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PubMed2003

Gene expression analysis in human fetal retinal explants treated with docosahexaenoic acid.

PURPOSE: To explore the effect of docosahexaenoic acid (DHA) on gene expression during human fetal retinal maturation. METHODS: Human fetal retinal explants were cultured in serum-free Waymouth's medium supplemented with DHA or oleic acid (OA), using bovine serum albumin (BSA) as the vehicle. After 14 days in culture, fatty acid composition was assessed, and the abundance of 2400 cDNAs was examined with a human cDNA microarray system. RESULTS: Transcript abundance remained unchanged for 82% and 90% of genes in the explants with added DHA or OA, respectively. Decreased expression was detected in 4% and 9% of genes, in explants supplemented with DHA or OA, respectively, whereas, 14% of genes in explants exposed to DHA and only 0.4% of genes in explants treated with OA showed increased expression. Transcripts displaying changes in abundance in explants supplemented with DHA encode for proteins involved in diverse biological functions, including neurogenesis, neurotransmission, and refinement of connectivity. These gene expression changes were not observed in explants supplemented with OA. CONCLUSIONS: The effect of DHA deficiency on retinal function during human development can be partly explained by modifications in retinal gene expression by direct or indirect mechanisms.

DNA, Complementary↗

PubMed1993

Circadian regulation of iodopsin gene expression in embryonic photoreceptors in retinal cell culture.

A circadian clock regulates a number of diverse physiological functions in the vertebrate eye. In this study, we show that mRNA for the red-sensitive cone pigment, iodopsin, fluctuates with a circadian rhythm in chicken retina. Transcript levels increase in the late afternoon just prior to the time of cone disc shedding. Furthermore, iodopsin mRNA levels are regulated similarly by a circadian oscillator in primary cultures of dispersed embryonic chick retina. Nuclear run-on experiments show that the circadian regulation of iodopsin transcript abundance occurs at the level of gene transcription. Our results provide a demonstration of clock-regulated gene expression in a vertebrate preparation maintained in cell culture.

Animals↗

PubMed1997

Cloning and characterization of a serine protease from the human malaria vector, Anopheles gambiae.

The nucleotide and deduced amino acid sequence of a serine protease (AgSp24D) from the human malaria vector, Anopheles gambiae, is presented. The gene product is a 271 amino acid protein that contains the conserved serine, histidine and aspartic acid residues found in serine proteases, and has the highest identity to a serine protease of unknown function from Drosophila melanogaster. In situ hybridization to the polytene chromosomes detects a single band at 24D. Northern analysis reveals only low levels of transcripts in larvae and pupae, but more abundant transcription products occur in adults. Interestingly, this analysis also shows that adult males express much higher levels of AgSp24D mRNA than females. In addition, Plasmodium-refractory mosquitoes express higher levels of AgSp24D mRNA than susceptible mosquitoes although the biological significance of this remains to be examined. The thorax is the primary site for expression in the adults. The lack of a dramatic increase in AgSp24D mRNA levels following blood feeding suggests that this protease is not involved in digestive processes. Transcriptional induction does not follow cold shock, septic wounding, bacterial injection, laminarin injection or CM-Sephadex bead injection.

Amino Acid Sequence↗

PubMed1995

Molecular cloning and functional expression of human parathyroid calcium receptor cDNAs.

