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At least 487 records · Page 27Linked to original sources
PubMed2006

Search for novel gene markers of traumatic brain injury by time differential microarray analysis.

Neuronal and glial cell death caused by axonal injury sometimes contributes to whole brain pathology after traumatic brain injury (TBI). We show that neuroprotection by 2 types of immunosuppressants, cyclosporin A (CsA) and tacrolimus (FK506), in a cryogenic brain injury model results from inhibition of calcineurin and protection from mitochondrial damage caused by formation of a mitochondrial permeability transition pore induced by cyclophilin D (CyPD), one of the prolyl cis/trans isomerase family members. We evaluated why CsA is neuroprotective by microarray analysis of gene expression in the cryogenic brain injury rat model. Analyses of expression patterns demonstrated that expression of over 14,000 genes changed between the groups with and without CsA treatment, and about 350 genes among them were extracted showing a significant difference. We learned that the differential expression of several gene targets showed specific patterns in a time-dependent manner. These results may help elucidate the mechanisms of neuronal cell death after TBI and the neuroprotective effects of CsA after TBI.

Animals↗
PubMed1995

Comparative expressed-sequence-tag analysis of differential gene expression profiles in PC-12 cells before and after nerve growth factor treatment.

Nerve growth factor-induced differentiation of adrenal chromaffin PC-12 cells to a neuronal phenotype involves alterations in gene expression and represents a model system to study neuronal differentiation. We have used the expressed-sequence-tag approach to identify approximately 600 differentially expressed mRNAs in untreated and nerve growth factor-treated PC-12 cells that encode proteins with diverse structural and biochemical functions. Many of these mRNAs encode proteins belonging to cellular pathways not previously known to be regulated by nerve growth factor. Comparative expressed-sequence-tag analysis provides a basis for surveying global changes in gene-expression patterns in response to biological signals at an unprecedented scale, is a powerful tool for identifying potential interactions between different cellular pathways, and allows the gene-expression profiles of individual genes belonging to a particular pathway to be followed.

Animals↗
PubMed2002

Analysis of differential lipofection efficiency in primary and established myoblasts.

In this study we have compared the process of lipid-mediated transfection in primary and established myoblasts, in an attempt to elucidate the mechanisms responsible for the scarce transfectability of the former. We determined the metabolic stability of cytoplasmically injected and lipofected DNA in primary and established myoblasts and carried out a comparative time course analysis of luciferase reporter-gene expression and DNA stability. The efficiency of the transcription-translation machinery of the two cell types was compared by intranuclear injection of naked plasmid DNA encoding luciferase. Subcellular colocalization of fluorescein-labeled lipopolyplexes with specific endosomal and lysosomal markers was performed by confocal microscopy to monitor the intracellular trafficking of plasmid DNA during transfection. The metabolic stability of plasmid DNA was similar in primary and established myoblasts after both lipofection and cytoplasmic injection. In both cell types, lipofection had no detectable effect on the rate of cell proliferation. Confocal analysis showed that nuclear translocation of transfected DNA coincided with localization in a compartment devoid of endosome- or lysosome-specific marker proteins. The residency time of plasmid DNA in this compartment differed for primary and established myoblasts. Our findings suggest that the lower transfectability of primary myoblasts is mostly due to a difference in the intracellular delivery pathway that correlates with more rapid delivery of internalized complex to the lysosomal compartment.

Cell Division↗
PubMed2001

Differential display analysis of mutants for the transcription factor Pdr1p regulating multidrug resistance in the budding yeast.

The transcription factor Pdr1p recognizes Pdr1p/Pdr3p-response element (PDRE) to activate genes involved in multidrug resistance of the budding yeast. To identify novel targets of Pdr1p, we compared transcriptomes among the yeast cells bearing wild, disrupted and gain-of-function alleles of PDR1 using a high-throughput fluorescent differential display PCR. Consequently, we identified 20 transcripts apparently regulated by Pdr1p, which are derived from well-known target genes as well as those that have never been described in the context of drug resistance. Intriguingly, among the latter, a previously unrecognized gene bearing a small putative open reading frame preceded by a functional PDRE was found.

Base Sequence↗
PubMed1997

Early diagnosis by genetic analysis of differentiated thyroid cancer metastases in small lymph nodes.

