Assessment of genetic markers and glioblastoma stem-like cells in activation of dendritic cells

Glioblastoma (GBM) is the most common and aggressive intraparenchymal primary brain tumor in adults. The principal reasons for the poor outcomes of GBM are the high rates of recurrence and resistance to chemotherapy. The aim of this study was to determine the role of tailored cellular therapy for GBM with a poor prognosis and compare the activity of dendritic cells (DCs) that have encountered GBM cells. Detecting the correlations between methylation and expression of MGMT and PTEN genes and GBM cancer stem cells (CSCs) markers after co-cultures with a mononuclear cell cocktail are also aims for this study. Allogenic umbilical cord blood (UCB)-derived DCs were labeled with the CD11a and CD123 for immature DCs, and CD80 and CD11c for mature DCs. CD34, CD45, and CD56 cells were isolated from allogenic UCB for using in DCs maturation. GBM CSCs were detected with CD133/1 and CD111 antibodies after co-culture studies. DC activation was carried out via GBM cells including CD133 and CD111 cells and a mononuclear cells cocktail including CD34, CD45, and CD56 natural killer cells. Real-time PCR was performed to detect the expression and promoter methylation status of PTEN and MGMT genes. The expression of CSCs markers was found in all GBM cases, and a statistically significant correlation was found among them after co-culture studies. The most pronounced affinity of DCs to GBM cells was observed at dilutions between 1/4 and 1/256 in co-cultures. There was a statistically significant correlation between cellularity and granularity ratios for CD123 and CD11c. PTEN and MGMT gene expression and methylation values were evaluated with respect to CSCs expression and no statistical significance was found. Activation of DCs might associate with CSCs and the mononuclear cells cocktail including CD34, CD45, and CD56 cells which were obtained from allogenic UCB.     

