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Marian Hajduch

Publications and source records attributed to Marian Hajduch.

14 recordsLinked to original sources
PubMed2006

Generalization of DNA microarray dispersion properties: microarray equivalent of t-distribution.

BACKGROUND: DNA microarrays are a powerful technology that can provide a wealth of gene expression data for disease studies, drug development, and a wide scope of other investigations. Because of the large volume and inherent variability of DNA microarray data, many new statistical methods have been developed for evaluating the significance of the observed differences in gene expression. However, until now little attention has been given to the characterization of dispersion of DNA microarray data. RESULTS: Here we examine the expression data obtained from 682 Affymetrix GeneChips with 22 different types and we demonstrate that the Gaussian (normal) frequency distribution is characteristic for the variability of gene expression values. However, typically 5 to 15% of the samples deviate from normality. Furthermore, it is shown that the frequency distributions of the difference of expression in subsets of ordered, consecutive pairs of genes (consecutive samples) in pair-wise comparisons of replicate experiments are also normal. We describe a consecutive sampling method, which is employed to calculate the characteristic function approximating standard deviation and show that the standard deviation derived from the consecutive samples is equivalent to the standard deviation obtained from individual genes. Finally, we determine the boundaries of probability intervals and demonstrate that the coefficients defining the intervals are independent of sample characteristics, variability of data, laboratory conditions and type of chips. These coefficients are very closely correlated with Student's t-distribution. CONCLUSION: In this study we ascertained that the non-systematic variations possess Gaussian distribution, determined the probability intervals and demonstrated that the K(alpha) coefficients defining these intervals are invariant; these coefficients offer a convenient universal measure of dispersion of data. The fact that the K(alpha) distributions are so close to t-distribution and independent of conditions and type of arrays suggests that the quantitative data provided by Affymetrix technology give "true" representation of physical processes, involved in measurement of RNA abundance. REVIEWERS: This article was reviewed by Yoav Gilad (nominated by Doron Lancet), Sach Mukherjee (nominated by Sandrine Dudoit) and Amir Niknejad and Shmuel Friedland (nominated by Neil Smalheiser).

Journal Article↗
PubMed2006

Nonribosomal cyclic peptides: specific markers of fungal infections.

Some cyclic peptides and depsipeptides are synthesized in microorganisms by large multienzymes called nonribosomal peptide synthetases. The structures of peptide products originating in this way are complex and diverse and are microorganism-specific. This work proposes the use of fungal cyclic peptides and depsipeptides as extremely specific markers of fungal infections. Since a reliable molecular tool for diagnosing fungal infections at an early stage is still missing, we present mass spectrometry as a new, modern, broadband (with respect to fungal strain) and specific tool for clinical mycologists. More than 40 different fungal species can be rapidly characterized according to specific families of cyclic peptides, and in some cases, a particular fungal strain can be identified on the basis of its cyclopeptide profile. This paper is also aimed at initiating discussion on the biological role of these secondary metabolites, especially of those synthesized by medically important strains. Proven cytotoxic, anti-inflammatory or immunosuppressive activities of some cyclic peptides indicate that these molecules may contribute to the synergistic array of fungal virulence factors and support microbial invasion during fungal infection. In addition to an overview on recent mass spectrometric protocols for cyclic peptide sequencing, the structures of new peptides from Paecilomyces and Pseudallescheria are presented.

Biomarkers↗
PubMed2006

A duplication dup(4)(q28q35.2) de novo in a newborn.

We report here a case of a newborn with hypotrophy and somatic stigmatization: microcephaly, facial dysmorphism, heart defect and immunodeficiency syndrome. The proband's karyotype was 46,XY,dup(4)(q28q35.2) de novo with chromosomal breaks in 4% of metaphases. We demonstrate the usefulness of a combination of physical examination, classical cytogenetics, FISH and PCR techniques in order to establish correct diagnosis because of overlap of some clinical and cytogenetic features of Nijmegen breakage syndrome (NBS) and duplication 4q in our patient. Although FISH technique detected translocation t(14q;21q) in 4 metaphases, deletion 657del5 in exon 6 of the NBS1 gene associated with NBS in Slavic population was not confirmed. We compare in this report similarity of the clinical picture of our patient, NBS cases and other patients carrying a duplication of the distal part of 4q as described in the literature.