Parathyroid cells express a cell surface receptor, coupled to the mobilization of intracellular Ca2+, that is activated by increases in the concentration of extracellular Ca2+ and by a variety of other cations. This "Ca2+ receptor" (CaR) serves as the primary physiological regulator of parathyroid hormone secretion. Alterations in the CaR have been proposed to underlie the increases in Ca2+ set-point seen in primary hyperparathyroidism due to parathyroid adenoma. We have isolated human CaR cDNAs from an adenomatous parathyroid gland. The cloned receptor, expressed in Xenopus oocytes, responds to extracellular application of physiologically relevant concentrations of Ca2+ and other CaR agonists. The rank order of potency of CaR agonists displayed by the native receptor (Gd3+ > neomycin B > Ca2+ > Mg2+) is maintained by the expressed receptor. The nucleotide sequence of the human CaR cDNA predicts a protein of 1078 amino acids with high sequence similarity to a bovine CaR, and displays seven putative membrane-spanning regions common to G protein-coupled receptors. The deduced protein sequence shows potential sites for N-linked glycosylation and phosphorylation by protein kinase C and has a low level of sequence similarity to the metabotropic glutamate receptors. Comparison of the cDNA sequence to that of the normal human CaR gene showed no alteration in the coding region sequence of the CaR in this particular instance of parathyroid adenoma. Human cDNA clones with differing 5'-untranslated regions were isolated, suggesting alternative splicing of the parathyroid CaR mRNA. A rare variant cDNA clone representing a 10 amino acid insertion into the extracellular domain was also isolated. Northern blot analysis of normal and adenomatous parathyroid gland mRNA identified a predominant transcript of approximately 5.4 kilobases, and less abundant transcripts of approximately 10, 4.8 and 4.2 kilobases in RNA from the adenoma. While there is no evidence for alteration of the primary amino acid sequence of the CaR in this adenoma, modulation of CaR biosynthesis through alternative RNA processing may play a role in set-point alterations.

Adenoma↗

PubMed2005

Differential transcriptional activity of plant-pathogenic begomoviruses in their whitefly vector (Bemisia tabaci, Gennadius: Hemiptera Aleyrodidae).

Plant-pathogenic begomoviruses have a complex association with their whitefly vector and aspects concerning virus genetic activity (genome replication and gene transcription) within the insect remain highly controversial. Virus transcript abundance was assessed by quantifying selected gene transcripts of Tomato mottle virus (ToMoV, a New World bipartite begomovirus) and Tomato yellow leaf curl virus (TYLCV, an Old World monopartite begomovirus) in whiteflies (Bemisia tabaci biotype B) after feeding on virus-infected tomato plants and after subsequent transfer to cotton, a plant that is immune to the selected begomoviruses. Real-time RT-PCR was performed using specific primers for three ToMoV genes (AV1, BC1 and BV1) and three TYLCV genes (V1, V2 and C3). The ToMoV gene transcripts rapidly became undetectable in whiteflies following transfer from tomato to cotton, probably because degradation was not accompanied by new synthesis. On the other hand, TYLCV transcripts increased after transfer of whiteflies to cotton, indicating active TYLCV transcription. Interestingly, the difference observed in ToMoV and TYLCV transcripts in the vector parallel observations on the different biological effects of these viruses on whiteflies, i.e. TYLCV, but not ToMoV, reduces whitefly fitness.

Animals↗

PubMed2004

Transcriptional regulation of proline biosynthesis in Medicago truncatula reveals developmental and environmental specific features.

The model legume plant Medicago truncatula accumulates free proline in response to hyperosmotic stress as do many other organisms. In order to analyse the transcriptional regulation of proline biosynthesis in M. truncatula, three cDNAs encoding Delta(1)-pyrroline-5-carboxylate synthetase (P5CS1, P5CS2; EC not assigned) and ornithine delta-aminotransferase (OAT; EC 2.6.1.13) were isolated. The cDNAs shared high homologies with the other plant sequences and genomic organization analysis indicated the presence of two P5CS and two putative OAT genes. The two P5CS genes showed differing transcript level regulation according to organs and in response to osmotic stress. MtP5CS1 steady-state transcript levels in the different plant organs were correlated with proline levels but transcript abundance was unaffected by osmotic stresses. MtP5CS2 transcripts were poorly detected in all organs but were strongly accumulated in shoots of salt-stressed plants. We suggest a specific of MtP5CS1 and MtP5CS2 as a housekeeping product and as a stress specific isoform, respectively. MtOAT transcripts were predominantly detected in roots and shoots of unstressed plants. Salt-stress treatment induced the accumulation of MtOAT transcripts in the whole plant whatever the developmental stage. In salt-stressed roots, a positive correlation was found between proline and MtOAT transcript accumulation. These results suggest that both ornithine and glutamate biosynthesis pathways contribute to the osmotic stress-induced proline accumulation in M. truncatula.

Journal Article↗

PubMed2006

Two-dimensional transcriptome profiling: identification of messenger RNA isoform signatures in prostate cancer from archived paraffin-embedded cancer specimens.

