Cases of allergic coronary syndrome (Kounis syndrome) : what we should know.

Kounis syndrome (KS) is an acute coronary syndrome that occurs with allergic, hypersensitivity, anaphylactic, or anaphylactoid reactions associated with mast cell activation, and entails significant morbidity and mortality risks. We present four cases of acute coronary syndrome developing after insect bites, chemotherapy, and coronary stent implantation. Two patients were lost due to anaphylactic shock-related multiorgan failures and sudden cardiac death. Since a wide range of drugs, foods, environmental conditions, and disease states may be associated with KS, all physicians must be aware of the syndrome.

Treatment of critically ill patients with acute hypercarbic respiratory failure by average volume-assured pressure support mode.

OBJECTIVES: Average volume-assured pressure support (AVAPS), a dual mode, delivers a set tidal volume (TV) per kg by adjusting the pressure between upper and lower inspiratory positive airway pressures (IPAP). Thus, ventilation is presumed to be happened effectively by sending a guaranteed TV. This study was aimed to evaluate the effectiveness of AVAPS mode in critically ill patients with acute hypercarbic respiratory failure (HRF) and compare the results with bilevel positive airway pressure-spontaneous/timed (BPAP-S/T) mode. METHODS: Sixty patients were assigned to BPAP-S/T (n = 29) and AVAPS modes (n = 31). Maximum IPAP was started at 20 cmH2 O and minimum IPAP was set at 5 cmH2 O higher than expiratory positive airway pressure (EPAP) in AVAPS mode. IPAP was started at 15 cmH2 O in BPAP-S/T mode. IPAP levels were titrated up to 30 cmH2 O during noninvasive mechanic ventilation (NIMV) with a targeted TV of 6-8 mL/kg. Patients were followed for 5 days. RESULTS: No differences were found in pH, paCO2 , HCO3 , TV and EPAP between the two groups when compared separately by days. Maximum IPAP levels were significantly high in AVAPS mode in all times (P < 0.001). The length of stay (LOS) in intensive care unit (ICU) (P = 0.994) and hospital (P = 0.509), hours of NIMV use per day (P = 0.101) and NIMV success rate (P = 0.931) were identical between the two groups. ICU (P = 0.931), hospital (P = 0.800), 6-month (P = 0.919) and 1-year (P = 0.645) mortality rates were also not different between the both groups. CONCLUSIONS: AVAPS mode had similar efficiency with BPAP-S/T mode regarding the NIMV treatment success in critically ill patients with acute HRF.

Leptospirosis: a six-case report from west black sea, Turkey.

Leptospirosis is a ubiquitous acute bacterial zoonosis. This report describes six cases presenting to our hospital with symptoms such as fever and muscle pain and diagnosed as leptospirosis. All cases presented with fever, muscle pain, and lethargy and were engaged in activities such as farming, hunting, and fishing. Thrombocytopenia and impaired liver function tests were found in all patients, increased creatine-kinase in five, and increased creatinine in four. Leptospirosis was diagnosed using polymerase chain reaction (PCR). The course of the disease resulted in cure in three cases, chronic kidney disease sequelae in one, and death in two. In conclusion, the possibility of leptospirosis should be considered in patients presenting with non-specific symptoms such as fever and muscle pain and developing thrombocytopenia, and liver and kidney function disorder. Risk factors should also be investigated when taking histories. Early diagnosis and antibiotic therapy being started as quickly as possible are important in terms of the course of the disease.

Increased risk of genetic and epigenetic instability in human embryonic stem cells associated with specific culture conditions.

