Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “differential analysis”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 469 records · Page 26Linked to original sources
PubMedDate not supplied

Leishmania mexicana amazonensis: differential display analysis and cloning of mRNAs from attenuated and infective forms.

The virulence of Leishmania mexicana is determined by the concerted action of several parasite molecules. These cells lose their infectivity to host macrophages after prolonged cultivation in axenic growth media. Both virulent and attenuated variants of the parasite cells were cloned. The differential display reverse transcription-polymerase chain reaction technique was employed to understand whether this natural attenuation of the parasite cells is accompanied by differential expression of selected genes in those cells. Twelve different dinucleotide-anchored oligo(dT) antisense primers were used to make cDNAs from poly(A)+ mRNAs isolated from a clonal population of virulent and avirulent cells following a protocol optimized for Leishmania mRNAs. Those cDNAs were subjected to amplifications using each of the three different arbitrary decanucleotide primers and the corresponding anchored oligo(dT) primer. This procedure revealed four virulent-specific cDNA probes and one avirulent-specific cDNA probe. Differential expressions of these genes were confirmed by northern hybridization using the cloned cDNA probes. These results indicate that differential expression of genes may be the key in determining the molecular basis of leishmanial virulence.

Animals↗
PubMed2005

Analysis of differentially expressed genes in nitric oxide-exposed human monocytic cells.

In this study we examined the gene expression pattern of *NO-dependent genes in U937 and Mono Mac 6 monocytes exposed to the synthetic NO-donor DPTA-NO using microarray technology. cDNA microarray data were validated by Northern blot analysis and quantitative real-time PCR. This approach allowed the identification of 17 *NO-sensitive genes that showed at least a twofold difference in expression, in both U937 cells and Mono Mac 6 cells exposed to 500 microM DPTA-NO for 4 h. NO-stimulated genes belong to various functional groups, including transcription factors, signaling molecules, and cytokines. Among the selected genes, 11 (ATF-4, c-maf, SGK-1, PBEF, ATPase 8, NADH dehydrogenase 4, STK6, TRAF4-associated factor 1, molybdopterin synthase, CKS1, and CIDE-B) have not been previously reported to be sensitive to *NO. Because several *NO-stimulated genes are transcription factors, we analyzed the mRNA expression profile in U937 cells exposed to DPTA-NO for 14 h. We found that long-term *NO treatment influenced transcription rates of a rather limited set of genes, including CIDE-B, BNIP3, p21/Cip1, molybdopterin synthase, and TRAF4-associated factor 1. To accelerate formation of nitrosating species, U937 cells were exposed to DPTA-NO along with suboptimal concentrations of 2-phenyl-4,4,5,5-tetramethylimidazole-1-oxyl 3-oxide (PTIO). PTIO-mediated increase in nitrosating species remarkably enhanced *NO-dependent induction of IL-8, p21/Cip1, and MKP-1 and built a specific gene expression profile.

Alkenes↗
PubMed2000

Identification of rice blast fungal elicitor-responsive genes by differential display analysis.

In order to study molecular interactions that occur between rice and rice blast fungus upon infection, we isolated fungal elicitor-responsive genes from rice (Oryza sativa cv. Milyang 117) suspension-cultured cells treated with fungal elicitor prepared from the rice blast fungus (Magnaporthe grisea) employing a method that combined mRNA differential display and cDNA library screening. Data base searches with the isolated cDNA clones revealed that the OsERG1 and OsERG2 cDNAs share significant similarities with the mammalian Ca2+-dependent lipid binding (C2) domains. The OsCPX1 cDNA is highly homologous to peroxidases. The OsHin1 cDNA exhibits homology to the tobacco hin1 gene, whose expression is induced by avirulent pathogens. The OsLPL1 and OsMEK1 cDNAs share homologies with lysophospholipases and serine/threonine mitogen-activated protein (MAP) kinase kinases, respectively. The OsWRKY1 and OsEREBP1 cDNAs are homologous to transcription factors, such as the WRKY protein family and the AP2/EREBP family, respectively. Transcripts of the OsERG1, OsHin1, and OsMEK1 genes were specifically elevated only in response to the avirulent race KJ301 of the rice blast fungus. Our study yielded a number of elicitor-responsive genes that will not only provide molecular probes, but also contribute to our understanding of host defense mechanisms against the rice blast fungus.