The expression of specific mRNA isoforms may uniquely reflect the biological state of a cell because it reflects the integrated outcome of both transcriptional and posttranscriptional regulation. In this study, we constructed a splicing array to examine approximately 1,500 mRNA isoforms from a panel of genes previously implicated in prostate cancer and identified a large number of cell type-specific mRNA isoforms. We also developed a novel "two-dimensional" profiling strategy to simultaneously quantify changes in splicing and transcript abundance; the results revealed extensive covariation between transcription and splicing in prostate cancer cells. Taking advantage of the ability of our technology to analyze RNA from formalin-fixed, paraffin-embedded tissues, we derived a specific set of mRNA isoform biomarkers for prostate cancer using independent panels of tissue samples for feature selection and cross-analysis. A number of cancer-specific splicing switch events were further validated by laser capture microdissection. Quantitative changes in transcription/RNA stability and qualitative differences in splicing ratio may thus be combined to characterize tumorigenic programs and signature mRNA isoforms may serve as unique biomarkers for tumor diagnosis and prognosis.

Aged↗

PubMed2004

Leptin receptor expression in fetal lung increases in late gestation in the baboon: a model for human pregnancy.

Leptin produced by both adipose tissue and the placental trophoblast, has been proposed to regulate numerous aspects of human conceptus development. Although recent animal studies have suggested an additional role for the polypeptide in fetal lung maturation, no evidence has been reported in primates. Therefore, we employed the baboon (Papio sp.), a well-characterized primate model for human pregnancy, to determine the presence and ontogeny of leptin receptor in fetal lung with advancing gestation. Lungs were collected from fetal baboons, early in gestation (days 58-62, n = 4), at mid gestation (days 98-102, n = 4), and late in gestation (days 158-165, n = 4) (term 184 days). mRNA transcripts for leptin (LEP) and both long and short intracellular domain isoforms of the leptin receptor (LEP-R(L) and LEP-R(S)) were assessed by RT-PCR. leptin receptor protein was evaluated by immunoblotting and cell types expressing leptin receptor were identified in late pregnancy by immunohistochemistry. Fetal serum leptin concentrations, determined by RIA, remained relatively unchanged at 5.7 +/- 1.1 ng/ml (mean +/- s.e.m.) in mid pregnancy and 8.4 +/- 3.0 ng/ml in late pregnancy (P > 0.05). Although leptin were detectable in fetal lung, no changes in transcript abundance were apparent with advancing gestation. However, transcripts for both LEP-R(L) and LEP-R(S) receptor isoforms increased several-fold (P < 0.05) in fetal lung between mid and late gestation, while leptin receptor protein was detectable only in late pregnancy. leptin receptor was localized in distal pulmonary epithelial cells, including type II pneumocytes. In conclusion, leptin is present in the fetal baboon and its receptor is enhanced during late gestation in cells responsible for the synthesis of pulmonary surfactant. Collectively, these and past findings may suggest a modulatory role for the polypeptide in pulmonary development and/or may identify leptin receptor as a physiological marker of primate fetal lung maturity.

Animals↗

PubMed1990

Molecular evidence for the presence of growth hormone receptors in the bovine mammary gland.

GH receptor messenger RNA (mRNA) was identified and characterized in mammary tissue from normal and GH-treated lactating cows using Northern and in-situ hybridization analyses. One major GH receptor transcript of 4.4 kilobases and a less abundant transcript of 9.2 kilobases were detected in mammary tissue from both normal and GH-treated cows. In-situ hybridization analysis revealed that the GH receptor gene is primarily expressed in the alveolar epithelial cells of mammary tissue. These results are evidence that the lactating mammary gland may synthesize GH receptors. On the basis of these observations it seems likely that the lactating bovine mammary gland is a GH target tissue. This finding challenges the widely accepted view that GH does not directly regulate mammary growth or function.

Animals↗

PubMed2002

cDNA array identification of genes regulated in rat renal medulla in response to vasopressin infusion.