The self-renewal and differentiation capacities of human pluripotent stem cells (hPSCs) make them a promising source of material for cell transplantation therapy, drug development, and studies of cellular differentiation and development. However, the large numbers of cells necessary for many of these applications require extensive expansion of hPSC cultures, a process that has been associated with genetic and epigenetic alterations. We have performed a combinatorial study on both hESCs and hiPSCs to compare the effects of enzymatic vs. mechanical passaging, and feeder-free vs. mouse embryonic fibroblast feeder substrate, on the genetic and epigenetic stability and the phenotypic characteristics of hPSCs. In extensive experiments involving over 100 continuous passages, we observed that both enzymatic passaging and feeder-free culture were associated with genetic instability, higher rates of cell proliferation, and persistence of OCT4/POU5F1-positive cells in teratomas, with enzymatic passaging having the stronger effect. In all combinations of culture conditions except for mechanical passaging on feeder layers, we noted recurrent deletions in the genomic region containing the tumor suppressor gene TP53, which was associated with decreased mRNA expression of TP53, as well as alterations in the expression of several downstream genes consistent with a decrease in the activity of the TP53 pathway. Among the hESC cultures, we also observed culture-associated variations in global gene expression and DNA methylation. The effects of enzymatic passaging and feeder-free conditions were also observed in hiPSC cultures. Our results highlight the need for careful assessment of the effects of culture conditions on cells intended for clinical therapies.

Investigation of antitumor effects of sorafenib and lapatinib alone and in combination on MCF-7 breast cancer cells.

BACKGROUND: Breast cancer evolution and tumor progression are controlled by complex interactions between steroid receptors and growth factor receptor signaling. Aberrant growth factor receptor signaling can augment or suppress estrogen receptor function in hormone-dependent breast cancer cells. Thus, we aimed to investigate antitumor effects of sorafenib and lapatinib alone and in combination on MCF-7 breast cancer cells. MATERIALS AND METHODS: Cytotoxicity of the sorafenib and lapatinib was tested in MCF-7 cells by XTT assays. 50, 25, 12.5 and 6.25µM concentrations of sorafenib and 200, 100, 50 and 25µM concentrations of lapatinib were administered alone and in combination. Results were evaluated as absorbance at 450nM and IC50 values are calculated according to the absorbance data RESULTS: Both sorafenib and lapatinib showed concentration dependent cytotoxic effects on MCF-7 cells. Sorafenib exerted cytotoxic effects with an IC50 value of 32.0µM; in contrast with lapatinib the IC50 was 136.6µM. When sorafenib and lapatinib combined, lapatinib increased cytotoxic effects of sorafenib at its ineffective concentrations. Also at the concentrations where both drugs had cytotoxic effects, combination show strong anticancer effects and killed approximately 70 percent of breast cancer cells. CONCLUSIONS: Combinations of tyrosine kinase inhibitors and cytotoxic agents or molecular targeted therapy has been successful for many types of cancer. The present study shows that both sorafenib and lapatinib alone are effective in the treatment of breast cancer. Also a combination of these two agents may be a promising therapeutic option in treatment of breast cancer.

Recurrent variations in DNA methylation in human pluripotent stem cells and their differentiated derivatives.

Human pluripotent stem cells (hPSCs) are potential sources of cells for modeling disease and development, drug discovery, and regenerative medicine. However, it is important to identify factors that may impact the utility of hPSCs for these applications. In an unbiased analysis of 205 hPSC and 130 somatic samples, we identified hPSC-specific epigenetic and transcriptional aberrations in genes subject to X chromosome inactivation (XCI) and genomic imprinting, which were not corrected during directed differentiation. We also found that specific tissue types were distinguished by unique patterns of DNA hypomethylation, which were recapitulated by DNA demethylation during in vitro directed differentiation. Our results suggest that verification of baseline epigenetic status is critical for hPSC-based disease models in which the observed phenotype depends on proper XCI or imprinting and that tissue-specific DNA methylation patterns can be accurately modeled during directed differentiation of hPSCs, even in the presence of variations in XCI or imprinting.

Specific lectin biomarkers for isolation of human pluripotent stem cells identified through array-based glycomic analysis.

