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https://www.readbyqxmd.com/read/27913847/patulin-transformation-products-and-last-intermediates-in-its-biosynthetic-pathway-e-and-z-ascladiol-are-not-toxic-to-human-cells
#1
Joanna Tannous, Selma P Snini, Rhoda El Khoury, Cécile Canlet, Philippe Pinton, Yannick Lippi, Imourana Alassane-Kpembi, Thierry Gauthier, André El Khoury, Ali Atoui, Ting Zhou, Roger Lteif, Isabelle P Oswald, Olivier Puel
Patulin is the main mycotoxin contaminating apples. During the brewing of alcoholic beverages, this mycotoxin is degraded to ascladiol, which is also the last precursor of patulin. The present study aims (1) to characterize the last step of the patulin biosynthetic pathway and (2) to describe the toxicity of ascladiol. A patE deletion mutant was generated in Penicillium expansum. In contrast to the wild strain, this mutant does not produce patulin but accumulates high levels of E-ascladiol with few traces of Z-ascladiol...
December 2, 2016: Archives of Toxicology
https://www.readbyqxmd.com/read/27913638/ms23-a-master-basic-helix-loop-helix-factor-regulates-the-specification-and-development-of-tapetum-in-maize
#2
Guo-Ling Nan, Jixian Zhai, Siwaret Arikit, Darren Morrow, John Fernandes, Lan Mai, Nhi Nguyen, Blake C Meyers, Virginia Walbot
Successful male gametogenesis involves orchestration of sequential gene regulation for somatic differentiation in pre-meiotic anthers. We report here the cloning of Male Sterile23 (Ms23), encoding an anther-specific predicted basic helix-loop-helix (bHLH) transcription factor required for tapetal differentiation; transcripts localize initially to the precursor secondary parietal cells then predominantly to daughter tapetal cells. In knockout ms23-ref mutant anthers, five instead of the normal four wall layers are observed...
December 2, 2016: Development
https://www.readbyqxmd.com/read/27913546/diagnosing-von-willebrand-disease-genetic-analysis
#3
Anne Goodeve
Investigation of a patient with possible von Willebrand disease (VWD) includes a range of phenotypic analyses. Often, this is sufficient to discern disease type, and this will suggest relevant treatment. However, for some patients, phenotypic analysis does not sufficiently explain the patient's disorder, and for this group, genetic analysis can aid diagnosis of disease type. Polymerase chain reaction and Sanger sequencing have been mainstays of genetic analysis for several years. More recently, next-generation sequencing has become available, with the advantage that several genes can be simultaneously analyzed where necessary, eg, for discrimination of possible type 2N VWD or mild hemophilia A...
December 2, 2016: Hematology—the Education Program of the American Society of Hematology
https://www.readbyqxmd.com/read/27913357/introducing-a-stable-bootstrap-validation-framework-for-reliable-genomic-signature-extraction
#4
Nikolaos-Kosmas Chlis, Ekaterini S Bei, Michael Zervakis
The application of machine learning methods for the identification of candidate genes responsible for phenotypes of interest, such as cancer, is a major challenge in the field of bioinformatics. These lists of genes are often called genomic signatures and their linkage to phenotype associations may form a significant step in discovering the causation between genotypes and phenotypes. Traditional methods that produce genomic signatures from DNA Microarray data tend to extract significantly different lists under relatively small variations of the training data...
November 29, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/27913249/comparison-of-the-transcriptomic-profile-of-hepatic-human-induced-pluripotent-stem-like-cells-cultured-in-plates-and-in-a-3d-microscale-dynamic-environment
#5
Eric Leclerc, Keiichi Kimura, Marie Shinohara, Mathieu Danoy, Morgane Le Gall, Taketomo Kido, Atsushi Miyajima, Teruo Fujii, Yasuyuki Sakai
We have compared the transcriptomic profiles of human induced pluripotent stem cells after their differentiation in hepatocytes like cells in plates and microfluidic biochips. The biochips provided a 3D and dynamic support during the cell differentiation when compared to the 2D static cultures in plates. The microarray have demonstrated the up regulation of important pathway related to liver development and maturation during the culture in biochips. Furthermore, the results of the transcriptomic profile, coupled with immunostaining, and RTqPCR analysis have shown typical biomarkers illustrating the presence of responders of biliary like cells, hepatocytes like cells, and endothelial like cells...
