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PubMed2006

Options available for profiling small samples: a review of sample amplification technology when combined with microarray profiling.

The possibility of performing microarray analysis on limited material has been demonstrated in a number of publications. In this review we approach the technical aspects of mRNA amplification and several important implicit consequences, for both linear and exponential procedures. Amplification efficiencies clearly allow profiling of extremely small samples. The conservation of transcript abundance is the most important issue regarding the use of sample amplification in combination with microarray analysis, and this aspect has generally been found to be acceptable, although demonstrated to decrease in highly diluted samples. The fact that variability and discrepancies in microarray profiles increase with minute sample sizes has been clearly documented, but for many studies this does appear to have affected the biological conclusions. We suggest that this is due to the data analysis approach applied, and the consequence is the chance of presenting misleading results. We discuss the issue of amplification sensitivity limits in the light of reports on fidelity, published data from reviewed articles and data analysis approaches. These are important considerations to be reflected in the design of future studies and when evaluating biological conclusions from published microarray studies based on extremely low input RNA quantities.

Gene Expression Profiling↗
PubMed2004

Simple cDNA normalization using kamchatka crab duplex-specific nuclease.

We developed a novel simple cDNA normalization method [termed duplex-specific nuclease (DSN) normalization] that may be effectively used for samples enriched with full-length cDNA sequences. DSN normalization involves the denaturation-reassociation of cDNA, degradation of the double-stranded (ds) fraction formed by abundant transcripts and PCR amplification of the equalized single-stranded (ss) DNA fraction. The key element of this method is the degradation of the ds fraction formed during reassociation of cDNA using the kamchatka crab DSN, as described recently. This thermostable enzyme displays a strong preference for cleaving ds DNA and DNA in DNA-RNA hybrid duplexes compared with ss DNA and RNA, irrespective of sequence length. We developed normalization protocols for both first-strand cDNA [when poly(A)+ RNA is available] and amplified cDNA (when only total RNA can be obtained). Both protocols were evaluated in model experiments using human skeletal muscle cDNA. We also employed DSN normalization to normalize cDNA from nervous tissues of the marine mollusc Aplysia californica (a popular model organism in neuroscience) to illustrate further the efficiency of the normalization technique.

Animals↗
PubMed1999

Characterization of a palmitoyl-acyl carrier protein thioesterase (FatB1) in cotton.

The relatively high level of palmitic acid (22 mol%) in cotton seeds may be due in part to a palmitoyl-acyl carrier protein (ACP) thioesterase (PATE), which prefers C16:0-ACP as its substrate. In embryo extracts, PATE activity was highest at the maximum rate of reserve accumulation (oil and protein), occurring about 30-35 d post anthesis. Thioesterase activity toward oleoyl-ACP was relatively similar at all developmental stages examined, but was considerably lower than the PATE activity. In developing seeds and in cotyledons and hypocotyls of seedlings, the PATE activity predominated. A cotton PATE cDNA clone isolated by screening a cDNA library with a heterologous Arabidopsis FatB1 probe has a 1.7-kb insert sequence with an open reading frame of 410 amino acids, lacking codons for the three N-terminal amino acids. The predicted amino acid sequence of the cotton PATE preprotein has a characteristic stromal-targeting domain and a 63% identity to the Arabidopsis long-chain acyl ACP-thioesterase FatB1 sequence. Alkaline blot hybridization of cotton genomic DNA with the Arabidopsis FatB1 probe suggested the presence of at least two FatB1 thioesterase genes in cotton. Relative cotton FatB1 transcript abundance was compared by RT-PCR and slot blot analysis in total RNA extracts from embryos, seedlings and leaves of mature plants. The cotton FatB1 mRNA apparently was expressed in all tissues but paralleled the profiles of PATE enzyme activity and seed oil accumulation in embryos.

Acyl Carrier Protein↗
PubMed2003

Regulation of NRT1 and NRT2 gene families of Arabidopsis thaliana: responses to nitrate provision.