Blotting, Northern↗
PubMed2004

Deconstructing positive affect in later life: a differential functionalist analysis of joy and interest.

Positive affect, an index of psychological well-being, is a known predictor of functionality and health in later life. Measures typically studied include joy, happiness, and subjective well-being, but less often interest--a positive emotion with functional properties that differ from joy or happiness. Following differential emotions theory, the present study measured trait joy and interest in a population-based sample of 1,118 adults aged 65-86 years. As predicted, trait joy was associated with greater religious participation, while trait interest was associated with greater education. Joy was associated with lower morbidity and stress while interest was not. Interest was, in fact, associated with greater stress. Both emotions were positively associated with social support. We use the pattern of predictors to develop a functionalist conceptualization of these two emotions in later life, concluding that it is worthwhile to treat interest and joy as partially-independent positive affects contributing differentially to human emotionality and later life adaptation.

Adaptation, Psychological↗
PubMed2002

Proteomic analysis of differential protein expression in human nasopharyngeal carcinoma cells induced by NAG7 transfection.

Nasopharyngeal carcinoma (NPC) is a commonly occurring tumor in southern China and south east Asia. A genetic factor has now been recognized to be associated with this cancer. A new gene, named NAG7, was cloned from the common minimal deletion region in 3p25.3-26.3. In order to investigate the function of NAG7 gene, proteomic methods were used to find and identify the differential proteins and expected to elucidate the mechanism of NAG7. The NAG7 eukaryotic expression vector was constructed and transfected into NPC cell line HNE1 with liposome. Twenty-two differential protein spots in transfected cells were found significant and reproducible using high-resolution two-dimensional electrophoresis. Nine proteins that were up-regulated and seven proteins that were down-regulated were identified by matrix assisted laser desorption/ionization time of flight mass spectrometry and database analysis. These proteins included growth arrest specific protein, DNA binding protein, caspase 6, pinch protein and ras-related protein rab-36, which are involved in cell cycling, transcription regulation, signaling pathways and apoptosis. NAG7 may exert its functions by mediating differential expression of these proteins.

Animals↗
PubMed1999

Identification, N-terminal region sequencing and similarity analysis of differentially expressed proteins in Paracoccidioides brasiliensis.

Paracoccidioides brasiliensis is the causal agent of paracoccidioidomycosis, which is a systemic mycosis in Latin America. This human pathogen is a dimorphic fungus existing as mycelium (26 degrees C) and in infected tissues as a yeast form (36 degrees C). The in vitro differentiation process is reversible and dependent on temperature shift. In the present study, the total proteins from both forms of P. brasiliensis (isolate Pb01) were analysed by two-dimensional electrophoresis. Differentially expressed proteins were identified. Two of these proteins, PbM46 (mycelium) and PbY20 (yeast), were submitted to automated protein sequencing of their N-terminal regions. The 15 amino acid residue sequence of PbM46, AITKIFALKVYDSSG, is similar to enolases from several sources, and specially those from Saccharomyces cerevisiae (80%) and Candida albicans (67%), when compared to the NR database at NCBI using the BLASTP program. The 34 amino acid residue sequence of PbY20, APKIAIVFYSLYGHIQKLAEAQKKGIEAAGGTAD, could probably represent an allergen protein since it is very similar (90%) to the minor allergen protein of Alternaria alternata and 82% similar to the allergen protein of Cladosporium herbarum. This comparative analysis of proteins from mycelium and yeast forms has allowed the identification and characterization of differentially expressed proteins, probably related to differential gene expression in P. brasiliensis.

Amino Acid Sequence↗
PubMed1997

Dipole source analysis may differentiate benign focal epilepsy of childhood with occipital paroxysms from symptomatic occipital lobe epilepsy.