Abnormalities, Multiple↗
PubMed2005

Influence of esterification and modification of A-ring in a group of lupane acids on their cytotoxicity.

The aim of this work was to find an optimal ester group for preparation of lupane derivatives connecting high cytotoxicity with good chemical and pharmacological properties. Activities of methyl-, pivaloyloxymethyl- (Pom-), and acetoxymethyl- (Acm-) esters were compared with the activity of free acids. Although the methyl- and Pom-esters were generally less active than free acids, some Acm-esters had cytotoxicity similar to or even better than the starting compounds. Cytotoxic activity was measured in five cancer cell lines.

Carboxylic Acids↗
PubMed2005

Correlation of cytotoxic activity of betulinines and their hydroxy analogues.

This research is based on intention to prepare and test 3beta-hydroxy and 3beta,28-dihydroxy analogues of new pro-apoptotic derivatives (betulinines) using selective hydrolysis procedure and strategic protective groups. The evaluation of cytotoxicity of prepared compounds on several tumor cell lines using an MTT test was our interest. It was found that hydrolysis of acetates in betulinines afforded compounds with higher cytotoxicity in case of 18-lupene-21-ones (e.g., ethyl 3beta-hydroxy-21-oxolup-18-en-28-oate), whereas hydrolysis of the 18-lupene-21,22-diones gave less active derivatives.

Antineoplastic Agents↗
PubMed2005

Synthesis of phthalates of betulinic acid and betulin with cytotoxic activity.

Synthesis of 3beta-O-phthalic esters from betulinic acid and its esters and synthesis of phthalic esters from betulin and its monoacetates using classical acylation procedure with phthalic anhydride. The evaluation of cytotoxicity of the prepared compounds was using numbers of tumor cell lines in MTT test. It was discovered that hemiphthalic esters had better cytotoxicity than starting compounds as betulinic acid or quite inactive betulin.

Acylation↗
PubMed2005

Protein fingerprints of anti-cancer effects of cyclin-dependent kinase inhibition: identification of candidate biomarkers using 2-D liquid phase separation coupled to mass spectrometry.

The purpose of this study was to apply a recently introduced proteomic based approach to identify candidate biomarkers of the response to anticancer activity of cyclin-dependent kinase inhibitor, bohemine. Mapping of the total protein expression of CEM lymphoblastic leukemia cells following bohemine treatment was performed by 2-D liquid phase separation. Proteins were fractionated by isoelectric points in pH gradient in the first dimension and each of these pI protein fractions was further separated by hydrophobicity using non-porous silica reverse phase chromatography in the second dimension. 2-D protein expression maps of control untreated and bohemine treated cells were generated and inter-sample comparison was performed. Most of the differentially expressed proteins were present at a decreased level after bohemine treatment while there were four proteins, which were up regulated. These proteins representing candidate biomarkers of cancer cell response to the treatment were selected for identification by mass spectrometry. Our results demonstrating down regulation of three histone variants, different in their pI and hydrophobicity, in response to bohemine indicated that anti-mitotic and anti-cancer activities of this compound may be associated with epigenetic regulation at the level of chromatin structure. Furthermore, crk-like adaptor scaffolding protein represents a new important protein family affected by bohemine. This strategy is valuable for comprehensive proteomic analysis of cellular protein targets and pathways that are relevant to anticancer activity of cyclin-dependent kinase inhibition.

Animals↗
PubMed2004

Synthesis of A-seco derivatives of betulinic acid with cytotoxic activity.

