Two-way Hierarchical Clustering Research Articles

Phenotypic tendency of achene yield and oil contents in sunflower hybrids

ABSTRACTThe knowledge about heterosis breeding of achene yield in sunflower is known; however, dissection of the genetic components of achene yield and seed quality traits is limited. Therefore, the prescribe study was conducted using Line × Tester design to determine combining abilities, and about the maternal-and-paternal gene actions involved in achene yield and seed quality traits in 21 single cross hybrids. Significant mean differences for achene yield and seed quality traits were observed, with total attributed variation (R2 = 0.89). Principal component analysis (P < 0.05) explained 92.6% variation and using factor analysis, we found factor 1 had primary variables (AW, AL, AT, HD, PH, PC, LA and OC) contributed 35.6% variation to achene yield. Combining ability analysis showed the positive general combining ability for E%, HD, PH, 100 AW and AYP in parental inbred lines, whilst, hybrids had positive specific combining ability for E%, HD, PH, 100 AW, DTF, DTM, OA, LA, OC and AYP. Females contributed significantly higher (P < 0.05) for AYP, E%, HD, NWPH, PH, 100 AW, LA and OA than that of males. Two-way hierarchical clustering showed the most promising hybrid H5 (A-18 × G-79) in Cluster V. The hybrid H5 also showed heterosis, heterobeltosis and commercial heterosis, therefore, genetic exploitation of H5 is highly desirable in future breeding to map QTLs/genes in arid/semi-arid zones and /or similar growing conditions to boost up yield and seed quality traits.

Clinical, microbiologic, and immunologic determinants of mortality in hospitalized patients with HIV-associated tuberculosis: A prospective cohort study.

BackgroundIn high-burden settings, case fatality rates are reported to be between 11% and 32% in hospitalized patients with HIV-associated tuberculosis, yet the underlying causes of mortality remain poorly characterized. Understanding causes of mortality could inform the development of novel management strategies to improve survival. We aimed to assess clinical and microbiologic determinants of mortality and to characterize the pathophysiological processes underlying death by evaluating host soluble inflammatory mediators and determined the relationship between these mediators and death as well as biomarkers of disseminated tuberculosis.Methods and findingsAdult patients with HIV hospitalized with a new diagnosis of HIV-associated tuberculosis were enrolled in Cape Town between 2014 and 2016. Detailed tuberculosis diagnostic testing was performed. Biomarkers of tuberculosis dissemination and host soluble inflammatory mediators at baseline were assessed. Of 682 enrolled participants, 576 with tuberculosis (487/576, 84.5% microbiologically confirmed) were included in analyses. The median age was 37 years (IQR = 31–43), 51.2% were female, and the patients had advanced HIV with a median cluster of differentiation 4 (CD4) count of 58 cells/L (IQR = 21–120) and a median HIV viral load of 5.1 log10 copies/mL (IQR = 3.3–5.7). Antituberculosis therapy was initiated in 566/576 (98.3%) and 487/576 (84.5%) started therapy within 48 hours of enrolment. Twelve-week mortality was 124/576 (21.5%), with 46/124 (37.1%) deaths occurring within 7 days of enrolment. Clinical and microbiologic determinants of mortality included disseminated tuberculosis (positive urine lipoarabinomannan [LAM], urine Xpert MTB/RIF, or tuberculosis blood culture in 79.6% of deaths versus 60.7% of survivors, p = 0.001), sepsis syndrome (high lactate in 50.8% of deaths versus 28.9% of survivors, p < 0.001), and rifampicin-resistant tuberculosis (16.9% of deaths versus 7.2% of survivors, p = 0.002). Using non-supervised two-way hierarchical cluster and principal components analyses, we describe an immune profile dominated by mediators of the innate immune system and chemotactic signaling (interleukin-1 receptor antagonist [IL-1Ra], IL-6, IL-8, macrophage inflammatory protein-1 beta [MIP-1β]/C-C motif chemokine ligand 4 [CCL4], interferon gamma-induced protein-10 [IP-10]/C-X-C motif chemokine ligand 10 [CXCL10], MIP-1 alpha [MIP-1α]/CCL3), which segregated participants who died from those who survived. This immune profile was associated with mortality in a Cox proportional hazards model (adjusted hazard ratio [aHR] = 2.2, 95%CI = 1.9–2.7, p < 0.001) and with detection of biomarkers of disseminated tuberculosis. Clinicians attributing causes of death identified tuberculosis as a cause or one of the major causes of death in 89.5% of cases. We did not perform longitudinal sampling and did not have autopsy-confirmed causes of death.ConclusionsIn this study, we did not identify a major contribution from coinfections to these deaths. Disseminated tuberculosis, sepsis syndrome, and rifampicin resistance were associated with mortality. An immune profile dominated by mediators of the innate immune system and chemotactic signaling was associated with both tuberculosis dissemination and mortality. These findings provide pathophysiologic insights into underlying causes of mortality and could be used to inform the development of novel treatment strategies and to develop methods to risk stratify patients to appropriately target novel interventions. Causal relationships cannot be established from this study.