Four low-affinity (NRT1), and seven high-affinity (NRT2) nitrate transporter gene homologues have been identified in Arabidopsis thaliana. We investigated the transcript abundances of all eleven genes in shoot and root tissues in response to the provision of 1 mM NO(3)(-), using relative quantitative RT-PCR. Based upon this criterion, genes were classified as nitrate-inducible, nitrate-repressible, or nitrate-constitutive. AtNRT1.1, 2.1, and 2.2 were strongly induced by NO(3)(-), peaking at 3-12 h and subsequently declining. By contrast AtNRT2.4 showed only modest induction both in shoots and roots. Expression of AtNRT2.5, one of the nitrate-repressible genes, was strongly suppressed by nitrate provision in both roots and shoots. The last group, characterized by a constitutive expression pattern, included AtNRT1.2, 1.4, 2.3, 2.6, and 2.7. Correlation coefficients between (13)NO(3)(-) influx from 100 micro M and 5 mM [NO(3)(-)], suggest that high- and low-affinity transport systems are mediated primarily by AtNRT2.1 and AtNRT1.1, respectively. Functional roles for the other members of these families remain uncertain.

Amino Acid Sequence↗
PubMed2005

Characterization of mitochondrial alternative NAD(P)H dehydrogenases in Arabidopsis: intraorganelle location and expression.

The intramitochondrial location of putative type II NAD(P)H dehydrogenases (NDs) in Arabidopsis was investigated by measuring the ability of isolated mitochondria to take up precursor proteins generated from cDNAs using an in vitro translation system. The mature proteins of NDA1, NDA2 and NDC1 were judged to be located on the inside of the inner membrane because they were protected from protease added after the mitochondrial outer membrane had been ruptured. In contrast, NDB1, NDB2 and NDB4 were not protected from protease digestion in mitochondria with ruptured outer membranes and were deemed to be located on the outside of the inner membrane. Expression of all ND genes was measured using quantitative reverse transcription-PCR (RT-PCR) to determine transcript abundance, and compared with expression of alternative oxidase, uncoupler proteins and selected components of the oxidative phosphorylation complexes. NDA1 and NDB2 were the most prominently expressed members in a variety of tissues, and were up-regulated in the early daytime in a diurnal manner. Analysis of array data suggested that NDA1 clustered closest to the gene encoding the P-subunit of glycine decarboxylase. Taken together with the diurnal regulation of NDA1 observed here and in other studies, this suggests that NDA1 plays a role in integrating metabolic activities of chloroplasts and mitochondria. NDA2, NDB2 and Aox1a were up-regulated in a coordinated manner under various treatments, potentially forming a complete respiratory chain capable of oxidizing matrix and cytosolic NAD(P)H. NDB1 and NDC1 were down-regulated under the same conditions and may be regarded as housekeeping genes.

Arabidopsis↗
PubMed2001

Gene expression profiling of cultured human bronchial epithelial and lung carcinoma cells.

Lung cancer is a complex collection of diseases that is thought to begin with single mutated progenitor cells and culminates in any of several clinically described pathologies. Our knowledge of the molecular events that lead to different lung cancer types--small cell carcinoma, squamous cell carcinoma, adenocarcinoma, and large cell carcinoma--is incomplete. Nonetheless, it is evident that genetic changes that impact multiple molecular networks are involved in the generation of each specific phenotype. Due to the obvious complexity of these processes, the simultaneous quantitative monitoring of changes in the expression of genes that define these networks can provide mechanistic information to increase our understanding of the molecular basis for human pulmonary carcinogenesis. To this end, we have employed a commercially available human cDNA array (Atlas Human Array, Clontech Laboratories) to systematically screen for alterations in the expression of 600 genes in normal human bronchial epithelial (NHBE) cells as well as in several lung carcinoma lines. Studies on the reproducibility and variability of array results indicate that a 2-fold or greater difference in the expression of a particular gene could be considered a real difference in transcript abundance. Accuracy of gene expression as measured in the array was verified by comparing mRNA levels of the proto-oncogene c-myc in the array with results obtained by traditional Northern blot analysis and by quantitative RT-PCR. Gene expression profiles were compared within and among cell types. The differential expression of 17 genes, including downregulation of MRP8 and MRP14 and upregulation of CYP1B1, was observed in all four carcinoma lines compared to NHBE cells. The direction of all 17 gene expression differences, either upregulation or downregulation relative to NHBE cells, was the same for all four carcinoma lines, underscoring their common molecular features. Each lung tumor line also exhibited a number of unique differences compared to both normal cells and the other tumor cell lines. These differences may be due to differences in the cellular origin and/or pathology of the cell lines studied.

