Heat Map Clustering Analysis Research Articles

Volatile Profile of Sparkling Wines Produced with the Addition of Mannoproteins or Lees before Second Fermentation Performed with Free and Immobilized Yeasts

Heat map and hierarchical cluster analysis showed that sparkling wines produced with immobilized yeasts contained mostly higher levels of compounds that impart positive notes to wines. Fisher ratio pointed out nine volatile compounds as the main components responsible for differentiation of samples treated with mannoproteins/lees and others. Principal component analysis (PCA) showed differences between the sparkling wines produced with and without adjuvants (commercial mannoproteins or lees). Sparkling wines aged without adjuvants presented higher levels of decanoic and dodecanoic acids (fatty/metallic aroma), while the use of mannoproteins or lees resulted in higher content of some fruity esters, nerolidol and β-damascenone. Therefore, the combination of immobilized yeast and aging on mannoproteins or lees seems to be the most promising treatment to obtain the volatile profile that positively influence wine quality.

Vitamin D (FokI) Receptor Gene Polymorphism is associated with Vitamin D Deficiency and Chronic Musculoskeletal Pain. A meta-analysis.

Background: Musculoskeletal pain is the most common chronic pain experienced by older adults. The aim of this study is to explore the associations between vitamin D (FOKI) receptor gene polymorphism (VDR) and vitamin D deficiency (VDD) and chronic musculoskeletal pain. Methods: Cross-sectional studies published in English from January 2000 to January 2015which reported prevalence of chronic pain (CP) and chronic musculoskeletal pain (CMP) were included in this systematic review and meta-analysis. A heat map was used to visualize and observe the correlation between VDR and CMP, CP and VDD. Results: 20 studies (N = 216,365) were included in the analysis, which showed an overall pooled prevalence estimate of CMP and CP as 30.6 per 100 (95 % CI: 30.59, 30.69) and 27.9 per 100 (95 % CI: 27.68, 28.24) respectively. The heat map clustering analysis visualizes the similarity between CP and CMP. Moreover, a direct correlation was observed between the three disease conditions (namely CMP, CP, and VDD) and FokI VDR polymorphism (FF). Spearman's correlation analyses with adjusted r2 revealed that there is a statistically significant interaction effect of the FF genotype and VDD on CMP (r2 = 0.19, p = 0.03), a marginally significant interaction effect of the ff genotype and VDD on CMP (r2 = 0.11, p = 0.08). VDD was also associated with increased CMP (r2 = 0.19, p = 0.028). The pooled estimates of the prevalence of CMP in this review were found to be high. Conclusion: FokI VDR gene polymorphism (FF) plays an important role in the relationship between VDD and CMP.

Reconstruction of microbial community structures as evidences for soil redox coupled reductive dechlorination of PCP in a mangrove soil

The aim was to investigate the influence of pentachlorophenol (PCP) on the soil microbial communities and the coupled mechanism between PCP reductive dechlorination and soil redox under anaerobic condition. Accordingly, a slurry incubation experiment was carried out in which bacterial and archaeal communities were detected by MiSeq amplicon sequencing. The original microbial community balance was gradually disrupted and new microbial structure was reconstructed subsequently through self-regulation and acclimation during PCP transformation, coupling with the changes of soil biogeochemical redox dynamics. The phylum Bacteroidetes predominated during the earlier PCP dechlorination period and then was progressively replaced by Proteobacteria and Firmicutes groups when PCP was mostly transformed into 2,3,4,5-TeCP and 3,4,5-TCP. Heatmap and hierarchical cluster analysis revealed the Clostridium-like, Geobacter-like and Dehalococcoides-like organisms enriched concurrently during PCP reductive dechlorination processes. The relative abundance changes of the redox-active microorganisms, together with their relevance to the corresponding biogeochemical redox processes, showed that PCP dechlorination, Fe(III) and SO42− reduction, as well as methanogenesis were coupled terminal electron accepting processes. The combined analysis of the microbial function, the affinity for substrates (H2 and acetate) and the sensitivity for PCP toxicity by microorganisms might explain why electron transport chain has changed in soil biogeochemical redox process. Our study offers a comprehensive description of the impact of PCP on the soil microbial community structures, which could be very useful for understanding the regulation of soil nutrient and energy transfer during biogeochemical cycling processes in soils with significant inputs of exogenous pollutants.

