopes and immune-related molecules, and analysis tools for T cell and B cell epitope prediction, vaccine design, and protein structure comparisons. There is an agreeable synergy between the growing collections in immune-related databases and the growing sophistication of analysis software; the databases provide the foundation for developing predictive computational tools, which in turn enable more rapid identification of immune responses to populate the databases. Collectively, these resources contribute to improved understanding of immune responses and escape, and evolution of pathogens under immune pressure. The public health implications are vast, including designing vaccines, understanding autoimmune diseases, and defining the correlates of immune protection.

Amino Acid Sequence↗
PubMed2004

Ribozyme expression systems.

We have succeeded in constructing an effective system for the expression of ribozymes under the control of a human tRNAVal promoter, which ensures a high level of production of ribozymes in vivo. The engineered tRNAVal-driven ribozymes, based on computer-predicted secondary structure, were relatively stable and were transported to the cytoplasm, where they could be colocalized with their target RNA. The activity of the exported ribozymes was significantly higher than that of ribozymes that remained in the nucleus. This chapter examines the methods for construction of the appropriate vector that can produce tRNA-driven ribozymes with high-level intracellular activity and for analysis of the constructs in cells.

Base Sequence↗
PubMed2006

A locus for renal malformations including vesico-ureteric reflux on chromosome 13q33-34.

Congenital anomalies of kidney and urinary tract (CAKUT), including vesico-ureteric reflux (VUR), are major causes of ESRD in childhood. Herein is reported evidence for a locus on 13q33q34 associated with CAKUT. Deletion mapping of chromosome 13q was performed in four children with CAKUT using 31 microsatellite markers on peripheral blood genomic DNA that was obtained from the patients and their parents. mRNA expression of the positional candidate genes was compared with sequences in electronic databases in silico and also studied in adult and fetal mouse kidneys using reverse transcription-PCR. The children (three girls; age range 5 to 17 yr) had varying severity of developmental delay and other organ system involvement. The spectrum of CAKUT included high-grade VUR (n = 2), renal dysplasia (n = 2), and hydronephrosis (n = 1). Both the children with VUR had evidence of renal failure with one of them developing ESRD. Deletion mapping identified a 7-Mb critical region flanked by markers D13S1311 and D13S285. There are 33 genes (12 known; 21 computer predicted) in this region. In silico expression studies showed matches for 14 of these genes in the kidneys and 10 in the bladder expressed sequenced tags databases. Mouse kidney studies showed that of the 24 genes examined, several had variable expression through the different stages of renal development, whereas five of the genes were not expressed at all. Herein is reported a new locus on chromosome 13q33q34 that can be associated with VUR with several genes showing mRNA expression patterns that suggest their potential for involvement in renal/urinary tract developmental anomalies.

Adolescent↗
PubMed1999

A computer program for conducting incinerator risk assessments.

In 1994, the United States Environmental Protection Agency (USEPA) developed a screening methodology for conducting indirect exposure risk assessments for combustion facilities. The United States Army Center for Health Promotion and Preventive Medicine currently utilizes this methodology in conjunction with other USEPA guidance documents to perform human health risk assessments (HHRAs). The HHRAs require the development of complex human health models using spreadsheet software packages which estimate various media concentrations of contaminants in the environment. Since the quality assurance/quality control procedures associated with verifying the model's results are extremely time consuming, a computer program was developed using Microsoft Excel to minimize the amount of time needed. This discussion describes the 6 steps taken in developing this computer program, which are: (1) understanding the problem; (2) establishing the structure of each table in the spreadsheets; (3) developing an algorithm to solve the problem; (4) writing code; (5) running the program; and (6) testing the results. The automated process of having the computer predict health risk and hazards for each potentially exposed individual saves a tremendous amount of time because each calculated value is placed in the correct spreadsheet cell location. In addition to the time needed to develop human health spreadsheets, this program also minimizes the potential for reducing human error.

Algorithms↗
PubMed1990

Structure and expression of osteonectin mRNA in human tissue.