November 29, 2016: Genomics
https://www.readbyqxmd.com/read/27913132/rapid-identification-of-candida-spp-frequently-involved-in-invasive-mycoses-by-using-flow-through-hybridization-and-gene-chip-fhgc-technology
#6
Chen Li, Xiurong Ding, Zhizhong Liu, Juanjuan Zhu
The incidence of invasive fungal infections in immunocompromised patients has increased in recent decades. Rapid and accurate identification of these pathogenic fungi is crucial for initiating a timely, safe, and effective antifungal therapy. Here we developed a microarray based on flow-through hybridization gene chip technology. The microarray was tested for its specificity using a panel of reference and blinded clinical isolates. The results proved that this microarray was highly discriminative, leading to the unequivocal identification of each species, including Candida famata and the highly related species Candida parapsilosis, Candida orthopsilosis, and Candida metapsilosis...
November 29, 2016: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/27912775/a-novel-long-non-coding-rna-lnc-gnat1-1-is-low-expressed-in-colorectal-cancer-and-acts-as-a-tumor-suppressor-through-regulating-rkip-nf-%C3%AE%C2%BAb-snail-circuit
#7
Chunxiang Ye, Zhanlong Shen, Bo Wang, Yansen Li, Tao Li, Yang Yang, Kewei Jiang, Yingjiang Ye, Shan Wang
BACKGROUND: The role of long non-coding RNAs (lncRNAs) in colorectal cancer (CRC) progression has not fully been elucidated. This study was designed to report the identification of a novel lncRNA, lnc-GNAT1-1, and its functional role in CRC progression. METHODS: lncRNA expression profile microarray was performed in three paired primary and liver metastatic tissues of CRC, and a novel lncRNA, lnc-GNAT1-1, was identified to be a potential functional lncRNA. Quantitative real-time PCR was used to detect its expression in CRC tissues, cell lines, and patients' plasma, cell fractionation was used to evaluate its subcellular location...
December 3, 2016: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/27912765/rna-seq-based-digital-gene-expression-analysis-reveals-modification-of-host-defense-responses-by-rice-stripe-virus-during-disease-symptom-development-in-arabidopsis
#8
Feng Sun, Peng Fang, Juan Li, Linlin Du, Ying Lan, Tong Zhou, Yongjian Fan, Wenbiao Shen, Yijun Zhou
BACKGROUND: Virus infection induces and suppresses host gene expression on a global level. Rice stripe virus (RSV) is the type species of the genus Tenuivirus and infects rice and Arabidopsis plants. Microarray-based and next generation sequencing-based transcriptomic approaches have been used to study rice-RSV interactions. However, our knowledge of the response of Arabidopsis plants to RSV infection is limited, and it requires further investigation to determine the similarities (or differences) in virus-host interactions between monocot and dicot hosts infected with RSV...
December 2, 2016: Virology Journal
https://www.readbyqxmd.com/read/27911910/molecular-markers-of-radiation-induced-attenuation-in-intrahepatic-plasmodium-falciparum-parasites
#9
Miranda S Oakley, Nitin Verma, Hong Zheng, Vivek Anantharaman, Kazuyo Takeda, Yamei Gao, Timothy G Myers, Phuong Thao Pham, Babita Mahajan, Nirbhay Kumar, Davison Sangweme, Abhai K Tripathi, Godfree Mlambo, L Aravind, Sanjai Kumar
Experimental immunization with radiation attenuated sporozoites (RAS) and genetically attenuated sporozoites has proved to be a promising approach for malaria vaccine development. However, parasite biomarkers of growth attenuation and enhanced immune protection in response to radiation remain poorly understood. Here, we report on the effect of an attenuating dose of γ-irradiation (15 krad) on the Plasmodium falciparum sporozoite (PfSPZ) ultrastructure by electron microscopy, growth rate of liver stage P. falciparum in liver cell cultures, and genome-wide transcriptional profile of liver stage parasites by microarray...
2016: PloS One
https://www.readbyqxmd.com/read/27911895/dna-microarray-detection-of-18-important-human-blood-protozoan-species
#10
Mu-Xin Chen, Lin Ai, Jun-Hu Chen, Xin-Yu Feng, Shao-Hong Chen, Yu-Chun Cai, Yan Lu, Xiao-Nong Zhou, Jia-Xu Chen, Wei Hu
BACKGROUND: Accurate detection of blood protozoa from clinical samples is important for diagnosis, treatment and control of related diseases. In this preliminary study, a novel DNA microarray system was assessed for the detection of Plasmodium, Leishmania, Trypanosoma, Toxoplasma gondii and Babesia in humans, animals, and vectors, in comparison with microscopy and PCR data. Developing a rapid, simple, and convenient detection method for protozoan detection is an urgent need. METHODOLOGY/PRINCIPAL FINDINGS: The microarray assay simultaneously identified 18 species of common blood protozoa based on the differences in respective target genes...
