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PubMed1997

Puberty influences expression of phospholipid hydroperoxide glutathione peroxidase (GPX4) in rat testis: probable hypophysis regulation of the enzyme in male reproductive tract.

Mammalian spermatozoa are unusually rich in polyunsaturated fatty acids, a property that predisposes them to the deleterious effects of oxygen free radicals. Mouse and human spermatozoa utilize glutathione peroxidase, (GPX), to inactivate oxygen free radicals. In the GPX super-family there is the enzyme phospholipid hydroperoxide glutathione peroxidase (GPX4) that specifically protects membrane phospholipids against peroxidation. GPX4 is present, primarily, in testis where its enzymatic activity seems to be present only after puberty. In order to clarify this question we utilized total RNA from rat testis, liver and lung to carry out cDNA synthesis and the following RT-PCR amplification of cDNA products by using specific primers of rat liver sequence. RT-PCR products of the expected size for GPX4 (525 bp) were obtained from the three tissues. At last, these fragments were submitted to sequencing analysis. Here we demonstrate that the sequence analysis of rat testis GPX4 coding region is identical to that of rat liver and lung; however puberty influences the expression pattern of rat testis GPX4. In fact Northern blot analysis of total RNA from normal and pre-puberal hypophysectomized rats demonstrates the absence of a specific GPX4 mRNA in total RNA from pre-puberal hypophysectomized rat testis; on the other hand this specific transcript is present in both normal rat testis and liver and in pre-puberal hypophysectomized rat liver. Expression pattern of GPX4 is very low in lung both in post-puberal and pre-puberal hypophysectomized rats. Therefore hypophysis could regulate GPX4 transcript in rat testis.

Amino Acid Sequence↗
PubMed1998

Cloning and expression of the catalytic domain from rat hepatoma H35 cell GDP-fucose:GM1 alpha 1-->2fucosyltransferase, an enzyme which is activated during early stages of chemical carcinogenesis in rat liver.

A ganglioside GM1-specific alpha 1-->2fucosyltransferase is induced during the early stages of chemical carcinogenesis with N-2-acetylaminofluorene (AAF) in rat liver hepatocytes. The induction of this enzyme gives rise to the expression of a fucose-containing ganglioside with the same determinant structure as blood group B on a GM1 ganglioside core. Fucoganglioside synthesis is not found in normal rat liver but is elevated in premalignant liver and is often highly expressed in derived rat hepatoma cell lines. Based upon the consensus sequence from portions of previously cloned human, rabbit, and rat alpha 1-->2fucosyltransferase enzymes, primers were designed which were used in RT-PCR experiments with rat hepatoma H35 cell total RNA to generate cDNAs encoding the extracellular, catalytic domain of the H35 cell alpha 1-->2fucosyltransferase. Sequencing of these PCR fragments showed them to encode a novel enzyme with high homology to other cloned enzymes, particularly secretor alpha 1-->2fucosyltransferases. The derived sequence indicated that the 3' portion of the gene was virtually identical to the alpha 1-->2fucosyltransferase B (FTB) fragment reported earlier in rat PROb colon-adenocarcinoma cells (J-P. Piau et al. Biochem. J. 300, 623-626, 1994). A PCR product corresponding to the H35 cell alpha 1-->2fucosyltransferase was obtained from total RNA isolated from F344 rat liver after 0.03% N-2-acetylaminofluorene administration. No PCR product was obtained from total RNA isolated from normal F344 liver using PCR primers for the H35 cell alpha 1-->2fucosyltransferase. The H35 cell alpha 1-->2fucosyltransferase was expressed in the pPROTA vector and the derived fusion protein demonstrated the ability to transfer fucose to ganglioside GM1 but not to the neolacto-series acceptor nLcOse4Cer.

2-Acetylaminofluorene↗
PubMed1995

Secondary structure in the 3' UTR of EGF and the choice of reverse transcriptases affect the detection of message diversity by RT-PCR.