A cDNA encoding osteonectin was isolated from a human bone cell cDNA library and used to examine osteonectin protein structure, mRNA structure and expression in human tissue. The deduced protein sequence shows complete identity with a recently isolated placental form and extensive homology to mouse and bovine counterparts. The protein is rich in cysteine residues, which are conserved between species except for cys 194 which is only present in the bovine. In the human, osteonectin mRNA is of two sizes, 2.3 and 3.0 kb, the former being dominant in all tissues studied. Human mRNA was detected in the Ewing sarcoma and in non-bone cell and tissue sources. The potential folded structure of osteonectin mRNA was estimated, based on computer predictions, and indicates the presence of a bulge at the 5' end of the message which includes the start of translation. Southern analysis of human genomic DNA using radiolabeled osteonectin cDNA as probe demonstrates a simple banding pattern confirming earlier studies that the osteonectin gene is present in one copy per haploid human genome.

Amino Acid Sequence↗
PubMed1998

Bovine ornithine decarboxylase gene: cloning, structure and polymorphisms.

Bovine ornithine decarboxylase (ODC) genomic clones were isolated from a bacteriophage lambda DASH genomic library. A total of 9452 bp sequence was determined which covers the entire sequence of the bovine ODC gene. Sequence analysis showed that the bovine ODC gene consisted of 12 exons which encode a protein identical to that inferred from a bovine ODC cDNA. Comparison of the structure and nucleotide sequence of the bovine, human and mouse ODC genes revealed that the gene was highly conserved. Primer extension analysis demonstrated that the transcription start point of bovine ODC mRNA was located 378 bp upstream from the A residue in the translation initiation codon. The 5'-untranslated region (UTR) of ODC mRNA was highly G + C rich, particularly in its 5'-most portion, and computer predictions suggested a very stable secondary structure for this region, with an overall free energy of formation of -134.4 kcal/mol. Conserved sequences and potential promoter elements including a TATA box, a possible CCAAT element, SP1 ranscription factor binding sites (GC boxes) and cAMP response elements (CRE) were identified in the 5'-flanking region of the gene. Two polymorphic restriction sites, a TaqI and a MspI, were mapped to the ODC gene and PCR-based methods for detection of the 2 polymorphisms were developed.

5' Untranslated Regions↗
PubMed2026

Comparative genomics reveals hidden biosynthetic diversity in Streptomyces spp. and metal-dependent regulatory features associated with untapped specialized metabolites.

The genus Streptomyces is one of the richest sources of bioactive natural products; however, a substantial proportion of its biosynthetic gene clusters (BGCs) remain cryptic and their metabolic products are unresolved. Advances in genome mining and computational prediction now enable comprehensive exploration of this hidden biosynthetic repertoire. In this study, whole-genome sequencing and comparative genomic analyses were performed on three three newly isolated Streptomyces strains to evaluate their specialized metabolic potential. Genome assemblies were annotated and systematically analyzed using antiSMASH, DeepBGC, GECCO, and PRISM to identify, cross-validate, and functionally characterize BGCs while predicting their associated secondary metabolite scaffolds. Taxonomic analyses based on Average Nucleotide Identity (ANI), phylogenomics, and BLAST identified the isolates as Streptomyces thinghirensis, Streptomyces novocaesareae, and Streptomyces griseorubens. Applying the consensus framework across the three Streptomyces genomes yielded 43 cryptic BGCs, lacking close similarity to reference BGCs in the MIBiG database, of which 26 were classified as HIGH, 10 as MEDIUM, and 7 as LOW confidence. Notably, numerous BGCs exhibited low abundance to characterized reference clusters, indicating a high potential for previously undescribed biosynthetic pathways and novel metabolite scaffolds. Comparative analyses further revealed strain-specific biosynthetic architectures together with putative metal-responsive regulatory systems; Fur, Zur, and Nur, which were frequently associated with specialized metabolite biosynthetic loci. Collectively, these findings demonstrate the effectiveness of integrated genome-mining strategies for prioritizing cryptic biosynthetic gene clusters and highlight the remarkable biosynthetic potential of newly identified Streptomyces isolates as a source of novel natural products.

comparative genomics↗
PubMed2001

Identification of the epitopes on HCV core protein recognized by HLA-A2 restricted cytotoxic T lymphocytes.