The aim of the study was to distinguish Benign Focal Epilepsy of Childhood with Occipital Paroxysms (BEOP) from its symptomatic counterpart on the basis of the location of the sources of the interictal EEG spikes. Patients were classified into two groups: idiopathic BEOP and symptomatic occipital lobe epilepsy. Source analysis of the averaged occipital spikes was performed using a homogeneously conducting sphere as the volume conductor model. Results showed a statistically significant difference in the eccentricity, i.e., the distance of the occipital spike focus from the centre of the head. The dipole sources of the occipital spikes in the BEOP group were found to be located more superficially than in the symptomatic group, corresponding in six of the nine cases with a source position estimated to be within the cortical layer just below the skull. The eccentricity of the symptomatic occipital spikes suggests a location deeper than the cortical layer. The results were validated in two patients from the symptomatic group. In one patient the estimated deeper dipole source location corresponded with a deeper location of spike activity observed during ECoG; in the other patient's ECoG, spike activity was observed superficially but over an extended area. The discrepancy between estimated and real location may be explained by the method of dipole source analysis used. It is concluded that the finding of a superficial dipole source location of the occipital spikes provides an indication for the diagnosis BEOP (sensitivity: 67%; specificity: 74%).

Adolescent↗
PubMed2005

Identification of a gene induced in conjugation-promoted cells of toxic marine dinoflagellates Alexandrium tamarense and Alexandrium catenella using differential display analysis.

Marine dinoflagellates Alexandrium tamarense and Alexandrium catenella produce toxins that cause paralytic shellfish poisoning (PSP). A detailed mechanism of encystment is necessary for a better understanding of bloom dynamics and the toxic effect of these organisms. In this study, a cDNA that was up-regulated in conjugation-promoted cells at encystment was identified using differential display. It encoded a polypeptide of 195 amino acids with a molecular weight of 20,900 Da. The deduced amino acid sequence of this cDNA showed 62% similarity with the polypeptide encoded by SPS19, a gene that is activated specifically during spore maturation and spore wall formation in Saccharomyces cerevisiae. Therefore, the cDNA obtained was termed an SPS19 homolog in this study. The expression levels of the SPS19 homolog were highest immediately after the promotion of conjugation and decreased sequentially later, a pattern similar to that of SPS19 in the sporulation of S. cerevisiae in terms of the time of induction and the duration of expression. These similarities between the SPS19 homolog and SPS19 suggested that the putative function of the SPS19 homolog might be an involvement in encystment. RT-PCR showed that the expression of the SPS19 homolog was highest in conjugation-promoted cells but low in vegetative cells. The SPS19 homolog was believed to be expressed constantly in order for cells to respond rapidly to environmental changes and ensure encystment. Characterization of the identified gene might help in understanding the mechanism of encystment.

Amino Acid Sequence↗
PubMed1979

Risk factor analysis in differentiated thyroid cancer.

Six hundred patients with primary differentiated thyroid carcinoma had follow-up studies for a minimum of 15 years and a maximum of 45 years. Recurrence rate and death rate were significantly different in defined high-risk and low-risk groups of patients. These basic risk groups were defined by age and sex alone; low risk consisted of men 40 years of age and younger and women 50 years of age and younger whereas the high-risk group were older patients. Recurrence and death rates in patients at high risk were 33% and 27% while respective figures for patients at low risk were 11% and 4%. In more recent years these results have shown significant improvement. Basic risk group definition outweighed the effect of pathologic type, local disease extension, type of treatment, and site of recurrence or metastasis. For instance, radioactive iodine cured 70% of patients at low risk with metastatic disease but only 10% of patients at high risk. Less aggressive biologic behavior of thyroid cancer before the age of menopause implies that an estrogen-rich milieu may alter the effects of initiating and promoting factors in carcinogenesis. It also suggests that therapeutic trials of estrogen be undertaken in progressive metastatic differentiated thyroid cancer.

Adenocarcinoma↗
PubMed2005

The analysis of differentially expressed novel transcripts in diapausing and diapause-activated eggs of Bombyx mori.

