An improved procedure for utilizing terminal transferase to add homopolymers to the 3' termini of DNA

TAS-Seq is a robust and sensitive amplification method for bead-based scRNA-seq

Single-cell RNA-sequencing (scRNA-seq) is valuable for analyzing cellular heterogeneity. Cell composition accuracy is critical for analyzing cell-cell interaction networks from scRNA-seq data. However, droplet- and plate-based scRNA-seq techniques have cell sampling bias that could affect the cell composition of scRNA-seq datasets. Here we developed terminator-assisted solid-phase cDNA amplification and sequencing (TAS-Seq) for scRNA-seq based on a terminator, terminal transferase, and nanowell/bead-based scRNA-seq platform. TAS-Seq showed high tolerance to variations in the terminal transferase reaction, which complicate the handling of existing terminal transferase-based scRNA-seq methods. In murine and human lung samples, TAS-Seq yielded scRNA-seq data that were highly correlated with flow-cytometric data, showing higher gene-detection sensitivity and more robust detection of important cell-cell interactions and expression of growth factors/interleukins in cell subsets than 10X Chromium v2 and Smart-seq2. Expanding TAS-Seq application will improve understanding and atlas construction of lung biology at the single-cell level.

Tailing DNA aptamers with a functional protein by two-step enzymatic reaction

An efficient, quantitative synthetic strategy for aptamer-enzyme conjugates was developed by using a two-step enzymatic reaction. Terminal deoxynucleotidyl transferase (TdT) was used to first incorporate a Z-Gln-Gly (QG) modified nucleotide which can act as a glutamine donor for a subsequent enzymatic reaction, to the 3'-OH of a DNA aptamer. Microbial transglutaminase (MTG) then catalyzed the cross-linking between the Z-QG modified aptamers and an enzyme tagged with an MTG-reactive lysine containing peptide. The use of a Z-QG modified dideoxynucleotide (Z-QG-ddUTP) or a deoxyuridine triphosphate (Z-QG-dUTP) in the TdT reaction enables the controlled introduction of a single or multiple MTG reactive residues. This leads to the preparation of enzyme-aptamer and (enzyme)n-aptamer conjugates with different detection limits of thrombin, a model analyte, in a sandwich enzyme-linked aptamer assay (ELAA). Since the combination of two enzymatic reactions yields high site-specificity and requires only short peptide substrates, the methodology should be useful for the labeling of DNA/RNA aptamers with proteins.

Amplified on-chip fluorescence detection of DNA hybridization by surface-initiated enzymatic polymerization

We describe the incorporation of multiple fluorophores into a single stranded DNA (ssDNA) chain using terminal deoxynucleotidyl transferase (TdT), a template-independent DNA polymerase that catalyzes the sequential addition of deoxynucleotides (dNTPs) at the 3'-OH group of an oligonucleotide primer; we term this methodology surface initiated enzymatic polymerization (SIEP) of DNA. We found that long (>1 Kb) ssDNA homopolymer can be grown by SIEP, and that the length of the ssDNA product is determined by the monomer to oligonucleotide initiator ratio. We observed efficient initiation (≥50%) and narrow polydispersity of the extended product when fluorescently labeled nucleotides are incorporated. TdT's ability to incorporate fluorescent dNTPs into a ssDNA chain was characterized by examining the effect of the molar ratios of fluorescent dNTP to natural dNTP on the degree of fluorophore incorporation and the length of the polymerized DNA strand. These experiments allowed us to optimize the polymerization conditions to incorporate up to ~50 fluorescent Cy3-labeled dNTPs per kilobase into a ssDNA chain. With the goal of using TdT as an on-chip labeling method, we also quantified TdT mediated signal amplification on the surface by immobilizing ssDNA oligonucleotide initiators on a glass surface followed by SIEP of DNA. The incorporation of multiple fluorophores into the extended DNA chain by SIEP translated to a ~45 fold signal amplification compared to the incorporation of a single fluorophore. SIEP was then employed to detect hybridization of DNA, by the posthybridization, on-chip polymerization of fluorescently labeled ssDNA that was grown from the 3'-OH of target strands that hybridized to DNA probes that were printed on a surface. A dose-response curve for detection of DNA hybridization by SIEP was generated, with a ~1 pM limit of detection and a linear dynamic range of 2 logs.

Molecular cloning of cDNA for Avena phytochrome

We have isolated several cDNA clones for phytochrome, a plant regulatory photoreceptor. A cDNA library was constructed by using etiolated Avena poly(A)(+) RNA enriched for phytochrome mRNA by size fractionation. Replicate arrays of colonies were differentially screened with cDNA probes made from poly(A)(+) RNA that had been either enriched in or depleted of phytochrome mRNA. Of the colonies hybridizing preferentially with the enriched probe, several contained plasmids that specifically selected phytochrome mRNA when assayed by hybridization-selection and translation. The largest such plasmid, pAP-2, was used to isolate clones from an Avena genomic library. One of these genomic clones was then used to screen a second cDNA library in an attempt to identify full-length phytochrome clones. The largest of the plasmids thus obtained, pAP-3, contains a 3.4-kilobasepair (kbp) insert, verified to contain phytochrome sequences by hybridization-selection and translation. Sequence analysis of pAP-2 and pAP-3 revealed that the two clones are identical in sequence through a 2.4-kbp region in which they overlap. However, the pAP-2 insert contains, in addition, 1.5 kbp of sequence of unknown origin, the apparent result of a recombination event. Blots of poly(A)(+) RNA hybridized with (32)P-labeled pAP-2 or pAP-3 show a single mRNA band at 4.2 kilobases. Blot analysis of RNA from dark-grown and from red-irradiated tissue demonstrates that a previously reported light-induced decrease in translatable phytochrome mRNA results from a decrease in physical abundance of this mRNA.