The secondary structure in mRNA is essential for many processes, but it can present a technical problem in making full-length cDNA with reverse transcriptases. Furthermore, different reverse transcriptases have differing abilities to transcribe through regions with secondary structure, which can alter the products obtained by reverse-transcribing RNA and then PCR-amplifying the product (RT-PCR). We have been interested in studying the posttranscriptional regulation of epidermal growth factor by RT-PCR and have tested the ability of several reverse transcriptases to reverse transcribe the 3'-untranslated region (3'UTR), a region that contains substantial secondary structure. When low levels of either total RNA or poly(A)+ mRNA were used, we found avian myeloblastosis virus reverse transcriptase (AMV-RT) to be the most robust of all the enzymes tested. Furthermore, contrary to reports that AMV-RT is inhibited by tRNA--which should make it less effective than Moloney murine leukemia virus reverse transcriptase (MMLV-RT) at reverse-transcribing total RNA--adding tRNA to poly(A)+ RNA actually increased the amount of specific RT-PCR product obtained with AMV-RT while it decreased the amount of product and enhanced mispriming with MMLV-RT. We found that pre-incubation of the oligo(dT) primer with total RNA at elevated temperature prior to reverse transcription improved the efficiency of both native and modified MMLV-RTs. These findings support the concept that secondary structures in RNA differentially affect the abilities of different reverse transcriptases to detect transcript diversity and raise the possibility that such structures could affect quantitation using RT-PCR with internal mRNA standards.

Avian Myeloblastosis Virus↗
PubMed1992

Search for Coxsackievirus B3 RNA in idiopathic dilated cardiomyopathy using gene amplification by polymerase chain reaction.

A polymerase chain reaction (PCR) amplification assay was developed to detect Coxsackievirus B3 ribonucleic acid (RNA) in blood and myocardial tissue of explanted hearts from 40 patients who underwent cardiac transplantation and in 1 normal heart. Twenty-one patients were affected by idiopathic dilated cardiomyopathy of different duration and 19 by coronary artery disease. Coxsackievirus B3 in vitro infected Vero cells and cells infected by related human enteroviruses (Coxsackievirus B2, B4, and poliovirus 1) were used as reaction controls. PCR was performed using 4 pairs of primers homologous to Coxsackie-virus B3 sequences. Three sets were located in regions of the genome conserved at nucleotide level between several enterovirus species (replicase gene, 5' noncoding region), while one was located in a Coxsackievirus B3-specific region (VP1 gene). Total RNA was prepared by acid guanidinium isothiocyanate extraction from tissue stored frozen at -80 degrees C. One microgram of total RNA was retrotranscribed with either antisense primer or with random hexanucleotide primers and then subjected to 40 cycles of amplification. PCR products were separated by electrophoresis on a 10% polyacrylamide gel, electrotransferred to a nylon membrane and then hybridized to oligonucleotide probes specific for the coxsackievirus B3 genome radiolabeled with radioactive isotope of phosphorous. All pairs of primers yielded specific amplification products when tested on Coxsackievirus B3-infected Vero cells, with a sensitivity of 1 infected cell out of 10(5) to 10(6) cells starting from 1 microgram total RNA. Primer sets for regions of Coxsackievirus B3 genome highly conserved between related enteroviral species gave positive amplification also when challenged with RNA from cells infected by Coxsackievirus B2, B4 and poliovirus 1.

Adult↗
PubMed1995

Load effects on gene expression during cardiac hypertrophy.