In this study, the relationships between the chemical structure and cytotoxic activity of betulinic acid (1) derivatives were investigated. Eight lupane derivatives (1-8), one of them new (6), five diosphenols (9-13), four of them new (10-13), two new norderivatives (14 and 15), five seco derivatives (16-20), four of them new (16, 17, 19, and 20), and three new seco-anhydrides (21-23) were synthesized from 1, and their activities were compared with the activities of known compounds. The effects of substitution on the A-ring and esterification of the carboxyl group in position 28 on cytotoxicity were of special interest. Significant cytotoxic activity against the T-lymphoblastic leukemia cell line CEM was found in diosphenols 9 and 13 (TCS(50) 4 and 5 micromol/L) and seco-anhydrides 22 and 23 (TCS(50) 7 and 6 micromol/L). All compounds were also tested on cancer cell lines HT 29, K562, K562 Tax, and PC-3, and these confirmed activity of diosphenols 9, 10, and 11 and anhydride 22. Diosphenols, as the most promising group of derivatives, were further tested on four more lines (A 549, DU 145, MCF 7, SK-Mel2).

Antineoplastic Agents, Phytogenic↗
PubMed2004

The analysis of correlations between drug resistance and clinical/laboratory measures found in a group of children with all treated by ALL-BFM 90 protocol.

This study was designed to assess the predictive value of an MTT (3-[4,5-dimethylthiazol-2,5-diphenyl] tetrazolium bromide) in vitro assay for the evaluation of leukemic cell resistance/sensitivity to cytotoxic drugs, and to compare these results with clinical and laboratory parameters in cases of childhood acute lymphoblastic leukemia (ALL).The chemoresistance of leukemic cells was ascertained by means of an MTT assay in 32 previously untreated children with ALL. The children were treated using the protocol ALL-BFM 90. Statistical correlations were made between in vitro drug resistance to anti-cancer drugs: prednisolone (PRED), vincristine (VCR),daunorubicin (DNR), etoposide (VP-16) and cytosine arabinoside (ARA-C) and in vivo clinical and laboratory parameters: age, sex, risk factor (RF), leukocytes (WBC)and absolute number of blast cells (BC) at diagnosis (BC0), BC at day 8 (BC8), the percentage of blast cells in bone marrow at day 15 (BM15) and at day 33 (BM33),and leukocyte surface antigens CD3, CD4, CD5, CD8, CD10, CD19, CD20, HLADR.

Adolescent↗
PubMed2003

Analysis of state-specific phosphorylation of proteins by two-dimensional gel electrophoresis approach.

In this paper we focus on the detection of specific state of protein phosphorylation within a complex protein mixture separated by two-dimensional gel electrophoresis followed by immunoblotting. The availability of antibodies that specifically recognize the phosphorylated residue(s) of proteins make this approach feasible as exemplified by the study of the regulatory mechanisms of the cell cycle. The major advantage of the presented approach is its relative simplicity and sensitivity that allows specific detection of protein phosphorylation and distinguishes different phosphorylation sites of target protein. Current findings demonstrate that this method represents a reasonable alternative to the use of other tools to study protein phosphorylation.

Electrophoresis, Gel, Two-Dimensional↗
PubMed2002

Herbal composition PC-SPES for management of prostate cancer: identification of active principles.

BACKGROUND: The herbal mixture PC-SPES, used to manage advanced prostate cancer, has proven thrombogenic and highly estrogenic in clinical trials. However, attempts to identify the active compounds in PC-SPES have yielded incongruous results. Moreover, warfarin was identified in the serum of a patient taking PC-SPES who experienced a bleeding disorder. To determine the active components in PC-SPES potentially responsible for these effects, we analyzed PC-SPES lots manufactured from l996 through mid-2001. METHODS: Antineoplastic activity of PC-SPES and its individual component extracts was determined by colony-forming assays with several prostate cancer cell lines, and estrogenicity was determined by analyzing expression of an estrogen-responsive reporter gene in breast cancer cells. High-pressure liquid chromatography was used to isolate, identify, and quantify components of PC-SPES. Components were also identified by proton nuclear magnetic resonance, gas chromatography/mass spectrometry, and mass spectra analysis. RESULTS: PC-SPES lots manufactured from 1996 through mid-1999 contained the synthetic compounds indomethacin (range = 1.07-13.19 mg/g) and diethylstilbestrol (range = 107.28-159.27 micro g/g) and were two to six times more antineoplastic and up to 50 times more estrogenic than lots manufactured after the spring of 1999. In lots manufactured after mid-1999, gradual declines in the concentrations of indomethacin (from 1.56 to 0.70 mg/g), diethylstilbestrol (from 46.36 to 0.00 micro g/g), and total phytosterols (from 0.586 to 0.085 mg/g) were observed. Warfarin was identified for the first time in lots manufactured after July 1998 (range = 341-560 micro g/g). In the August 2001 lot, increases were found in concentrations of the natural products licochalcone A (from 27.6 to 289.2 micro g/g) and baicalin (from 12.5 to 38.8 mg/g). CONCLUSIONS: The phytochemical composition of PC-SPES varied by lot, and chemical analyses detected various amounts of the synthetic drugs diethylstilbestrol, indomethacin, and warfarin and several natural products. To qualify for clinical pharmacologic exploration, nutritional supplements including herbal mixtures should meet standards of quality control under the Good Manufacturing Practice system, and the manufacturers of such supplements should provide reliable analytical quality assurance.