A partial cDNA clone for porcine glucosephosphate isomerase: isolation, characterization and use in detection of restriction fragment length polymorphisms

A cDNA library for porcine skeletal muscle was established in the vector pBR322. The library was screened with an oligonucleotide probe coding for a hexapeptide from glucosephosphate isomerase (Gpi). A positive clone with an insert of about 450 bp and restriction sites for PstI, BamHI and PvuII was isolated. A 362-bp PstI fragment was sequenced and shown to contain the codons for the hexapeptide as well as the remaining 29 amino acids of this Gpi peptide. The PstI fragment was used to probe pig genomic DNA. The restriction enzymes PvuII and SacI detected a set of polymorphisms with five bands, behaving as a set of insertion/deletion polymorphisms.

Engineering infectious foot-and-mouth disease virus in vivo from a full-length genomic cDNA clone of the A/AKT/58 strain

Two full-length genomic cDNA clones, pTA/FMDV and pCA/FMDV, were constructed that contained three point-mutants [A174G and A308G (not present in pTA/FMDV); T1029G] in the genome compared with the wild type A/AKT/58 strain of foot-and-mouth disease virus. These two viruses were rescued by co-transfection of pCA/FMDV with pCT7RNAP, which can express T7 RNA polymerase in BHK-21 cell-lines, or by transfection of the in vitro transcribed RNA. Their biological properties were analyzed for their antigenicity, virulence in suckling-mice (LD50) and growth kinetics in BHK-21 cells. The in vivo rescued viruses showed high pathogenicity for 3-day-old unweaned mice (LD50=10(-7.5)). However, the in vitro transcribed RNA derived from pTA/FMDV had lower pathogenicity for suckling-mice (LD50=10(-6)), and the in vivo transcribed RNA recovered from pCA/FMDV co-transfected with pCT7RNAP showed no significant differences from the wild type virus. These data showed that recovery of the infectious foot-and-mouth disease virus directly from the use of in vivo techniques was better than from in vitro methods. Furthermore, the reverse genetic procedure technique was simplified to a faster one-step procedure based on co-transfection with pCT7RNAP. These results suggest that in vivo RNA transcripts may be more valuable for engineering recombinant foot-and-mouth disease virus than in vitro RNA transcripts, and may contribute to further understanding of the biological properties, such as replication, maturation and quasispecies, of the foot-and-mouth disease virus.

Detection of meiotic DNA breaks in mouse testicular germ cells

The study of location and intensity of double-strand breaks (DSBs) in mammalian systems is more challenging than in yeast because, unlike yeast, the progression through meiosis is not synchronous and only a small fraction of all testis cells are actually at the stage where DSB formation is initiated. We devised a quantitative approach that is sensitive enough to detect the position of rare DNA strand breaks in mouse germ cell-enriched testicular cell populations. The method can detect DNA breaks at any desired location in the genome but is not specific for DSBs-overhangs, nicks, or gaps with a free 3' OH group are also detected. The method was successfully used to compare testicular cells from mouse strains that possess or lack an active recombination hot spot at the H2-Ea gene. Breaks that were due to meiotic hot spot activity could be distinguished from the background of DNA breaks. This highly sensitive approach could be used to study other biological processes where rare DNA breaks are generated.

Analysis of oligonucleotide microarrays by 3' end labeling using fluorescent nucleotides and terminal transferase

A simple enzymatic labeling procedure is described to determine spot quality in oligonucleotide microarrays. By using fluorescently labeled dideoxynucleotides or ribonucleotides as substrate for terminal deoxynucleotidyl transferase (TdT), a single fluorophore can be covalently attached at the 3' end of each oligonucleotide probe molecule in the spot. Fluorescein-12-ddUTP CyTM3-ddUTP Cy5-UTP, and Cy3-UTP were compared as TdT substrates for 3' end labeling an array of 1273 hexamer probes. Cy5-UTP was found to show minimal bias toward probe base composition and is therefore well suited for quantitative analysis of microarray spots where the oligonucleotide probes are coupled via a 5' end linkage to the solid phase.

Mouse strains with an active H2-Ea meiotic recombination hot spot exhibit increased levels of H2-Ea-specific DNA breaks in testicular germ cells

We devised a sensitive method for the site-specific detection of rare meiotic DNA strand breaks in germ cell-enriched testicular cell populations from mice that possess or lack an active recombination hot spot at the H2-Ea gene. Using germ cells from adult animals, we found an excellent correlation between the frequency of DNA breaks in the 418-bp H2-Ea hot spot and crossover activity. The temporal appearance of DNA breaks was also studied in 7- to 18-day-old mice with an active hot spot during the first waves of spermatogenesis. The number of DNA breaks detected rose as leptotene and zygotene spermatocytes populate the testis with a peak at day 14 postpartum, when leptotene, zygotene, and early pachytene spermatocytes are the most common meiotic prophase I cell types. The number of DNA breaks drops precipitously 1 day later, when middle to late pachytene spermatocytes become the dominant subtype. The recombination-related breaks in the hot spot likely reflect SPO11-induced double-strand breaks and/or recombination intermediates containing free 3' hydroxyl groups.

Cloning, chromosomal mapping, and characteristic 5'-UTR sequence of murine cytosolic sialidase

We have totally sequenced a cytosolic sialidase [EC 3.2.1.18] by RT-PCR from the murine thymus (murine thymic sialidase, MTS) which has a 1844-base length (encoding 385 amino acids including two sialidase motifs) and is the longest cytosolic sialidase ever reported. MTS has high and relatively low homologies with those of mammalian cytosolic sialidases from the mouse brain (99%), rat (91%), and human skeletal muscle (75%), and those of the mouse lysosomal (47%) and membrane-bound (51%) sialidases, respectively. Chromosomal mapping, being the first report of mouse cytosolic sialidase gene, showed that the MTS gene is localized to the distal part of mouse chromosome 1D and to rat chromosome 9q36. RT-PCR with the site-specific primers revealed that the coding region was expressed in all organs tested, but expressions including the 5'-UTR were barely detectable except for in the upper-thymic fraction. Also, soluble sialidase activity in the thymus was the highest of these organs. There were mRNA instability signals and AT-rich regions in 143 bp of MTS 5'-end.