HTLV-1-associated genes as potential biomarkers for endometrial cancer.

Endometrial carcinoma (EC) is a malignant neoplasm of the endometrial epithelium, which may be diagnosed by pathological investigations. The aim of the current study was to identify new markers for the diagnosis of EC using machine learning. The association between human T cell lymphotropic virus type 1 (HTLV-1) infection and endometrial cancer risk have not been widely reported. It remains ambiguous whether HTLV-1 infection is associated with several types of cancer. The present study investigated the association between HTLV-1 infection-associated genes and EC risk. RNA sequencing uterine cancer expression data were downloaded from The Cancer Genome Atlas (TCGA) database. Differentially expressed genes (DEGs) were identified between normal and matched tumor samples. A total of 41 genes were selected by an overlap between HTLV-1 infection pathway-associated genes and the DEGs. Two-way hierarchical clustering analysis (HCA) and a support vector machine (SVM) classifier were constructed using the 41 genes. The accuracy of the candidate genes in risk-stratifying the samples was 100%. The accuracy of the proposed SVM model was 100%. In addition, the classification power of the SVM model was validated using a merged dataset (TCGA and the Genotype-Tissue Expression project). This predictive feature achieved reliable outcomes with risk-stratifying samples of almost 99% in two-way HCA, and an accuracy yield of 98% of the SVM classifier. In conclusion, the 41 genes identified in the current study may be implicated in the development of EC and may be of prognostic value for the disease. The results obtained the current study suggest that HTLV-1 may be potentially associated with EC and highlight potential disease mechanisms.

Immunophenotyping Using Targeted RNA NGS Recapitulates Traditional AML and CLL FLOW Fingerprints

IntroductionFlow cytometry is the gold standard for diagnosing hematologic cancers based on morphologic detection and analysis of a few expensive and delicate immunological markers. On the other hand, targeted RNA sequencing panels are not sample or marker limited; in fact, 50ng of RNA stored for up to 6 months could yield results for thousands of markers. We hypothesized that an RNA-Seq-based targeted immuno-oncology gene expression panel could recapitulate the FLOW diagnostic patterns of AML and CLL routinely used in a clinical laboratory.MethodsA custom panel of 2207 genes was constructed including 58 typical FLOW markers and well-referenced immune and oncology markers. Housekeeping genes were added to normalize between batches. A total of 52 CLL, 15 AML, and 20 normal clinical samples were tested in parallel with a clinically validated leukemia/lymphoma flow cytometry panel and targeted RNA-Seq. Paired-end 76 x 76 cycles sequencing was performed using Illumina NextSeq. Bowtie analysis suite was performed to determine gene expression. Unsupervised analysis was first performed to identify patterns associated with clinical diagnosis or sequencing artifacts. Two-way hierarchical clustering of genes having a median expression of >1 fpkm and at least 2 fold differential expression than the median in 10% of the samples revealed a strong CLL profile and a less pervasive AML profile without any supervised analysis. To determine which genes in the profiles were significantly associated with AML or CLL, genes with >5 fold differential expression were assessed after Benjamini-Hochberg correction with single tailed T-tests. Further, each FLOW marker was individually tested using a 1-way ANOVA. Pathway analysis was performed on GO terms using the Fischer exact test. All corrected p-values <0.05 were considered significant.ResultsIn general, the FLOW marker gene expression data highly correlated with protein marker expression and was adequate for rendering proper diagnosis. Overall, CLL had a strong immune-oncology pattern with 10+ flow markers including CD19, CD5, CD2, CD200, CD22, CD79, FCER2, IL3RA, IL2RA, PDCD1, and MS4A1 significantly associated with CLL. In addition, 295 other genes including immune targets like CD74, CD33, CD34, CD48, CD40, and gene targets like PAX5, BCL2, PARP3 further help classify CLL. Forty-three of these genes are involved in immune response pathway (p<1.9x10-17). In contrast, two markers used for FLOW (CD34 and CD52) could classify AML with RNA, and 218 other genes including immune (CD3E/G, CD23, CD48, CD6, CD33) and molecular markers (HOXA10, HOXA9, and TGFBR2) could be used to further classify AML. Interestingly, these genes were significantly enriched for T cell co-stimulation (p<2.0x10-18) and other T cell receptor signaling pathways. To determine whether other immune genes may be used to differentiate CLL or AML, hierarchical clustering of the top 200 genes significantly expressed in either CLL or AML was performed. We could clearly identify two clusters of genes which characterize CLL from other disease types: 1) 110 genes which were highly expressed in CLL, but expressed at low levels in both normal and AML samples, 2) 28 genes with low expression in CLL, but highly expressed in both normal and AML samples. Conversely, few genes were able to characterize AML from normal or CLL samples, including BMP1, NPM2, and FLT3, which were highly expressed in AML samples, but were expressed at low levels in both normal and CLL samples.ConclusionBased on our preliminary study, we have shown that protein marker expression determined by flow are reproduced by our RNA expression panel. Importantly, we are able to classify and diagnose CLL and AML samples based on their RNA expression profiles. DisclosuresWong:NeoGenomics: Employment. Funari:NeoGenomics: Employment.

