Low Molecular Weight Ribonucleic Acid Research Articles

S2Snet: deep learning for low molecular weight RNA identification with nanopore.

Ribonucleic acid (RNA) is a pivotal nucleic acid that plays a crucial role in regulating many biological activities. Recently, one study utilized a machine learning algorithm to automatically classify RNA structural events generated by a Mycobacterium smegmatis porin A nanopore trap. Although it can achieve desirable classification results, compared with deep learning (DL) methods, this classic machine learning requires domain knowledge to manually extract features, which is sophisticated, labor-intensive and time-consuming. Meanwhile, the generated original RNA structural events are not strictly equal in length, which is incompatible with the input requirements of DL models. To alleviate this issue, we propose a sequence-to-sequence (S2S) module that transforms the unequal length sequence (UELS) to the equal length sequence. Furthermore, to automatically extract features from the RNA structural events, we propose a sequence-to-sequence neural network based on DL. In addition, we add an attention mechanism to capture vital information for classification, such as dwell time and blockage amplitude. Through quantitative and qualitative analysis, the experimental results have achieved about a 2% performance increase (accuracy) compared to the previous method. The proposed method can also be applied to other nanopore platforms, such as the famous Oxford nanopore. It is worth noting that the proposed method is not only aimed at pursuing state-of-the-art performance but also provides an overall idea to process nanopore data with UELS.

A Novel Low Molecular Weight Ribonucleic Acid (RNA) Related to Transforming Growth Factor α Messenger RNA

Human transforming growth factor alpha (TGF alpha) is coded for by an mRNA of about 4800 nucleotides. The cDNA sequence demonstrates that the 50 amino acid TGF alpha is embedded in a larger 160 amino acid precursor protein. We report here that in addition to the 4800 nucleotide TGF alpha mRNA, there is a novel second RNA species of about 350 nucleotides that hybridizes to a human TGF alpha cDNA probe. This small RNA species has been found in the RNA of several human tumor cells including HT1080, A549, A431, A2058, and A673. We have demonstrated an inverse relationship between the amounts of the 4800 nucleotide TGF alpha mRNA and the 350 nucleotide novel RNA in these human cells. Restriction enzyme cleavage of a human TGF alpha cDNA probe into three separate domains consisting of a processed coding region and 5'- and 3'-preprocessed coding and untranslated regions showed that only the 3'-untranslated region hybridized to the 350 nucleotide RNA. Using sense and anti-sense single-stranded 3'-untranslated region probes, we determined that the 350 nucleotide RNA band may be composed of multiple species of RNA which are related to the anti-sense DNA strand that is opposite to the strand that codes for the 4800 nucleotide TGF alpha mRNA.

Application of rapid biochemical methods for detecting avocado sunblotch disease

SUMMARYThe method of Palukaitis & Symons (1980) for extracting low molecular weight ribonucleic acids from plant tissue was improved by CF‐11‐cellulose chromatography and further simplified for use in routine biochemical indexing for avocado sunblotch viroid (ASBV). Extracts were prepared routinely at 10 g dry weight equivalents (DWE) of tissue per ml; more concentrated than previously possible with many avocado cultivars. Conditions for assaying extracts of ASBV were standardised and the lower limits for detection determined as 80–230 ng ASBV/g DWE of tissue for polyacrylamide gel electrophoresis (PAGE) and 1 ng/g DWE of tissue for complementary DNA (cDNA) probe assays. The concentration of ASBV in a single infected tree varied from 5 to 5000 ng/g DWE between branches, but only to a minor degree between mature leaves and young blossoms within branches.Six independent sources of sunblotch disease were examined and all proved positive for ASBV by PAGE. The ASBV extracted from five of these sources hybridised with cDNA prepared from the sixth or standard source (Hass/SB‐1), with hybridisation values ranging from 43% to 89%. In a survey of 76 trees intended for propagation in Australia, all of 17 trees previously accepted as healthy on the basis of graft transmission tests were negative for ASBV by PAGE and had cDNA hybridisation values ranging from 1.8% to 12.1%. Amongst 59 trees apparently free of sunblotch symptoms but not previously indexed, only one tree was positive for ASBV by both PAGE and cDNA probe assay. The other 58 trees were negative by PAGE but had hybridisation values ranging from 1.0% to 42.8%. Forty‐nine trees had values consistent with known healthy trees (<12% hybridisation), while the results of the remaining nine trees will require confirmation by additional tests before a conclusion about ASBV is made.The cDNA probe assay successfully detected ASBV in avocado seedlings graft inoculated with Hass/SB‐1, 1–2 months before symptoms were displayed but not until 6 months after inoculation. Methods for improving the cDNA probe assay still further are discussed.

Cytoplasmic low molecular weight ribonucleic acid species of chick embryonic muscles, a potent inhibitor of messenger ribonucleic acid translation in vitro.

Cytoplasmic low molecular weight ribonucleic acid species of chick embryonic muscles, a potent inhibitor of messenger ribonucleic acid translation in vitro.