AIM: To identify hepatitis C virus(HCV) core protein epitopes recognized by HLA-A2 restricted cytotoxic T lymphocyte (CTL). METHODS: Utilizing the method of computer prediction followed by a 4h(51)Cr release assay confirmation. RESULTS: The results showed that peripheral blood mononuclear cells (PBMC) obtained from two HLA-A2 positive donors who were infected with HCV could lyse autologous target cells labeled with peptide "ALAHGVRAL (core 150-158)". The rates of specific lysis of the cells from the two donors were 37.5% and 15.8%, respectively. Blocking of the CTL response with anti-CD4 mAb caused no significant decrease of the specific lysis. But blocking of CTL response with anti-CD8 mAb could abolish the lysis. CONCLUSION: The peptide (core 150-158) is the candidate epitope recognized by HLAA2 restricted CTL.

Amino Acid Sequence↗
PubMed2004

Site-specific inhibitors of NADPH oxidase activity and structural probes of flavocytochrome b: characterization of six monoclonal antibodies to the p22phox subunit.

The integral membrane protein flavocytochrome b (Cyt b) is the catalytic core of the human phagocyte NADPH oxidase, an enzyme complex that initiates a cascade of reactive oxygen species important in the elimination of infectious agents. This study reports the generation and characterization of six mAbs (NS1, NS2, NS5, CS6, CS8, and CS9) that recognize the p22(phox) subunit of the Cyt b heterodimer. Each of the mAbs specifically detected p22(phox) by Western blot analysis but did not react with intact neutrophils in FACS studies. Phage display mapping identified core epitope regions recognized by mAbs NS2, NS5, CS6, CS8, and CS9. Fluorescence resonance energy transfer experiments indicated that mAbs CS6 and CS8 efficiently compete with Cascade Blue-labeled mAb 44.1 (a previously characterized, p22(phox)-specific mAb) for binding to Cyt b, supporting phage display results suggesting that all three Abs recognize a common region of p22(phox). Energy transfer experiments also suggested the spatial proximity of the mAb CS9 and mAb NS1 binding sites to the mAb 44.1 epitope, while indicating a more distant proximity between the mAb NS5 and mAb 44.1 epitopes. Cell-free oxidase assays demonstrated the ability of mAb CS9 to markedly inhibit superoxide production in a concentration-dependent manner, with more moderate levels of inhibition observed for mAbs NS1, NS5, CS6, and CS8. A combination of computational predictions, available experimental data, and results obtained with the mAbs reported in this study was used to generate a novel topology model of p22(phox).

Amino Acid Sequence↗
PubMed2026

Functional screening of ZIP8 naturally occurring variants identifies pathogenic mutations and trafficking defects.

The rapid expansion of human genomic data has revealed a large number of naturally occurring variants, creating a major challenge for functional annotation. The human metal transporter SLC39A8 (ZIP8) is a clinically important, promiscuous divalent metal transporter, yet most of its documented variants remain uncharacterized. Here, we developed a workflow to functionally evaluate ZIP8 variants by integrating laser ablation inductively coupled plasma time-of-flight mass spectrometry (LA-ICP-TOF-MS) with scaled-up cell-based transport assays. Using this method, we systematically analyzed 33 naturally occurring missense variants located in the extracellular domain (ECD) of ZIP8. The assay enables direct quantification of intracellular metal accumulation with substantially improved throughput (~150 samples per hour). Functional screening identified 14 potential pathogenic variants with significantly reduced transport activity. Comparison with computational predictions revealed a moderate correlation between activity and AlphaMissense pathogenicity scores (R2 = 0.423), while an error rate of ~20% underscores the need for experimental validation. Flow cytometry analysis showed that most loss-of-function variants exhibit impaired trafficking of the protein to the cell surface possibly due to mutation-caused protein misfolding or instability. Structural mapping of activity-compromised variants, together with functional assessment of the ZIP8-ECD, highlights the importance of this domain in ZIP8 expression and intracellular trafficking. Together, this work establishes a scalable approach for functional screening of metal transporter variants and provides new insights into the structure-function relationships of ZIP8.

Journal Article↗
PubMed2026

Integrated Pan-Cancer, Single-Cell, and Spatial Transcriptomic Analyses Identify ZDHHC12 as a Biomarker Associated with Macrophage Infiltration and the Immune Landscape in Glioma.