Adenocarcinoma↗
PubMed2003

Aux/IAA gene family is conserved in the gymnosperm, loblolly pine (Pinus taeda).

We isolated five members of the Aux/IAA gene family in loblolly pine (Pinus taeda L.). Degenerate primers complementary to conserved regions of angiosperm Aux/IAA genes were used to amplify fragments that were, in turn, used as probes to screen a cDNA library constructed from auxin-treated hypocotyls. The five unique clones, named PTIAA1-5, contain the four highly conserved domains that are characteristic of the Aux/IAA proteins. All clones contain the bipartite nuclear localization signal (NLS) between Domains I and II that is predicted in most angiosperm Aux/IAA genes, but only one, PTIAA2, contains the conserved NLS in Domain IV. The five invariant residues in Domain II that have been found to constitute part of a protein destabilization element in Arabidopsis thaliana (L.) Heynh. are conserved in all the PTIAAs. A postulated phosphorylation site located between Domains I and II and proximal to the conserved bipartite NLS was conserved in 20 out of 36 genes in this analysis, including the pine genes. Transcripts of all five PTIAAs accumulated specifically in the hypocotyls in response to exogenous auxin treatment and were induced by all auxins tested. Transcript abundance above basal levels in response to 1-naphthaleneacetic acid treatment was first detected after 10 min (PTIAA3) to 3 h (PTIAA2) in the different genes and remained above basal levels throughout 7 days. Induction of PTIAA2 was inhibited by the protein synthesis inhibitor cycloheximide, indicating that PTIAA2 is a secondary response gene. Phylogenetic analysis showed that all five pine genes clustered within a single class (Class I) of the dendrogram. Clone PTIAA2 has a sequence that is relatively distinct from the other four and is the most closely related to the angiosperm genes of Class I. Class I contains both primary and secondary auxin response genes, suggesting that it is the original lineage and that other gene classes have evolved subsequent to the angiosperm/gymnosperm divergence.

Amino Acid Sequence↗
PubMed2005

Expression of senescence-associated genes in the leaves of silver birch (Betula pendula).

Development was monitored throughout the entire life span of silver birch (Betula pendula Roth.) leaves. The focus was on senescence-related changes in photosynthesis and gene expression. The youngest fully developed leaves were compared with older senescing leaves in two silver birch lines: the wild-type line R and a late-senescing line R3.1. Line R3.1 was found among transgenic lines produced with a plasmid containing sense-RbcS and nptII under the control of the 35S CaMV promoter. Compared with the wild type, line R3.1 showed no general change in the mRNA levels of RbcS or Rubisco protein; therefore, it can be considered a line whose phenotype is due to insertional mutagenesis. Leaf senescence started earlier in line R than in line R3.1. Senescence was characterized by declining photosynthesis as indicated by decreases in chlorophyll fluorescence, the amount and activity of Rubisco, and the level of the ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit (RbcS1) mRNA. Some well-known senescence-associated genes (SAGs) encoding cysteine proteinases (Cyp1, Cyp2) and a pathogenesis-related gene (Pr1) were associated with leaf senescence. The expression pattern of Cyp1 indicated that it could serve as a molecular marker of leaf senescence in silver birch. Several genes related to energy metabolism, antioxidants and phenylpropanoid biosynthesis showed enhanced expression during leaf senescence. A distinct pattern in transcript abundance during leaf development was revealed for some of the identified SAGs.

Betula↗
PubMed2005

Nematode-induced changes of transporter gene expression in Arabidopsis roots.

Root-knot plant-parasitic nematodes (Meloidogyne spp.) account for much of the damage inflicted to plants by nematodes. The feeding sites of these nematodes consist of "giant" cells, which have characteristics of transfer cells found in other parts of plants. Increased transport activity across the plasma membrane is a hallmark of transfer cells, and giant cells provide nutrition for nematodes; therefore, we initiated a study to identify the transport processes that contribute to the development and function of nematode-induced feeding sites. The study was conducted over a 4-week period, during which time the large changes in the development of giant cells were documented. The Arabidopsis ATH1 GeneChip was used to identify the many transporter genes that were regulated by nematode infestation. Expression of 50 transporter genes from 18 different gene families was significantly changed upon nematode infestation. Sixteen transporter genes were studied in more detail using real-time reverse-transcriptase polymerase chain reaction to determine transcript abundance in nematode-induced galls that contain giant cells and uninfested regions of the root. Certain genes were expressed primarily in galls whereas others were expressed primarily in the uninfested regions of the root, and a third group was expressed evenly throughout the root. Multiple transport processes are regulated and these may play important roles in nematode feeding-site establishment and maintenance.

