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article

How to preserve and handle fish liver samples to conserve RNA integrity

Eeva-Riikka Vehniäinen, Maiju Ruusunen, Pekka J. Vuorinen, Marja Keinänen, more

Environmental Science and Pollution Research > 2019 > 26 > 17 > 17204- 17213

As transcriptomic studies are becoming more and more common, it is important to ensure that the RNA used in the analyses is of good quality. The RNA integrity may be compromised by storage temperature or freeze-thaw cycles, but these have not been well studied in poikilothermic fishes. This work studied the effects of tissue storage time and temperature, and freeze-thaw cycles of tissue and extracted...

article

Have you tried spermine? A rapid and cost-effective method to eliminate dextran sodium sulfate inhibition of PCR and RT-PCR

Łukasz Krych, Witold Kot, Katja M.B. Bendtsen, Axel K. Hansen, more

Journal of Microbiological Methods > 2018 > 144 > C > 1-7

The Dextran Sulfate Sodium (DSS) induced colitis mouse model is commonly used to investigate human inflammatory bowel disease (IBD). Nucleic acid extracts originating from these animals are often contaminated with DSS, which is a strong inhibitor of many enzymatic based molecular biology reactions including PCR and reverse-transcription (RT). Methods for removing DSS from nucleic acids extracts exist...

article

Differential expression of PR genes in response to Phytophthora capsici inoculation in resistant and susceptible black pepper (Piper nigrum L.) lines

V. V. Vandana, R. Suseela Bhai

European Journal of Plant Pathology > 2018 > 150 > 3 > 713-724

Differential expression of three important genes encoding pathogenesis related proteins (PR proteins) viz. β-1,3-glucanase (PR-2), osmotin (PR-5) and cytosolic ascorbate peroxidase (cAPX, PR-9) were carried out in Phytophthora susceptible (Sreekara) and resistant (04-P24) black pepper lines compared to uninoculated plants using quantitative reverse transcription PCR (qRT-PCR). Upon Phytophthora capsici...

article

Heterologous expression of PDH47 confers drought tolerance in indica rice

Dhanawantari L. Singha, Narendra Tuteja, Dimple Boro, Girindra Nath Hazarika, more

Plant Cell, Tissue and Organ Culture (PCTOC) > 2017 > 130 > 3 > 577-589

In response to challenge of producing rice plants tolerant to drought stress, Pea DNA Helicase 47 (PDH47) from Pisum sativum under the control of constitutive 35S CaMV promotor was introduced into indica rice cultivar ASD16 mediated through Agrobacterium tumefaciens using immature embryos as explant. PCR positive transgenic rice lines showed varied levels of PDH47 transcripts as evident by semi-quantitative...

article

Expression of α‐glucosidase during morphological differentiation in the basidiomycetous fungus Pholiota microspora

Gang Zhu, Mirai Hayashi, Norihiro Shimomura, Takeshi Yamaguchi, more

Journal of Basic Microbiology > 56 > 9 > 1036 - 1045

The α‐glucosidase gene from Pholiota microspora, designated PnGcs, was amplified and characterized. The open reading frame region of PnGcs, from ATG to the stop codon, is 2937 bp and encodes a protein of 979 amino acids with a signal peptide of 20 amino acids at the N‐terminus. The predicted amino acid sequence of PnGcs indicated that it is a glycoside hydrolase family 31 protein. Quantitative reverse...

article

Reference genes selection for quantitative gene expression studies in Pinus massoniana L.

Hu Chen, Zhangqi Yang, Ying Hu, Jianhui Tan, more

Trees > 2016 > 30 > 3 > 685-696

Key message Evaluation and selection of reference genes in Pinus massoniana L. (PM) for gene expression studies of various tissues, floral organ development, and abiotic stress. Abstract An important prerequisite for obtaining accurate gene expression results using quantitative real-time PCR is the selection of...

article

Wheat WCBP1 encodes a putative copper-binding protein involved in stripe rust resistance and inhibition of leaf senescence

Xin Li, Taiguo Liu, Wanquan Chen, Shengfu Zhong, more

BMC Plant Biology > 2015 > 15 > 1 > 1-15

Background Stripe rust, a highly destructive foliar disease of wheat (Triticum aestivum), causes severe losses, which may be accompanied by reduced photosynthetic activity and accelerated leaf senescence. Methods We used suppression subtractive hybridization (SSH) to examine the mechanisms of resistance in the resistant wheat line L693 (Reg. No. GP-972, PI 672538), which was derived from a lineage...

article

Expression patterns of sex‐determination genes in single male and female embryos of two Bactrocera fruit fly species during early development

J. L. Morrow, M. Riegler, M. Frommer, D. C. A. Shearman

Insect Molecular Biology > 23 > 6 > 754 - 767

In tephritids, the sex‐determination pathway follows the sex‐specific splicing of transformer (tra) mRNA, and the cooperation of tra and transformer‐2 (tra‐2) to effect the sex‐specific splicing of doublesex (dsx), the genetic double‐switch responsible for male or female somatic development. The Dominant Male Determiner (M) is the primary signal that controls this pathway. M, as yet uncharacterized,...

article

Cloning, expression and phylogenetic analysis of a divergent laccase multigene family in Auricularia auricula-judae

XiuZhi Fan, Yan Zhou, Yang Xiao, ZhangYi Xu, more

Microbiological Research > 2014 > 169 > 5-6 > 453-462

Laccases (p-diphenol: oxygen oxidoreductase; EC 1.10.3.2) are multi-copper oxidases encoded by gene family in white rot fungi. Auricularia auricula-judae is one kind of white rot fungi with a soft, jelly-like texture and an ear-like shape. In the present study, seven laccase genes containing the signature sequences L1–L4 were isolated from A. auricula-judae strain Au916 on the basis of the mycelium-derived...

article

Selection and evaluation of novel reference genes for quantitative reverse transcription PCR (qRT-PCR) based on genome and transcriptome data in Brassica napus L.