Myocyte death in the failing human heart is gender dependent

Cardiovascular disease is delayed and less common in women than in men. Myocyte death occurs in heart failure, but only apoptosis has been documented; the role of myocyte necrosis is unknown. Therefore, we tested whether necrosis is as important as apoptosis and whether myocyte death is lower in women than in men with heart failure. Molecular probes were used to measure the magnitude of myocyte necrosis and apoptosis in 7 women and 12 men undergoing transplantation for cardiac failure. Myocyte necrosis was evaluated by detection of DNA damage with blunt end fragments, whereas apoptosis was assessed by the identification of double-strand DNA cleavage with single base or longer 3' overhangs. An identical analysis of these forms of cell death was performed in control myocardium. Heart failure showed levels of myocyte necrosis 7-fold greater than apoptosis in patients of both sexes. However, cell death was 2-fold higher in men than in women. Heart failure resulted in a 13-fold and 27-fold increase in necrosis in women and men, respectively. Apoptosis increased 35-fold in women and 85-fold in men. The differences in cell death between women and men were confirmed by the electrophoretic pattern of DNA diffusion and laddering of isolated myocytes. The lower degree of cell death in women was associated with a longer duration of the myopathy, a later onset of cardiac decompensation, and a longer interval between heart failure and transplantation. In conclusion, myocyte necrosis and apoptosis affect the decompensated human heart; each contributes to the evolution of cardiac failure. However, the female heart is protected, at least in part, from necrotic and apoptotic death signals.

Expression of mRNA encoding insulin-like growth factors I and II by uterine tissues and placenta during pregnancy in the rat

The uterus and the placenta synthesize insulin-like growth factors (IGFs) and insulin-like binding proteins (IGFBPs). These growth factors are implicated in processes of proliferation and differentiation that occur in the uterus. To determine the patterns of expression of IGFs during rat pregnancy we used in situ hybridization with digoxigenin labeled probes on uterus from day 7 to day 16 of pregnancy. In early gestation days (7-8) both IGF mRNAs showed similar tissue distribution with relative abundance in the stroma and circular muscle layer. On days 11 and 12 expression for IGF-I mRNA was found in the mesometrial decidua and metrial gland and in the ectoplacental cone while clear expression of IGF-II mRNA could only be found in the latter. On days 13 and 14, expression for IGF-I mRNA could be detected in the mesometrial decidua and metrial gland but no expression was observed for IGF-II mRNA. A gradient of IGF-I mRNA expression could be observed in the placenta on day 16, with the trophoblastic cells of the basal zone expressing the signal with stronger intensity than in the labyrinthine zone. For IGF-II mRNA the highest expression was associated with the labyrinthine zone. Endovascular trophoblast was positive for both mRNAs. The spatial and temporal patterns of expression suggests a role for IGFs in the process of decidualization as well as in the establishment, growth and differentiation of the various trophoblast cells of the placenta.

Extensive Junctional Diversity in Ig Light Chain Genes from Early B Cell Progenitors of μMT Mice

Nontemplated (N) nucleotide additions contribute significantly to the junctional diversity of all Ag receptor chains in adult mice except Ig light (L) chains, primarily because terminal deoxynucleotidyl transferase (TdT) expression is turned off at the time of their rearrangement in pre-B cells. However, because some Ig L chain gene rearrangements are detectable earlier during B cell ontogeny when TdT expression is thought to be maximal, we have examined the junctional processing of κ- and λ-chain genes of CD45(B220)+CD43+ pro-B cells from μMT mice. We found that both κ and λ coding junctions formed in these B cell precursors were extensively diversified with N-region additions. Together, these findings demonstrate that Ig L chain genes are equally accessible to TdT in pro-B cells as Ig heavy chain genes. Surprisingly, however, the two L chain isotypes differed in the pattern of N addition, which was more prevalent at the λ-chain locus. We observed the same diversity pattern in pre-B cells from TdT-transgenic mice. These results suggest that some aspects of TdT processing could be influenced by factors intrinsic to the sequence of Ig genes and/or the process of V(D)J recombination itself.

Infectious transcripts from cloned genome-length cDNA of porcine reproductive and respiratory syndrome virus

The 5'-terminal end of the genomic RNA of the Lelystad virus isolate (LV) of porcine reproductive and respiratory syndrome virus was determined. To construct full-length cDNA clones, the 5'-terminal sequence was ligated to cDNA clones covering the complete genome of LV. When RNA that was transcribed in vitro from these full-length cDNA clones was transfected into BHK-21 cells, infectious LV was produced and secreted. The virus was rescued by passage to porcine alveolar lung macrophages or CL2621 cells. When infectious transcripts were transfected to porcine alveolar lung macrophages or CL2621 cells, no infectious virus was produced due to the poor transfection efficiency of these cells. The growth properties of the viruses produced by BHK-21 cells transfected with infectious transcripts of LV cDNA resembled the growth properties of the parental virus from which the cDNA was derived. Two nucleotide changes leading to a unique PacI restriction site directly downstream of the ORF7 gene were introduced in the genome-length cDNA clone. The virus recovered from this mutated cDNA clone retained the PacI site, which confirmed the de novo generation of infectious LV from cloned cDNA. These results indicate that the infectious clone of LV enables us to mutagenize the viral genome at specific sites and that it will therefore be useful for detailed molecular characterization of the virus, as well as for the development of a safe and effective live vaccine for use in pigs.