With the aim of identifying possible gene targets for direct or indirect regulation by vasopressin in the renal medulla, we have carried out cDNA array experiments in inner medullas of Brattleboro rats infused with the V(2) receptor-selective vasopressin analog desamino-Cys1,d-Arg8 vasopressin (dDAVP) for 72 h. Of the 1,176 genes on the array, 137 transcripts were increased by 2-fold or more, and 10 transcripts were decreased to 0.5-fold or less. Quantitative, real-time RT-PCR measurements confirmed increases seen for six selected transcripts (Wilms' tumor protein, beta-arrestin 2, neurofibromin, casein kinase IIbeta, aquaporin-3, and aquaporin-4). To correlate changes in mRNA expression with changes in protein expression, we carried out quantitative immunoblotting for 28 of the proteins whose cDNAs were on the array. For several targets including aquaporin-2, transcript abundance and protein abundance changes did not correlate. However, for most genes examined, changes in mRNA abundances were associated with concomitant protein abundance changes. Targets with demonstrated increases in both protein and mRNA abundances included neurofibromin, casein kinase IIbeta, the beta-subunit of the epithelial Na channel (beta-ENaC), 11beta-hydroxysteroid dehydrogenase type 2, and c-Fos. Additional cDNA arrays revealed that several transcripts that were increased in abundance after 72 h of dDAVP were also increased after 4 h, including casein kinase IIbeta, beta-ENaC, aquaporin-3, UT-A, and syntaxin 2. These studies have identified several transcripts whose abundances are regulated in the inner medulla in response to infusion of dDAVP and that could play roles in the regulation of salt and water excretion.

11-beta-Hydroxysteroid Dehydrogenase Type 2↗

PubMed1995

Expression of neuronal acetylcholine receptor genes in vertebrate skeletal muscle during development.

Of the 15 nicotinic ACh receptor genes identified in vertebrates, only four (alpha 1, beta 1, gamma, and delta) have been shown to be expressed in embryonic skeletal muscle at early times. In mammalian muscle a fifth gene (epsilon) replaces the gamma gene in expression at later times. The remaining 10 nicotinic receptor genes identified to date (alpha 2-alpha 8, beta 2-beta 4) are expressed in the nervous system and are considered neuronal genes. Using RNase protection assays, we show here that four of the neuronal-type genes (alpha 4, alpha 5, alpha 7, and beta 4) are expressed in developing chick skeletal muscle. Two of them (alpha 4 and alpha 7) decline substantially in transcript abundance between embryonic days 11 and 17, as does alpha 1, while the other two (alpha 5 and beta 4) show only moderate decreases over the same time period. At embryonic day 8, alpha 7 transcripts are nearly 20% as abundant as alpha 1 transcripts. In situ hybridizations confirm the presence of alpha 7 transcripts in muscle cells both in cell culture and in embryonic tissue. No evidence was found for expression of the alpha 2, alpha 3, alpha 8, or beta 3 genes in muscle. Immunoprecipitations and immunoblot analysis using subunit-specific monoclonal antibodies reveal alpha 7 protein in muscle, and the amount of protein rises and declines with the amount of alpha 7 mRNA during development. Sucrose gradient analysis demonstrates that the alpha 7 protein is present in muscle as a species of 10S, the size expected for a nicotinic receptor. The alpha 7 species in muscle binds alpha-bungarotoxin but does not contain alpha 1 subunits, indicating that the two kinds of alpha-type gene products segregate during assembly. The results suggest that neuronal AChRs may play a role in early muscle development.

Animals↗

PubMed1985

A study of mitochondrial and nuclear transcription with cloned cDNA probes. Changes in the relative abundance of mitochondrial transcripts after stimulation of quiescent mouse fibroblasts.

From a cDNA library constructed in pBR322 we have isolated and studied a set of clones corresponding to mRNAs whose abundance changes when serum-deprived murine fibroblasts are stimulated to enter the cell cycle. A subset of these clones was derived from mRNA species whose abundance decreased during the G1 period following serum stimulation; all but one of these clones turned out to be clones of mitochondrial poly(A)mRNAs. There was no detectable change in the rate of transcription of the mitochondrial genome compared with the nuclear genome, and the lengths of the poly(A) segments on both mRNA species did not change significantly after serum stimulation. We conclude that the apparent decline in the relative abundance of the mitochondrial mRNAs is the result of a relative increase in the processing and/or transport of nuclear mRNA.