December 2016: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/27911272/foxo4-expression-is-related-to-stem-cell-like-properties-and-resistance-to-treatment-in-diffuse-large-b-cell-lymphoma
#11
Kyung Ju Ryu, Chaehwa Park, Mineui Hong, Young Hyeh Ko, Won Seog Kim, Seok Jin Kim
Cancer stem cells are proposed to be responsible for resistance to chemotherapeutic agents, including doxorubicin. As phenylbutyrate enhances cancer stem cell properties, we analyzed surviving lymphoma cells after treatment with doxorubicin and phenylbutyrate. Human B-cell lymphoma cell lines, including Toledo, BJAB, Daudi, and Raji were incubated with IC90 concentrations of doxorubicin (300 nM) or phenylbutyrate (8 mM). After 48 h, live cells were sorted and analyzed for their resistance to treatment by examining gene expression profiles using cDNA microarray and biological characteristics...
November 29, 2016: Oncotarget
https://www.readbyqxmd.com/read/27911271/immunoglobulin-superfamily-genes-are-novel-prognostic-biomarkers-for-breast-cancer
#12
Yue Li, Maoni Guo, Zhenkun Fu, Peng Wang, Yan Zhang, Yue Gao, Ming Yue, Shangwei Ning, Dianjun Li
Breast cancer progression is associated with dysregulated expression of the immunoglobulin superfamily (IgSF) genes that are involved in cell-cell recognition, binding and adhesion. Despite widespread evidence that many IgSF genes could serve as effective biomarkers, this potential has not been realized because the studies have focused mostly on individual genes and not the entire network. To gain a global perspective of the IgSF-related biomarkers, we constructed an IgSF-directed neighbor network (IDNN) and an IgSF-directed driver network (IDDN) by integrating multiple levels of data, including IgSF genes, breast cancer driver genes, protein-protein interaction (PPI) networks and gene expression profiling data...
November 29, 2016: Oncotarget
https://www.readbyqxmd.com/read/27911093/dna-microarray-profiling-highlights-nrf2-mediated-chemoprevention-targeted-by-wasabi-derived-isothiocyanates-in-hepg2-cells
#13
Phoebe Zapanta Trio, Atsuyoshi Kawahara, Shunsuke Tanigawa, Kozue Sakao, De-Xing Hou
6-MSITC and 6-MTITC are sulforaphane (SFN) analogs found in Japanese Wasabi. As we reported previously, Wasabi isothiocyanates (ITCs) are activators of Nrf2-antioxidant response element pathway, and also inhibitors of pro-inflammatory cyclooxygenase-2. This study is the first to assess the global changes in transcript levels by Wasabi ITCs, comparing with SFN, in HepG2 cells. We performed comparative gene expression profiling by treating HepG2 cells with ITCs, followed by DNA microarray analyses using HG-U133 plus 2...
December 2, 2016: Nutrition and Cancer
https://www.readbyqxmd.com/read/27910960/unc-5-homolog-b-unc5b-is-one-of-the-key-downstream-targets-of-n-%C3%AE-acetyltransferase-10-naa10
#14
Huiyu Xu, Yong Han, Bing Liu, Rong Li
N-α-acetyltransferase 10 (Naa10) displays alpha (N-terminal) acetyltransferase activity. It functions as a major modulator of cell growth and differentiation. Until now, a few downstream targets were found, but no studies have concerned about which gene is the early event of Naa10 downstream target. As we know, the earlier events may play more significant role in Naa10 pathway. Through construction of Naa10 stably knocked down H1299 cell line, we discovered cell morphological changes induced by Naa10. Moreover, potential function of Naa10 in cell morphogenesis was also indicated using cDNA microarray analysis of the Naa10 stably knock-down cell line...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27910946/ki-67-in-endometrial-cancer-scoring-optimization-and-prognostic-relevance-for-window-studies
#15
Sarah Kitson, Vanitha N Sivalingam, James Bolton, Rhona McVey, Mashid Nickkho-Amiry, Melanie E Powell, Alexandra Leary, Hans W Nijman, Remi A Nout, Tjalling Bosse, Andrew G Renehan, Henry C Kitchener, Richard J Edmondson, Emma J Crosbie
Ki-67, a marker of cellular proliferation, is increasingly being used in pre-surgical window studies in endometrial cancer as a primary outcome measure. Unlike in breast cancer, however, there are no guidelines standardizing its measurement and its clinical relevance as a response biomarker is undetermined. It is, therefore, imperative that Ki-67 scoring protocols are optimized and its association with patient survival rigorously evaluated, in order to be able to clinically interpret the results of these studies...