Determination of radiation-induced DNA strand breaks in individual cells by non-radioactive labelling of 3' OH ends

To quantify DNA strand breaks generated by ionizing radiation in single cells with preserved morphology, the number of radiation-induced 3' OH ends of nuclear DNA was determined by enzymatic labelling. Confluent CHO-K1 cells were irradiated with doses up to 100 Gy. After fixation and permeabilization of the cell monolayer the nuclear DNA was labelled with Digoxigenin-11-dUTP using terminal transferase. The incorporated nucleotide was detected with an anti-Digoxigenin antibody conjugated with alkaline phosphatase. The phosphatase bound was quantified by a colour reaction and the integrated optical densities of the cell nuclei were measured. For doses ranging from 20 to 100 Gy a linear relationship between dose and labelling signal was obtained. Repair experiments showed a fast component of repair with a half-time of about 14 min, followed by a slower decline to background values, which were reached after 6-8 h. This method allows the measurement of radiation-induced DNA strand breaks in morphologically preserved single cells in a reproducible way, which may be of importance in the prediction of tumour response in radiotherapy.

Efficient second-strand cDNA synthesis using T7 DNA polymerase

We present a second-strand cDNA synthesis method that takes advantage of both the very high processivity and the very high 3' exonuclease activity of T7 DNA polymerase. The first strand is synthesized with reverse transcriptase using oligo(dT) as a primer. After alkaline hydrolysis of the mRNA template, a tract of dT residues is synthesized with terminal transferase at the 3' end of the first strand. The second strand is synthesized using oligo(dA) as a primer. Several oligo(dA) molecules probably anneal to the poly(dT) tract. Because the 3' exonuclease activity of T7 DNA polymerase is very high, the region of the tract annealed to these oligo(dA) molecules is digested. However, the region of the tract annealed to the very oligo(dA) molecule used as a primer for second-strand synthesis is protected. The resulting cDNA molecules could be cloned with a high efficiency. The size distribution of cloned c-myc DNAs was estimated by Southern blot analysis of phage DNA prepared from the amplified library and by analysis of isolated clones. The results indicate that this method allows to obtain full-length cDNA clones with a high efficiency.

In situ hybridization for epidermal growth factor receptor (EGFR) external domain transcripts in prostatic adenocarcinoma

We examined prostatic adenocarcinomas from 19 formalin fixed radical prostatectomy specimens for EGFR by in situ hybridization employing a 24 base synthetic biotin-labeled oligonucleotide probe complementary to the 5' end of EGFR mRNA. All slides were examined by light microscopy using a 25x objective. Each field was given three values: 1) Gleason grade (1-5), 2) Nuclear grade [small (< 5.0 mu), intermediate (5-10 mu), large (> 10 mu)], and 3) EGFR staining intensity score (0, absent; 1, weak; 2+, moderate to strong). A total 851 25x fields of prostatic adenocarcinoma were studied. All cancers demonstrated at least some degree of cytoplasmic EGFR message. The EGFR intensity score correlated best with tumor nuclear size. No correlation with Gleason grade was observed. Cytoplasmic staining was also identified in the basal cell layer of benign glands, high grade prostatic intraepithelial neoplasia, stromal nodules, transitional epithelium, periurethral glands, and ganglion cells. Competitive hybridization experiments using an unlabeled EGFR probe showed markedly diminished hybridization signal, while in situ hybridization with a biotin-labeled EGFR sense probe was negative. Immunohistochemistry on 13 of the tumors with 2 monoclonal antibodies against EGFR showed staining in only 1/13 and 10/13 tumors. EGFR expression appears to be most prominent in tumors of high nuclear grade. Further studies will be necessary to explore this growth factor as a prognostic variable in this tumor.

Mutation creates an open reading frame within the 5' untranslated region of macaque erythrocyte carbonic anhydrase (CA) I mRNA that suppresses CA I expression and supports the scanning model for translation

A variant allele at the CA I locus that produces a deficiency of erythrocyte-specific CA I occurs as a widespread polymorphism in pigtail macaques from southeast Asia. Sequence analyses revealed a C----G substitution 12 nucleotides downstream of the cap site in the variant erythrocyte CA I mRNA. This mutation forms a new AUG start site and an open reading frame coding for 26 amino acids that terminates 6 nucleotides before the normal AUG initiation codon for CA I. It appears that the presence of this upstream open reading frame greatly diminishes reinitiation of translation from the normal start site, resulting in trace levels of CA I in erythrocytes. Preferential use of the first AUG codon supports the scanning model for translation initiation in eukaryotes.

The demonstration of a subset of carcinoid tumours of the appendix by in situ hybridization using synthetic probes to proglucagon mRNA

Previous studies using immunohistochemistry have shown variable hormone production by carcinoid tumours of the appendix. In order to confirm the existence of a specific subset of these tumours, in situ hybridization using synthetic oligonucleotide probes to detect pre-proglucagon and pre-proinsulin mRNA was performed in formalin-fixed, paraffin-embedded material from eight tubular carcinoids, 12 insulin carcinoids, and two mucinous carcinoids. The results were correlated with standard silver and mucin stains. All tubular carcinoids but none of the insular or mucinous carcinoids contained proglucagon mRNA. Proinsulin mRNA was not detected in any of the tumours. Tubular carcinoids of the appendix constitute a definable subset of appendiceal carcinoids which have a similar distribution and prognosis to typical insular carcinoids and can be diagnosed on haematoxylin and eosin-stained sections confirmed by routine special stains. The main need for recognition is to avoid confusion with mucinous carcinoids, which have a worse prognosis and may require more aggressive treatment.

The expression of parathyroid hormone messenger RNA in normal and abnormal parathyroid tissue

The distribution and expression of preproparathyroid hormone (PTH) mRNA were investigated in parathyroid tissue from 57 parathyroidectomy specimens. PTH mRNA was detected by in situ hybridization using digoxigenin-labelled oligonucleotide probes. Cell morphology was seen to correlate with PTH mRNA expression. Strong expression of PTH mRNA was confined to cells which on haematoxylin and eosin staining had large vesicular nuclei. These included both vacuolated and non-vacuolated cells. Chief cells with small dark nuclei and scanty cytoplasm had little or no expression. In both adenoma and chief cell hyperplasia, the striking difference from normal was the greatly increased proportion of cells expressing PTH mRNA. In adenomas, the rim of uninvolved parathyroid tissue showed PTH mRNA expression similar to that of normal parathyroid. In hyperplasia, there was frequently concordance of staining within individual nodules. The findings establish morphological criteria for activity of parathyroid tissue and support current concepts of the different pathogenesis of hyperplasia and adenoma. The expression of PTH mRNA in oxyphil change and parathyroid carcinoma was also investigated.