Improved Representation of Biological Information by Using Correlation as Distance Function for Heatmap Cluster Analysis

Heatmap cluster figures are often used to represent data sets in the omic sciences. The default option of the frequently used R heatmap function is to cluster data according to Euclidean distance, which groups data mainly to their numerical value and not to its relative behaviour. The disadvantage of using the default clustering dendrograms of R is demonstrated. Instead, a script is provided that uses correlation as distance function, which better reveals biologically meaningful information. This optimized script was used to detect heterotic groups in Vitamaize hybrids (purple maize with high nutraceutical value). A field trial with different genetic combinations was performed through an agricultural phenomics approach (holistic evaluation of the phenotype). The grain yield data and other phenotypic variables were represented through heatmap figures. In the data set of Mexican tropical maize germplasm, at least three heterotic groups were detected, in contrast to only two heterotic groups reported earlier in temperate yellow maize from USA and Europe. This optimized script for heatmap correlation bicluster can also be used to better represent metabolomic fingerprints and transcriptomic data sets.

Microbiological study on bioremediation of 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) contaminated soil by agricultural waste composting.

This paper studied the degradation of 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) in contaminated soil under composting and natural conditions, respectively. BDE-47 residue in agricultural waste-composting pile was determined during 45-day composting. The microbial communities were determined by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), and the relationships between the DGGE results and physico-chemical parameters were evaluated by redundancy analysis (RDA) and heatmap-clustering analysis. The results showed that the degradation rate of BDE-47 was significantly higher in agricultural waste-composting pile compared with control group, which was enhanced up to almost 15% at the end of composting. There were different environmental factors which affected the distribution of composting bacterial and fungal communities. The bacterial community composition was more significantly affected by the addition of BDE-47 compared with other physico-chemical parameters, and BDE-47 had stronger influences on bacterial community than fungal community during the composting. Meanwhile, the most variation in distribution of fungal community was explained by pile temperature.

Simultaneous analysis of multiple neurotransmitters by hydrophilic interaction liquid chromatography coupled to tandem mass spectrometry

Neurotransmitters are endogenous metabolites that allow the signal transmission across neuronal synapses. Their biological role is crucial for many physiological functions and their levels can be changed by several diseases. Because of their high polarity, hydrophilic interaction liquid chromatography (HILIC) is a promising tool for neurotransmitter analysis. Due to the large number of HILIC stationary phases available, an evaluation of the column performances and retention behaviors has been performed on five different commercial HILIC packing materials (silica, amino, amide and two zwitterionic stationary phases). Several parameters like the linear correlation between retention and the distribution coefficient (logD), the separation factor k and the column resolution Rs have been investigated and the column performances have been visualized with a heat map and hierarchical clustering analysis. An optimized and validated HILIC-MS/MS method based on the ZIC-cHILIC column is proposed for the simultaneous detection and quantification of twenty compounds consisting of neurotransmitters, precursors and metabolites: 3-methoxytyramine (3-MT), 5-hydroxyindoleacetic acid (5-HIAA), 5-hydroxy-L-tripthophan, acetylcholine, choline, L-3,4-dihydroxyphenylalanine (L-DOPA), dopamine, epinephrine, γ-aminobutyric acid (GABA), glutamate, glutamine, histamine, histidine, L-tryptophan, L-tyrosine, norepinephrine, normetanephrine, phenylalanine, serotonin and tyramine. The method was applied to neuronal metabolite profiling of the central nervous system of the freshwater snail Lymnaea stagnalis. This method is suitable to explore neuronal metabolism and its alteration in different biological matrices.

Differential expression of extracellular matrix and growth factors by embryoid bodies in hydrodynamic and static cultures.