Metabolism of low molecular weight ribonucleic acids in early sea urchin embryos

There are three major low molecular weight RNAs (150-300 nucleotides) larger than 5S rRNA present in sea urchin embryos. Two of these are localized in the nucleus and one is localized in the cytoplasm. The nuclear species contain "capped" 5' termini, with a cap I structure. These RNAs are synthesized starting in late cleavage and continuing through pluteus. Relative to 5S RNA there is a 10-fold change in the rate of synthesis of these RNAs, due primarily to a decrease in their rate of transcription after blastula. The RNAs are metabolically stable and the nuclear RNA genes are reiterated 50--100 times in the genome. Significant amounts of these RNAs are present in sea urchin eggs, enough to supply the embryo during early cleavage, prior to initiation of their synthesis.

Avocado Affected by Sunblotch Disease Contains Low Molecular Weight Ribonucleic Acid.

When extracts from infected and healthy avocado tissue were electrophoresed in polyacrylamide gels to separate the nucleic acids, an RNA with an Rf of 0.57 was present in all preparations from infected avocado but absent from healthy tissue. Sunblotch affected material from both Calif. and Australia contained the same RNA, which has a mol. wt. similar to that of other viroids and is believed to be the sunblotch agent. Avocado material may be much more easily tested for the presence of the sunblotch disease agent by detecting the SB-RNA than by the previously employed time-consuming, grafting technique.

Human leukemic cells: Characteristics of modified methylated minor bases of low molecular weight ribonucleic acids

RNAs isolated from cells derived from human leukemia (CCRF-CEM), infectious mononucleosis (CCRF-RKB, SB), and a normal donor (CCRF-SLT) were resolved into 4 peaks on Sephadex G-100 columns. tRNA (4S or peak IV) showed a higher ratio of 6-methyladenosine, N 2, N 2 -dimethylguanosine and 5-methylcytosine in RKB and SB cells as compared with CEM and SLT cells. Striking differences were observed in 7-methylguanosine; there was a 4–5-fold increase in CEM cells, and a 2-fold increase in RKB and SB, as compared with SLT cells. The total content of modified minor bases, including pseudo-uridine, showed no significant quantitative differences in the 4.6S RNA (peak III) RNA. A 3–4-fold increase was seen in the 7-methylguanosine content of 5.5S (peak II) isolated from CEM cells as compared to RKB, SB and SLT cells. 3-Methylcytosine was found only in CEM, and higher ratios of minor bases were found in 5.5S RNA isolated from CEM, as compared with SLT, RKB, and SB cells. These observations are of particular interest in view of increased excretion of methylated purines in urines of patients or animals with cancer, and may reflect increased methylation reactions and/or increased metabolic turnover of methylated bases in the tumor-bearing host.

Multiple forms of potato spindle-tuber metavirus ribonucleic acid.

Multiple infectious low-molecular weight ribonucleic acids from Scopolia sinensis plants, infected with potato spindle tuber metavirus were isolated by Bio-Gel P-200 gel filtration columns and the slowest-moving form (infectious peak III) was eluted with bulk of 4 S-RNA.

Modified Nucleosides of Nuclear and Nucleolar Low Molecular Weight Ribonucleic Acid

Abstract Modified nucleosides have been found in some types of low molecular weight nuclear RNA of Novikoff hepatoma ascites cells in addition to 4 S RNA. The low molecular weight nuclear RNA species have been defined on the basis of their size as well as their content of uridylic acid as 4 S, 4.5 S, 5 S, U-1, U-2, and U-3 RNA (Busch, H., and Smetana, K. (1970) The Nucleolus, p. 285, Academic Press, New York). In particular, the U-2 RNA contained 11 pseudouridine residues and the unusual nucleoside, N2,N2-dimethyl 7-methyl guanosine, which was not found in transfer RNA or any other nuclear RNA except U-3. Nuclear 4.5 S RNAiii contained 3 pseudouridine residues and 1 residue each of N6-methyl adenosine and N2-methyl guanosine. Nuclear 5 S RNAiii contained 2 pseudouridine residues. Although the content of modified nucleosides in the 4 S RNAs from cytoplasm, ribosomes, and nuclei was the same, significantly lower amounts of dihydrouridine and N2-methyl guanosine were found in the nucleolar 4 S RNA. No modified nucleosides were found in 4.5 S RNAi, 4.5 S RNAii, 5 S RNAi, 5 S RNAii, U-1a RNA, and 5.5 S RNA.