Demonstration of insulin and glucagon mRNA in routinely fixed and processed pancreatic tissue by in-situ hybridization

Human insulin and glucagon mRNA were identified in routinely processed pancreatic tissue by non-radioactive in-situ hybridization using digoxigenin-labelled oligonucleotide probes. Cocktails of synthetic oligonucleotides complementary to human insulin and glucagon mRNA were labelled with digoxigenin using terminal deoxynucleotidyl transferase (Tdt). Specific hybrids were detected with alkaline phosphatase-labelled anti-digoxigenin antibody and visualized by BCIP-nitroblue tetrazolium indicator substrate. The results showed highly sensitive and specific staining of islet cells on a range of routinely formalin-fixed and paraffin-embedded tissues. Post-mortem pancreatic tissue from adults and stillborn neonates yielded acceptable signals as long as tissue morphology was well preserved. Preliminary investigations using pancreatic endocrine cell tumours gave clear easily interpretable signals which were comparable to conventional immunostaining. The application of this technique promises to be of value in the investigation of pancreatic disease.

Macronuclear and micronuclear configurations of a gene encoding the protein synthesis elongation factor EF 1 alpha in Stylonychia lemnae

The micronuclear and macronuclear configurations of a gene encoding the protein synthesis elongation factor EF 1 alpha in the hypotrich ciliate Stylonychia lemnae were compared. The two sequences are generally colinear. The coding sequence of the micronuclear gene is, however, interrupted by a 64 bp insert flanked by a 2 bp direct repeat in a gene region which is moderately conserved among EF 1 alpha genes of different organisms. The insertion site is distinct from known intron positions in eukaryotic EF 1 alpha genes. The insert sequence shows inverted repeats at its ends and thus exhibits typical features of an internal eliminated sequence (IES). Comparison with other such sequences in the related organism Oyxtricha nova shows that the IES falls into a new group of such elements. The macronuclear gene exhibits a strikingly limited codon usage, which cannot be simply explained by the overall base composition of the DNA but probably also relates to the very high copy number of the macronuclear gene and the putative high amount of the gene product.

Interleukin-1 mRNA-expressing macrophages in human chronically inflamed gingival tissues

Interleukin-1 (IL-1)-producing cells in inflamed gingival tissues obtained from patients with periodontitis were examined by combined immunohistochemistry and in situ hybridization. Macrophages, T cells, B cells, and endothelial cells were visualized in the lesions by the immunoperoxidase method using specific antibodies to each cell type. Subsequent in situ hybridization using 35S-labeled synthetic oligonucleotide probes complementary to human IL-1 alpha and IL-1 beta mRNA showed IL-1 transcripts in macrophages predominantly but not in T cells or B cells. Neither fibroblasts nor keratinocytes contained the IL-1 message to any significant extent. Endothelial cells also were essentially negative for IL-1 messages. These findings indicate that IL-1 is produced principally by macrophages in inflamed gingival tissues of humans.

In situ hybridization of immunoglobulin light chain mRNA in paraffin sections using biotinylated or hapten-labelled oligonucleotide probes

An in situ hybridization technique has been developed for the detection of immunoglobulin light chain mRNA in routine pathology specimens. The method detects kappa or lambda constant region sequences using a cocktail of synthetic oligonucleotide probes labelled with biotin or fluorescein 5-isothiocyanate (FITC) reporter molecules. The probes were labelled at flanking sites chemically by primary amine directed acylation and by 'homopolymer tailing' with terminal deoxynucleotidyl transferase using non-radioactive nucleotide analogues. The mRNA was unmasked in the formalin-fixed tissue sections by digestion with varying concentrations of proteinase K, and the hybrids were demonstrated using alkaline phosphatase with either a streptavidin/biotin based four-stage system or an anti-FITC antibody based detection system. Alkaline phosphatase was visualized using a Fast Red naphthol-capture method and the sections were counterstained with haematoxylin. The results confirm that the method is specific for kappa or lambda mRNA and show that specific mRNAs can be detected in routine formalin-fixed sections using non-radioactive techniques with retention of good morphology. The method reliably detects light chain mRNA in cells expressing secretory immunoglobulin. The protocol can also be applied to tissue rich in endogenous biotin by using hapten-labelled probes.

Early Changes in Gene Expression during the Transition from Vegetative to Generative Growth in the Long-Day Plant Sinapis alba

Changes in gene expression during flower formation were studied in the long-day plant Sinapis alba. The day length dependence was exploited to synchronize flower formation in a large population of mustard plants. After an inductive light treatment, apices were harvested after different lengths of time, and changes in gene expression were analyzed. Two major groups of genes were identified whose expression was affected during flower formation. Transcripts of the first group (group I) were present at low concentration in the apex of noninduced plants. They began to accumulate strongly after the end of the inductive light period. They reached a maximum 2 days to 10 days after flower induction and then declined slowly. Transcripts of the second group of genes (group II) could be detected for the first time 10 days after flower induction. Within a very short time, these transcripts accumulated dramatically and reached a maximum 15 days after flower induction before beginning to decline. They dropped beyond the limit of detection before the flower reached maturity.