We report a PCR-based technique for detecting thyroid cancer metastases in small nodes <1.5 cm diameter by the amplification of thyroid specific transcripts TSH-receptor and thyroglobulin. A 100% correspondence with the histopathological diagnosis was observed in the 41/46 nodes (89%) in which an adequate sample was obtained at fine needle aspiration. The genetic analysis resulted more sensitive and accurate than both the cytological analysis (28% inadequate samples, 17% false negative diagnoses) and the thyroglobulin measurement in the aspirates (39% false negatives). The PCR-based genetic analysis may provide a useful tool for diagnosis and follow-up of thyroid cancer.

Biopsy, Needle↗
PubMed2002

Differential display analysis of presenilin 1-deficient mouse brains.

Missense mutations in presenilin 1 (PS1) gene are the most common cause of early onset familial Alzheimer's disease (FAD). AD pathogenic PS1 mutations result in elevated gamma-secretase cleavage of APP and diminished S3-site cleavage of Notch. We have previously described a PS1-hypomorphic mouse line that could survive postnatally with markedly reduced gamma-secretase cleavage of APP and S3-site cleavage of Notch, resulting in a Notch developmental phenotype similar to PS1-null mice. This model was exploited to identify genes whose expression is altered due to the loss of PS1. A global gene expression study by differential display was performed on whole brains of PS1-hypomorphic mice and their wild type siblings. In total, more than 16,000 bands corresponding to cDNAs were compared between the mutant and wild-type brains. This analysis identified 19 cDNAs showing significantly altered expression resulting from PS1 deficiency. Four of the identified cDNAs corresponded to genes that could be associated with AD or presenilin function. Hypoxia inducible factor 1a (Hif1a), NPRAP (delta-catenin) and cell division cycle 10 (CDC10) showed significantly reduced expression in the PS1-hypomorphic compared to wild-type brains, whereas expression of nucleoside diphosphate kinase sub-unit A (NDPK-A) was markedly elevated in the respective brains. Clarification of the possible role of these genes in AD and the basis for their differential expression induced by PS1-deficiency may provide insight into the disease, presenilin function and consequences of its loss, as well as possible deleterious effects of AD therapeutics aimed at inhibiting PS1.

Alzheimer Disease↗
PubMed2006

Comparing calpain- and caspase-3-mediated degradation patterns in traumatic brain injury by differential proteome analysis.

A major theme of TBI (traumatic brain injury) pathology is the over-activation of multiple proteases. We have previously shown that calpain-1 and -2, and caspase-3 simultaneously produced alphaII-spectrin BDPs (breakdown products) following TBI. In the present study, we attempted to identify a comprehensive set of protease substrates (degradome) for calpains and caspase-3. We further hypothesized that the TBI differential proteome is likely to overlap significantly with the calpain- and caspase-3-degradomes. Using a novel HTPI (high throughput immunoblotting) approach and 1000 monoclonal antibodies (PowerBlottrade mark), we compared rat hippocampal lysates from 4 treatment groups: (i) naïve, (ii) TBI (48 h after controlled cortical impact), (iii) in vitro calpain-2 digestion and (iv) in vitro caspase-3 digestion. In total, we identified 54 and 38 proteins that were vulnerable to calpain-2 and caspase-3 proteolysis respectively. In addition, the expression of 48 proteins was down-regulated following TBI, whereas that of only 9 was up-regulated. Among the proteins down-regulated in TBI, 42 of them overlapped with the calpain-2 and/or caspase-3 degradomes, suggesting that they might be proteolytic targets after TBI. We further confirmed several novel TBI-linked proteolytic substrates, including betaII-spectrin, striatin, synaptotagmin-1, synaptojanin-1 and NSF (N-ethylmaleimide-sensitive fusion protein) by traditional immunoblotting. In summary, we demonstrated that HTPI is a novel and powerful method for studying proteolytic pathways in vivo and in vitro.

Animals↗
PubMed2002

DNA microarray analysis of differential gene expression in Borrelia burgdorferi, the Lyme disease spirochete.