Hemodynamic load is a primary regulator of cardiac mass. A potential proximal event in this regulatory pathway is thought to be the induction of immediate early genes, and markers of this process include the re-expression of genes for fetal sarcomeric proteins and the ventricular expression of atrial natriuretic factor (ANF). Previous in vivo models which have examined these questions have often neither quantified myocardial loading nor accounted for covariables which may affect gene expression such as the renin-angiotensin-aldosterone system, the sympathetic nervous system, or baroreceptors. Thus, whether load alone is sufficient to induce immediate early genes, which may ultimately result in cardiac hypertrophy, remains unknown. In the present study two models of right ventricular (RV) pressure overload were created by partially occluding the pulmonary artery (PA), either with a balloon catheter for 1 or 4 h, or with a surgically placed PA band for 12, 24, or 48 h. Serum catecholamine concentrations were determined in a subset of RV pressure overload cats at basal state, after 5 min of balloon inflation, and after 1 h of balloon inflation to examine the effects of this systemic trophic factor on IEG induction. Northern blot analysis for c-fos, egr-1, alpha-skeletal actin, and ANF from paired RV and left ventricular (LV) RNA allowed the effect of load (selectively increased in the RV) to be separated from other systemic variables (present in both ventricles). The relative signal intensities of the optical density of RV and LV mRNA autoradiograms were determined from northern blots, alternate lanes of which were loaded with 7.5 micrograms of total RNA from RV and LV tissue from the same cat. Partial PA occlusion caused RV systolic pressure to increase from a control value of 22 +/- 1 mmHg to 57 +/- 6 mmHg after 1 h, 59 +/- 5 mmHg after 4 h, and 58 +/- 5 mmHg after 48 h of RV pressure overload (RVPO). Serum norepinephrine and epinephrine levels at both 5 and 60 min of RVPO were not significantly different from basal levels. The RV/LV ratios of mRNA for both egr-1 and c-fos were equal in control and 48 h PA banded animals, but were increased in the 1 and 4 h balloon RVPO cats. The RV/LV ratio of mRNA for alpha-skeletal actin was equal in the basal state and did not increase after 12, 24, or 48 h of RVPO. After 48 h of RVPO, total RNA was increased in the RV compared with the LV (1.9 +/- 0.1 v 1.1 +/- 0.1 micrograms/g tissue, P < 0.05). ANF expression was present in the RV after 48 h of RVPO, but absent in same-animal LV and all control ventricles. Thus, while increased load alone did not alter the expression of alpha-skeletal actin, it was sufficient both to induce increased expression of two distinct classes of immediate early genes, as well as ANF, and to increase total RNA, indicating hypertrophic growth initiation.

Animals↗
PubMed1979

RNA synthesis of vesicular stomatitis virus-infected cells: in vivo regulation of replication.

Pulse-labeling of vesicular stomatitis virus-infected HeLa and BHK cells with [3H]uridine throughout the infectious cycle demonstrated two peaks of uridine incorporation into virus-specific RNA molecules. By separating total RNA synthesis into replication and transcription products, we showed that replication occurs over a shorter period of time in one peak synthesis. The biphasic nature of uridine incorporation is in part due to a general membrane phenomenon of reduced metabolite transport during vesicular stomatis virus infection and in part due to the apparent uncoupling of replication and transcription. A change in the ratio of newly synthesized plus and minus strands of the genome length (42S) RNA was found as the infection proceeded. Early in the infection, plus-stranded 42S RNA comprised 40% of the total genome length RNA synthesis, whereas late in infection, only 15 to 20% of the 42S RNA synthesized was complementary to the virion minus strand. Our data suggest that the rate of synthesis of plus-stranded 42S RNA was constant throughout the infection. The rate of virus release was determined by monitoring the uptake of [3H]uridine into released virus particles. Virus maturation and release are closely associated with the assembly of 42S RNA-containing nucleocapsids.

Animals↗
PubMed1990

Arginine vasopressin gene regulation in the homozygous Brattleboro rat.