Early Changes in Gene Expression during the Transition from Vegetative to Generative Growth in the Long-Day Plant Sinapis alba

Changes in gene expression during flower formation were studied in the long-day plant Sinapis alba. The day length dependence was exploited to synchronize flower formation in a large population of mustard plants. After an inductive light treatment, apices were harvested after different lengths of time, and changes in gene expression were analyzed. Two major groups of genes were identified whose expression was affected during flower formation. Transcripts of the first group (group I) were present at low concentration in the apex of noninduced plants. They began to accumulate strongly after the end of the inductive light period. They reached a maximum 2 days to 10 days after flower induction and then declined slowly. Transcripts of the second group of genes (group II) could be detected for the first time 10 days after flower induction. Within a very short time, these transcripts accumulated dramatically and reached a maximum 15 days after flower induction before beginning to decline. They dropped beyond the limit of detection before the flower reached maturity.

Localization of preprogalanin mRNA in rat brain: in situ hybridization study with a synthetic oligonucleotide probe

Galanin is a peptide containing 29 amino acid residues that is present in both the central and peripheral nervous systems. Galanin has multiple putative biological functions including regulation of hormone release, stimulation of feeding behaviour, and effects on blood pressure. This study examined the distribution of neurones expressing preprogalanin mRNA in the rat brain by in situ hybridization of a specific 35S-labelled oligonucleotide. Preprogalanin mRNA was detected in several regions of brain, with high concentrations in the paraventricular, periventricular, supraoptic, dorsomedial and arcuate nuclei of the hypothalamus; the locus coeruleus and dorsal raphe nucleus in the pons; and the nucleus tractus solitarii and ventrolateral reticular nucleus in the medulla. These findings are consistent with studies of the cellular localization of galanin-like immunoreactivity in rat brain, and further suggest the involvement of galanin in the regulation of several functions ranging from water balance to blood pressure control.

Infectious foot-and-mouth disease virus derived from a cloned full-length cDNA

A full-length cDNA plasmid of foot-and-mouth disease virus has been constructed. RNA synthesized in vitro by means of a bacteriophage SP6 promoter inserted in front of the cDNA led to the production of infectious particles upon transfection of BHK-21 cells. These particles were also found to be highly infectious for primary bovine kidney cells as well as for baby mice. The difficulty in cloning the foot-and-mouth disease virus cytidyl tract in Escherichia coli was circumvented by joining two separate cloned parts, representing the S and L fragments of the genome, and, in a second step, inserting a dC-dG homopolymer. Homopolymeric sequences of up to 25 cytidyl residues did not lead to the production of virus. Replicons containing poly(C) tracts long enough to permit virus replication were first established in yeast cells. One of these constructs could also be maintained in E. coli and was used to produce infectious RNA in vitro. The length of the poly(C) sequence in this cDNA plasmid was 32 nucleotides. However, the poly(C) tracts of two recombinant viruses found in transfected BHK-21 cells were 60 and 80 nucleotides long, respectively. Possible mechanisms leading to the enlargement of the poly(C) tract during virus replication are discussed.

Cloning and sequencing of protochlorophyllide reductase

Putative protochlorophyllide reductase cDNA clones (252 and 113) were isolated from an etiolated-oat (Avena sativa) cDNA library. These were used to indirectly characterize a further clone, p127, isolated from a lambda-phage gt11 cDNA library. The latter (1.15 kb in length) was sequenced, and the derived amino acid sequence was shown to be remarkably similar to that derived from chemical analysis of a CNBr-cleavage fragment of the purified reductase, p127 codes for more than 95% of the reductase protein.

Detection of mouse hepatitis virus nonstructural proteins using antisera directed against bacterial viral fusion proteins

Mouse hepatitis virus, strain A59 cDNAs were inserted into the procaryotic fusion vector pGE374. RecA/viral/LacZ tripartite fusion proteins were synthesized from these plasmids and purified from E. coli. Antisera were raised in rabbits against these fusion proteins. Viral nonstructural proteins were detected in infected murine fibroblasts and glial cells. The anti-gene B, ORF1 sera detect a 30K cytoplasmic protein while the anti-gene E, ORF2 sera detect a 9.6K protein. Sera raised against proteins encoded in cDNAs from 5' portions of gene A immunoprecipitate the 200-250K polypeptides synthesized in vitro from genome RNA. Antisera raised against proteins encoded in both 5' and 3' portions of gene A immunoprecipitate membrane associated polypeptides of 150K and greater than 600K from MHV infected cells.

Fluorescent in-situ hybridization to detect cellular RNA by flow cytometry and confocal microscopy

A fluorescent in-situ hybridization procedure was developed which is suitable for detection of specific cellular RNA in cells fixed in suspension. The procedure was originally developed for analysis of single-cell suspensions by flow cytometry. The resulting fluorescent cells proved to have their 3-D morphology perfectly preserved. The spatial distribution of specific ribosomal RNA and messenger RNA could then be analysed by confocal microscopy of individual cells. In the hybridization procedure, biotinylated single-stranded RNA probes were used that were produced by transcription from cloned DNA fragments. Detection of poly-(A)+ RNA was performed with a poly-biotin-d(U)-tailed oligo-d(T) probe. Bound probe was detected using streptavidin-fluorescein isothiocyanate. For flow cytometry, nuclear DNA was counterstained with di-amidine-2-phenyl indol. Multi-parameter flow cytometry was used to quantify the fluorescence intensity, i.e. the hybridization signal, of thousands of cells. Confocal scanning microscopy on individual cells revealed the intracellular distribution of the target RNA. The distribution of ribosomal RNA and poly-(A)+ RNA mRNA in mouse bone marrow and the human leukaemia cell line HL60 cells was investigated. Ribosomal RNA was confined to the cytoplasm of the cells, although in many cells the nucleoli could also be distinguished. Poly-(A)+ RNA in HL60 cells was found both in the cytoplasm and nucleus. A granular cytoplasmic distribution was seen in part of these cells.