The Cancer Prevention Project of Philadelphia: preliminary findings examining diversity among the African diaspora

ABSTRACT Objective: Cancer mortality inequity among persons of African Ancestry is remarkable. Yet, Black inclusion in cancer biology research is sorely lacking and warrants urgent attention. Epidemiologic research linking African Ancestry and the African Diaspora to disease susceptibility and outcomes is critical for understanding the significant and troubling health disparities among Blacks. Therefore, in a cohort of diverse Blacks, this study examined differences in genetic ancestry informative markers (AIMs) in the DNA repair pathway and the cancer related biomarker 4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL). Methods: Participants completed a questionnaire and provided bio-specimens. AIMs in or around DNA repair pathway genes were analyzed to assess differences in minor allele frequency (MAF) across the 3 ethnic subgroups. NNAL concentration in urine was measured among current smokers. Results: To date the cohort includes 852 participants, 88.3% being Black. Of the 752 Blacks, 51.3% were US-born, 27.8% were Caribbean-born, and 19.6% were Africa-born. Current and former smokers represented 14.9% and 10.0%, respectively. US-born Blacks were more likely to be smokers and poor metabolizers of NNAL. Two-way hierarchical clustering revealed MAF of AIMs differed across the 3 ethnic subgroups. Conclusion: Our findings are consistent with the emerging literature demonstrating Black heterogeneity underscoring African Ancestry genetic subgroup differences – specifically relevant to cancer. Further investigations, with data harmonization and sharing, are urgently needed to begin to map African Ancestry cancer biomarkers as well as race, and race by place\\region comparative biomarkers to inform cancer prevention and treatment in the era of precision medicine.

Integrated Genome-Wide Analysis of Gene Expression and DNA Copy Number Variations Highlights Stem Cell-Related Pathways in Small Cell Esophageal Carcinoma.

Purpose/Objectives. Primary small cell esophageal carcinoma (SCEC) represents a rare and aggressive malignancy without any prospective clinical trial or established treatment strategy at present. Although previous studies have indicated similarities between SCEC and small cell lung cancer (SCLC) in terms of their clinical manifestations, pathology, and morphology, very little genetic information is available on this highly malignant tumor. At present, patients with SCEC are staged and treated according to the guidelines established for SCLC. However, early recurrence and distant metastasis are common, and long-time survivors are rare. Current options available for patients with relapsed SCEC are fairly unsatisfactory, and their prognosis is generally poor. Novel therapeutic approaches against SCEC are therefore urgently needed and require a deeper understanding of the underlying genetic mechanisms. The current investigation aims to characterize the gene expression profile and copy number variations (CNVs) in SCEC to clarify molecular markers and pathways that may possess clinical significance. Materials/Methods. De novo expression array was carried out on three matched sets of primary SCEC and adjacent normal tissue samples procured from the institutional tissue bank, utilizing the Affymetrix HG U133 Plus 2.0 Array. After individual tissue normalization, the statistical software GeneSpring GX 12.5 was used to determine differentially expressed genes (DEGs) in the tumors relative to their paired normal tissues. Gene enrichments in addition to functional annotation and gene interaction networks were performed using DAVID 6.8 and STRING 10.0, respectively. A gene alteration was determined to be recurrent if it was observed in at least 2 samples. Chromosomes X and Y were not included in calculations as gender differences are a known source of analysis bias. The DEGs of at least one SCEC sample could be mapped to the CNV regions (fold change (FC) ≥ 2 and false discovery rate (FDR) < 0.01) after gene expression profiling by RefSeq Transcript ID. These overlapped genes were subjected to the functional annotation using DAVID 6.8. In order to elucidate the effect of CNV on mRNA expression, we integrated the genome-wide copy number data and gene expression in 3 paired samples. CNV-associated gene expression aberration (CNV-FC) was calculated for the recurrent DEGs using previously published integrated microarray data as reference. Pearson's correlation coefficient was employed to determine if there was a statistical correlation between the gene expression log2 ratios and their copy numbers using the SPSS 19.0 software. Genes that possessed CNV-FC ≥ 2 and r ≥ 0.6 (p < 0.05) were determined to be genes potentially associated with cancer. Results. High-quality DNA and total RNA were first extracted from both SCEC and normal tissues. Microarray data showed significant upregulation in WNT gene sets and downregulation in the PTEN and notch gene sets in SCEC. Functional annotation showed that genes associated with DNA replication, mitosis, cell cycle, DNA repair, telomere maintenance, RB, and p53 pathways were significantly altered in SCEC compared to corresponding noncancerous tissues (Benjamini p < 0.05). Thirteen recurrent CNVs were found in all SCEC samples by array CGH. Chromosomal regions with gain were located in 14q11.2, and regions with loss were located in 4q22.3-23.3, 3q25.31-q29, 5p15.31-15.2, 8q21.11-24.3, and 9p23-13.1 in all samples. In two samples, the 14q11.2-32.33 region was amplified, whereas 3p26.3-25.3, 4p16.3-11, 4q11-22.3, 4q23-25, 8p23.3, and 16p13.3 were deleted. We further identified 306 genes that consistently differed in copy number and expression (194 upregulated and 112 downregulated) between the SCEC and noncancerous tissues in all three samples. These genes were significantly enriched with those involved in cell cycle, mitosis, DNA repair, P53 pathway, and RB pathway, according to their functional annotation. These 306 DEGs also included network genes of the above pathways such as NUF2, CCNE2, NFIB, ETV5, KLF5, ATAD2, NDC80, and ZWINT. In addition, 39 individual DEGs demonstrated a minimum 2-fold copy number-associated expression change (median: 5.35, 95% CI: 4.53–16.98) and Pearson's correlation coefficient ≥ 0.6 (p < 0.05), of which PTP4A3 showed the highest correlation (CNV-FC = 21362.13; Pearson's correlation coefficient = 0.9983; p = 0.037). Two distinct groups of genes belonging to each SCEC and nonmalignant tissues were observed upon unsupervised two-way (genes and samples) hierarchical clustering. Conclusions. The current investigation is the first to produce data regarding the genomic signature of SCEC at the transcription level and in relation to CNVs. Our preliminary data indicate possible key roles of WNT and notch signaling in SCEC and overexpressed PTP4A3 as a potential therapeutic target. Further validation of our findings is warranted.