Rapid and dependable methods for isolating human pluripotent stem cell (hPSC) populations are urgently needed for quality control in basic research and in cell-based therapy applications. Using lectin arrays, we analyzed glycoproteins extracted from 26 hPSC samples and 22 differentiated cell samples, and identified a small group of lectins with distinctive binding signatures that were sufficient to distinguish hPSCs from a variety of non-pluripotent cell types. These specific biomarkers were shared by all the 12 human embryonic stem cell and the 14 human induced pluripotent stem cell samples examined, regardless of the laboratory of origin, the culture conditions, the somatic cell type reprogrammed, or the reprogramming method used. We demonstrated a practical application of specific lectin binding by detecting hPSCs within a differentiated cell population with lectin-mediated staining followed by fluorescence microscopy and flow cytometry, and by enriching and purging viable hPSCs from mixed cell populations using lectin-mediated cell separation. Global gene expression analysis showed pluripotency-associated differential expression of specific fucosyltransferases and sialyltransferases, which may underlie these differences in protein glycosylation and lectin binding. Taken together, our results show that protein glycosylation differs considerably between pluripotent and non-pluripotent cells, and demonstrate that lectins may be used as biomarkers to monitor pluripotency in stem cell populations and for removal of viable hPSCs from mixed cell populations.

A bioinformatic assay for pluripotency in human cells.

Pluripotent stem cells (PSCs) are defined by their potential to generate all cell types of an organism. The standard assay for pluripotency of mouse PSCs is cell transmission through the germline, but for human PSCs researchers depend on indirect methods such as differentiation into teratomas in immunodeficient mice. Here we report PluriTest, a robust open-access bioinformatic assay of pluripotency in human cells based on their gene expression profiles.

Equivalence of conventionally-derived and parthenote-derived human embryonic stem cells.

BACKGROUND: As human embryonic stem cell (hESC) lines can be derived via multiple means, it is important to determine particular characteristics of individual lines that may dictate the applications to which they are best suited. The objective of this work was to determine points of equivalence and differences between conventionally-derived hESC and parthenote-derived hESC lines (phESC) in the undifferentiated state and during neural differentiation. METHODOLOGY/PRINCIPAL FINDINGS: hESC and phESC were exposed to the same expansion conditions and subsequent neural and retinal pigmented epithelium (RPE) differentiation protocols. Growth rates and gross morphology were recorded during expansion. RTPCR for developmentally relevant genes and global DNA methylation profiling were used to compare gene expression and epigenetic characteristics. Parthenote lines proliferated more slowly than conventional hESC lines and yielded lower quantities of less mature differentiated cells in a neural progenitor cell (NPC) differentiation protocol. However, the cell lines performed similarly in a RPE differentiation protocol. The DNA methylation analysis showed similar general profiles, but the two cell types differed in methylation of imprinted genes. There were no major differences in gene expression between the lines before differentiation, but when differentiated into NPCs, the two cell types differed in expression of extracellular matrix (ECM) genes. CONCLUSIONS/SIGNIFICANCE: These data show that hESC and phESC are similar in the undifferentiated state, and both cell types are capable of differentiation along neural lineages. The differences between the cell types, in proliferation and extent of differentiation, may be linked, in part, to the observed differences in ECM synthesis and methylation of imprinted genes.

Friedreich's ataxia induced pluripotent stem cells model intergenerational GAA⋠TTC triplet repeat instability.

The inherited neurodegenerative disease Friedreich's ataxia (FRDA) is caused by GAA⋅TTC triplet repeat hyperexpansions within the first intron of the FXN gene, encoding the mitochondrial protein frataxin. Long GAA⋅TTC repeats cause heterochromatin-mediated gene silencing and loss of frataxin in affected individuals. We report the derivation of induced pluripotent stem cells (iPSCs) from FRDA patient fibroblasts by transcription factor reprogramming. FXN gene repression is maintained in the iPSCs, as are the global gene expression signatures reflecting the human disease. GAA⋅TTC repeats uniquely in FXN in the iPSCs exhibit repeat instability similar to patient families, where they expand and/or contract with discrete changes in length between generations. The mismatch repair enzyme MSH2, implicated in repeat instability in other triplet repeat diseases, is highly expressed in pluripotent cells and occupies FXN intron 1, and shRNA silencing of MSH2 impedes repeat expansion, providing a possible molecular explanation for repeat expansion in FRDA.

DNA methylation in embryonic stem cells.