A general method for the induction and screening of antisera for cDNA-encoded polypeptides: antibodies specific for a coronavirus putative polymerase-encoding gene

A prokaryotic vector, pGE374, containing the recA and lacZ genes, out-of-frame, was used for the expression of cDNA derived from the putative polymerase-encoding gene of the coronavirus mouse hepatitis virus strain A59 (MHV-A59). The pGE374/viral recombinant vector generates a tripartite bacterial/viral protein composed of a segment of the RecA protein at the N terminus, the coronaviral sequences in the middle, and an enzymatically active beta-galactosidase at the C terminus. Rabbits immunized with such recombinant proteins generated antibodies to the MHV-A59 portion of the tripartite protein. Because the MHV-A59 polymerase proteins have been difficult to identify during infection, we used a novel method to demonstrate the viral specificity of the antiserum. The viral cDNA was excised from the expression vector, and transferred to a pGem vector, downstream from and in-frame with a portion of the cat gene. This construct contained a bacteriophage RNA polymerase promoter that enabled the cell-free synthesis of a fusion protein that was used to verify that antibodies were generated to the expressed viral DNA. This strategy was shown to successfully result in the specific generation of antibodies to the encoded information of the viral cDNA. Furthermore, this method has general applicability in the generation and characterization of antibodies directed against proteins encoded in cDNAs.

Expression and cellular localization of amyloid beta-protein precursor transcripts in normal human brain and in Alzheimer's disease

Two classes of amyloid beta-protein precursors which differ by the presence of a serine protease inhibitor domain have been described. We have used synthetic oligonucleotide probes to investigate the tissue distribution and cellular localization of mRNAs encoding the two classes of amyloid beta-protein precursors. RNA blot analysis showed that transcripts encoding the protease inhibitor sequence are ubiquitously expressed in peripheral and central tissues. By contrast, transcripts lacking the protease inhibitor domain were only found in the central nervous system. By in situ hybridization on cerebral cortex and hippocampal formation both types of transcripts were present exclusively in nerve cells and they appeared to be produced by the same cells. A reduction in the transcript lacking the protease inhibitor domain was observed in frontal cortex from Alzheimer's disease patients. The present results indicate that there exists no correlation between the distribution of amyloid amyloid beta-protein precursor mRNAs and the tissue and cellular pathology of Alzheimer's disease; they also suggest that an overproduction of amyloid beta-protein precursor mRNA is unlikely to be responsible for amyloid beta-protein deposition in Alzheimer's disease.

cDNA cloning and predicted amino acid sequence of Glycera dibranchiata monomer hemoglobin IV

The three major monomer hemoglobins from Glycera dibranchiata erythrocytes isolated in this laboratory were sequenced from their N-termini. A stretch of amino acid sequence identity was used to determine the sequence of a mixed oligodeoxynucleotide that would be complementary to all 12 possible mRNA sequences coding for the amino acids. A cDNA library was constructed by using poly(A+) RNA from G. dibranchiata erythrocytes, the library was probed with the oligonucleotide, and the longest positive inserts found were subcloned into a sequencing plasmid and then sequenced. The first one was 745 bases long, containing 85 bases of 5'-untranslated RNA, an open reading frame of 444 bases coding for 148 amino acids, and a 3'-untranslated region of 216 bases. The predicted amino acid sequence matches the first 25 amino acids of G. dibranchiata monomer globin component IV. The sequence contains an N-terminal methionine plus 18 other mostly conservative sequence changes compared to the published sequence of Imamura et al. (1972), which appears from our partial sequencing to be monomer globin component II. We confirm the presence of leucine in the E7 position, which is histidine in most myoglobins and hemoglobins.

In situ hybridization demonstration of poly-adenylated RNA sequences in formalin-fixed paraffin sections using a biotinylated oligonucleotide poly d(T) probe

An in situ hybridization technique has been developed for assessing poly(A)+ RNA preservation in routine pathology specimens. The method detects poly-adenylated RNA sequences in tissue sections using a biotinylated polydeoxythymidine (poly d(T)) probe. The probe was prepared from single-stranded 25-30 base oligo d(T) and was biotinylated using the enzyme terminal deoxynucleotide transferase with biotin-11-dUTP and dTTP in the ratio 1:4. The hybridization protocol uses varying concentrations of proteinase K to unmask mRNA sequences and the biotin-labelled hybrids are demonstrated after hybridization under standard conditions by the application of streptavidin and biotinylated alkaline phosphatase. Alkaline phosphatase was visualized using a Fast Red naphthol-capture method and the sections were counterstained with haematoxylin. The results have confirmed that the method is specific for poly(A)+ RNA and shows that poly(A)+ RNA can be demonstrated in routine formalin-fixed sections using non-radioactive techniques with retention of morphology. It also provides a means of optimizing the hybridization conditions for specific mRNA probes and produces a staining pattern demonstrating the relative level of poly(A)+ RNA per cell which may reveal new information about cell activity and tissue function.

Gene-specific labeling of chromatin for electron microscopy

In restriction enzyme digested Xenopus laevis erythrocyte chromatin, the 5S oocyte genes were specifically labeled with colloidal gold so they could be identified in an electron microscopic study. Nuclei were digested first with HindIII restriction endonuclease followed by T7 exonuclease to leave single-stranded 3' tails on the fragments. A biotinylated 15-mer oligonucleotide complementary to the tail on the 3' end of the 5S gene was annealed to the chromatin, and streptavidin complexed colloidal gold was bound to it. In a spread for electron microscopy the labeled fragments were readily recognized.

Localization of GABAA receptor alpha-subunit mRNAs in relation to receptor subtypes

The distribution of 3 GABAA receptor alpha-subunit mRNAs in various regions of bovine brain has been investigated using in situ hybridization. Whereas the alpha 2- and alpha 3-transcripts are of low abundance in all regions except striatum, the alpha 1-transcript is considerably enriched in the inferior colliculus, olfactory bulb and substantia nigra, and appears to be correlated with benzodiazepine type I receptor localization.