The frequency of promoter DNA hypermethylation is decreased in colorectal neoplasms of familial adenomatous polyposis.

Familial adenomatous polyposis (FAP) is an inherited disorder characterized by numerous colorectal adenomatous polyps with predisposition to the development of colorectal cancer (CRC). Here, we conducted genome-wide DNA methylation analysis of FAP neoplasms, including seven cancer samples and 16 adenoma samples, using an Infinium 450K BeadArray. As controls for sporadic colorectal neoplasms and mucosae, we used Infinium 450k data from 297 CRC samples, 45 colorectal adenoma samples, and 37 normal mucosa samples with reference to The Cancer Genome Atlas and other databases. Unsupervised two-way hierarchical clustering analysis of FAP and sporadic CRC/adenoma revealed that CRC was classified into four DNA methylation epigenotypes (MEs): high-ME (HME), intermediate-ME (IME), low-ME (LME), and normal-like ME (NME). Five FAP neoplasms (two cancer and three adenoma) were clustered with IME, whereas 18 FAP neoplasms (five cancer and 13 adenoma) were clustered into NME. IME FAP neoplasms significantly correlated with KRAS mutations, similar to sporadic CRC. Within IME cases, however, aberrant DNA methylation was significantly less frequent in FAP neoplasms than sporadic neoplasms, and these unmethylated genes included WNT family genes and several types of oncogenes. In summary, FAP neoplasms were classified into at least two molecular subtypes, i.e., NME in the majority of cases showing mostly no aberrant methylation and IME in some cases accompanied by KRAS mutations but less frequent aberrant DNA methylation than sporadic neoplasms, suggesting that FAP may follow a tumorigenesis pathway different from that of sporadic CRC.

Characterization of Sulfur-Compounds as Chemotaxonomic Markers in the Essential Oils of Allium Species by Solvent-Free Microwave Extraction and Gas Chromatography–Mass Spectrometry

Allium species were examined to authenticate the chemotaxonomic controversy about these plants by analyzing their extracted compound profiles. Essential oils of various species were isolated using conventional hydro-distillation and solvent-free microwave extraction (SFME). A comparison of the isolation procedures was performed. The presence of sulfur compounds in the Allium genus is a prominent characteristic for their medicinal uses. These components were characterized using two-way hierarchical cluster analysis (HCA) and principal component analysis (PCA). The variation of sulfur-compounds was performed by qualitative analysis of Allium species by gas chromatography–mass spectrometry (GC–MS). 2,4-Dimethyl-5,6-dithia-2,7-nonadienal, 4,6-diethyl-1,2,3,5-tetrathiolane, and 5,7-diethyl-1,2,3,4,6-pentathiepane were revealed as potential chemotaxonomic markers for all of the Alliums examined in this study. These markers may be used to provide improved systematics for other Allium species.

