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PubMed1999

Error Analysis of Three Spherotensiometric Methods.

The error analysis in the determination of interfacial tension and contact angle using sphere tensiometry was fulfilled using the total differential analysis. The average error in interfacial tension for all three methods (the maximum force point method, two points method (F0 and H0/R) and process curve method) is smaller than 0.05 mN/m and average error in contact angle is smaller than 0.9 degrees. Copyright 1999 Academic Press.

Journal Article↗
PubMed2026

Prognostic model based on calcium-related genes predicts prognosis and reveals the immune landscape of acute myeloid leukemia.

Acute myeloid leukemia (AML) exhibits heterogeneous outcomes and lacks reliable prognostic markers. As a critical regulator of cell fate, the prognostic value of calcium signaling in AML requires investigation. This study aimed to construct a calcium-related gene (CRG)-based prognostic model for AML. Differential analysis on RNA-seq data was conducted for AML from The Cancer Genome Atlas and Gene Expression Omnibus (GEO). Intersecting differentially expressed genes and CRGs yielded AML-associated differentially expressed CRGs (DECRGs). A prognostic model was developed using univariate/multivariate Cox regression and least absolute shrinkage and selection operator (LASSO) and validated in a GEO dataset. Bioinformatics analyses explored the links between risk groups and immune characteristics, genomic mutations, and drug sensitivity. Key genes' effects on cell proliferation, apoptosis, and differentiation were verified in vitro using CCK-8 assay, colony formation assay, and flow cytometry. The 13-DECRG-based model distinguished high- and low-risk patients in both training and validation cohorts, with high-risk patients showing a worse prognosis. The risk score was an independent prognostic factor. Immune analysis revealed a unique immune microenvironment for the high-risk group. CAMK2A overexpression inhibited cell proliferation and colony-forming ability, promoted cell apoptosis, and induced an increased proportion of CD11b- and CD14-positive cells. In vitro experiments indicated CAMK2A-induced suppression of AML cells' malignant phenotype by activating the P53 signaling pathway. An AML CRG-based model with favorable risk stratification performance was constructed. In vitro experiments revealed CAMK2A-induced inhibition of the malignant phenotype via suppressing proliferation, promoting apoptosis, and facilitating myeloid differentiation in AML cells. This study provides novel evidence for understanding CRGs in AML as well as the potential functions of CAMK2A.

Journal Article↗
PubMedDate not supplied

Identification of genes induced by taxol application using a combination of differential display RT-PCR and DNA microarray analysis.

The differential display reverse transcriptional polymerase chain reaction (DD-RT-PCR) was used to hunt for cDNA fragments specifically expressed by taxol treatment of HeLa cells. Forty-eight cDNA clones were differentially displayed through the experiments. The cDNA fragments obtained were separately spotted onto glass slides to prepare a tailor-made DNA chip. The gene expression pattern of differentially displayed cDNA fragments were checked by DNA microarray analysis.

Cloning, Molecular↗
PubMed2004

Identification of genes differentially expressed in T cells following stimulation with the chemokines CXCL12 and CXCL10.

BACKGROUND: Chemokines are involved in many biological activities ranging from leukocyte differentiation to neuronal morphogenesis. Despite numerous reports describing chemokine function, little is known about the molecular changes induced by cytokines. METHODS: We have isolated and identified by differential display analysis 182 differentially expressed cDNAs from CXCR3-transfected Jurkat T cells following treatment with CXCL12 or CXCL10. These chemokine-modulated genes were further verified using quantitative RT-PCR and Western blot analysis. RESULTS: One hundred and forty-six of the cDNAs were successfully cloned, sequenced, and identified by BLAST. Following removal of redundant and non-informative clones, seventeen mRNAs were found to be differentially expressed post treatment with either chemokine ligand with several representing known genes with established functions. Twenty-one genes were upregulated in these transfected Jurkat cells following both CXCL12 and CXCL10, four genes displayed a discordant response and seven genes were downregulated upon treatment with either chemokine. Identified genes include geminin (GEM), thioredoxin (TXN), DEAD/H box polypeptide 1 (DDX1), growth hormone inducible transmembrane protein (GHITM), and transcription elongation regulator 1 (TCERG1). Subsequent analysis of several of these genes using semi-quantitative PCR and western blot analysis confirmed their differential expression post ligand treatment. CONCLUSIONS: Together, these results provide insight into chemokine-induced gene activation and identify potentially novel functions for known genes in chemokine biology.