MASH Suite Pro: A Comprehensive Software Tool for Top-Down Proteomics

Top-down mass spectrometry (MS)-based proteomics is arguably a disruptive technology for the comprehensive analysis of all proteoforms arising from genetic variation, alternative splicing, and posttranslational modifications (PTMs). However, the complexity of top-down high-resolution mass spectra presents a significant challenge for data analysis. In contrast to the well-developed software packages available for data analysis in bottom-up proteomics, the data analysis tools in top-down proteomics remain underdeveloped. Moreover, despite recent efforts to develop algorithms and tools for the deconvolution of top-down high-resolution mass spectra and the identification of proteins from complex mixtures, a multifunctional software platform, which allows for the identification, quantitation, and characterization of proteoforms with visual validation, is still lacking. Herein, we have developed MASH Suite Pro, a comprehensive software tool for top-down proteomics with multifaceted functionality. MASH Suite Pro is capable of processing high-resolution MS and tandem MS (MS/MS) data using two deconvolution algorithms to optimize protein identification results. In addition, MASH Suite Pro allows for the characterization of PTMs and sequence variations, as well as the relative quantitation of multiple proteoforms in different experimental conditions. The program also provides visualization components for validation and correction of the computational outputs. Furthermore, MASH Suite Pro facilitates data reporting and presentation via direct output of the graphics. Thus, MASH Suite Pro significantly simplifies and speeds up the interpretation of high-resolution top-down proteomics data by integrating tools for protein identification, quantitation, characterization, and visual validation into a customizable and user-friendly interface. We envision that MASH Suite Pro will play an integral role in advancing the burgeoning field of top-down proteomics.With well-developed algorithms and computational tools for mass spectrometry (MS)¹ data analysis, peptide-based bottom-up proteomics has gained considerable popularity in the field of systems biology (1–9). Nevertheless, the bottom-up approach is suboptimal for the analysis of protein posttranslational modifications (PTMs) and sequence variants as a result of protein digestion (10). Alternatively, the protein-based top-down proteomics approach analyzes intact proteins, which provides a “bird''s eye” view of all proteoforms (11), including those arising from sequence variations, alternative splicing, and diverse PTMs, making it a disruptive technology for the comprehensive analysis of proteoforms (12–24). However, the complexity of top-down high-resolution mass spectra presents a significant challenge for data analysis. In contrast to the well-developed software packages available for processing data from bottom-up proteomics experiments, the data analysis tools in top-down proteomics remain underdeveloped.The initial step in the analysis of top-down proteomics data is deconvolution of high-resolution mass and tandem mass spectra. Thorough high-resolution analysis of spectra by horn (THRASH), which was the first algorithm developed for the deconvolution of high-resolution mass spectra (25), is still widely used. THRASH automatically detects and evaluates individual isotopomer envelopes by comparing the experimental isotopomer envelope with a theoretical envelope and reporting those that score higher than a user-defined threshold. Another commonly used algorithm, MS-Deconv, utilizes a combinatorial approach to address the difficulty of grouping MS peaks from overlapping isotopomer envelopes (26). Recently, UniDec, which employs a Bayesian approach to separate mass and charge dimensions (27), can also be applied to the deconvolution of high-resolution spectra. Although these algorithms assist in data processing, unfortunately, the deconvolution results often contain a considerable amount of misassigned peaks as a consequence of the complexity of the high-resolution MS and MS/MS data generated in top-down proteomics experiments. Errors such as these can undermine the accuracy of protein identification and PTM localization and, thus, necessitate the implementation of visual components that allow for the validation and manual correction of the computational outputs.Following spectral deconvolution, a typical top-down proteomics workflow incorporates identification, quantitation, and characterization of proteoforms; however, most of the recently developed data analysis tools for top-down proteomics, including ProSightPC (28, 29), Mascot Top Down (also known as Big-Mascot) (30), MS-TopDown (31), and MS-Align+ (32), focus almost exclusively on protein identification. ProSightPC was the first software tool specifically developed for top-down protein identification. This software utilizes “shotgun annotated” databases (33) that include all possible proteoforms containing user-defined modifications. Consequently, ProSightPC is not optimized for identifying PTMs that are not defined by the user(s). Additionally, the inclusion of all possible modified forms within the database dramatically increases the size of the database and, thus, limits the search speed (32). Mascot Top Down (30) is based on standard Mascot but enables database searching using a higher mass limit for the precursor ions (up to 110 kDa), which allows for the identification of intact proteins. Protein identification using Mascot Top Down is fundamentally similar to that used in bottom-up proteomics (34), and, therefore, it is somewhat limited in terms of identifying unexpected PTMs. MS-TopDown (31) employs the spectral alignment algorithm (35), which matches the top-down tandem mass spectra to proteins in the database without prior knowledge of the PTMs. Nevertheless, MS-TopDown lacks statistical evaluation of the search results and performs slowly when searching against large databases. MS-Align+ also utilizes spectral alignment for top-down protein identification (32). It is capable of identifying unexpected PTMs and allows for efficient filtering of candidate proteins when the top-down spectra are searched against a large protein database. MS-Align+ also provides statistical evaluation for the selection of proteoform spectrum match (PrSM) with high confidence. More recently, Top-Down Mass Spectrometry Based Proteoform Identification and Characterization (TopPIC) was developed (http://proteomics.informatics.iupui.edu/software/toppic/index.html). TopPIC is an updated version of MS-Align+ with increased spectral alignment speed and reduced computing requirements. In addition, MSPathFinder, developed by Kim et al., also allows for the rapid identification of proteins from top-down tandem mass spectra (http://omics.pnl.gov/software/mspathfinder) using spectral alignment. Although software tools employing spectral alignment, such as MS-Align+ and MSPathFinder, are particularly useful for top-down protein identification, these programs operate using command line, making them difficult to use for those with limited knowledge of command syntax.Recently, new software tools have been developed for proteoform characterization (36, 37). Our group previously developed MASH Suite, a user-friendly interface for the processing, visualization, and validation of high-resolution MS and MS/MS data (36). Another software tool, ProSight Lite, developed recently by the Kelleher group (37), also allows characterization of protein PTMs. However, both of these software tools require prior knowledge of the protein sequence for the effective localization of PTMs. In addition, both software tools cannot process data from liquid chromatography (LC)-MS and LC-MS/MS experiments, which limits their usefulness in large-scale top-down proteomics. Thus, despite these recent efforts, a multifunctional software platform enabling identification, quantitation, and characterization of proteins from top-down spectra, as well as visual validation and data correction, is still lacking.Herein, we report the development of MASH Suite Pro, an integrated software platform, designed to incorporate tools for protein identification, quantitation, and characterization into a single comprehensive package for the analysis of top-down proteomics data. This program contains a user-friendly customizable interface similar to the previously developed MASH Suite (36) but also has a number of new capabilities, including the ability to handle complex proteomics datasets from LC-MS and LC-MS/MS experiments, as well as the ability to identify unknown proteins and PTMs using MS-Align+ (32). Importantly, MASH Suite Pro also provides visualization components for the validation and correction of the computational outputs, which ensures accurate and reliable deconvolution of the spectra and localization of PTMs and sequence variations.     

Levels of some trace elements and rheumatoid factor in sheep with brucellosis

Brucellosis is a zoonotic disease that is encountered in sheep rather frequently. In this study, 100 sheep diagnosed with brucellosis that had aborts and 40 healthy sheep were used as materials. Analyses for Cu, Zn, Fe, Cr, Ca, Mg, and K were performed with the atomic absorption spectrophotometric method on blood collected from vena jugularis of all the sheep and rheumatoid factor levels were determined by the nephelometry method. Although it was found that Cu, Ca, and rheumatoid factor values in the sera of the sheep with brucellosis were high when compared to the control group (p<0.001, p<0.05, p<0.001, respectively), their serum Zn values were low (p<0.05). No significant changes in serum Cr, Fe, K, and Mg levels were found.     

