Effect of data normalization on fuzzy clustering of DNA microarray data

BACKGROUND: Microarray technology has made it possible to simultaneously measure the expression levels of large numbers of genes in a short time. Gene expression data is information rich; however, extensive data mining is required to identify the patterns that characterize the underlying mechanisms of action. Clustering is an important tool for finding groups of genes with similar expression patterns in microarray data analysis. However, hard clustering methods, which assign each gene exactly to one cluster, are poorly suited to the analysis of microarray datasets because in such datasets the clusters of genes frequently overlap. RESULTS: In this study we applied the fuzzy partitional clustering method known as Fuzzy C-Means (FCM) to overcome the limitations of hard clustering. To identify the effect of data normalization, we used three normalization methods, the two common scale and location transformations and Lowess normalization methods, to normalize three microarray datasets and three simulated datasets. First we determined the optimal parameters for FCM clustering. We found that the optimal fuzzification parameter in the FCM analysis of a microarray dataset depended on the normalization method applied to the dataset during preprocessing. We additionally evaluated the effect of normalization of noisy datasets on the results obtained when hard clustering or FCM clustering was applied to those datasets. The effects of normalization were evaluated using both simulated datasets and microarray datasets. A comparative analysis showed that the clustering results depended on the normalization method used and the noisiness of the data. In particular, the selection of the fuzzification parameter value for the FCM method was sensitive to the normalization method used for datasets with large variations across samples. CONCLUSION: Lowess normalization is more robust for clustering of genes from general microarray data than the two common scale and location adjustment methods when samples have varying expression patterns or are noisy. In particular, the FCM method slightly outperformed the hard clustering methods when the expression patterns of genes overlapped and was advantageous in finding co-regulated genes. Thus, the FCM approach offers a convenient method for finding subsets of genes that are strongly associated to a given cluster

Highly Monodispersed PbS Quantum Dots for Outstanding Cascaded-Junction Solar Cells.

High-performance cascaded-junction quantum dot solar cells (CJQDSCs) are fabricated from as-prepared highly monodispersed lead sulfide QDs. The cells have a high power conversion of 9.05% and a short-circuit current density of 32.51 mA cm-2. A reliable and effective stratagem for fabricating high-quality lead sulfide quantum dots (QD) is explored through a "monomer" concentration-controlled experiment. Robust QDSC performances with different band gaps are demonstrated from the as-proposed synthesis and processing stratagems. Various potential CJQDSCs can be envisioned from the band edge evolution of the QDs as a function of size and ligands reported here

Unleashing the full potential of Hsp90 inhibitors as cancer therapeutics through simultaneous inactivation of Hsp90, Grp94, and TRAP1

Cancer therapeutics: Extending a drug's reach A new drug that blocks heat shock proteins (HSPs), helper proteins that are co-opted by cancer cells to promote tumor growth, shows promise for cancer treatment. Several drugs have targeted HSPs, since cancer cells are known to hijack these helper proteins to shield themselves from destruction by the body. However, the drugs have had limited success. Hye-Kyung Park and Byoung Heon Kang at Ulsan National Institutes of Science and Technology in South Korea and coworkers noticed that the drugs were not absorbed into mitochondria, a key cellular compartment, and HSPs in this compartment were therefore not being blocked. They identified a new HSP inhibitor that can reach every cellular compartment and inhibit all HSPs. Testing in mice showed that this inhibitor effectively triggered death of tumor cells, and therefore shows promise for anti-cancer therapy. The Hsp90 family proteins Hsp90, Grp94, and TRAP1 are present in the cell cytoplasm, endoplasmic reticulum, and mitochondria, respectively; all play important roles in tumorigenesis by regulating protein homeostasis in response to stress. Thus, simultaneous inhibition of all Hsp90 paralogs is a reasonable strategy for cancer therapy. However, since the existing pan-Hsp90 inhibitor does not accumulate in mitochondria, the potential anticancer activity of pan-Hsp90 inhibition has not yet been fully examined in vivo. Analysis of The Cancer Genome Atlas database revealed that all Hsp90 paralogs were upregulated in prostate cancer. Inactivation of all Hsp90 paralogs induced mitochondrial dysfunction, increased cytosolic calcium, and activated calcineurin. Active calcineurin blocked prosurvival heat shock responses upon Hsp90 inhibition by preventing nuclear translocation of HSF1. The purine scaffold derivative DN401 inhibited all Hsp90 paralogs simultaneously and showed stronger anticancer activity than other Hsp90 inhibitors. Pan-Hsp90 inhibition increased cytotoxicity and suppressed mechanisms that protect cancer cells, suggesting that it is a feasible strategy for the development of potent anticancer drugs. The mitochondria-permeable drug DN401 is a newly identified in vivo pan-Hsp90 inhibitor with potent anticancer activity

Importância dos Saca-Rabos (Herpestes Ichneumon) como Reservatório de Mycobacterium avium subsp. paratuberculosis. Deteção por Técnicas Tradicionais e Moleculares

Poster apresentado nas IV Jornadas de Genética, realizadas na UTAD, Vila Real, nos dias 1,2 e 3 de Março de 2012.Os saca-rabos (Herpestes ichneumon) também conhecidos por mangustos, são carnívoros diurnos selvagens que juntamente com a geneta (Genetta genetta) representam os exemplares da família Viverridae em Portugal. É uma espécie cinegética de caça menor que se alimenta de coelhos, roedores, aves, cobras, insectos e ovos. Neste estudo colheram-se amostras de 8 animais mortos por atropelamento e em ações de controlo de predadores, durante os anos de 2010 e 2011, nos concelhos de Idanha-a-Nova e Penamacor do distrito de Castelo Branco. As amostras colhidas foram fígado, pulmão, baço, intestino, rim, gânglio mesentérico, retrofaríngeo, mediastínico, amígdalas e fezes. As amostras foram submetidas à técnica de PCR e a cultura microbiológica em meios específicos. Em três saca-rabos (37,5%) detectou-se Mycobacterium avium subsp. paratuberculosis (Map) através da técnica de biologia molecular. Dois eram machos e um era fêmea. Map foi confirmado também em cultura nos dois machos. Sete saca-rabos (87,5%) apresentaram bactérias álcool-ácido resistentes compatíveis com Map em esfregaços de diferentes tecidos, quando corados pelo método de Ziehl-Neelsen. Estes resultados preliminares confirmam os saca-rabos como reservatório de Map no nosso país. Atualmente, estão a ser desenvolvidos mais estudos para a avaliação dos saca-rabos na dinâmica da infeção de Map em mamíferos selvagens

Discovery of new epigenomics-based biomarkers and the early diagnosis of neurodegenerative diseases

Treatment options for many neurodegenerative diseases are limited due to the lack of early diagnostic procedures that allow timely delivery of therapeutic agents to affected neurons prior to cell death. While notable advances have been made in neurodegenerative disease biomarkers, whether or not the biomarkers discovered to date are useful for early diagnosis remains an open question. Additionally, the reliability of these biomarkers has been disappointing, due in part to the large dissimilarities between the tissues traditionally used to source biomarkers and primarily diseased neurons. In this article, we review the potential viability of atypical epigenetic and/or consequent transcriptional alterations (ETAs) as biomarkers of early-stage neurodegenerative disease, and present our perspectives on the discovery and practical use of such biomarkers in patient-derived neural samples using single-cell level analyses, thereby greatly enhancing the reliability of biomarker application. © 2020 The Authors1