A six-long non-coding RNA signature predicts prognosis in melanoma patients.

The aim of this study was to identify long non-coding RNAs (lncRNAs) which may prove useful for risk-classifying patients with melanoma. For this purpose, based on a dataset from The Cancer Genome Atlas (TCGA), we selected and analyzed samples from melanoma stages I, II, III and IV, from which differentially expressed lncRNAs were identified. The lncRNAs were classified using two-way hierarchical clustering analysis and analysis of support vector machine (SVM), followed by Kaplan-Meier survival analysis. The prognostic capacity of the signature was verified on an independent dataset. lncRNA-mRNA networks were built using signature lncRNAs and corresponding target genes. The Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis was conducted on the target genes. A total of 48 differentially expressed lncRNAs were identified, from which 6 signature lncRNAs (AL050303 and LINC00707, LINC01324, RP11-85G21, RP4-794I6.4 and RP5-855F16) were identified. Two-way hierarchical clustering analysis revealed that the accuracy of the six-lncRNA signature in risk-stratifying samples was 84.84%, and the accuracy of the SVM classifier was 85.9%. This predictive signature performed well on the validation dataset [accuracy, 86.76; area under the ROC curve (AUROC), 0.816]. A total of 720 target genes of the 6 lncRNAs were selected for the lncRNA-mRNA networks. These genes were significantly related to mitogen-activated protein kinase (MAPK), the neurotrophin signaling pathway, focal adhesion pathways, and several immune and inflammation-related pathways. On the whole, we identified a six-lncRNA prognostic signature for risk-stratifying patients with melanoma. These lncRNAs may affect prognosis by regulating the MAPK pathway, immune and inflammation-related pathways, the neurotrophin signaling pathway and focal adhesion pathways.

MOLECULAR AND MORPHOLOGICAL EVALUATION OF POTATO GENOTYPES CULTIVATED IN SANDY SOIL

Twenty-six potato genotypes including seventeen cultivars were used to investigate the genetic diversity of potato plants (Solanum tuberosum L.) grown in Egyptian sandy soil using both morphological characteristics and molecular markers. The analysis of variance (ANOVA) of the potato yield traits and its components showed highly significant differences among the genotypes, the growing seasons and the interaction between genotypes and the growing seasons for all the studied traits. The NAP geno type gave the highest significant values for the yield traits and the highest percentage of the tuber size more than 70 mm in diameter trait. The NIZ genotype gave the highest significant value (146.5 g) for the tuber weight trait. On the other hand, OH, Cleopatra and Sophie potato genotypes showed the least significant values for tuber weight and tuber size traits. According to the two-way hierarchical cluster analysis, the potato genotypes were separated into three main cluster groups, while in the second way of the hierarchical clustering (traits clustering), the morphological traits were separated into two clusters. According to RAPD cluster analysis, the Mondial genotype was separated at the uppermost of the dendrogram apart of the other genotypes and the Red Sun genotype was separated at the lowermost of the dendrogram. The other 24 potato genotypes were separated into five clusters. Depending upon ISSR cluster analysis; the Mozart and ALF genotypes were separated apart of all other genotypes at the lowermost of the dendrogram, while the Mondial, Sophie, Liseta, NAP and Red Sun genotypes were distributed separately throughout the dendrogram. The other genotypes were separated into four clusters. Thus, it can be concluded that both morphological and molecular markers could be efficiently used to study the genetic diversity among potato genotypes. Although the morphological characteristics are affected with the environment, their results could be supported by the molecular markers results.

Identification of biomarkers for childhood obesity based on expressional correlation and functional similarity.

The aim of the current study was to identify potential biomarkers of childhood obesity, and investigate molecular mechanisms and candidate agents in order to improve therapeutic strategies for childhood obesity. The GSE9624 gene expression profile was downloaded from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) in omental adipose tissues were analyzed with limma package by comparing samples from obese and normal control children. Two-way hierarchical clustering was applied using the pheatmap package. The co-expression (CE) analysis was performed using online CoExpress software. Subsequent to functional classification via the GOSim package, the gene network enriched by DEGs was visualized using the Cytoscape package. The codon usage bias of the DEGs was then examined using the CAI program from the European Molecular Biology Open Software Suite. In total, 583 DEGs (273 upregulated genes and 310 downregulated genes) were observed in the omental adipose tissues between samples from obese and normal control children. Hierarchical clustering identified a significant difference between samples from obese and normal control children. Subsequent to CE analysis, 130 DEGs, which were classified into 4 clusters, were selected. The following 3 upregulated and 2 downregulated genes were identified to be significant: Upregulated genes, microtubule-associated protein tau (MAPT), destrin (actin depolymerizing factor) (DSTN) and spectrin, β, non-erythrocytic 1 (SPTBN1); downregulated genes, Rho/Rac guanine nucleotide exchange factor 2 (ARHGEF2) and spindle and kinetochore associated complex subunit 1 (SKA1). The top 3 amino acids were identified to be glycine, leucine and serine with a high bias. The DEGs MAPT, DSTN, SPTBN1, ARHGEF2 and SKA1 are suggested to be candidate biomarkers for childhood obesity.