As an initial step to define the molecular mechanism of initiation and termination of diapause during the embryogenesis of silkworms, Bombyx mori, mRNA transcripts from maintained and activated diapause eggs were compared with differential expression using cDNA array. Twenty-four individual cDNA transcripts were expressed differentially in a total of 1,468 different cDNAs. Among those clones, mRNA transcript from cytochrome oxidase subunit I (COI), which was detected to be 2-kb transcripts, gradually increased in diapause-activated eggs during early embryogenesis. Further analysis revealed that mRNA transcripts from silkworm COI were highly expressed in testis, fat body, and midgut during the larval stage. These results may indicate that the expression of silkworm COI mRNA is regulated developmentally as well as tissue-specifically.

Animals↗
PubMed2001

Plasmodium falciparum: differential display analysis of gene expression during gametocytogenesis.

With the Plasmodium falciparum genome sequencing near completion, functional analysis of individual parasite genes has become the major task of the postgenomic era. Understanding the expression patterns of individual genes is the initial step toward this goal. In this report, we have examined gene expression during gametocytogenesis of the malaria parasite, P. falciparum, using a modified differential display (DD) method. The modifications of this method include adjusting the dNTP mix, using upstream primers with higher AT contents, and reducing the extension temperature of the polymerase chain reaction (PCR). With a combination of 16 arbitrary upstream primers and 3 one-base-anchored oligo(dT) primers, we have successfully cloned 80 unique cDNA tags from stage IV-V gametocytes. Further analysis by dot blots and semiquantitative reverse transcriptase-PCR showed that at least 49 cDNAs had induced or elevated levels of expression in gametocytes. These results indicate that this modified DD procedure is suitable for large-scale identification of developmentally regulated genes in the AT-rich Plasmodium genome.

Animals↗
PubMed2005

Identification of novel biomarker candidates by differential peptidomics analysis of cerebrospinal fluid in Alzheimer's disease.

The objective of this work was the application of peptidomics technologies for the detection and identification of reliable and robust biomarkers for Alzheimer's disease (AD) contributing to facilitate and further improve the diagnosis of AD. Using a new method for the comprehensive and comparative profiling of peptides, the differential peptide display (DPD), 312 cerebrospinal fluid (CSF) samples from AD patients, cognitively unimpaired subjects and from patients suffering from other primary dementia disorders were analysed as four independent analytical sets. By combination with a cross validation procedure, candidates were selected from a total of more than 6,000 different peptide signals based on their discriminating power. Twelve candidates were identified using mass-spectrometric techniques as fragments of the possibly neuroprotective neuroendocrine protein VGF and another one as the complement factor C3 descendent C3f. The combination of peptide profiling and cross validation resulted in the detection of novel potential biomarkers with remarkable robustness and a close relation to AD pathophysiology.

Algorithms↗
PubMed1997

Product differentiation by analysis of DNA melting curves during the polymerase chain reaction.

A microvolume fluorometer integrated with a thermal cycler was used to acquire DNA melting curves during polymerase chain reaction by fluorescence monitoring of the double-stranded DNA specific dye SYBR Green I. Plotting fluorescence as a function of temperature as the thermal cycler heats through the dissociation temperature of the product gives a DNA melting curve. The shape and position of this DNA melting curve are functions of the GC/AT ratio, length, and sequence and can be used to differentiate amplification products separated by less than 2 degrees C in melting temperature. Desired products can be distinguished from undesirable products, in many cases eliminating the need for gel electrophoresis. Analysis of melting curves can extend the dynamic range of initial template quantification when amplification is monitored with double-stranded DNA specific dyes. Complete amplification and analysis of products can be performed in less than 15 min.

Benzothiazoles↗
PubMed2001

Improvement of RNA fingerprinting efficiency for the analysis of differential gene expression in human cardiac macro- and microvascular endothelial cells.