During development, cell fate specification and tissue development are orchestrated by the sequential presentation of soluble growth factors (GF) and extracellular matrix (ECM) molecules. Similarly, differentiation of stem cells in vitro relies upon the temporal presence of extracellular cues within the microenvironment. Hydrodynamic culture systems are not limited by volume restrictions and therefore offer several practical advantages for scalability over static cultures; however, hydrodynamic cultures expose cells to physical parameters not present in static culture, such as fluid shear stress and mass transfer through convective forces. In this study, the differences between static and hydrodynamic culture conditions on the expression of ECM and GF molecules during the differentiation of mouse embryonic stem cells were examined at both the gene and protein level. The expression of ECM and GF genes exhibited an early decrease in static cultures based on heat map and hierarchical clustering analysis and a relative delayed increase in hydrodynamic cultures. Although the temporal patterns of specific ECM and GF protein expression were comparable between static and hydrodynamic cultures, several notable differences in the magnitudes of expression were observed at similar time points. These results describe the establishment of an analytical framework that can be used to examine the expression patterns of ECM and GF molecules expressed by pluripotent stem cells undergoing differentiation as 3D multicellular aggregates under different culture conditions, and suggest that physical parameters of stem cell microenvironments can alter endogenous ECM and GF expression profiles that may, in turn, influence cell fate decisions.

Abstract 409: In vitro and in vivo characterization of protein biomarkers of metastasis in melanoma.

Abstract Metastasis is a major cause of death in cancer patients. We report here the use of a multiplex proteomic analysis approach to in vitro and in vivo identify biomarkers involved in melanoma invasion/metastasis. An in vitro quantitative profile of the secretome (>200 proteins) was done on non-metastatic melanoma cell lines (A375, LH, M14, DM.6, Lox, and WUmel19) and their metastatic RhoC-expressing counterparts (A375-RhoC, LH-RhoC, M14-RhoC, DM.6-RhoC, Lox-RhoC, and WUmel19-RhoC). A heat map cluster analysis was performed to characterize protein expression levels on metastatic vs. the non-metastatic melanoma cells and identify secreted markers with significantly altered expression that may be involved in tumor invasion, angiogenesis, and metastasis. An in vivo characterization, using an animal model of human melanoma pulmonary metastasis, has identified differential expression of tissue and circulating protein biomarkers in tumor and sera, respectively. Moreover, use of species-specific assays has allowed us to dissect the contribution of stroma (mouse) and tumor (human). Increased expression of a panel of markers, including IL-8, PLGF, FGF-2, follistatin, MMP-1, MMP-9, TIMP-1, TIMP-2, GDF15, NSE, OPN, and MIF was detected in vivo in both tumor and sera, indicating their roles in inducing angiogenesis, tumor invasion and metastasis. Cell signaling pathway multiplex analyses revealed the activation of PI3K/mTOR pathway in the tumor. Elevated levels of phosphorylated targets of PI3K/mTOR pathway, p70S6K (pT412), GSK3α (pS21), GSK3β (pS9), RPS6 (pS235/236), TSC2 (pS939) and mTOR (pS2448) were detected in the pulmonary tumor metastasis. Hence this human melanoma pulmonary metastasis model may prove to be a useful animal model for studying the actions of PI3K/mTOR inhibitors in melanoma metastasis. Altogether, these in vitro and in vivo studies using multiplex proteomic analysis may assist in the discovery of biomarkers and therapeutic targets for human melanoma interventions. Citation Format: Wen-Rong Lie, Michelle Becker-Hapak, Megan Chan, James Graham, Jehangir Mistry, Gerald Linette, Beatriz Carreno. In vitro and in vivo characterization of protein biomarkers of metastasis in melanoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 409. doi:10.1158/1538-7445.AM2013-409

Genome-wide Analysis of Aberrant DNA Methylation for Identification of Potential Biomarkers in Colorectal Cancer Patients