Antibiosis and bmyB Gene Presence As Prevalent Traits for the Selection of Efficient Bacillus Biocontrol Agents against Crown Gall Disease.

This study aimed to improve the screening method for the selection of Bacillus biocontrol agents against crown gall disease. The relationship between the strain biocontrol ability and their in vitro studied traits was investigated to identify the most important factors to be considered for the selection of effective biocontrol agents. In fact, previous selection procedure relying only on in vitro antibacterial activity was shown to be not suitable in some cases. A direct plant-protection strategy was performed to screen the 32 Bacillus biocontrol agent candidates. Moreover, potential in vitro biocontrol traits were investigated including biofilm formation, motility, hemolytic activity, detection of lipopeptide biosynthetic genes (sfp, ituC and bmyB) and production of antibacterial compounds. The obtained results indicated high correlations of the efficiency of the biocontrol with the reduction of gall weight (p = 0.000) and the antibacterial activity in vitro (p = 0.000). Moreover, there was strong correlations of the efficiency of the biocontrol (p = 0.004) and the reduction in gall weight (p = 0.000) with the presence of the bmyB gene. This gene directs the synthesis of the lipopeptide bacillomycin belonging to the iturinic family of lipopeptides. These results were also confirmed by the two-way hierarchical cluster analysis and the correspondence analysis showing the relatedness of these four variables. According to the obtained results a new screening procedure of Bacillus biocontrol agents against crown gall disease could be advanced consisting on two step selection procedure. The first consists on selecting strains with high antibacterial activity in vitro or those harbouring the bmyB gene. Further selection has to be performed on tomato plants in vivo. Moreover, based on the results of the biocontrol assay, five potent strains exhibiting high biocontrol abilities were selected. They were identified as Bacillus subtilis or Bacillus amyloliquefaciens. These strains were found to produce either surfactin or surfactin and iturin lipopeptides. In conclusion, our study presented a new and effective method to evaluate the biocontrol ability of antagonistic Bacillus strains against crown gall disease that could increase the efficiency of screening method of biocontrol agents. Besides, the selected strains could be used as novel biocontrol agents against pathogenic Agrobacterium tumefaciens strains.

Genetic Diversity of Fig (Ficus carica L.) Based on Morphological Characters and Two-Way Hierarchical Cluster Analysis

Genetic Diversity of Fig (Ficus carica L.) Based on Morphological Characters and Two-Way Hierarchical Cluster Analysis

Metabolic syndrome and the seminal cytokine network in morbidly obese males.

Given the increasing prevalence of metabolic syndrome (MetS) in males of reproductive age, the objective of this prospective case-controlled study was to investigate the impact of subacute systemic inflammation associated with MetS on seminal cytokines and standard sperm parameters in comparison with healthy men. Between 2011 and 2014, we recruited 27 patients with MetS out of 41 obese patients screened from an internal outpatient clinic. Twenty-seven age-matched healthy controls were enrolled from 54 men requesting vasectomy in a urological outpatient clinic. A multiplex analysis was performed to quantify simultaneously the level of 30 cytokines (Eotaxin, FGF, Fraktalkine, GCSF, GMCSF, Granzyme A, IFN-γ, IL-1α, IL-1β, IL-2, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-12p70, IL-13, IL-17A, IL-21, IP-10, I-TAC, MCP-1, MIG, MIP-1α, MIP-1β, RANTES, TNF-α, and VEGF) in each 50μL of blood and seminal plasma during the andrological work-up. Semen analysis was performed according to the WHO (Global status report on noncommunicable diseases, 2010) recommendations, including standard sperm parameters as well as peroxidase-positive leukocytes and polymorphonuclear elastase. Blood levels of C-reactive protein, interleukins 6 and 10 were elevated in MetS (p>0.001). Two-way hierarchical cluster analysis showed characteristic cytokine networks in semen greatly differing from those in blood, but not between MetS and controls. No deterioration of semen analysis was evident in men diagnosed with MetS. Our results suggest that there is no transmission of the systemic inflammation associated with MetS into semen based on cytokine profiles and that MetS does not impair standard semen parameters to a clinically significant extent.

Genotypes of cancer stem cells characterized by epithelial-to-mesenchymal transition and proliferation related functions.