BACKGROUND: The tumor immune microenvironment (TME) critically influences cancer progression and therapeutic response. However, the pan-cancer expression landscape, prognostic relevance, and spatial distribution of ZDHHC12 remain incompletely characterized. This study investigated the prognostic value of ZDHHC12 and its associations with immune microenvironmental features and drug sensitivity. METHODS: Data from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) datasets were used to evaluate ZDHHC12 expression and prognosis across cancer types. Immune infiltration analyses, single-cell RNA sequencing, and spatial transcriptomics were integrated to characterize the associations of ZDHHC12 with the cancer immunity cycle and the spatial architecture of glioma. Drug sensitivity and immunotherapy-related metrics were assessed using pharmacogenomic databases and computational prediction models. RESULTS: ZDHHC12 was aberrantly expressed across multiple tumors and was associated with patient prognosis. Its expression was broadly correlated with immune cell recruitment- and activation-related signatures. In glioma, single-cell and spatial transcriptomic analyses showed enrichment of ZDHHC12 in monocyte/macrophage populations and spatial co-localization with BAK1, CD68, and CD163. ZDHHC12 expression was also associated with predicted drug sensitivity and immunotherapy-related metrics. CONCLUSION: ZDHHC12 may serve as a candidate pan-cancer prognostic biomarker. In glioma, its expression is associated with macrophage-enriched and immunosuppressive microenvironmental features. Functional studies are required to establish causality and determine its therapeutic relevance.

GBM↗
PubMed2000

[Synthesis of the lupane group triterpenoids and there hepatoprotective activity].

Hemisuccinates, hemiphthalates, acetylsalicylates, cinnamates, and p-methoxycinnamates of lupeol, betulin, and 3-O-acetylbetulin were synthesized via interaction with corresponding acid anhydrides or acid chlorides. A number of betulin esters in position 3 and 28 were shown to exhibit a pronounced hepatoprotective effect similar to that of betulin and silibor. These experimental data were in a good agreement with the computer prediction of their biological activity. Betulin 3,28-bis-hemiphthalate was more effective than carsil in models of experimental hepatitis caused by carbon tetrachloride, tetracycline, and ethanol.

Animals↗
PubMed1976

Population replacement in Culex fatigans by means of cytoplasmic incompatibility. 2. Field cage experiments with overlapping generations.

Three experiments were carried out in field cages to test the principle of "transport" of a desirable gene or chromosome into a wild Culex fatigans population as a result of the sterility in cross-matings associated with cytoplasmic incompatibility. Cycling populations of Delhi origin were established in the cages and daily releases were made of the IS31B strain, which has Paris cytoplasm and carries a male-linked translocation. It was shown that, if sufficient releases were made to establish a majority of the Paris cytoplasmic type, complete replacement by this cytoplasmic type subsequently occurred. However, as a result of partial compatibility of males of the Delhi population with Paris females, "recombinant" males with Paris cytoplasm and no translocation were produced. In an experiment in which a continuous low rate of "immigration" of a strain of Delhi origin was simulated, a gradual increase of the Paris cytoplasm nontranslocated type occurred, and renewed IS31B releases were necessary after 5 months to restore the predominance of this type. The results are compared with computer predictions and discussed in relation to the transport of genes for filaria refractoriness or chromosome translocations into wild populations.

Animals↗
PubMed2001

5'UTR sequences of the glucocorticoid receptor 1A transcript encode a peptide associated with translational regulation of the glucocorticoid receptor.