Blotting, Western↗
PubMed2002

CpG DNA: recognition by and activation of monocytes.

Unmethylated CpG motifs present in bacterial DNA rapidly trigger an innate immune response characterized by the activation of Ig- and cytokine-secreting cells. Synthetic oligonucleotides (ODNs) containing CpG motifs mimic this activity, triggering monocytes to proliferate, secrete and/or differentiate. Analysis of hundreds of novel ODNs led to the identification of two structurally distinct classes of CpG motif that differentially activate human monocytes. ODNs of the "K"-type interact with Toll-like receptor 9 and induce monocytes to proliferate and secrete IL-6. In contrast, "D"-type ODNs trigger monocytes to differentiate into mature dendritic cells.

Animals↗
PubMed1990

Adenovirus infection of differentiated F9 cells results in a global shut-off of differentiation-induced gene expression.

Previous experiments have demonstrated a link between transcriptional regulatory mechanisms acting during F9 cell differentiation and transcription control by the adenovirus E1A gene. We have isolated a number of differentiation-specific genes by cDNA cloning to determine if E1A exerts a coordinated control over differentiation specific gene expression. The mRNAs encoded by these cDNAs were undetectable or only barely detectable in undifferentiated cells but then rose in concentration upon differentiation. Analysis of transcription rates in isolated nuclei revealed that all but one of the genes was transcriptionally regulated during differentiation. Interestingly, alpha 2-type IV collagen expression was activated by a post-transcriptional mechanism since the gene was transcribed in both undifferentiated and differentiated cells whereas the cytoplasmic mRNA was undetectable in undifferentiated cells but rose in abundance in parallel with other regulated transcripts. Adenovirus infection of differentiated F9 cells reduced the cytoplasmic mRNA levels of each of the differentiation specific genes to near that found in the undifferentiated cell. Of those genes that were transcriptionally activated by differentiation, adenovirus infection specifically inhibited transcription. In contrast, although the alpha 2 collagen mRNA levels were reduced by adenovirus infection similar to the other mRNAs, the control was post-transcriptional since transcription of the gene was unaffected. Thus, the mechanism for loss of gene expression mediated by E1A reflects the mechanism by which the gene was activated during differentiation. Based on these results we suggest that E1A controls the expression of the F9 cell phenotype by targeting a regulatory activity acting early in the differentiation program.

Adenoviruses, Human↗
PubMed1981

Analysis of filament population in different stages of fish and amphibian myogenesis.

In order to determine the participation of different types of filaments in particular phases of myogenic cell differentiation, analysis of filament population was done in embryonic somite cells of the trout (S. trutta) and in the cells of developing limb of the salamander larvae (S. salamandra L.). The following types of myogenic units were selected for the observation: undifferentiated mesenchymal cells (presumptive myoblasts), myoblasts prior to and post fusion and myotubules. Basing on morphological features four types of filaments were encountered: skein (4 nm), actin (8 nm), intermediate (12...14 nm) and myosin (14, 17, 21, 25 nm) filaments. Within the myosin filament population three different classes of filaments differing significantly from one another in their thickness (p less than 0.01) were found. In fish myogenic cells we have found myosin filaments of a thickness 17, 21, 25 nm, whereas in amphibian's cells, myosin filaments measured in thickness 14, 17, 21 nm respectively. The observed quantitative differences in the composition of myosin filament population might reflect their maturation process during sarcomere formation. As the process of differentiation of contractile units - sarcomeres and microfibrils develops, a distinctive quantitative predominance of 17 nm myosin filaments in fishes and 14 nm myosin filaments in amphibians becomes established.

Actins↗
PubMedDate not supplied

[Initial results of a study on morphonuclear parameters at the level of benign and primary neoplastic hepatic tissue].

This study characterises morphonuclear parameters from normal, cirrhotic, tumoral benign and malignant liver specimens obtained by computerized morphonuclear images analyses. The material is obtained by cytological aspirations or by imprint smears from liver biopsy. The monoparametric analysis differentiates a benign and a malignant cellular populations. In the malignant populations, two types are individualised: the well differentiated and the pleiomorphic hepatocarcinoma. The treatment of the data by canonical projections onto the factorial plan and by discriminant analysis allowed the selection of homogeneous cell populations belonging to each of the pathological groups described above.

Carcinoma, Hepatocellular↗
PubMedDate not supplied

Race of parents and infant birthweight in the United States.