DNA microarrays were used to survey the adaptive genetic responses of Borrelia burgdorferi (Bb) B31, the Lyme disease spirochete, when grown under conditions analogous to those found in unfed ticks (UTs), fed ticks (FTs), or during mammalian host adaptation (Bb in dialysis membrane chambers implanted in rats). Microarrays contained 95.4% of the predicted B31 genes, 150 (8.6%) of which were differentially regulated (changes of > or = 1.8-fold) among the three growth conditions. A substantial proportion (46%) of the differentially regulated genes encoded proteins with predicted export signals (29% from predicted lipoproteins), emphasizing the importance to Bb of modulating its extracellular proteome. For B31 cultivated at the more restrictive UT condition, microarray data provided evidence of a bacterial stringent response and factors that restrict cell division. A large proportion of genes were responsive to the FT growth condition, wherein increased temperature and reduced pH were prominent environmental parameters. A surprising theme, supported by cluster analysis, was that many of the gene expression changes induced during the FT growth condition were transient and largely tempered as B31 adapted to the mammalian host, suggesting that once Bb gains entry and adapts to mammalian tissues, fewer differentially regulated genes are exploited. It therefore would seem that although widely dissimilar, the UT and dialysis membrane chamber growth conditions promote more static patterns of gene expression in Bb. The microarray data thus provide a basis for formulating new testable hypotheses regarding the life cycle of Bb and attaining a more complete understanding of many aspects of Bb's complex parasitic strategies.

Animals↗
PubMed2026

Comprehensive Analysis of Differentially Expressed Genes and Immune Infiltration in Burn Injury: Key Biomarkers and Pathways.

BACKGROUND: Burn injuries trigger complex immune responses and gene expression changes, impacting wound healing and systemic inflammation. Understanding these changes is crucial for identifying biomarkers and therapeutic targets. METHODS: We analyzed two gene expression omnibus datasets (wound tissue [GSE8056] and blood [GSE37069]) to identify differentially expressed genes (DEGs) in burn injury samples versus controls. Immune cell proportions were assessed using CIBERSORT. Functional enrichment analyses (Gene Ontology and Kyoto Encyclopedia of Genes and Genomes) and protein-protein interaction networks were constructed to identify key genes and pathways. RESULTS: We identified 1170 upregulated and 1227 downregulated DEGs. Gene Ontology analysis revealed enrichment in neutrophil activation, inflammatory response, and extracellular matrix organization. Kyoto Encyclopedia of Genes and Genomes analysis highlighted cytokine-cytokine receptor interaction, TNF, and IL-17 signaling pathways. Immune infiltration analysis showed significant changes in neutrophils, macrophages (M1/M2), and T-cell subsets. Protein-protein interaction network analysis identified five hub genes: JUN, STAT1, Bcl2, MMP9, and TLR2. CONCLUSIONS: This study provides a comprehensive bioinformatic analysis of gene expression and immune responses in burn injuries. The identified DEGs, hub genes, and pathways offer insights into the immune response mechanisms and suggest potential targets for diagnostic and therapeutic interventions in burn injury management.

Burns↗
PubMed2002

Renal transcriptomes: segmental analysis of differential expression.

BACKGROUND/AIMS: Progress accomplished by complete genomes and cDNA-sequencing projects calls for methods that fully use these resources to study gene expression patterns in characterized cell populations. However, since the number of functional genes cannot be readily inferred from the genomic sequence, it is highly desirable to make use of methods enabling to study both known and unknown genes. METHODS: The method of serial analysis of gene expression provides short diagnostic cDNA tags without bias towards known genes. In addition, the frequency of each tag in the library conveys quantitative information on gene expression. A microassay was set-up to perform serial analysis of gene expression in minute samples such as those obtained by microdissecting nephron segments. RESULTS: Studies carried out in the thick ascending limb of Henle's loop and the collecting duct of the mouse kidney provided expression data for several thousand genes. Known markers were found appropriately enriched, and several of the thick ascending limb or collecting duct specific transcripts had no database match. CONCLUSIONS: The microassay for serial analysis of gene expression makes possible large-scale quantitative measurements of mRNA levels in nephron segments. The comprehensive picture generated by analyzing both known and unknown transcripts in defined cell populations should help to discover genes with dedicated functions.

Animals↗
PubMed2006

Microarray analysis distinguishes differential gene expression patterns from large and small colony Thymidine kinase mutants of L5178Y mouse lymphoma cells.