The Brattleboro rat, which has an autosomally recessive form of diabetes insipidus, has been reported to have a marked defect in the regulation of arginine vasopressin (AVP) gene expression. However, it is not known whether this is a primary genetic defect or occurs secondary to the urinary water losses which occur in the absence of circulating AVP in the Brattleboro rat. This present study was therefore undertaken to study AVP gene regulation in the Brattleboro rat after chronic AVP treatment by osmotic minipump for 2 wk. In Brattleboro rats without AVP treatment, neither urinary osmolality (Uosm) nor hypothalamic AVP mRNA was significantly changed after 24 h of fluid deprivation (Uosm, 413 +/- 33 to 588 +/- 44, NS; AVP mRNA, 39.33 +/- 2.95 to 46.39 +/- 2.71 pg/micrograms total RNA, NS). In contrast, when Brattleboro rats were treated with AVP for 2 wk, the regulation of AVP gene occurred in response to 24 h of fluid deprivation. In these studies, hypothalamic AVP mRNA was significantly increased compared with the Brattleboro rats still receiving AVP with free access of water (28.9 +/- 3.5 vs. 65.0 +/- 3.3 pg/micrograms total RNA, P less than 0.001). Further studies in Long-Evans rats demonstrate a similar response to a comparable degree of fluid deprivation as Uosm and AVP mRNA were significantly increased after 72 h of fluid deprivation (Uosm, 1,505 +/- 186 to 5,460 +/- 560 mosmol/kg, P less than 0.001; AVP mRNA, 31.7 +/- 3.9 to 77.5 +/- 4.6 pg/micrograms total RNA, P less than 0.001). These results indicate that AVP-replaced homozygous Brattleboro rats can regulate AVP gene expression normally in response to fluid deprivation. This finding indicates that the defect in AVP gene regulation in the Brattleboro rat not receiving AVP replacement is a secondary phenomenon rather than a primary genetic defect.

Animals↗
PubMed2004

[Progress towards the use of DNA microarray technology for the study of wild Plasmodium strains].

Plasmodium falciparum is still a major cause of mortality in the world. Due to growing drug resistance in most endemic countries, the use of tools allowing large-scale analysis of P. falciparum biology is increasingly urgent. In addition to gene sequence data, post-genomic methods including microarray-based transcript profiling allow complete Plasmodium gene expression. However, application of this technology has been limited to study of samples presenting large quantities of total RNA (8 microg to 50 microg). Indeed at least two replicas (one technical and one biological) are necessary to ensure the statistical strength of results. This constraint excludes the use of biological materials hardly available and of wild strain samples. Many methods have been developed to facilitate the use of microarray technology with smaller quantities of total RNA. Currently the use of amplification techniques, various fluorochrome markers, and labelled cDNA and/or RNA probes avoiding all amplification steps, to enhance detection sensitivity has enabled reliable assays to be performed with less material. However these enhancement techniques appear to have a biasing effect on results and the use of powerful new markers is still limited for technical and practical reasons. At the present time radioactive labeling is the most reliable technique for assays using small quantities of total RNA. This approach is not only compatible with competitive hybridization but also enables all microarray screening criteria. Findings from our laboratory support the effectiveness of radioactive labeling for microarray-based determinations on P. falciparum.

Animals↗
PubMed2006

Dynamic alteration of telomerase expression and its diagnostic significance in liver or peripheral blood for hepatocellular carcinoma.