Animals↗

PubMed1997

The PPS1 gene of Saccharomyces cerevisiae codes for a dual specificity protein phosphatase with a role in the DNA synthesis phase of the cell cycle.

We report the identification of the PPS1 gene of Saccharomyces cerevisiae. The deduced amino acid sequence of PPS1p shows similarity with protein-tyrosine phosphatases (PTPases) and is most closely related to a subfamily of PTPases that are capable of dephosphorylating phosphoseryl and phosphothreonyl residues as well as phosphotyrosyl residues. Analysis of the predicted amino acid sequence suggests that the protein consists of an active phosphatase domain, an inactive phosphatase-like domain, and an NH2-terminal extension. Mutation of the catalytic cysteinyl residue in the active phosphatase domain reduced the in vitro activity of the mutant protein to less than 0.5% of wild type activity, while mutation of the corresponding cysteinyl residue of the inactive phosphatase-like domain had no effect on in vitro activity. The PPS1 protein was expressed in Escherichia coli, and the protein was shown to catalyze the hydrolysis of p-nitrophenyl phosphate, dephosphorylate phosphotyrosyl, and phosphothreonyl residues in synthetic diphosphorylated peptides and to inactivate the human ERK1 protein. PPS1 transcript abundance is coregulated with that of the divergently transcribed DPB3 gene, which codes for a subunit of DNA polymerase II, with both transcripts showing peak abundance in S phase. pps1Delta mutant strains did not differ from PPS1 strains under any of the conditions tested, but overexpression of the PPS1 protein in S. cerevisiae led to synchronous growth arrest and to aberrant DNA synthesis. A screen for suppressors of this growth arrest identified the RAS2 gene as a multicopy suppressor of the PPS1p overexpression arrest. The arrest was not suppressed by the presence of multicopy RAS1, TPK2, or TPK3 genes or by the presence of 5 mM cAMP in the growth medium, suggesting that PPS1 functions in a pathway involving RAS2, but not TPK kinases or adenylate cyclase.

Alleles↗

PubMed1989

Ubiquitin mRNA is a major stress-induced transcript in mammalian cells.

Ubiquitin mRNA was found to be an abundant transcript which was induced by heat shock (HS), and certain other stresses in mammalian cells. In Chinese hamster cells, the 2 major ubiquitin transcripts of 2.6 kb and 1.7 kb were induced coordinately, while a minor ubiquitin transcript of 0.8 kb was not induced; the response was similar in human cells with induction of the 2.5 kb Ub C and 1.0 kb Ub B transcripts. A representative ubiquitin cDNA clone, isolated from a cDNA library derived from HS-treated Chinese hamster cells, coded for a typical tandem repeat polyubiquitin transcript. Only a portion of the 5' nontranslated sequence of this clone had homology with the previously published corresponding region in human Ub B mRNA. Oligonucleotide probes complementary to the portion of the 5' nontranslated sequence with homology to the human sequence and also portions with no homology hybridized only to the 1.7 kb transcript. There was coordinate induction of ubiquitin, HSP27, and HSP70 mRNA by HS as determined by both increased RNA and increased transcription. Ubiquitin mRNA was induced by certain DNA damaging agents, in particular the alkylating agent methylmethane sulfonate, or incubation in isoleucine-deficient medium under conditions where the other HSP mRNA were not.

Amino Acid Sequence↗

PubMed2025

Effect of transgene on salt tolerance of tobacco.

To explore the effects of salt-tolerance gene accumulation on salt tolerance in transgenic plant, we used four types of plant expression vector (N27, N28, N29, and N30) carrying mtlD, mtlD + gutD, mtlD + gutD + BADH, mtlD + gutD + BADH + sacB genes respectively, to transform tobacco through Agrobacterium-mediated method. Transgenic lines were identified through polymerase chain reaction (PCR) detection. Transgenic lines and non-transgenic plant (CK) were subjected to 6‰ sodium chloride solution stress; then, fluorescence quantitative PCR (FQ-PCR) and salt tolerance indexes were used to assess characteristics. PCR showed the exogenous genes had been integrated into the tobacco genome. FQ-PCR showed under clean water treatment the target genes were expressed in all transgenic plants at the transcriptional level. The transcript abundances of target genes changed with the number of genes increased, and improved following salt stress. Comparative analyses of salt tolerance indexes showed height growth, biomass (except for N29), chlorophyll content, net photosynthetic rate, Fv/Fm, and PI of all transgenic plants and CK were lower under salt stress than under clean water treatment, to varying degrees. However, the descent ratio was smaller in transgenic plants. A comprehensive evaluation of multiple salt-tolerance indicators performed using the membership function method showed the average salt tolerance of each vector transgenic line was higher than that of CK, and salt tolerance was greater in transgenic polyvalent gene lines than in transgenic monovalent gene lines. The average salt tolerance was N29 > N28 > N30 > N27 > CK. This study provides a theoretical and practical reference for salt tolerance breeding in other plants.