Cloning and synthesis of infectious cardiovirus RNAs containing short, discrete poly(C) tracts

Mengovirus RNA transcripts with 5' noncoding poly(C) tracts of C8, C12, and C13UC10 have been synthesized in vitro from cDNA clones and shown to be infectious to HeLa cells. A chimeric clone has also been constructed which links the 5' end from one mengovirus clone (299 nucleotides, containing C13UC10) to a 7,424-base fragment derived from the 3' end of encephalomyocarditis (EMC) virus. Progeny virus isolated after transfection with the clone-derived RNAs had the same poly(C) tracts, mengovirus-specific sequences, or EMC virus-specific sequences as the transcript from which it was derived. Although the cloned poly(C) tracts were considerably shorter than those found in viral RNA from mengovirus (C50UC10) or EMC virus (C115UCUC3UC10), the growth characteristics of the progeny viruses in HeLa cells were indistinguishable from those of the parental viruses, indicating the length of this tract does not play a significant restrictive role for cardiovirus infectivity in tissue culture.

A very small viral double-stranded RNA

UmV is a double-stranded RNA (dsRNA) virus of the corn fungal pathogen Ustilago maydis. UmV has no infectious cycle. Some UmV subtypes have viral dsRNAs encoding secreted toxins that kill sensitive cells of the same species and related species. There are three viral subtypes, P1, P4 and P6, which differ in the specificity of their secreted killer toxins. Each has three size classes of dsRNA: H (heavy), M (medium) and L (light). The L segments of UmV are unique in being derived from one end of the larger M segments. We have sequenced P1 L and placed it at the 3' end of the P1 M1 plus strand. In their overlapping regions, these dsRNAs are identical in sequence. In vitro translation of P1 M1 results in a peptide whose size is consistent with its being encoded by the non-L region of M1. P1 L is a very small dsRNA of 355 bp. It has no long open reading frames and produces no detectable in vitro translation product. The sequence of P1 L suggests that it is derived by a process unique among dsRNA viruses: replication and packaging of the 3' end fragment of a processed mRNA.

Hypoxanthine-guanine phosphoribosyltransferase. Genetic evidence for identical mutations in two partially deficient subjects

In past reports of hypoxanthine-guanine phosphoribosyltransferase (HPRT) deficiency a marked degree of molecular heterogeneity has been noted. We have previously described two apparently unrelated subjects with partial HPRT deficiency, G.S. and D.B., who have a mutant form of HPRT with remarkably similar alterations in physical and kinetic properties. The mutation in G.S. is a serine to leucine substitution at amino acid 110 as determined by amino acid sequence analysis. This mutant enzyme has been designated HPRTLondon. We have examined HPRT cDNA from D.B. using two different methods to determine if the similar properties of mutant HPRT from these two subjects are the result of a common mutation. HPRT cDNA clones were obtained by routine cloning techniques and by polymerase chain reaction amplification of single-stranded cDNA reverse transcribed from mRNA derived from subject D.B. Dideoxynucleotide sequencing revealed a single mutation, a C to T transition at bp 329 in clones generated by both methods. This mutation in D.B. predicts the identical amino acid substitution described in HPRTLondon. A C to T nucleotide transition at 329 in D.B. creates an Hpa I site in exon 4 of the HPRT gene. Southern blot analysis of genomic DNA isolated from lymphoblasts derived from G.S. and D.B. revealed that both have this additional Hpa I site, indicating that the similarly altered protein sequence is due to the identical transition in the HPRT gene.

Distinct GABAA receptor alpha subunit mRNAs show differential patterns of expression in bovine brain

Specific oligonucleotide probes have been used to visualize the regional and cellular distribution of the mRNAs encoding three structurally distinct GABAA receptor alpha subunits in bovine brain. In situ hybridization analysis showed that these transcripts differ in distribution and in relative abundance. In frontal cortex the alpha 1 and alpha 2 transcripts are most abundant in layers II-IV, whereas the alpha 3 mRNA is most abundant in layers V and VI. In the hippocampal complex, the alpha transcripts are differentially distributed in the entorhinal cortex and subiculum. The alpha 2 transcript is enriched in the dentate gyrus and CA4/CA3 regions of the hippocampus. In the cerebellum, essentially only the alpha 1 transcript is detectable in granule cells, Purkinje cells, and stellate/basket cells. These results suggest that the different alpha subunits represent components of distinct GABAA receptor subtypes.

Insulin/insulin-like growth factor I and other epigenetic modulators of myelin basic protein expression in isolated oligodendrocyte progenitor cells

The expression of myelin basic protein by the oligodendrocyte is an integral event in the maturation of central nervous system function. Although much is known concerning the various myelin basic protein species, their temporal expression, and processing of RNA transcripts, little is known about the epigenetic factors responsible for the regulation of myelin basic protein (MBP) expression. In this study, we present evidence that insulin/insulin-like growth factor-I can increase the levels of MBP protein in isolated oligodendrocyte progenitor cells cultured in a serumless, chemically defined medium (ODM). Insulin was found to increase MBP protein in a dose-responsive manner, reaching a maximal level at 72 hr of exposure. Both insulin-like growth factor-I (IGF-I) and insulin were demonstrated to have no effect on MBP RNA levels. These data indicate that insulin/IGF-I increased MBP protein levels at a level distal to transcription The dose response of insulin action suggests that it may have a MBP regulatory function, distinct from IGF-I. When added individually, the other supplements of ODM, transferrin (500 ng/ml), and basic fibroblast growth factor (5 ng/ml) had no effect on MBP expression. However, when all three components were combined, a synergistic effect resulting in increased MBP protein and total RNA levels was found. The phorbol ester 12-O-tetradecanoyl phorbol acetate was found to reduce intracellular MBP RNA levels. The cAMP analogue/dibutyryl cAMP had contrasting effects on MBP RNA levels; no effect occurred in cultures grown in fetal calf serum, but a reduction in RNA levels was found in cultures grown in ODM. These data suggest that only a select range of extrinsic factors may be involved in MBP regulation, and depending on the environmental milieu, epigenetic agents may modulate gene activity differently.