AIM: To investigate the dynamic alteration of telomerase expression during development of hepatocellular carcinoma (HCC) and its diagnostic implications in liver tissues or peripheral blood mononuclear cells for HCC. METHODS: Dynamic expressions of liver telomerase during malignant transformation of hepatocytes were observed in Sprague-Dawly (SD) rats fed with 0.05% of 2-fluoenyacetamide (2-FAA). Total RNA and telomerase were extracted from rat or human liver tissues. The telomerase activities in livers and in circulating blood were detected by a telomeric repeat amplification protocol-enzyme-linked immunosorbent assay (TRAP-ELISA), and its diagnostic value was investigated in patients with benign or malignant liver diseases. RESULTS: The hepatoma model displayed the dynamic expression of hepatic telomerase during HCC development. The telomerase activities were consistent with liver total RNA levels (r = 0.83, P<0.01) at the stages of degeneration, precancerosis, and cancerization of hepatocytes. In HCC patients, the telomerase levels in HCC tissues were significantly higher than in their adjacent non-cancerous tissues, but liver total RNA levels were lower in the former than in the latter. Although the circulating telomerase of HCC patients was abnormally expressed among patients with chronic liver diseases, the telomerase activity was a non-specific marker for HCC diagnosis, because the incidence was 15.7% in normal control, 25% in chronic hepatitis, 45.9% in liver cirrhosis, and 85.2% in HCC, respectively when absorbance value of telomerase activity was more than 0.2. If the value was over 0.6, the incidence was 60% in HCC group and 0% in any of the others (P<0.01) except in two cases with liver cirrhosis. However, the combination of circulating telomerase with serum alpha-fetoprotein level could increase the positive rate and the accuracy (92.6%, 125 of 135) of HCC diagnosis. CONCLUSION: The overexpression of telomerase is associated with HCC development, and its abnormality in liver tissues or in peripheral blood could be a useful marker for diagnosis and prognosis of HCC.

2-Acetylaminofluorene↗
PubMed1992

Transcriptional regulation of neuromodulin (GAP-43) in mouse neuroblastoma clone N1E-115 as evaluated by the RT/PCR method.

The steady-state level of the neuromodulin transcript in the neuron-like N1E-115 cell line was measured with a method combining reverse transcription and the polymerase chain reaction (RT/PCR). Total RNA was isolated from N1E-115 cells and treated with DNAse to remove residual DNA; cDNA was synthesized from this RNA by priming with random hexamers. For PCR amplification, primers for neuromodulin were designed for regions of the coding sequence that were identical in mouse, rat, and human. In one approach (the 'ratio method'), variations in RNA yield and cDNA synthesis efficiency were controlled for by amplifying a reference (housekeeping) gene (glyceraldehyde phosphate dehydrogenase; GAPDH). To control for inter-experimental variations in PCR amplification efficiencies the data were analyzed on semi-logarithmic plots, with which the relative levels of the starting templates could be determined by extrapolating the plots to cycle number zero (0). In another approach with RT/PCR (the 'spiking method'), the absolute level of N1E-115 neuromodulin cDNA was assessed by adding known amounts of cloned human neuromodulin template to the RT/PCR assay of N1E-115 nucleic acid and comparing the increased yield of product across cycles. When the spike was added at either the cDNA level (in the form of double-stranded DNA) or at the total RNA level (as sense RNA), the levels of N1E-115 calculated were virtually the same: 509 fg and 495 fg of coding region per ug total RNA in confluent N1E-115 cells, respectively. Treatment of N1E-115 cells with 2% dimethylsulfoxide for three days elevated neuromodulin mRNA levels 5.6-fold. Conversely, treatment of N1E-115 cells with 100 nM phorbol myristate acetate for 24 h decreased the level of neuromodulin mRNA by 70%. Under carefully controlled conditions and within certain limits of precision, the RT/PCR method appears to be suitable for assessing the level of low abundance mRNA under various pharmacologically-induced conditions.

Animals↗
PubMed1981

Preliminary characterization of the major RNA species from Plasmodium falciparum.

Polyacrylamide gel electrophoresis of the total RNA extracted from cultures of Plasmodium falciparum resolved two major RNA components with estimated molecular weights of 1.3 X 10(6) and 0.72 - 0.74 X 10(6). Oligo(dT)-cellulose column chromatography of the total cellular RNA indicates that more than 90% of the total radiolabeled RNA lacks substantial poly(A) sequences (poly(A)-). Resolution of the poly(A)- fraction on polyacrylamide or agarose gels indicates that the majority of the poly(A)- RNAs are the 1.3 X 10(6) and 0.72 - 0.74 X 10(6) species. This observation was confirmed by two-dimensional oligonucleotide fingerprint analysis of the total cellular RNA as well as the poly(A)- RNA components. Oligonucleotide fingerprint analysis confirmed that the small RNA species is not a breakdown or cleavage product of the larger RNA component. Base ratio analysis of the large and small RNA species indicate that they are typically protozoan type with a low guanine + cytosine (G + C) content. The findings that these two RNA species (i) are the major cellular RNA species, (ii) lack substantial poly(A) sequences, (iii) have estimated molecular weights similar to the ribosomal RNAs obtained from other protozoa, (iv) have a low G + C content (approximately equal to 35 - 37%), and (v) are distinct from one another, indicates that the 1.3 X 10(6) and 0.72 - 0.74 X 10(6) RNA components obtained from P. falciparum cultures are the major ribosomal RNAs.