Plants, Genetically Modified↗

PubMed2026

Translation of scRNA-seq to a clinical blood test for infection diagnostics.

INTRODUCTION: Early and accurate triage of patients with febrile illness is crucial for appropriate treatment. While standard inflammatory biomarkers are often nonspecific, transcriptome analysis of peripheral blood has diagnostic potential. However, bulk gene expression data is often confounded by changes in cell count proportions, a more robust quantification of gene expression in specific single-cell types, such as monocytes, is required to serve as a reliable clinical biomarker. AREAS COVERED: Various methods to obtain single-cell-type gene expression results, including the gold standard of gene expression analysis after cell sorting and single-cell RNA sequencing, which are difficult to implement in the routine settings are discussed. Other method to interrogate gene expression of a single cell-type is needed. Finally, monocyte cell-type specific ratio-based biomarker (RBB, called Direct Leukocyte Single cell-type Transcript Abundance, or DIRECT LS-TA) which can estimate single cell-type (monocyte) specific gene expression without cell sorting is introduced. EXPERT OPINION: Traditional diagnostic test for differentiating infection has several limitations requiring breakthrough including turn-around time and cost. DIRECT LS-TA provides a reliable way to quantify monocyte-specific gene expression that strongly correlates with gold-standard methods. It is more affordable than single-cell RNA sequencing and can be readily implemented in clinical laboratories using widely available quantitative PCR or digital PCR machines.

Humans↗

PubMed2005

Changes in gene expression in maize kernel in response to water and salt stress.

Increasing pressure on limited water resources for agriculture, together with the global temperature increase, highlight the importance of breeding for drought-tolerant cultivars. A better understanding of the molecular nature of drought stress can be expected through the use of genomics approaches. Here, a macroarray of approximately 2500 maize cDNAs was used for determining transcript changes during water- and salt-stress treatments of developing kernels at 15 days after pollination. Normalization of relative transcript abundances was carried out using a human nebulin control sequence. The proportions of transcripts that changed significantly in abundance upon treatment (>2-fold compared to the control) were determined; 1.5% of the sequences examined were up-regulated by high salinity and 1% by water stress. Both stresses induced 0.8% of the sequences. These include genes involved in various stress responses: abiotic, wounding and pathogen attack (abscisic acid response binding factor, glycine and proline-rich proteins, pathogenesis-related proteins, etc.). The proportion of down-regulated genes was higher than that for up-regulated genes for water stress (3.2%) and lower for salt stress (0.7%), although only eight genes, predominantly involved in energy generation, were down-regulated in both stress conditions. Co-expression of genes of unknown function under defined conditions may help in elucidating their roles in coordinating stress responses.

Down-Regulation↗

PubMed1994

Detection of circular and linear transcripts of Sry in pre-implantation mouse embryos: differences in requirement for reverse transcriptase.

Sry is the testes determining factor gene located on the Y chromosome. Expression of Sry had previously been found to occur during a short time frame of 10.5 to 12.5 days post coitum in the developing genital ridge. A recent study of the Sry transcript from adult testes found that the most abundant transcript is circular in nature. We have performed reverse transcription polymerase chain reactions with RNA from mouse preimplantation embryos ranging from the 2 cell stage to the blastocyst stage and report the detection of both circular and linear forms of Sry in the preimplantation embryo. In addition, we also demonstrate that the well described reverse transcriptase activity of Taq polymerase leads to a major difference in the mode of detection of the two forms.

Animals↗