Detailed 1977 national natality data are used to investigate social, demographic, and genetic effects on birthweight differentials. Analysis of birthweight differences among infants with white, black, and mixed black-white parents indicates that a portion of the observed weight differentials appear to be due to biologic factors. Infants with a black mother and father have the lowest mean birthweights, while infants with two white parents have the highest weights. Newborns with mixed-race parents have intermediate birthweight distributions. Multivariate analysis suggests that the effects of parental race on birthweight are not the result of maternal/obstetric differences among parents of the same or mixed race.

Adult↗
PubMed2026

META-DIFF: a k-mer-based pipeline that detects differentially abundant sequences in metagenomics whole genome sequencing.

Traditional case-control metagenomic studies are constrained by their dependence on taxonomic and functional databases. Because annotation occurs before differential analysis, they are limited to known elements and keep function and taxonomy separate. Although binning strategies have emerged to reconstruct genomes and mitigate this issue, they still require an assembly step, preventing the use of all available sequencing data. Here, we introduce META-DIFF, a pipeline based on differentially abundant k-mers independently of any prior annotation. From those k-mers, it reconstructs longer sequences and provides biological context, as well as the best set of unitigs to discriminate between conditions. Across both taxonomy-centric and functionally-centric benchmarks, it showed robust performance and displayed great reproducibility. It also behaved more conservatively than did other univariate methodologies, i.e. it maintained a high precision at the expense of recall, particularly in conditions of low fold-change and limited sequencing depth. The efficacy of META-DIFF was further validated through its application to a real-world colorectal cancer dataset, which produced both confirmatory and novel results compared with those of previous publications. The pipeline is able to exploit all reads and identify differentially abundant elements, including unknown DNA, prior to annotation. With the guidelines provided, META-DIFF provides users with great exploratory power to unravel microbiome changes.

Metagenomics↗
PubMed1996

Bladder squamous cell carcinomas express psoriasin and externalize it to the urine.

PURPOSE: To report a single biomarker, psoriasin (Mr 11.0 kd, pI 6.2), a calcium binding protein which is expressed largely by stratified squamous epithelia and is externalized to the urine of bladder squamous cell carcinoma (SCC) bearing patients. MATERIALS AND METHODS: Protein expression profiles of SCCs obtained immediately after surgery were analyzed by two-dimensional gel electrophoresis and Coomassie blue staining. Protein identity was determined by microsequencing and immunoblotting. Protein expression in cryosections was studied by immunofluorescence. RESULTS: Four patients with SCC were identified from 100 samples of patients with suspected transitional cell carcinoma (TCC). The protein profiles of the 4 SCCs (56-1, grade III, T4; 181-1, grade I, T3; 219-1, grade III, T3 and 239-1, grade not determined, T2-4) resembled that of keratinocytes, suggesting that these cells express an early developmental pattern of gene expression. Besides expressing markers characteristic of keratinizing stratified squamous epithelia, the SCCs exhibited psoriasin, a protein externalized to the medium by keratinocytes. Immunohistochemistry of 3 of the SCCs with psoriasin antibodies showed that the positive cells were confined chiefly to the "squamous pearls." The presence of psoriasin in the urine of the 4 SCC patients was demonstrated by two-dimensional gel immunoblotting. Similar analysis of 43 urines from patients with bladder tumors other than SCC revealed 7 positives, some of which may reflect squamous differentiation. Analysis of the urine of 13 control individuals (12 males matched by age and a 42-year-old female) revealed 2 positives. Immunoblotting of the SCC patients' serum proteins with psoriasin antibodies failed to reveal the protein. CONCLUSION: The results point towards psoriasin, alone or as part of a biomarker profile, as a potential marker for the noninvasive follow-up of patients with SCC.

Adult↗
PubMedDate not supplied

Osteogenic differentiation of mouse embryonic stem cells: differential gene expression analysis by cDNA microarray and purification of osteoblasts by cadherin-11 magnetically activated cell sorting.