Embryonic stem cells (ESCs) are pluripotent, self-renewing cells. These cells can be used in applications such as cell therapy, drug development, disease modeling, and the study of cellular differentiation. Investigating the interplay of epigenetics, genetics, and gene expression in control of pluripotence and differentiation could give important insights on how these cells function. One of the best known epigenetic factors is DNA methylation, which is a major mechanism for regulation of gene expression. This phenomenon is mostly seen in imprinted genes and X-chromosome inactivation where DNA methylation of promoter regions leads to repression of gene expression. Differential DNA methylation of pluripotence-associated genes such as Nanog and Oct4/Pou5f1 has been observed between pluripotent and differentiated cells. It is clear that tight regulation of DNA methylation is necessary for normal development. As more associations between aberrant DNA methylation and disease are reported, the demand for high-throughput approaches for DNA methylation analysis has increased. In this article, we highlight these methods and discuss recent DNA methylation studies on ESCs.

A new seed selection algorithm that maximizes local structural similarity in proteins.

The PHI-BLAST algorithm for protein sequence alignment takes a query sequence and searches a protein database for a small seed or region of high similarity and extends this alignment to produce the total alignment for sequences. Clearly, the success of this approach depends on the quality of the seeds. We propose an algorithm that maximizes the likelihood of seeds sharing the same local structure in both the query and known sequences. This was tested on the 2290 protein sequences in the PISCES database. Our new algorithm results in an effective a priori estimate of seed structural quality.

Improved K-means clustering algorithm for exploring local protein sequence motifs representing common structural property.

Information about local protein sequence motifs is very important to the analysis of biologically significant conserved regions of protein sequences. These conserved regions can potentially determine the diverse conformation and activities of proteins. In this work, recurring sequence motifs of proteins are explored with an improved K-means clustering algorithm on a new dataset. The structural similarity of these recurring sequence clusters to produce sequence motifs is studied in order to evaluate the relationship between sequence motifs and their structures. To the best of our knowledge, the dataset used by our research is the most updated dataset among similar studies for sequence motifs. A new greedy initialization method for the K-means algorithm is proposed to improve traditional K-means clustering techniques. The new initialization method tries to choose suitable initial points, which are well separated and have the potential to form high-quality clusters. Our experiments indicate that the improved K-means algorithm satisfactorily increases the percentage of sequence segments belonging to clusters with high structural similarity. Careful comparison of sequence motifs obtained by the improved and traditional algorithms also suggests that the improved K-means clustering algorithm may discover some relatively weak and subtle sequence motifs, which are undetectable by the traditional K-means algorithms. Many biochemical tests reported in the literature show that these sequence motifs are biologically meaningful. Experimental results also indicate that the improved K-means algorithm generates more detailed sequence motifs representing common structures than previous research. Furthermore, these motifs are universally conserved sequence patterns across protein families, overcoming some weak points of other popular sequence motifs. The satisfactory result of the experiment suggests that this new K-means algorithm may be applied to other areas of bioinformatics research in order to explore the underlying relationships between data samples more effectively.

Parallel protein secondary structure prediction based on neural networks.

Protein secondary structure prediction has a fundamental influence on today's bioinformatics research. In this work, binary and tertiary classifiers of protein secondary structure prediction are implemented on Denoeux belief neural network (DBNN) architecture. Hydrophobicity matrix, orthogonal matrix, BLOSUM62 and PSSM (position specific scoring matrix) are experimented separately as the encoding schemes for DBNN. The experimental results contribute to the design of new encoding schemes. New binary classifier for Helix versus not Helix ( approximately H) for DBNN produces prediction accuracy of 87% when PSSM is used for the input profile. The performance of DBNN binary classifier is comparable to other best prediction methods. The good test results for binary classifiers open a new approach for protein structure prediction with neural networks. Due to the time consuming task of training the neural networks, Pthread and OpenMP are employed to parallelize DBNN in the hyperthreading enabled Intel architecture. Speedup for 16 Pthreads is 4.9 and speedup for 16 OpenMP threads is 4 in the 4 processors shared memory architecture. Both speedup performance of OpenMP and Pthread is superior to that of other research. With the new parallel training algorithm, thousands of amino acids can be processed in reasonable amount of time. Our research also shows that hyperthreading technology for Intel architecture is efficient for parallel biological algorithms.