TNF combined with IFN-alpha accelerates NF-kappaB-mediated apoptosis through enhancement of Fas expression in colon cancer cells

Immunostaining and EMSA revealed that NF-kappaB was activated strongly by TNF/IFN-alpha compared to TNF alone in a human colon adenocarcinoma cell line, RPMI4788. Although inhibition of activated NF-kappaB, by using an NF-kappaB decoy, reduced cell viability after treatment with TNF only, NF-kappaB decoy resulted in recovery of cell viability after TNF/IFN-alpha treatment. Caspase-3 activity was increased in cells induced by TNF/IFN-alpha, while suppression of caspase-3 activity was observed in cells transfected with NF-kappaB decoy and then treated by TNF/IFN-alpha. On the other hand, Fas expression was strongly enhanced by TNF/IFN-alpha, and inhibition of TNF/IFN-alpha-induced NF-kappaB activation, by using NF-kappaB decoy, decreased Fas expression. Cell viability and caspase-3 activity decreased in cells treated with TNF/IFN-alpha and anti-FasL antibody. Taken together, our findings suggest that activated NF-kappaB induced by the crosstalk between TNF and IFN-alpha is a novel pro-apoptotic signal acting via enhancement of Fas expression.     

Medroxyprogesterone and tamoxifen augment anti-proliferative efficacy and reduce mitochondria-toxicity of epirubicin in FM3A tumor cells in vitro

We have shown that low doses of medroxyprogesterone acetate (MPA- 2.6 microM) and tamoxifen (TAM- 270 nM) could augment the effectiveness of epirubicin in breast tumor cells. In this study, we monitored early cell kinetics (24-96 h plating and S-phase) and mitochondrial morphology during chemo-endocrine treatments to delineate the epirubicin sensitizing mechanism. S-phase fractions with radioactive thymidine uptake, plating efficacy, and transmission electron microscopic analysis were taken for 24-h periods until the 7th day after drug treatments. Despite strongly enhancing the clonogenic killing, both MPA and TAM did not affect epirubicin induced early cytotoxicity. Instead, they augmented the S-phase inhibition, which was even more pronounced for TAM. Epirubicin induced prominent swelling and crista damage of mitochondria and fragmentation of nuclei. Mitochondria were a normal size during a combination of epirubicin with either MPA- or tamoxifen treatment, despite the persistence of chromatin fragmentation and strong synergism on the clonogenic killing of breast tumor cells. Low dosage endocrine agent-induced anthracycline sensitization may be independent of mitochondrial toxicity. Further studies would be worthwhile, since the uncoupling of mitochondrial toxicity from the anti-neoplastic effect may also mean obviated cardiac toxicity in clinic.     

An infantile case of Zellweger syndrome presented with Kabuki-like phenotype

Zellweger syndrome is a peroxisomal disorder resulting from the mutations in PEX genes generally presenting in the neonatal period with profound hypotonia seizures, inability to feed, liver cysts with hepatic dysfunction, chondrodysplasia punctata. Kabuki make-up syndrome is a multiple congenital anomalies and mental retardation syndrome with characteristic facial appearance, skeletal abnormalities, dermatoglyphic abnormalities, mental retardation and short stature. Abnormal liver functions and some atypical findings were also reported in some patients with Kabuki syndrome. In this report a case with late onset Zellweger syndrome who had some phenotypical findings which are also seen in Kabuki Syndrome will be presented. The inclusion of Zellweger syndrome into the differential diagnosis of the patients with Kabuki-like phenotype in addition to abnormal liver functions is emphasized.     

Two new records of Oribatula (Zygoribatula) species (Acari: Oribatida) from Turkey, with redescriptions

The oribatid mite fauna of Turkey is still relatively poorly known. The present paper adds two species of oribatid mites to the known Turkish fauna viz., Oribatula (Zygoribatula) debilitranslamellata (Kulijev, 1962) and O. (Z.) exilis (Nicolet, 1855). Both species are characterised by large, prominent lamellar cusps, with the lamellar setae inserted apically on the cusps, and by the presence of distinct translamellae. They can be distinguished, however, by the smaller lamellae, absence of cuspidal teeth, narrowly fusiform sensilli and, 13 pairs of thin, smooth, apically almost flagellate notogastral setae, in O. (Z.) debilitranslamellata, and by the wider lamellae, presence of cuspidal teeth, widely fusiform sensilli, and 14 pairs of thin, smooth notogastral setae, with seta c (1) slightly thicker and minutely barbed in O. (Z.) exilis. The following species have been previously reported from Turkey: O. (Z.) cognata (Oudemans, 1902), O. (Z.) undulata (Berlese, 1917), O. (Z.) terricola Van der Hammen, 1952, and O. (Z.) lanceolata Grobler, Bayram & Cobanoglu, 2004.