Cancer stem cells (CSCs), or cancer cells with stem cell-like properties, generally exhibit drug resistance and have highly potent cancer inducing capabilities. Genome-wide expression data collected at public repositories over the last few years provide excellent material for studies that can lead to insights concerning the molecular and functional characteristics of CSCs. Here, we conducted functional genomic studies of CSC based on fourteen PCA-screened high quality public CSC whole genome gene expression datasets and, as control, four high quality non-stem-like cancer cell and non-cancerous stem cell datasets from the Gene Expression Omnibus database. A total of 6,002 molecular signatures were taken from the Molecular Signatures Database and used to characterize the datasets, which, under two-way hierarchical clustering, formed three genotypes. Type 1, consisting of mainly glia CSCs, had significantly enhanced proliferation, and significantly suppressed epithelial-mesenchymal transition (EMT), related functions. Type 2, mainly breast CSCs, had significantly enhanced EMT, but not proliferation, related functions. Type 3, composed of ovarian, prostate, and colon CSCs, had significantly suppressed proliferation related functions and mixed expressions on EMT related functions.

Micro-habitats Utilizations, Feeding Niche Overlapping, and Management Systems Impacts on Community Tolerances of Wasp Species within Oil Palm Plantations.

A study on micro-habitats utilizations, feeding niche overlapping, and management systems impacts pertaining to hymenopteran community were evaluated at five chosen oil palm age stands within FELDA Sungai Tekam oil palm plantations, Pahang. Samplings were done within the duration of one year, employing the standard Malaise traps, starting from February 2013 till February 2014, involving both hot and wet seasons. 60 species, from 17 families and 35 subfamilies were successfully collected during the sampling periods. Eight defined micro-habitats were elaborated, with the subdivisions of major, minor, stable, and risky micro-habitat types. Management systems impacts were associated with the applications of chemical herbicides and fertilizers. Species groups were formed using Two-Way Hierarchical Cluster Dendrogram, following 75% of information remaining. Three species groups were formed for hot and wet seasons respectively, with the first group involved nearly half of the overall hymenopteran community. Beneficial nectariferous plants, heaps of chipped rotting oil palm trunks, and remnants of rotting forest logs were all the prominent micro-habitats associated will all cases of hymenopteran species groups, for both cases of major and minor micro-habitat types. Application of BASTA, Glyphosate-Type-A and Type-B herbicides, as well as NK-Mix, Borax, and GML chemical fertilizers were all highly correlated with hymenopteran species groups, showing the high tolerance of most hymenopteran species towards the employed management systems, with reference to minor micro-habitats. Strong feeding ecological niches and plexus values between species of similar species groups formed were specifically associated with discrete but connected minor micro-habitats with weaker food chains, collectively forming larger stable food webs within major micro-habitats. Suggestions on maintaining minor micro-habitats for the survival of most hymenopteran community, as well as the sustenance of their food sources were also discussed.

Micro-habitats Utilizations, Feeding Niche Overlapping, and Management Systems Impacts on Community Tolerances of Wasp Species within Oil Palm Plantations.

A study on micro-habitats utilizations, feeding niche overlapping, and management systems impacts pertaining to hymenopteran community were evaluated at five chosen oil palm age stands within FELDA Sungai Tekam oil palm plantations, Pahang. Samplings were done within the duration of one year, employing the standard Malaise traps, starting from February 2013 till February 2014, involving both hot and wet seasons. 60 species, from 17 families and 35 subfamilies were successfully collected during the sampling periods. Eight defined micro-habitats were elaborated, with the subdivisions of major, minor, stable, and risky micro-habitat types. Management systems impacts were associated with the applications of chemical herbicides and fertilizers. Species groups were formed using Two-Way Hierarchical Cluster Dendrogram, following 75% of information remaining. Three species groups were formed for hot and wet seasons respectively, with the first group involved nearly half of the overall hymenopteran community. Beneficial nectariferous plants, heaps of chipped rotting oil palm trunks, and remnants of rotting forest logs were all the prominent micro-habitats associated will all cases of hymenopteran species groups, for both cases of major and minor micro-habitat types. Application of BASTA, Glyphosate-Type-A and Type-B herbicides, as well as NK-Mix, Borax, and GML chemical fertilizers were all highly correlated with hymenopteran species groups, showing the high tolerance of most hymenopteran species towards the employed management systems, with reference to minor micro-habitats. Strong feeding ecological niches and plexus values between species of similar species groups formed were specifically associated with discrete but connected minor micro-habitats with weaker food chains, collectively forming larger stable food webs within major micro-habitats. Suggestions on maintaining minor micro-habitats for the survival of most hymenopteran community, as well as the sustenance of their food sources were also discussed.Â

A novel procedure on next generation sequencing data analysis using text mining algorithm