BACKGROUND: The Thymidine kinase (Tk) mutants generated from the widely used L5178Y mouse lymphoma assay fall into two categories, small colony and large colony. Cells from the large colonies grow at a normal rate while cells from the small colonies grow slower than normal. The relative proportion of large and small colonies after mutagen treatment is associated with a mutagen's ability to induce point mutations and/or chromosomal mutations. The molecular distinction between large and small colony mutants, however, is not clear. RESULTS: To gain insights into the underlying mechanisms responsible for the mutant colony phenotype, microarray gene expression analysis was carried out on 4 small and 4 large colony Tk mutant samples. NCTR-fabricated long-oligonucleotide microarrays of 20,000 mouse genes were used in a two-color reference design experiment. The data were analyzed within ArrayTrack software that was developed at the NCTR. Principal component analysis and hierarchical clustering of the gene expression profiles showed that the samples were clearly separated into two groups based on their colony size phenotypes. The Welch T-test was used for determining significant changes in gene expression between the large and small colony groups and 90 genes whose expression was significantly altered were identified (p < 0.01; fold change > 1.5). Using Ingenuity Pathways Analysis (IPA), 50 out of the 90 significant genes were found in the IPA database and mapped to four networks associated with cell growth. Eleven percent of the 90 significant genes were located on chromosome 11 where the Tk gene resides while only 5.6% of the genes on the microarrays mapped to chromosome 11. All of the chromosome 11 significant genes were expressed at a higher level in the small colony mutants compared to the large colony mutants. Also, most of the significant genes located on chromosome 11 were disproportionally concentrated on the distal end of chromosome 11 where the Tk mutations occurred. CONCLUSION: The results indicate that microarray analysis can define cellular phenotypes and identify genes that are related to the colony size phenotypes. The findings suggest that genes in the DNA segment altered by the Tk mutations were significantly up-regulated in the small colony mutants, but not in the large colony mutants, leading to differential expression of a set of growth regulation genes that are related to cell apoptosis and other cellular functions related to the restriction of cell growth.

Animals↗
PubMed1984

The quadrilateral analysis: a differential diagnosis for surgical orthodontics.

The integration of the diagnostic and treatment skills of both the orthodontist and the maxillofacial surgeon has become a standard procedure in the treatment of severe dentofacial dysplasias. Orthognathic surgery, surgery without prior tooth movement, is being replaced by an interdisciplinary approach as the treatment of choice. When a proper tooth-to-denture-base relationship is obtained, an ideal maxillomandibular relationship can be achieved surgically. The quadrilateral analysis enables the practitioner to obtain an individualized skeletal, dental, and soft-tissue assessment of each patient requiring treatment. It determines the direction and extent of the skeletal dysplasia in millimeter measurements and allows the clinician to outline the appropriate surgical orthodontic procedures. The quadrilateral analysis indicates that in a balanced facial pattern a 1:1 ratio exists between the maxillary bony base length (Max.Lth.) and the mandibular bony base length (Mand.Lth.); also that the average of the anterior lower facial height (ALFH) and the posterior lower facial height (PLFH) equals these bony base lengths. Simply stated, the Max.Lth. = Mand.Lth. = (formula; see text) An accurate diagnosis locates the area and quantifies the magnitude of skeletal dysplasia. Then the correct placement of a dentition within the denture bases and the appropriate surgery in the area of dysplasia can produce an individualized, balanced facial pattern.

Adolescent↗
PubMed2002

Complementary DNA cloning, sequence analysis and differential organ expression of beta-naphthoflavone-inducible cytochrome P4501A in Atlantic salmon (Salmo salar).

Cytochrome p4501A induction and subsequent enzyme expression is used as a biomarker for exposure to aryl hydrocarbon receptor active contaminants in fish and other species. In the present study, CYP1A cDNA (1912 bp, GenBank accession number AF364076) was cloned, sequenced and characterized from the liver of a beta-naphthoflavone (betaNF)-treated teleost, Atlantic salmon (Salmo salar), by reverse-transcriptase polymerase chain reaction (RT-PCR). The salmon CYP1A sequence contained a 5'-flanking region of 99 bp, an open reading frame of 1566 bp that encodes a 521 amino acid protein, a stop codon, and a 3'-untranslated region of 346 bp, and a single polyadenylated signal. The theoretical molecular mass and isoelectric point was 58.6 kDa and 6.17, respectively. Comparison of the deduced amino acid sequence of salmon cDNA with reported CYP1A genes showed identities of 73-88% with fish CYP1A, 51-54% with mammalian CYP1A1, 47-51% with mammalian CYP1A2 and 54% with frog p450. Phylogenetic analysis showed that salmon CYP1A clustered in the tree with rainbow trout CYP1A1 and eel CYP1A sequences. CYP1A mRNA induction in beta-naphthoflavone-treated salmon showed differential organ expression with a distinct single transcript pattern. A new specific molecular tool has been developed for the monitoring of environmental pollution using CYP1A mRNA from salmon as a biomarker.