Animals↗
PubMed2001

Simple, sensitive and accurate method for the quantification of prothrombin mRNA by using competitive PCR.

A method for the quantification of prothrombin (PT) mRNA species in hepatic tissues of rats was developed with the use of competitive PCR. To validate the quantification approach, sequential dilutions of total RNA from one of the samples were reverse transcribed. Their equivalent volumes were amplified together with a known amount of non-homologous competitor cDNA with identical nucleotide primers. The disparate sizes of target and competitor permitted the easy identification and quantification of bands in samples after densitometric analysis of ethidium bromide-stained agarose gels. Ratios of intensities of target and competitor bands were plotted against the initial amounts of total RNA species used, giving a linear relationship. The slope of this line was virtually identical with that obtained when the sample RNA was replaced with recombinant target cDNA, indicating that recombinant cDNA behaved in PCR identically with that made by reverse transcription and permitting the estimation of transcripts in reverse transcription reactions by using the recombinant counterpart of each as a standard. To avoid variation in the final results, the amount of competitor used in the assay was calculated separately from the equivalence point of the reverse-transcribed total RNA of one of the tissue samples; PCR was performed only for the minimum number of cycles required to detect products. A standard curve was made in each PCR run by amplifying differing amounts of recombinant cDNA species of PT or beta-actin together with a constant amount of its competitor. The numbers of transcripts in the tissues were then determined directly by PCR incorporating the same amount of respective competitor (as used in the standard curve) and comparing the ratios of products with the standard curve. Application of this method revealed that the median ratio of PT message to beta-actin message in hepatic tissues of 10 normal rats was 0.37, with a mean+/-S.D. of 0.37+/-0.07 (range 0.27-0.47). Although the method was developed for the quantification of PT transcripts in liver, it can easily be used for non-hepatic tissues as well. The technique is simple, quick and sensitive and requires only a very small amount of substrate.

Animals↗
PubMed2006

Identification of eukaryotic open reading frames in metagenomic cDNA libraries made from environmental samples.

Here we describe the application of metagenomic technologies to construct cDNA libraries from RNA isolated from environmental samples. RNAlater (Ambion) was shown to stabilize RNA in environmental samples for periods of at least 3 months at -20 degrees C. Protocols for library construction were established on total RNA extracted from Acanthamoeba polyphaga trophozoites. The methodology was then used on algal mats from geothermal hot springs in Tengchong county, Yunnan Province, People's Republic of China, and activated sludge from a sewage treatment plant in Leicestershire, United Kingdom. The Tenchong libraries were dominated by RNA from prokaryotes, reflecting the mainly prokaryote microbial composition. The majority of these clones resulted from rRNA; only a few appeared to be derived from mRNA. In contrast, many clones from the activated sludge library had significant similarity to eukaryote mRNA-encoded protein sequences. A library was also made using polyadenylated RNA isolated from total RNA from activated sludge; many more clones in this library were related to eukaryotic mRNA sequences and proteins. Open reading frames (ORFs) up to 378 amino acids in size could be identified. Some resembled known proteins over their full length, e.g., 36% match to cystatin, 49% match to ribosomal protein L32, 63% match to ribosomal protein S16, 70% to CPC2 protein. The methodology described here permits the polyadenylated transcriptome to be isolated from environmental samples with no knowledge of the identity of the microorganisms in the sample or the necessity to culture them. It has many uses, including the identification of novel eukaryotic ORFs encoding proteins and enzymes.