RNA fingerprinting by arbitrarily primed PCR (RAP-PCR) is a powerful tool to screen differential gene expression. However, PCR-based screening techniques show a high incidence of false positive results (40-90%). In order to increase the efficiency and feasibility of RAP-PCR, the original protocol was modified and applied to analyse differential gene expression in human coronary macro- (HCEC) and microvascular (HCMEC) endothelial cells. The major modifications introduced were: (i) the use of two primers for PCR amplification, instead of reverse-transcription primer alone; (ii) the use of three cycles at low stringency followed by further amplification at high stringency; (iii) optimization of amplification cycle number, template amount, and concentration of primers, dNTP, Mg(2+); (iv) detection of fingerprints by silver staining; and (v) direct sequencing using RAP-PCR primers. Analysis of untreated and TNF alpha -stimulated (100 U ml(-1)for 1, 4, and 24 h) HCEC and HCMEC displayed 11 differentially expressed products by 18 primer combinations. Confirmation of results by RT-PCR showed that the rate of false positives attributable to our screening method was less than 20%. Among detected RAP-PCR products, the expression of Mn-superoxide dismutase, A20 zinc finger protein, and three novel genes (A/a, 4/d, 7/c) was more strongly modulated by TNF in HCEC than HCMEC. A further novel gene (B/e) was strongly expressed in HCMEC while only barely detectable in HCEC. In conclusion, modification of RAP-PCR strongly reduced the incidence of false positives, eliminated a radioactive requirement, and allowed sequencing without prior cloning, supplying an improved technology able to identify new differentially expressed genes between macro- and microvascular endothelial cells.

Cells, Cultured↗
PubMed1992

DNA image cytometric analysis of differentiated thyroid adenocarcinoma specimens.

A total of 117 differentiated thyroid adenocarcinomas that had been removed by total thyroidectomy were studied. Seventy (60%) were papillary, 36 (30%) were follicular, and 11 (10%) were Hürthle cell adenocarcinomas. The mean length of follow-up was 57.7 months. Adverse prognostic factors according to multivariate analysis were adjacent tissue infiltration (p = 0.0004), histologic type (p = 0.0049), and patient age (p = 0.033). The nuclear DNA content of tumor cells and of morphologically normal adjacent tissue was assessed by image cytometry, and correlations between nuclear DNA content and prognostic factors were examined. Fifty-four (75%) adenocarcinomas were classified as aneuploid, 9 (13%) as diploid, and 9 (12%) as borderline. Thirty-four (60%) specimens of morphologically normal adjacent tissue were classified as aneuploid, 18 (32%) as diploid, and 5 (8%) as borderline. The correlation between tumor ploidy and selected prognostic factors was statistically significant for patient age (p = 0.004) and histologic type (p = 0.033). Despite the fact that ploidy could not be identified as a prognostic factor, we suggest that, because of its correlation with age and histologic type, it might prove prognostic if the number of patients were increased. We also emphasize the importance of evaluating morphologically normal adjacent tissue because of the high rates of aneuploidy in these areas.

Adenocarcinoma↗
PubMed1986

Metastatic tumors to the parotid and submandibular glands--analysis and differential diagnosis of 108 cases.

The distinction between primary salivary gland tumors and metastases of other primary tumors in salivary glands is of special importance for therapy and prognosis. In the files of the Salivary Gland Register, 10,944 cases were collected during 1965 and 1985. Among these cases, there were 108 cases of metastatic tumors to the parotid and submandibular gland. The pathohistological analysis of these tumors revealed the following data: 47 cases (43%) of metastatic tumors were localized in the parenchyma of the parotid gland (37 cases) or of the submandibular gland (10 cases). 61 cases (57%) displayed metastases in the lymph nodes of the parotid gland (38 cases) or of the submandibular gland (23 cases). The sublingual gland was free of metastatic tumors. 65 metastatic tumors originated from primary tumors in the neighborhood (head and neck). 32 tumors were carcinomas of the skin, 17 tumors were melanomas, and 13 tumors were nasopharyngeal cancers. Metastases of thyroid cancers were found in 3 cases. The relative frequency of metastases in the lymph nodes of the salivary glands is due to the intense drainage with lymph vessels and the presence of many lymph nodes which are localized especially in the gland parenchyma or around the parotid gland. 21 metastatic tumors originated from primary tumors distant from the head and neck region. There were metastases of lung cancers (7 cases), renal cancers (6 cases), mammary cancers (6 cases), colonic cancer (1 case) and uterus cancer (1 case). Clear cell carcinomas in salivary gland tissue should always be checked for a metastasis of a primary renal cancer.(ABSTRACT TRUNCATED AT 250 WORDS)

Aged↗