We have previously shown osteogenic differentiation of mouse embryonic stem (ES) cells and temporal enrichment with osteoblastic cells, by stimulation with serum-containing culture medium supplemented with beta-glycerophosphate, ascorbate, and dexamethasone. In our present study we have used similar culture conditions to further investigate osteogenic differentiation of mouse ES cells. Using reverse transcription-polymerase chain reaction (RT-PCR) we demonstrated the expression of genes associated with osteoblast differentiation including the bone matrix protein osteocalcin and the transcription factor Cbfa-1/runx2. Furthermore, results of cDNA microarray analysis, and subsequent RT-PCR analysis of differentiating ES cells after exposure to osteogenic stimuli, revealed a combination of upregulation of genes involved in osteoblast differentiation including osteopontin, HSP-47, and IGF-II coupled with downregulation of genes involved in differentiation of other phenotypes such as the neuroectoderm factor Stra-13. Finally, we have applied magnetically activated cell-sorting methods to ES cell cultures treated with osteogenic stimuli and, using an antibody to cadherin-11, have purified a subpopulation of cells with osteoblastic characteristics.

Animals↗
PubMed2002

Expression of endomembrane calcium pumps in colon and gastric cancer cells. Induction of SERCA3 expression during differentiation.

Calcium mobilization from the endoplasmic reticulum (ER) into the cytosol is a key component of several signaling networks controlling tumor cell growth, differentiation, or apoptosis. Sarco/endoplasmic reticulum calcium transport ATPases (SERCA-type calcium pumps), enzymes that accumulate calcium in the ER, play an important role in these phenomena. We report that SERCA3 expression is significantly reduced or lost in colon carcinomas when compared with normal colonic epithelial cells, which express this enzyme at a high level. To study the involvement of SERCA enzymes in differentiation, in this work differentiation of colon and gastric cancer cell lines was initiated, and the change in the expression of SERCA isoenzymes as well as intracellular calcium levels were investigated. Treatment of the tumor cells with butyrate or other established differentiation inducing agents resulted in a marked and specific induction of the expression of SERCA3, whereas the expression of the ubiquitous SERCA2 enzymes did not change significantly or was reduced. A similar marked increase in SERCA3 expression was found during spontaneous differentiation of post-confluent Caco-2 cells, and this closely correlated with the induction of other known markers of differentiation. Analysis of the expression of the SERCA3 alternative splice isoforms revealed induction of all three known iso-SERCA3 variants (3a, 3b, and 3c). Butyrate treatment of the KATO-III gastric cancer cells led to higher resting cytosolic calcium concentrations and, in accordance with the lower calcium affinity of SERCA3, to diminished ER calcium content. These data taken together indicate a defect in SERCA3 expression in colon cancers as compared with normal colonic epithelium, show that the calcium homeostasis of the endoplasmic reticulum may be remodeled during cellular differentiation, and indicate that SERCA3 constitutes an interesting new differentiation marker that may prove useful for the analysis of the phenotype of gastrointestinal adenocarcinomas.

Adenocarcinoma↗
PubMed2002

Brucella proteomes--a review.

The proteomes of selected Brucella spp. have been extensively analyzed by utilizing current proteomic technology involving 2-DE and MALDI-MS. In Brucella melitensis, more than 500 proteins were identified. The rapid and large-scale identification of proteins in this organism was accomplished by using the annotated B. melitensis genome which is now available in the GenBank. Coupled with new and powerful tools for data analysis, differentially expressed proteins were identified and categorized into several classes. A global overview of protein expression patterns emerged, thereby facilitating the simultaneous analysis of different metabolic pathways in B. melitensis. Such a global characterization would not have been possible by using time consuming and traditional biochemical approaches. The era of post-genomic technology offers new and exciting opportunities to understand the complete biology of different Brucella species.

Bacterial Proteins↗
PubMed2006

Thermodynamics of tryptophan-mediated activation of the trp RNA-binding attenuation protein.

The trp RNA-binding attenuation protein (TRAP) functions in many bacilli to control the expression of the tryptophan biosynthesis genes. Transcription of the trp operon is controlled by TRAP through an attenuation mechanism, in which competition between two alternative secondary-structural elements in the 5' leader sequence of the nascent mRNA is influenced by tryptophan-dependent binding of TRAP to the RNA. Previously, NMR studies of the undecamer (11-mer) suggested that tryptophan-dependent control of RNA binding by TRAP is accomplished through ligand-induced changes in protein dynamics. We now present further insights into this ligand-coupled event from hydrogen/deuterium (H/D) exchange analysis, differential scanning calorimetry (DSC), and isothermal titration calorimetry (ITC). Scanning calorimetry showed tryptophan dissociation to be independent of global protein unfolding, while analysis of the temperature dependence of the binding enthalpy by ITC revealed a negative heat capacity change larger than expected from surface burial, a hallmark of binding-coupled processes. Analysis of this excess heat capacity change using parameters derived from protein folding studies corresponds to the ordering of 17-24 residues per monomer of TRAP upon tryptophan binding. This result is in agreement with qualitative analysis of residue-specific broadening observed in TROSY NMR spectra of the 91 kDa oligomer. Implications for the mechanism of ligand-mediated TRAP activation through a shift in a preexisting conformational equilibrium and an induced-fit conformational change are discussed.

