scholarly journals CDNA Subtraction

2020 ◽  
Author(s):  
Keyword(s):  
2002 ◽  
Vol 10 (2) ◽  
pp. 93-102 ◽  
Author(s):  
L. Elaine Epperson ◽  
Sandra L. Martin

Hibernators in torpor dramatically reduce their metabolic, respiratory, and heart rates and core body temperature. These extreme physiological conditions are frequently and rapidly reversed during the winter hibernation season via endogenous mechanisms. This phenotype must derive from regulated expression of the hibernator’s genome; to identify its molecular components, a cDNA subtraction was used to enrich for seasonally upregulated mRNAs in liver of golden-mantled ground squirrels. The relative steady-state levels for seven mRNAs identified by this screen, plus five others, were measured and analyzed for seasonal and stage-specific differences using kinetic RT-PCR. Four mRNAs show seasonal upregulation in which all five winter stages differ significantly from and are higher than summer (α2-macroglobulin, apolipoprotein A1, cathepsin H, and thyroxine-binding globulin). One of these mRNAs, α2-macroglobulin, varies during the winter stages with significantly lower levels at late torpor. None of the 12 mRNAs increased during torpor. The implications for these newly recognized upregulated mRNAs for hibernation as well as more global issues of maintaining steady-state levels of mRNA during torpor are discussed.


2001 ◽  
Vol 360 (1) ◽  
pp. 107-115 ◽  
Author(s):  
Abinash Chandra MISTRY ◽  
Shinji HONDA ◽  
Shigehisa HIROSE

Using a Japanese-eel (Anguilla japonica) gill cDNA subtraction library, two novel β-d-galactose-binding lectins were identified that belong to group VII of the animal C-type lectin family. The eel C-type lectins, termed eCL-1 and eCL-2, are simple lectins composed of 163 amino acid residues, including a 22-residue signal peptide for secretion and a single carbohydrate-recognition domain (CRD) of ∼ 130 residues typical of C-type lectins. The galactose specificity of the CRD was suggested by the presence of a QPD motif and confirmed by a competitive binding assay. Using Ruthenium Red staining, the lectins were shown to bind Ca2+ ions. SDS/PAGE showed that native eCL-1 and eCL-2have an SDS-resistant octameric structure (a tetramer of disulphide-linked dimers). Northern and Western blot analyses demonstrated high-level expression of eCL-1 and eCL-2 mRNAs and their protein products in gills from freshwater eels, which decreased markedly when the eels were transferred from freshwater to seawater. Immunohistochemistry showed that the eel lectins are localized in the exocrine mucous cells of the gill.


2003 ◽  
pp. 601-609 ◽  
Author(s):  
Damian L. Weaver ◽  
César Núñez ◽  
Clare Brunet ◽  
Victoria Bostock ◽  
Gerard Brady
Keyword(s):  
Rt Pcr ◽  

2004 ◽  
Vol 16 (2) ◽  
pp. 245
Author(s):  
O. Suzuki ◽  
T. Hata ◽  
M. Koura ◽  
Y. Noguchi ◽  
K. Takano ◽  
...  

During the first month after birth, synchronous follicular growth occurs in the ovary of immature mice (first wave). Previously, we showed that mouse oocytes during the first wave were more competent developmentally in older females (Suzuki O et al., 2002 Theriogenology 57, 628 abst), although the numbers of mature oocytes did not differ with female age (17, 18, and 24 days old). In this study, we examined the genetic factors that affect the developmental competence of mouse oocytes during the first wave using suppression subtractive hybridization (SSH). Oocytes collected from 17- and 24-day-old B6D2F1 females (D17 and D24, respectively) without hormonal treatment were matured in Waymouth medium supplemented with pyruvate (0.23mM), antibiotics, bovine fetuin (1mgmL−1), and polyvinylpyrrolidone (3mgmL−1). After 17-h culture at 37°C in an atmosphere of 5% CO2, 5% O2, and 90% N2, total RNA was isolated from oocytes whose germinal vesicles had broken down (mature oocytes), separately, in three independent culture groups per age (each group contained oocytes from four animals) using Cell-to-cDNA Cell Lysis Buffer (Ambion, Austin, TX, USA). Some of the total RNA from each independent group was pooled by age (total of RNA from approximately 100 oocytes per age) and used for SSH. A SMART cDNA Synthesis Kit (Clontech, Palo Alto, CA, USA) was used to reverse-transcribe total RNA to cDNA. SSH was performed with a PCR-Select cDNA Subtraction Kit (Clontech). The subtracted PCR products were cloned into pGEM-T vector (Promega, Madison, WI, USA). Clones from the subtracted library (D24−D17) were sequenced and their identities were examined using the NCBI BLAST search. The differential expression of candidate genes preferentially expressed in mature D24 oocytes suggested by SSH was confirmed with cDNA transcribed separately in the three independent culture groups per age using real-time quantitative PCR with an ABI Prism 7900HT with TaqMan technology (Applied Biosystems, Foster City, CA, USA). Of 513 clones sequenced, the top six preferentially-expressed candidate genes in more developmentally-competent D24 oocytes were spindlin (20 clones), bmi-1 (4 clones), cyclin B1 (4 clones), E330034G19Rik (4 clones), Jagged1 (4 clones), and Ndfip2 (4 clones). The expression of spindlin in mature D24 oocytes (relative threshold cycle: −3.8±0.7, mean±SD) was confirmed to be approximately 11-fold higher than in D17 oocytes (−0.3±1.5) when GAPDH was used as an internal control (P<0.05, t-test). Quantitative analyses of mRNA expression of the remaining genes are now under way. Our results suggest that spindlin is one of the key factors leading to the acquisition of developmental competence in mouse oocytes during folliculogenesis. Supported by JSPS KAKENHI (No.145716000) and MHLW.