Colorectal cancer is one of the leading causes of mortality worldwide. Genome wide analysis studies have identified sequence mutations causing loss-of-function that are associated with disease occurrence and severity. Epigenetic modifications, such DNA methylation, have also been implicated in many cancers but have yet to be examined in the East Asian population of colorectal cancer patients. Biopsies of tumors and matched non-cancerous tissue types were obtained and genomic DNA was isolated and subjected to the bisulphite conversion method for comparative DNA methylation analysis on the Illumina Infinium HumanMethylation27 BeadChip. Totals of 258 and 74 genes were found to be hyper- and hypo-methylated as compared to the individual's matched control tissue. Interestingly, three genes that exhibited hypermethylation in their promoter regions, CMTM2, ECRG4, and SH3GL3, were shown to be significantly associated with colorectal cancer in previous studies. Using heatmap cluster analysis, eight hypermethylated and 10 hypomethylated genes were identified as significantly differentially methylated genes in the tumour tissues. Genome-wide methylation profiling facilitates rapid and simultaneous analysis of cancerous cells which may help to identify methylation markers with high sensitivity and specificity for diagnosis and prognosis. Our results show the promise of the microarray technology in identification of potential methylation biomarkers for colorectal cancers.

Genomewide DNA Methylation Analysis Reveals Specific Signatures in Childhood B-Lymphoblastic Leukemias,

Abstract 3476Childhood B-cell acute lymphoblastic leukemias (B-ALL) arise from diverse genetic events. Gene dysregulation through abnormal DNA methylation is also believed to play an important role in the tumorigenesis of B-ALL but has not been thoroughly investigated in a large set yet.We performed a genome-wide methylation analysis for 238 childhood B-ALL patients, including 77 hyperdiploid and 64 t(12;21)(p13;q22) [ETV6/RUNX1–fusion] patients, using the Infinium HD450 Methylation array (Illumina). The methylation profile was compared with that of 24 normal precursor B-cell samples, including pro-B, pre-B-I, pre-B-II and immature B cells, which were obtained from 8 normal fetuses and separated by flow cytometry using a panel of antibodies targeting the CD antigens 3/13/19/33/34/56, and IgM antibodies. A total of 3,641 CpGs in 1,953 genes, including 1,007 polycomb target genes, were differently methylated in B-ALL compared to normal precursor B-cells (at a P value below 1.0×10−4; beta difference>0.5). The Ingenuity Pathway Analysis System demonstrated that genes involve in the G-protein coupled receptor signaling are significantly demethylated or hypermethylated (P=8.7×10−6), followed by genes in antigen presentation, B-cell development, cyclic adenosine monophosphate (cAMP)-mediated signaling, and calcium-induced T-lymphocyte apoptosis pathways (P=6.1×10−5, 6.1×10−5, 1.0×10−4, and 1.2×10−3, respectively). Gene Set Enrichment Analysis revealed that genes containing motifs for SP1, LEF1, MAZ, TCF3, MLLT7, NFAT, ETS2, MYOD1, FOXA1, and VSX1 molecules were significantly enriched (P<1.0×10−16).Hyperdiploid patients had 37 significantly hypermethylated and 70 significantly demethylated genes compared to ETV6/RUNX1–fusion patients (at a P value below 1.0×10−4; beta difference>0.5). Many of those genes were involved in the molecular mechanism of cancer (P=6.9×10−5), with several genes showing large differences in methylation status between hyperdiploid and ETV6/RUNX1. Heatmap generation and clustering analysis identified a demethlyation cluster and a hypermethylation cluster specific for hyperdiploid, and a demethylation cluster for ETV6/RUNX1. In addition, we discovered evidence of a highly variable CpG cluster, by which each cytogenetics group could be divided into two separate subgroups. Some genes in the cluster are previously shown to have an important role in hematopoiesis. An integrative analysis using the preexisting expression database for B-ALL identified that differences in methylation beta values between hyperdiploid and ETV6/RUNX1 generally have an inverse correlation with differences in expression levels. By filtering both methylation and expression data, we could identify several genes that may potentially attribute to the biological difference between hyperdiploid and ETV6/RUNX1.These data indicate that numerous genes are aberrantly hypermethylated or demethylated in B-ALL, with changes in some genes having a significant impact on the leukemogenesis as well as on the biologic differences in each B-ALL subgroup. Heterogeneity in methylation profile also appears to be present even within a well-established cytogenetics group. Disclosures:No relevant conflicts of interest to declare.