Amino Acids↗
PubMed2003

A functional genomic study to identify differential gene expression in the preterm and term human myometrium.

The mechanisms that lead to the onset of human parturition are still unknown, although selected critical factors have been identified. To investigate the changes in myometrial gene expression associated with parturition, we used two macroarrays each containing 1176 different complementary human cDNA clones. Methods involving hierarchical clustering and conventional statistical analysis allowed us to generate a profile of genes expression at three stages of late pregnancy: preterm (29 wk amenorrhea); full term, not in labor (38 wk amenorrhea); and full term in labor (39 wk amenorrhea). Only 4% of the genes investigated were differentially expressed between the preterm and term groups (P < 0.05). These genes could be clustered as groups of either down-regulated or up-regulated transcripts. The changes in transcript abundance were particularly marked between the preterm and term stages of gestation, whereas the differences between term not in labor and term in labor were less pronounced. The parturition was characterized by a massive down-regulation of a large panel of developmental, cell adhesion molecule and proliferation-related genes, along with the up-regulation of inflammatory, contraction and apoptosis associated genes. We propose that the mechanisms of parturition consist primarily in the arrest of the processes of myometrial development, a step that might be essential to allow the uterus to recover appropriate contractile function before delivery.

Adult↗
PubMed2001

Molecular biology of channel catfish gonadotropin receptors: 1. Cloning of a functional luteinizing hormone receptor and preovulatory induction of gene expression.

There is little known about the molecular biology of piscine gonadotropin receptors, and information about gene expression during reproductive development is particularly lacking. We have cloned the LH receptor (LHR) in the channel catfish (cc), and examined its gene expression throughout a reproductive cycle. A cDNA encoding the receptor was isolated from the testis using reverse transcription-polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends procedures. It encoded a 696-amino acid protein that showed the greatest homology (46-50% identity) with the known LHRs and lesser similarity with FSH receptors and thyroid-stimulating hormone receptors (44-47% and 42-44% identity, respectively). In addition, two characteristics unique to the LHRs were conserved in the cloned receptor and the encoding gene: presence of an intron corresponding to intron 10 in mammals and turkey and occurrence of a double cysteine residue in the cytoplasmic tail for potential palmitoylation. The ccLHR gene was well expressed in the gonads and kidney and merely detectable in the gills, muscle, and spleen. The isolated cDNA encoded an active ccLHR protein, as the recombinant receptor expressed in COS7 cells activated a cAMP response element-driven reporter gene (luciferase) upon exposure to hCG in a dose-dependent manner. Seasonal changes in the ovarian expression of the ccLHR gene, as examined by measuring the transcript abundance by quantitative real-time RT-PCR, remained rather low during most of the reproductive cycle but was acutely induced around the time of spawning. This pattern of expression correlates well with the reported expression of its ligand (LH) in fishes and concurs with the notion that LH is a key regulator of the periovulatory maturational events.

Amino Acid Sequence↗
PubMed2001

Molecular biology of the channel catfish gonadotropin receptors: 2. Complementary DNA cloning, functional expression, and seasonal gene expression of the follicle-stimulating hormone receptor.