Amino Acid Sequence↗
PubMed2001

Differential display analysis of hemocytes from schistosome-resistant and schistosome-susceptible intermediate hosts.

Hemocytes from schistosome-resistant and schistosome-susceptible Biomphalaria glabrata differ fundamentally in their behavior towards an invading parasite. When the schistosome infects a resistant snail host it is quickly surrounded by hemocytes, encapsulated and destroyed. Hemocytes from susceptible hosts fail to kill the parasite. To detect the differences between these two host phenotypes, we used differential-display reverse-transcription PCR (DDRT-PCR), based on RNA extracted from isolated hemocytes. A number of differentially expressed fragments from resistant and susceptible snails were detected by DDRT-PCR and confirmed using single-strand conformation polymorphism. These methods proved to be sensitive enough to allow comparison and verification of differential gene expression in our system, where only small numbers of cells are available. The most interesting phenotype-specific fragments detected so far show sequence homologies to an adhesion molecule, defensin, serine/ threonine kinases, peroxidases and glycosidases.

Animals↗
PubMed2003

Multi-stage analysis of differential gene expression in BALB/C mouse liver development by high-density microarrays.

The development of a complex organ such as the liver relies on precise temporal and spatial gene expression patterns during ontogenesis. The unique adult phenotype is a result of a cascade of transcriptional events that finally trigger gene expression in a liver-specific fashion. Development in mice starts at embryonic stage E8.5-9.5 with the expression of several genes typically associated with liver tissue. While the role of some genes and their expression is well studied, little is known about the complex expression pattern changes during embryonic and fetal liver development. High-density oligonucleotide microarrays, which allow simultaneous expression analysis of 12,488 mouse mRNA transcripts and EST sequences, were used to study the gene expression profiles in day 7.5 embryonic tissue, in micro-dissected fetal liver tissue from day 11.5 and day 13.5 embryos, and in adult liver. In pairwise comparisons of all stages, a total of 4242 distinct genes or ESTs were found to be differentially regulated. Cross-comparisons of data from all stages detected the highest number of differentially regulated genes in E11.5 fetal liver tissue versus adult liver (3063 genes) and the lowest number in E11.5 versus E13.5 fetal liver tissue (517 genes). Using adult liver as reference tissue, 212 genes were regulated exclusively in E7.5 embryonic tissue, 303 genes in E11.5 and 198 in E13.5 fetal liver tissue. Expression profiles of the 31 genes with significant regulation at all stages as well as of a number of known developmentally regulated genes were compared with published results and interpreted. The gene expression profiles detected by microarray hybridization were independently confirmed for selected genes by quantitative RT-PCR. Our data presented here suggest that a relatively small number of stage-specific genes exist, which may be of particular importance for liver development, growth and differentiation. Furthermore, the microarray approach led to the identification of a number of genes, which have not yet been associated with liver organogenesis and maturation.

Animals↗
PubMed1982

Structural analysis of differentiation antigens Mo1 and Mo2 on human monocytes.

Mo1 and Mo2 are membrane differentiation antigens expressed by human monocytes, and in the case of Mo1, by granulocytes and null cells. Mo1 antigen expression is resistant to protease treatment of intact monocytes while Mo2 is protease sensitive; Mo2 antigenic activity is regenerated by trypsin-treated monocytes during culture under conditions that favor protein synthesis. Further biochemical analysis reveals that Mo1 is associated with a glycoprotein consisting of two subunits of 94,000 and 155,000 MW. Mo2 resides on a glycoprotein of 55,000 MW. Immunoprecipitation of Mo1- and Mo2-bearing structures from lysates of internally labeled cells indicates that these proteins are synthesized by human monocytes.

Antibodies, Monoclonal↗
PubMed2001

PCR-based microsatellite analysis for differentiation and genetic monitoring of nine inbred SENCAR mouse strains.

Sixteen DNA microsatellites or simple sequence length polymorphisms (SSLPs), generated by polymerase chain reaction (PCR) were selected for use in the genetic quality control of the nine inbred SENCAR strains currently available. The SENCAR strains constitute a powerful tool for mechanistic studies of multi-stage skin carcinogenesis, as well as for studies to understand the underlying genetic basis of resistance to tumour promotion and progression. SSLP analysis is a fast and economical way for detecting genetic contamination (unexpected outcrosses) among these closely-related albino strains, where standard immunological and biochemical markers have been shown to be insufficient.

Animals↗