Anti-Inflammatory Agents, Non-Steroidal↗
PubMed2002

Fluridil, a rationally designed topical agent for androgenetic alopecia: first clinical experience.

BACKGROUND: Fluridil, a novel topical antiandrogen, suppresses the human androgen receptor. While highly hydrophobic and hydrolytically degradable, it is systemically nonresorbable. In animals, fluridil demonstrated high local and general tolerance. OBJECTIVE: To evaluate the safety and efficacy of a topical anti- androgen, fluridil, in male androgenetic alopecia. METHODS: In 20 men, for 21 days, occlusive forearm patches with 2, 4, and 6% fluridil, isopropanol, and/or vaseline were applied. In 43 men with androgenetic alopecia (AGA), Norwood grade II-Va, 2% fluridil was evaluated in a double-blind, placebo-controlled study after 3 months clinically by phototrichograms, hematology, and blood chemistry including analysis for fluridil, and at 9 months by phototrichograms. RESULTS: Neither fluridil nor isopropanol showed sensitization/irritation potential, unlike vaseline. In all AGA subjects, baseline anagen/telogen counts were equal. After 3 months, the average anagen percentage did not change in placebo subjects, but increased in fluridil subjects from 76% to 85%, and at 9 months to 87%. In former placebo subjects, fluridil increased the anagen percentage after 6 months from 76% to 85%. Sexual functions, libido, hematology, and blood chemistry values were normal throughout, except that at 3 months, in the spring, serum testosterone increased within the normal range equally in placebo and fluridil groups. No fluridil or its decomposition product, BP-34, was detectable in the serum at 0, 3, or 90 days. CONCLUSION: Topical fluridil is nonirritating, nonsensitizing, nonresorbable, devoid of systemic activity, and anagen promoting after daily use in most AGA males.

Administration, Topical↗
PubMed2002

Application of proteomics in the search for novel proteins associated with the anti-cancer effect of the synthetic cyclin-dependent kinases inhibitor, bohemine.

The purpose of this study was to use the proteomics approach, which is based on high resolution two-dimensional electrophoresis coupled with multivariate correspondence analysis and mass spectrometry, to classify objectively the biochemical basis of the anti-cancer activity of the synthetic cyclin-dependent kinase inhibitor, bohemine (BOH). The changes in the cell cycle and corresponding protein composition of the A549 human lung adenocarcinoma cell line after treatment with BOH were evaluated and proteins differentially expressed in the BOH treated A549 cells, compared to the untreated A549 counterparts, were selected. Thirteen of these candidate proteins associated with the drug effects in vitro were identified by mass spectrometry. Many of these proteins fall into one of three functional categories: i) metabolic pathways (glycolysis, nucleic acid synthesis and NADPH production), ii) stress response and protein folding, and iii) cytoskeleton and exocytosis. Changes in protein expression patterns corresponded to a higher resistance of A549 lung carcinoma cells to BOH when compared to the CEM leukaemia cell line. These protein changes reflect a fine balance of the resistant versus the susceptible phenotype in response to the drug. Since BOH is a selective cyclin-dependent kinase inhibitor, changes in the protein expression pattern can be more generally associated with cell cycle regulation as evidenced by inhibition of cell cycling in A549 cells. Our conclusions further underline the importance of cell cycle control in both the cellular signalling and metabolic pathways.

Antineoplastic Agents↗