Molecular cloning of the channel catfish FSH receptor is reported together with temporal changes in the gene expression throughout a reproductive cycle. A cDNA encoding the receptor was isolated from the testis using reverse transcription-polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE) procedures. The cDNA coded for a 662-amino acid protein that was most identical (51%-59%) to salmon gonadotropin receptor I and the FSH receptors of higher vertebrates, and less identical to LH receptors and thyrotropin receptors (45%-49% and 46%-47%, respectively). In addition, PCR analysis of the genomic DNA showed the absence of the LH receptor-specific intron. Expression of the channel catfish FSH receptor gene was highly restricted to the testis and ovary, except for a low-level expression in the spleen. Transfected COS cells expressed an active recombinant receptor as determined by the ligand-specific activation of a cAMP-responsive reporter gene (luciferase). The recombinant receptor was activated by human FSH and, to a small extent, hCG. Seasonal changes in the ovarian expression of the FSH receptor gene, examined by measuring the transcript abundance by quantitative real-time RT-PCR, showed a rise around the time of onset of ovarian recrudescence and a decrease prior to spawning. This pattern of seasonal expression of FSH receptor differs significantly from that of the LH receptor, which we reported recently. The differential expression of the two gonadotropin receptor genes, in addition to the differential secretion of the gonadotropic hormones, seem to be critical for the regulation of steroidogenesis and other gonadal physiological processes.

Amino Acid Sequence↗
PubMed1990

Identification of B epitopes in human papillomavirus type 16 E7 open reading frame protein.

Human papillomavirus (HPV) type 16 is implicated in the aetiology of anogenital dysplasia which may progress to malignancy. HPV-16 DNA is actively transcribed in cervical carcinomas, the most abundant transcripts being from the E6 and E7 early open reading frames. The E7 protein has been shown to have transforming activity in vitro. In this report we define four immunodominant B epitopes within the protein corresponding to the E7 gene, using a panel of murine monoclonal antibodies. Three epitopes are linear and lie within the N-terminal region of the molecule, and are unique to the HPV-16 E7 protein. One epitope is non-linear and presumed to be conformational. At least three of the four epitopes of the E7 protein are detectable by immunoprecipitation from an HPV-16-infected cervical carcinoma cell line. The demonstrated immunogenicity of the E7 protein allows us to deduce that this molecule may be a potential candidate for incorporation in a vaccine against cervical cancer.

Amino Acid Sequence↗
PubMed2025

Structural basis for the function of long noncoding RNA Pnky in neural stem cells.

LncRNA Pnky is a trans-acting regulator of neural stem cell (NSC) differentiation, but the molecular mechanisms by which Pnky regulates neurogenesis is unknown. A fundamental step towards mechanistic understanding is to determine whether a lncRNA has folded structure that underlies biological function. Using chemical probing and high-throughput analysis, we determined the secondary structure of Pnky folded in vitro and in cellulo. Pnky adopts a compact structure in vitro with distinct modules and evidence of tertiary interactions. In cellulo, Pnky structure is remarkably similar to the in vitro conformation. We used locked nucleic acid oligonucleotides to interrogate the entire Pnky transcript for function in NSCs and identified regions that when targeted increased neurogenesis - phenocopying Pnky knockdown - without decreasing transcript abundance. Our findings provide a structural basis for the role of Pnky in neurogenesis and, more broadly, illustrate how structural maps combined with phenotypic data can advance fundamental understanding of lncRNA mechanism.

LNA-ASOs↗
PubMed1988

Destruction of a translationally controlled mRNA in Xenopus oocytes delays progesterone-induced maturation.

The maternal mRNA D7 is a moderately abundant transcript in Xenopus laevis whose expression is highest in, and perhaps restricted to, oogenesis and early embryogenesis. The nucleotide sequence of cloned D7 cDNA was determined and shown to have the capacity to code for a 31-kD protein. This amino acid sequence was searched against a protein data base, and no homologous proteins were found. Antibodies directed against D7 recognize in Xenopus embryos a soluble, cytoplasmic protein with an apparent molecular weight on SDS gels of 36,000. The D7 protein is absent from oocytes and first begins to accumulate during oocyte maturation. Its levels are highest during the first day of embryonic development and then decrease; D7 protein was not detected in adult tissues. D7 mRNA was selectively destroyed by injection into oocytes of antisense oligodeoxynucleotides. Analysis of injected oocytes by Northern and Western blotting showed site-specific cleavage and subsequent degradation of the D7 mRNA and the failure of the D7 protein to accumulate during progesterone-induced maturation. The loss of D7 protein affects the maturation process itself, significantly delaying the time course of germinal vesicle breakdown. Thus, D7 is a newly described protein involved in oocyte maturation.