We have recently reported that glucocorticoid receptor (GR) transcript 1A, one of the five mouse GR splice variants (1A-1E), encodes membrane GR (mGR), which subsequently participates in mediating the apoptotic effects of glucocorticoids (GCs); all transcripts vary at their 5'UTR. Computer analysis of the entire1026 bp comprising the 5'UTR of transcript 1A identified five putative translation start sites at positions 85, 217, 478, 628, and 892 with the potential to encode peptides of 33, 93, 6, 18, and 41 amino acids, respectively. We then separately generated point mutations at these five upstream AUG codons of the GR 1A cDNA and performed in vitro transcription/translation experiments to investigate the regulatory effects of these sites on GR synthesis. GR translation products were immuno-captured with BUGR-2 antibody (Ab), then subjected to Western blot analysis. Mutation of the uAUG codon-2 completely inhibited GR synthesis, while mutations at the other four uAUG codons had no significant effect on the translation of transcript 1A. Antibodies (Abs) against the uORF-2 and uORF-5 protein products were used to perform Western blot analysis on cytosolic proteins from S-49 cells (which express GR transcript 1A), U937 cells transfected with GR 1A cDNA, or in vitro translation products from this cDNA. This assay identified an intense immunoreactive band of approximately 8.5 kDa recognized only with Ab to the uORF-2 peptide; this size is consistent with the computer-predicted size of the uORF-2 product, suggesting that the uORF-2 product is indeed synthesized in cells. No peptide was identified with Ab to uORF-5 peptide. Indirect fluorescent Ab staining, confocal microscopy and FACS analysis all showed that the ORF-2 peptide is localized both in the interior of the cell and at the plasma membrane. Using Ab to ORF-2 peptide for immunoadsorption we then asked whether cellular factors interact with the product of uORF-2. Immuno-captured uORF-2 peptide levels correlated with the concentrations of several salt-wash-sensitive cellular proteins, suggesting that protein-protein interactions occur between this upstream open reading frame (uORF) product and other factors. The uORF-2 product, however, does not appear to directly interact with GR, since there was no reciprocal immuno-capture between these two proteins. In summary, our results show that cells can synthesize the uORF-2 peptide, blocking of the synthesis of the uORF-2 peptide product abolishes translation of GR from the GR 1A transcript, and the peptide product of uORF-2 interacts with other cellular factors which might be involved in translation of GR.

5' Untranslated Regions↗
PubMed1998

Determination of T and B Cell Epitopes of Aspergillus fumigatus Ribotoxin and Heat Shock Protein.

Ribotoxin Asp f1 and heat shock protein Asp hsp1 from Aspergillus fumigatus represent the major components of A. fumigatus allergic complex. Eight computer predicted peptides corresponding to probable T epitopes of Asp f1 (4 peptides) and Asp hsp1 (4 peptides) have been synthesized according to the primary sequence of the proteins. The peptides Asp f1 15-27, 87-99 and Asp hsp 84-96, able to bind high affinity sera from mice BALB/c immunized with crude A. fumigatus extract, were considered to represent B cell epitopes. To screen T cell epitopes among the peptides splenocytes from mice immunized with crude A. fumigatus extract were stimulated in vitro with A. fumigatus or peptides, and their Ab production was analyzed. Spontaneous A. fumigatus-specific Ab production was found in unstimulated control. In cultures stimulated with 20 &mgr;g/ml of A. fumigatus preparation Ab production was blocked by 92%. The peptide Asp f1 87-99 decreased synthesis of A. fumigatus-specific Abs by 80%. The peptide Asp f1 15-27 and those overlapping hsp1 18-31 and 22-36 induced 34-37% decrease in Ab production. Other A. fumigatus-derived or irrelevant peptides did not affect specific Ab production. Thus, these peptides, containing T cell epitope, may be considered as potential candidates for peptide-based immunotherapy of allergic aspergillosis.

Journal Article↗
PubMed1992

Mutations away from splice site recognition sequences might cis-modulate alternative splicing of goat alpha s1-casein transcripts. Structural organization of the relevant gene.

alpha s1-Casein variants F and D, synthesized in goat milk at lower levels than variant A, essentially differ from it by internal deletions of 37 and 11 amino acid residues, respectively. Northern blot analysis of mRNAs encoding alpha s1-casein F and A and sequencing of the relevant cloned cDNAs, as well as sequencing of in vitro amplified genomic fragments, revealed multiple alternatively processed transcripts, from the F allele. Although correctly spliced messengers were identified, most of the FmRNAs lacked three exons. These exons, further identified as exons 9, 10, and 11, together encode the 37 amino acid residues present in alpha s1-casein variant A but missing in variant F. Exon 9 codes for the sequence present in variant A but deleted in variant D. A single nucleotide deletion in exon 9 and two insertions, 11 and 3 base pairs in length, in the downstream intron, were identified as mutations potentially responsible for the alternative skipping of these 3 exons. From a computer-predicted secondary structure it appeared that the 11-base pair insertion might be involved in base-pairing interactions with the intron 5' splice site which might consequently be less accessible to U1 snRNA. We also report here the complete structural organization of the goat alpha s1-casein transcription unit, deduced from polymerase chain reaction experiments. It contains 19 exons scattered within a nucleotide stretch nearly 17-kilobase pairs long.

Amino Acid Sequence↗