Acanthamoeba↗
PubMed1994

Investigations into size heterogeneity of the alpha B-crystallin mRNA.

alpha B-crystallin is expressed in a variety of developmental, physiological and pathological conditions in a number of tissues. Based on northern blots of total RNA, the existence of at least two size classes of alpha B-crystallin mRNAs has been reported, one smaller predominant species, 0.8-0.9 kb, and the other 1.2 to 1.4 kb. This heterogeneity has been attributed to alternative upstream transcriptional initiation. We have investigated the origin of the size heterogeneity of alpha B-crystallin mRNA by using 5'-upstream-, coding- and 3'-untranslated-region probes in RNAse protection and northern blot assays. RNAse protection assays indicate that there is only one predominant initiation site as previously reported and that the second polyadenylation signal is not used in the rat gene. Importantly, northern blot data obtained with coding region-only probe shows that the size of alpha B mRNA detected in the heart and the lens is similar (0.78 kb) in poly A+ as well as in total RNA. On the other hand, in the brain and in the lung, the larger hybridizing species (1.05 kb and 1.22 kb respectively) seen in total RNA are not detected in poly A+RNA which shows a 0.95 kb species in both tissues. The 5' upstream probe (-1 to -499) produces weak hybridization patterns in the brain and the lung, similar to those obtained with coding region-only probe. The 5' probe did not show hybridization in the heart and the lens RNAs. These data suggest that upstream initiations represent a minor population of transcripts and that higher size transcripts (about 500 bp larger) actually represent non-polyadenylated RNAs that may not contribute to the generation of the actual gene product.

Animals↗
PubMed2004

Pregnancy-associated changes in genome-wide gene expression profiles in the liver of cow throughout pregnancy.

The objective of the present study was to fabricate and use a bovine liver complementary DNA (cDNA) microarray to profile genome-wide gene expressions in the liver of cow throughout pregnancy. A cDNA library was prepared from liver total RNA collected from cows during estrous cycle and pregnancy, and from fetuses at different stages of pregnancy. The sequenced clones were compiled and annotated by basic local alignment search tool (BLASTn) and spotted onto glass slides. The annotated liver array represented 2675 genes. Of which, 1442 were known genes while 617 sequences had matches with sequences found in expressed sequence tags databases. In addition, 616 unknown sequences were found and these sequences may possibly be identified as candidates for novel bovine genes. For gene expression profiling studies, total RNA from livers of cows slaughtered on days 19, 27-28, 49-58, 150, and 245 of pregnancy (test RNAs) was separately reverse transcribed and labeled with either cyanine 5-fluorescent dye (Cy5) or Cy3. The test samples were individually compared with liver total RNA collected from nonpregnant cycling cows (control RNA) after reverse transcription and labeling with the opposite dye following a two-color hybridization method. After scanning, image acquisition, and normalization, genes that showed either more than 1.5-fold (test/control) induction or repression were selected for further analyses. Hierarchical clustering algorithm showed a clear induction of most liver genes on days 27-28 of pregnancy. Self-organizing maps algorithm identified groups of genes whose differential expression patterns were similar across pregnancy. In conclusion, we described fabrication of a bovine liver cDNA microarray, and demonstrate, for the first time, differential expression patterns of a large number of coregulated liver genes in parallel throughout pregnancy in the bovine.

Algorithms↗
PubMed1998

Expression of smooth muscle caldesmon in developing chicken gizzard.