December 2, 2016: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/27910945/thyroid-transcription-factor-1-distinguishes-subependymal-giant-cell-astrocytoma-from-its-mimics-and-supports-its-cell-origin-from-the-progenitor-cells-in-the-medial-ganglionic-eminence
#16
Jen-Fan Hang, Chih-Yi Hsu, Shih-Chieh Lin, Chih-Chun Wu, Han-Jui Lee, Donald Ming-Tak Ho
Subependymal giant cell astrocytoma is a benign brain tumor mostly associated with tuberous sclerosis complex. However, it may be misinterpreted as other high-grade brain tumors due to the presence of large tumor cells with conspicuous pleomorphism and occasional atypical features, such as tumor necrosis and endothelial proliferation. In this study, we first investigated thyroid transcription factor-1 (TTF-1) expression in a large series of subependymal giant cell astrocytomas and other histologic and locational mimics to validate the diagnostic utility of this marker...
December 2, 2016: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/27910818/histomorphometric-and-transcriptome-evaluation-of-early-healing-bone-treated-with-a-novel-human-particulate-dentin-powder
#17
Yu-Chih Huang, Wei-Zhen Lew, Sheng-Wei Feng, Wei-Yi Lai, Yoshimitsu Abiko, Haw-Ming Huang
Human particulate dentin (HPD) shows potential as an alternative bone grafting material. However, the mechanism of bone healing at the molecular level after grafting with HPD is unclear. This study assessed the histological and global gene expression of bone tissues grafted with HPD. The HPD was prepared to 250-500 µm in size. X-ray diffraction (XRD) and energy dispersive x-ray spectroscopy (EDX) were performed to confirm the crystal structure, organic compound residues, and surface morphology, respectively...
December 2, 2016: Biomedical Materials
https://www.readbyqxmd.com/read/27910771/induction-of-flavin-containing-monooxygenase-in-mice-by-oral-administration-of-phellinus-baumii-agaricomycetes-extract
#18
Batbayar Sainkhuu, Beom Su Park, Ha Won Kim
Phellinus baumii is a yellow mushroom long used in alternative medicine in Korea and other central Asian countries. To identify genes affected by a single or 7-day oral administration of a water extract of Ph. Baumii, mouse liver tissue was analyzed using microarrays. The results showed that 8 and 23 genes were upregulated and 3 and 11 genes downregulated more than 3-fold by single and multiple oral administrations of 100 mg/kg PBE, respectively. Among the upregulated genes, the expression of 3 flavin-containing monooxygenase (Fmo) family genes, Fmo2-4, was upregulated in a concentration-dependent manner...
2016: International Journal of Medicinal Mushrooms
https://www.readbyqxmd.com/read/27910032/cytogenetic-nomenclature-and-reporting
#19
Marian Stevens-Kroef, Annet Simons, Katrina Rack, Rosalind J Hastings
A standardized nomenclature is critical for the accurate and consistent description of genomic changes as identified by karyotyping, fluorescence in situ hybridization and microarray. The International System for Human Cytogenomic Nomenclature (ISCN) is the central reference for the description of karyotyping, FISH, and microarray results, and provides rules for describing cytogenetic and molecular cytogenetic findings in laboratory reports. These laboratory reports are documents to the referring clinician, and should be clear, accurate and contain all information relevant for good interpretation of the cytogenetic findings...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27910023/array-based-comparative-genomic-hybridization-acgh
#20
Chengsheng Zhang, Eliza Cerveira, Mallory Romanovitch, Qihui Zhu
Copy number variations (CNVs) in the genomes have been suggested to play important roles in human evolution, genetic diversity, and disease susceptibility. A number of assays have been developed for the detection of CNVs, including fluorescent in situ hybridization (FISH), array-based comparative genomic hybridization (aCGH), PCR-based assays, and next-generation sequencing (NGS). In this chapter, we describe a microarray method that has been used for the detection of genome-wide CNVs, loss of heterozygosity (LOH), and uniparental disomy (UPD) associated with constitutional and neoplastic disorders...
2017: Methods in Molecular Biology
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