Allosteric Regulation↗
PubMed1984

Differentiation of human erythroid cells is associated with increased O-glycosylation of the major sialoglycoprotein, glycophorin A.

Glycophorin A, the major human erythrocyte sialoglycoprotein, is found exclusively on cells of the erythroid lineage. The amino acid sequence is known, and glycophorin A isolated from mature erythrocytes contains a single N-glycosidic and 15 O-glycosidic oligosaccharides. Monoclonal antibodies against erythrocyte glycophorin A reacted weakly with erythroid precursors while a monospecific rabbit antiserum reacted strongly with immature and mature red cells. Glycophorin A was isolated from cells representing various stages of erythropoiesis in normal bone marrow, from blood cells of neonates with erythroblastosis fetalis, and from the erythroleukemic cell lines K562 and HEL before and after induced differentiation. Analysis of the oligosaccharides showed less O-glycosylation of glycophorin A in erythroid precursors. The degree of glycosylation increased concomitantly with differentiation.

Bone Marrow Cells↗
PubMed1992

Disruption of synchrony between parasite growth and host cell division is a determinant of differentiation to the merozoite in Theileria annulata.

The multinucleated macroschizont stage of the protozoon Theileria annulata is an intracellular parasite of bovine leukocytes. The parasite induces the host cell to proliferate, and divides in synchrony with the immortalised host cell. Differentiation to the next stage occurs within the host cell culminating in the release of merozoites and destruction of the leukocyte. In this study clones of Theileria annulata macroschizont-infected cell lines were isolated by limiting dilution and tested for differentiation to the merozoite stage (merogony). Two cloned cell lines underwent differentiation with enhanced efficiency, while two others were of lower efficiency. Quantification was carried out using monoclonal antibodies, which showed that over 90% of the cells in an enhanced cloned cell line could be induced to differentiate. By carrying out induction at 41 degrees C for limited periods of time followed by culture at 37 degrees C evidence was obtained that differentiation to the merozoite is a two-step process: a preliminary reversible phase, followed by a second irreversible phase of differentiation. Analysis of the nuclear number of the macroschizont and the growth rate of the cloned cell lines showed that the ability to differentiate was associated with an increase in nuclear number (size) of the macroschizont, generated by a disruption in the synchrony between parasite growth and host cell division. We believe that these results reveal a relationship between a reduction in parasite division and differentiation, and that there are similarities between stage differentiation in parasites and cellular differentiation in higher eukaryotes.

Animals↗
PubMed2026

narrowPASEF: A Sample-Aware diaPASEF Method Optimization Strategy Improving Differential Proteomics Performance on Low-Abundance Proteins.

Recent instrumental and computational innovations in mass-spectrometry-based proteomics offer new promise in biomarker discovery, thanks to unprecedented proteome coverage and depth. Data-independent acquisition (DIA) methods are very promising in this context as they allow improved proteome coverage, reduced missing value rates, and enhanced quantification precision. However, DIA methods also suffer from their own challenges, such as increased data complexity, cycle times, and background noise. In this work, we propose a sample-aware diaPASEF method optimization strategy for a timsTOF platform. Thorough method optimizations have first been conducted on standard HeLa lysates. Then, a ground-truth calibrated sample series, consisting of a range of UPS amounts spiked into a complex Arabidopsis background, was used to mimic differential analyses under controlled conditions. These benchmark experiments demonstrate clear benefits of using narrowPASEF for differential protein discovery. Finally, our strategy was applied to real use case biological samples to conduct a differential analysis of purified mouse astrocyte cells across two different conditions. narrowPASEF improved the proteome depth by 13%, considering proteins quantified with a coefficient of variation (CV) of <20%, and led to a 68% (435 vs 729) increase in differentially expressed proteins. These results provide an opportunity for a more precise and comprehensive analysis of the biological functions of biomarkers, offering a more profound understanding of the disease mechanisms. The benefits of our sample-aware narrowPASEF strategy demonstrated the most substantial impact on low-abundance proteins. Overall, these results show promise for more valuable and robust biomarker discoveries in the future.

Proteomics↗