Caldesmon is an actin/calmodulin/tropomyosin protein located in the thin filaments of smooth muscle cells and microfilaments of nonmuscle cells. Two isoforms of caldesmon, h- and l-types, shown to exist in vertebrate smooth and nonmuscle cells respectively, are produced by alternative splicing of the caldesmon mRNA encoded by a single gene. To study the expression of smooth muscle specific h-caldesmon during the differentiation of mesenchymal cells into smooth muscle cells, soluble protein and total RNA from the gizzard primordium in the gut region of 5-day and gizzards of 7-, 9-, 13-, 17- and 21-day embryos and 2-days post-hatch chicks were extracted and analyzed for caldesmon expression at both protein and mRNA levels. Western blot analysis of proteins and immunofluorescence microscopy of tissue section were carried out using an antibody specific for h-caldesmon. Total RNA was analyzed by Northern blotting using a caldesmon cDNA probe, and h- and l-caldesmon cDNAs were identified due to the difference in their molecular sizes (4.8 and 4.1 kb respectively). The mRNA was also analyzed by reverse transcribed-polymerase chain reaction (RT-PCR) and Southern blot analysis. Our results show that the I-caldesmon mRNA was expressed at higher levels in the gizzard primordium during the early stages of development, and decreased gradually during growth. The h-caldesmon protein and mRNA, not expressed at day 5, is minimally expressed at day 7 and is fully turned on by day 9. Additionally, sequence analyses of the RT-PCR products of I-caldesmon showed that it lacked the spacer region, as predicted. RT-PCR analysis of total RNA gave two h-caldesmon fragments. These two fragments were identified as two different isoforms of h-caldesmon since they both contained the spacer region. They also showed homology in the region of exon 4 had differences in the region of exon 3b.

Animals↗
PubMed1981

Four fluorochromes for the demonstration and microfluorometric estimation of RNA.

Microfluorometric estimates of total RNA were made in selected test material stained with berberine sulfate, acridine orange, and Hoechst 33258. These measurements were compared with those obtained with propidium iodide, which is known to interact only with double-stranded nucleic acids. It was observed that all of the fluorochromes, including propidium iodide, yielded very similar patterns of fluorescence in the various types of material tested. In isolated thymocyte and hepatocyte nuclei stained with either propidium iodide or Hoechst 33258 at pH 2, it was evident that RNA could be estimated only indirectly by measuring the amount of fluorescence before and after extraction with RNase. It was apparent that the total fluorescence of small thymocyte nuclei was affected much less by RNase extraction than that of 2c hepatocyte nuclei. Attempts to obtain direct estimates of RNA by exposing the preparations to DNase were not successful: the fluorescence of thymocyte nuclei dropped almost to zero, and hepatocyte nuclei could no longer be assigned to distinct ploidy classes. In addition, since the highly condensed chromatin of thymocyte nuclei was stained much more prominently than the looser chromatin of hepatocyte nuclei with Hoechst 33258, it was apparent that this fluorochrome - when used at pH 2 - has potential usefulness as a "probe" of organizational differences in chromatin.

Acridine Orange↗
PubMed1982

[Effect of gibberellic acid on RNA synthesis in dwarf peas].

The effect of gibberellic acid (GA) on total RNA and polysomal poly-[A]+-RNA synthesis in epicotylia and embryos of dwarf pea of two varieties differing in their physiological sensitivity to GA was studied. It was found that incubation with GA increases the accumulation of total RNA in pea epicotylia, var. "Pioner" and "Polzunok". The maximal stimulation of RNA accumulation makes up to 40% for the low sensitivity variety "Polzunok" and 150% for the highly sensitive variety "Pioner". GA increases the synthesis of polysomal poly (A)+-mRNA in 5-year-old pea sprouts and that of newly synthesized poly (A)+-mRNA in epicotylian polysomes of both varieties 5, 24, 48 and 72 hrs after incubation with GA. GA at concentrations of 10(-6) and 10(-5) stimulates the incorporation of [3H]uridine into polysomal mRNA during the first 1--3 hours after treatment and enhances the accumulation of newly synthesized mRNA in pea embryonic polyribosomes. The stimulating effect is directly proportional to the dose of the hormone. The mechanisms of GA effect on the transcription and translation in pea plant cells are discussed.

Gibberellins↗