BackgroundNext-generation sequencing (NGS) technologies have provided researchers with vast possibilities in various biological and biomedical research areas. Efficient data mining strategies are in high demand for large scale comparative and evolutional studies to be performed on the large amounts of data derived from NGS projects. Topic modeling is an active research field in machine learning and has been mainly used as an analytical tool to structure large textual corpora for data mining.MethodsWe report a novel procedure to analyse NGS data using topic modeling. It consists of four major procedures: NGS data retrieval, preprocessing, topic modeling, and data mining using Latent Dirichlet Allocation (LDA) topic outputs. The NGS data set of the Salmonella enterica strains were used as a case study to show the workflow of this procedure. The perplexity measurement of the topic numbers and the convergence efficiencies of Gibbs sampling were calculated and discussed for achieving the best result from the proposed procedure.ResultsThe output topics by LDA algorithms could be treated as features of Salmonella strains to accurately describe the genetic diversity of fliC gene in various serotypes. The results of a two-way hierarchical clustering and data matrix analysis on LDA-derived matrices successfully classified Salmonella serotypes based on the NGS data. The implementation of topic modeling in NGS data analysis procedure provides a new way to elucidate genetic information from NGS data, and identify the gene-phenotype relationships and biomarkers, especially in the era of biological and medical big data.ConclusionThe implementation of topic modeling in NGS data analysis provides a new way to elucidate genetic information from NGS data, and identify the gene-phenotype relationships and biomarkers, especially in the era of biological and medical big data.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-016-1075-9) contains supplementary material, which is available to authorized users.

CSF/plasma HIV-1 RNA discordance even at low levels is associated with up-regulation of host inflammatory mediators in CSF

IntroductionHIV-1 RNA can be found at higher levels in cerebrospinal fluid (CSF) than in plasma, termed CSF/plasma discordance. The clinical significance of CSF/plasma discordance is not known and the degree of discordance considered important varies. We aimed to determine whether a panel of CSF cytokines, chemokines and associated mediators were raised in patients with CSF/plasma discordance at different levels. MethodsA nested case-control study of 40 CSF samples from the PARTITION study. We used a cytometric bead array to measure CSF mediator concentrations in 19 discordant and 21 non-discordant samples matched for plasma HIV-1 RNA. Discordant samples were subdivided into ‘high discordance’ (>1log10) and ‘low discordance’ (0.5–1log10, or ultrasensitive discordance). CSF mediators significant in univariate analysis went forward to two-way unsupervised hierarchical clustering based on the patterns of relative mediator concentrations. ResultsIn univariate analysis 19 of 21 CSF mediators were significantly higher in discordant than non-discordant samples. There were no significant differences between samples with high versus low discordance. The samples grouped into two clusters which corresponded to CSF/plasma discordance (p<0.0001). In cluster one all mediators had relatively high abundance; this included 18 discordant samples and three non-discordant samples. In cluster two all mediators had relatively low abundance; this included 18 non-discordant samples and one non-discordant sample with ultrasensitive discordance only. ConclusionsCSF/plasma discordance is associated with potentially damaging neuroinflammatory process. Patients with discordance at lower levels (ie. 0.5–1log10) should also be investigated as mediator profiles were similar to those with discordance >1log10. Sensitive testing may have a role to determine whether ultrasensitive discordance is present in those with low level CSF escape.

RNA Sequencing Quantification of Xenobiotic-Processing Genes in Various Sections of the Intestine in Comparison to the Liver of Male Mice.

Previous reports on tissue distribution of xenobiotic-processing genes (XPGs) have limitations, because many non-cytochrome P450 phase I enzymes have not been investigated, and one cannot compare the real mRNA abundance of multiple XPGs using conventional quantification methods. Therefore, this study aimed to quantify and compare the mRNA abundance of all major XPGs in the liver and intestine using RNA sequencing. The mRNA profiles of 304 XPGs, including phase I, phase II enzymes, phase II cosubstrate synthetic enzymes, xenobiotic transporters, as well as xenobiotic-related transcription factors, were systematically examined in the liver and various sections of the intestine in adult male C57BL/6J mice. By two-way hierarchical clustering, over 80% of the XPGs had tissue-divergent expression, which partitioned into liver-predominant, small intestine-predominant, and large intestine-predominant patterns. Among the genes, 54% were expressed highest in the liver, 21% in the duodenum, 4% in the jejunum, 6% in the ileum, and 15% in the large intestine. The highest-expressed XPG in the liver was Mgst1; in the duodenum, Cyp3a11; in the jejunum and ileum, Ces2e; and in the large intestine, Cyp2c55. Interestingly, XPGs in the same family usually exhibited highly different tissue distribution patterns, and many XPGs were almost exclusively expressed in one tissue and minimally expressed in others. In conclusion, the present study is among the first and the most comprehensive investigations of the real mRNA abundance and tissue-divergent expression of all major XPGs in mouse liver and intestine, which aids in understanding the tissue-specific biotransformation and toxicity of drugs and other xenobiotics.