Hongli Yang, Jing Liu, Shunmou Huang, Tingting Guo, more

Gene > 2014 > 538 > 1 > 113-122

Selection of reference genes in Brassica napus, a tetraploid (4×) species, is a very difficult task without information on genome and transcriptome. By now, only several traditional reference genes which show significant expression differentiation under different conditions are used in B. napus. In the present study, based on genome and transcriptome data of the rapeseed Zhongshuang-11 cultivar, 14...

article

Cloning and characterization of two allelic glyceraldehyde-3-phosphate dehydrogenase genes in Auricularia auricula-judae

Xiuzhi Fan, Yan Zhou, Yang Xiao, Yinbing Bian

World Journal of Microbiology and Biotechnology > 2014 > 30 > 1 > 181-189

Two allelic variants of the gpd gene, Gpd ^a and Gpd ^b, were isolated based on a putative glyceraldehyde-3-phosphate dehydrogenase encoding sequence from the transcriptome of Auricularia auricula-judae strain Au916. The two alleles were found to have a 73 bp length discrepancy and 39 SNP variations. Both of the genomic DNA sequences of two alleles were interrupted by five introns, and encoded a...

article

Gene expression signatures that can discriminate oral leukoplakia subtypes and squamous cell carcinoma

Nobuo Kondoh, Shuri Ohkura, Masaaki Arai, Akiyuki Hada, more

Oral Oncology > 2007 > 43 > 5 > 455-462

The purpose of this study is to generate a classifier for oral squamous cell carcinoma (OSCC) and leukoplakias (LPs), and evaluate its diagnostic potential. In order to identify marker gene candidates, differential gene expression between LPs and OSCCs were examined by cDNA microarray. The expression of 118 marker gene candidates was further evaluated by quantitative reverse transcription-PCR (QRT-PCR)...

article

Constitutional high expression of an APC mRNA isoform in a subset of attenuated familial adenomatous polyposis patients

Tiziana Venesio, Antonella Balsamo, Christian Sfiligoi, Luca Fuso, more

Journal of Molecular Medicine > 2007 > 85 > 3 > 305-312

Familial adenomatous polyposis is an inherited condition associated with hundreds to thousands of colorectal adenomas conferring a very high risk of cancer at a young age. In addition to “classical” form, there is also an attenuated polyposis, with fewer than 100 polyps and a delayed age of cancer onset. Both classical and attenuated polyposis are characterized by a relevant phenotypic heterogeneity...

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Keywords

QUANTITATIVE REVERSE TRANSCRIPTION PCR (13)
TRANSCRIPTOME (3)
REFERENCE GENE (2)
PINUS MASSONIANA L. (1)
APC GENE (1)
AURICULARIA AURICULA-JUDAE (1)
PUCCINIA STRIIFORMIS (1)
TRITICUM AESTIVUM (1)
ABIOTIC STRESS (1)
AGROBACTERIUM (1)
ALLELE (1)
ALTERNATIVE SPLICING (1)
ATTENUATED FAMILIAL ADENOMATOUS POLYPOSIS (AFAP) (1)
AURICULARIA AURICULA-JUDAE (1)
B. NAPUS (1)
BACTROCERA (1)
BLEACHED KRAFT PULP MILL EFFLUENT (1)
CYTOCHROME P450 (1)
CYTOSOLIC ASCORBATE PEROXIDASE (1)
DEAD-BOX HELICASES (1)
DEXTRAN SODIUM SULFATE (1)
DOMINANT MALE DETERMINER (1)
DSS (1)
DSS INHIBITION (1)
FLORAL ORGAN DEVELOPMENT (1)
FRUITING BODY FORMATION (1)
GENE EXPRESSION PROFILING (1)
GENETIC TRANSFORMATION (1)
GH31 (1)
GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE (1)
HEAD AND NECK/ORAL CANCER (1)
INDICA RICE (1)
LACCASE (1)
LEUKOPLAKIA (1)
LIVER (1)
MICROARRAY (1)
MRNA ISOFORM (1)
NORMALIZATION (1)
OSMOTIN (1)
PATHOGENESIS RELATED PROTEINS (1)
PDH47 (1)
PHOTOSYNTHESIS (1)
PHYLOGENETIC ANALYSIS (1)
QUANTITATIVE PCR (1)
RNA INTEGRITY (1)
RT-QPCR (1)
SAMPLE STORAGE (1)
SEX‐DETERMINATION (1)
SINGLE‐EMBRYO (1)
SNP (1)
SPERMINE (1)
STABILITY (1)
SUPPRESSION SUBTRACTIVE HYBRIDIZATION (1)
Α‐GLUCOSIDASE (1)
Β-1,3-GLUCANASE (1)
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Elsevier (4)
Wiley (2)

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