2012 ◽  
Vol 92 (1) ◽  
pp. 80-91 ◽  
Author(s):  
Takumi Okawa ◽  
Yuzo Kurio ◽  
Masahiro Morimoto ◽  
Toshiharu Hayashi ◽  
Takayuki Nakagawa ◽  
...  

Blood ◽  
2002 ◽  
Vol 100 (5) ◽  
pp. 1742-1754 ◽  
Author(s):  
Jung Hoon Ahn ◽  
Yoon Lee ◽  
ChoonJu Jeon ◽  
Sang-Jin Lee ◽  
Byung-Hak Lee ◽  
...  

Recent studies on dendritic cell (DC)–associated genes have been performed using monocyte-derived DCs (MoDCs) in different maturation stages. In our approach, to uncover the novel DC-associated genes and their expression profiles among the different DC subsets, we constructed a subtracted DC-cDNA library from CD1a+, CD14+, and CD11c− DCs by subtracting the genes shared with T cells, B cells, and monocytes, and we then screened the libraries with the aid of microarray technique. The genes showing remarkable specificity to DCs in the microarray analysis were selected and confirmed by semiquantitative reverse transcriptase–polymerase chain reaction. Our investigations revealed the following: (1) Genes highly expressed in myeloid DCs are those involved in antigen uptake/processing/presentation, cell metamorphosis, or chemotaxis. (2) Most of the genes previously identified in MoDCs, such as TARC, ferritin L-chain, lysosomal acid lipase, α- and β-tubulin, osteopontin (Eta-1), and others, are not markedly expressed in CD11c− DCs regardless of their maturation status. On the other hand, specific transcription factors and MHC class II molecules, such as interferon regulatory factor-4 (IRF4) and HLA-DR, are similarly expressed in both DC subsets. (3) CD14+ DCs retain unique features of tissue DCs, as evidenced by the gene expression profile of “no CCR7 but more CCR1” and “no TARC but abundant MCP1 and Eta-1.” (4) The genes for immunoglobulin (Ig) superfamily Z39Ig, CD20-like precursor, glycoprotein NMB (GPNMB), transforming growth factorβ (TGF-β)–induced protein (TGFBI), myeloid DAP12-associated lectin (MDL-1), and 6 novel genes are newly identified as being associated with the phenotypic expression of the DC subsets. These identifications provide important molecular information for further functional studies of the DC subsets.


2012 ◽  
Vol 93 (4) ◽  
pp. 706-715 ◽  
Author(s):  
Grace Fatima ◽  
Ganeshan Mathan ◽  
Vijay Kumar

The pleiotropic HBx protein of hepatitis B virus is linked functionally to the development of hepatocellular carcinoma (HCC) via effectors and signalling pathways of the host. To identify such effectors in a macrocarcinogenic environment, a PCR-based cDNA subtraction analysis was carried out in the X15-myc oncomouse model of HCC. Altogether, 19 categories of genes, mainly involved in protein biosynthesis and the electron-transport chain, were found to be upregulated in the liver of these mice. Ribosomal protein S27a (RPS27a), which is a natural fusion protein of N-terminal ubiquitin and C-terminal extension protein (CEP), topped the list of expressed genes, with >20-fold higher expression compared with its normal level. Sustained and elevated expression of RPS27a in the mouse liver and its moderate expression in cell culture in the presence of HBx suggested an indirect role of RPS27a in hepatocarcinogenesis. Nevertheless, a remarkable change in the intracellular distribution of ubiquitin from cytoplasm to late-endosomal lysosomes, and of CEP from nucleoli to the perinucleolar region/nuclear foci, was observed in the presence of HBx. RPS27a accelerated the progression of the cell cycle and cooperated with HBx in this process. Further, the knockdown of RPS27a expression by RNA interference in an HBx microenvironment led to retarded cell-cycle progression and reduced cell size. Thus, these results suggest strongly that RPS27a could be an effector of HBx-mediated hepatocarcinogenesis.


1994 ◽  
Vol 22 (5) ◽  
pp. 878-879 ◽  
Author(s):  
Theodorus B.M. Hakvoort ◽  
Aad C.J. Leegwater ◽  
Frits A.M. Michiels ◽  
Robert A.F.M. Chamuleau ◽  
Wouter H. Lamers

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