Amino Acid Sequence↗
PubMed1988

Expression of a collagen gene in mesenchyme lineages of the Strongylocentrotus purpuratus embryo.

We have previously described cloning of an exon of a sea urchin collagen gene and shown that its expression is temporally regulated during embryogenesis, beginning during blastula formation. We have now localized the protein encoded by the gene and the sites of its mRNA synthesis in the developing embryo. Antibody to a synthetic peptide reacts with a 208,000 Mr protein that is digestible by collagenase. Fractionation of pluteus stage embryos demonstrates that the protein is localized primarily with cells that form the syncytium of primary mesenchyme that elaborates the larval endoskeleton; furthermore, immunofluorescence localizes the epitope to the periphery of the endoskeleton in situ. Transcripts of the gene accumulate only in mesenchyme cells, especially those of the primary mesenchyme lineage. Measurements of absolute transcript abundance show that collagen mRNA is present in blastula primary mesenchyme cells at 600-700 copies per cell and at about fourfold lower amounts in other mesenchyme cells.

Animals↗
PubMed2005

Massive genome erosion and functional adaptations provide insights into the symbiotic lifestyle of Sodalis glossinidius in the tsetse host.

Sodalis glossinidius is a maternally transmitted endosymbiont of tsetse flies (Glossina spp.), an insect of medical and veterinary significance. Analysis of the complete sequence of Sodalis' chromosome (4,171,146 bp, encoding 2,432 protein coding sequences) indicates a reduced coding capacity of 51%. Furthermore, the chromosome contains 972 pseudogenes, an inordinately high number compared with that of other bacterial species. A high proportion of these pseudogenes are homologs of known proteins that function either in defense or in the transport and metabolism of carbohydrates and inorganic ions, suggesting Sodalis' degenerative adaptations to the immunity and restricted nutritional status of the host. Sodalis possesses three chromosomal symbiosis regions (SSR): SSR-1, SSR-2, and SSR-3, with gene inventories similar to the Type-III secretion system (TTSS) ysa from Yersinia enterolitica and SPI-1 and SPI-2 from Salmonella, respectively. While core components of the needle structure have been conserved, some of the effectors and regulators typically associated with these systems in pathogenic microbes are modified or eliminated in Sodalis. Analysis of SSR-specific invA transcript abundance in Sodalis during host development indicates that the individual symbiosis regions may exhibit different temporal expression profiles. In addition, the Sodalis chromosome encodes a complete flagella structure, key components of which are expressed in immature host developmental stages. These features may be important for the transmission and establishment of symbiont infections in the intra-uterine progeny. The data suggest that Sodalis represents an evolutionary intermediate transitioning from a free-living to a mutualistic lifestyle.

Adaptation, Physiological↗
PubMed2002

Comparison of RNA expression profiles based on maize expressed sequence tag frequency analysis and micro-array hybridization.

Assembly of 73,000 expressed sequence tags (ESTs) representing multiple organs and developmental stages of maize (Zea mays) identified approximately 22,000 tentative unique genes (TUGs) at the criterion of 95% identity. Based on sequence similarity, overlap between any two of nine libraries with more than 3,000 ESTs ranged from 4% to 20% of the constituent TUGs. The most abundant ESTs were recovered from only one or a minority of the libraries, and only 26 EST contigs had members from all nine EST sets (presumably representing ubiquitously expressed genes). For several examples, ESTs for different members of gene families were detected in distinct organs. To study this further, two types of micro-array slides were fabricated, one containing 5,534 ESTs from 10- to 14-d-old endosperm, and the other 4,844 ESTs from immature ear, estimated to represent about 2,800 and 2,500 unique genes, respectively. Each array type was hybridized with fluorescent cDNA targets prepared from endosperm and immature ear poly(A(+)) RNA. Although the 10- to 14-d-old postpollination endosperm TUGs showed only 12% overlap with immature ear TUGs, endosperm target hybridized with 94% of the ear TUGs, and ear target hybridized with 57% of the endosperm TUGs. Incomplete EST sampling of low-abundance transcripts contributes to an underestimate of shared gene expression profiles. Reassembly of ESTs at the criterion of 90% identity suggests how cross hybridization among gene family members can overestimate the overlap in genes expressed in micro-array hybridization experiments.

Contig Mapping↗