The Nucleotide Sequence of a Low Molecular Weight Ribonucleic Acid from Cells Infected with Adenovirus 2

Abstract A low molecular weight RNA was isolated from human cells infected with adenovirus 2 and its nucleotide sequence deduced to be pG-G-G-C-A-C-U-C-U-U-C-C-G-U-G-G-U-C-U-G-G-U-G-G-A-U-A-A-A-U-U-C-G-C-A-A-G-G-G-U-A-U-C-A-U-G-G-C-(G-U-G-G-A-C-G-A-C-C)-G-G-G-G-U-U-C-G-A-A-C-C-C-C-G-G-A-U-C-C-G-U-G-A-U-C-C-A-U-G-C-G-G-U-U-A-C-C-G-U-C-C-G-C-C-G-C-C-C-G-U-G-C-G-U-C-G-A-A-C-C-C-A-G-G-U-G-U-G-C-G-A-C-G-U-C-A-G-A-C-A-A-C-G-G-G-G-G-A-G-C-G-C-U-C-C-U-Uoh. To determine this sequence, we analyzed the products of extensive digestion of this RNA with T1 RNase, pancreatic RNase, and spleen acid ribonuclease, the products of extensive T1 RNase digests of partially methylated RNA, the products of pancreatic RNase digestion of RNA modified with a water-soluble carbodiimide, the products of limited digestion of the RNA with T1 RNase, and the oligonucleotides produced by spleen acid nuclease digestion of the limited T1 RNase digestion products.

Infectious low-molecular weight ribonucleic acid from tomato

Summary Potato spindle tuber virus (PSTV) was extracted from tomato leaves and purified by precipitation with cetyltrimethylammonium bromide and by chromatography on DEAE-cellulose. Analysis of viral activity using the local lesion host, Scopolia sinensis , revealed a 40 fold increase in infectivity. Further analysis of the purified virus by centrifugation in sucrose gradients and by electrophoresis in polyacrylamide gels showed that peak infectivity corresponded to a particle size of 4–5 Svedberg units. Susceptibility of the virus to exonuclease activity was also examined, and in some cases infectivity was decreased by 98 per cent upon incubation with venom phosphodiesterase.

A low molecular weight ribonucleic acid synthesized by Escherichia coli in the presence of chloramphenicol: Characterization and relation to normally synthesized 5 s ribonucleic acid

A low molecular weight RNA synthesized by Escherichia coli cells during exposure to chloramphenicol (100 μg/ml.) has properties which are similar, though not identical, to those of normally synthesized ribosomal 5 s RNA. We call it Cam-5 s RNA. Radioactive Cam-5 s RNA is annealed to E. coli DNA in a manner similar to that of normal 5 s RNA, and this hybridization can be inhibited in a competitive fashion by normal non-radioactive 5 s RNA. Cam-5 s RNA can replace normal 5 s RNA, when larger ribosomal subunits are reconstituted from lithium chloridetreated ribosomal cores and lithium chloride-split proteins. By thermal denaturation, the secondary structure of Cam-5 s RNA can be reversibly changed in a fashion similar to that of normal 5 s RNA, but none of the forms of Cam-5 s RNA coincide with the corresponding forms of normal 5 s RNA when they are co-chromatographed on columns of methylated albumin—kieselguhr. When 5 s RNA and Cam-5 s RNA are subjected to limited degradation by ribonuclease T 1 and fractionated by acrylamide gel electrophoresis, similar large partial digestion fragments are obtained from both RNA's. The over-all base compositions of Cam-5 s RNA and normal 5 s RNA are quite similar, and no methylated or other modified nucleotides could be detected in alkaline hydrolysates of Cam-5 s RNA which were fractionated in two dimensions by electrophoresis and descending chromatography. Two-dimensional fractionations of Cam-5 s RNA completely digested by pancreatic or T 1 ribonuclease demonstrate that the primary structure of Cam-5 s RNA is essentially identical to that of normal 5 s RNA except for the presence of different 5′-terminal nucleotide sequences: in Cam-5 s RNA, the normal 5′-terminal sequence pUpG- is absent and the following sequences are found, in a combined yield of one mole: pApUpUpUpG-, pUpUpUpG- and pUpUpG-. The RNA chains (Cam-5 s RNA) which have these 5′-terminal sequences are slightly longer than the 5′-terminus of normal 5 s RNA and probably represent precursor forms of mature 5 s RNA.

Low molecular weight ribonucleic acid in rabbit reticulocyte ribosomes

A low molecular weight RNA which we call “lRNA” is released from the 30 s ribosomal RNA or the large ribosomal subunit of rabbit reticulocyte ribosomes by treatment which disrupts base pairing. Separation of the two RNA species may occur at a relatively low temperature (43 °C in 0.01 m-phosphate buffer, pH 7.6) indicating that only a small number of bases, not more than about six, are involved in pairing. The fact that the temperature of RNA release from ribosomes is about the same as that from the isolated RNA indicates that ribosomal proteins do not stabilize the interaction between the two RNA species in the ribosome. No ribosomal proteins are released along with RNA. Reassociation of the two RNA chains occurs when they are annealed together from 65 °C in standard saline citrate buffer. Purification of the RNA in amounts sufficient for measurements of its molecular weight, composition and secondary structure, and the results of these studies, are reported.

Patterns of Ribonucleic Acid Synthesis in T5-infected Escherichia coli: III. SEPARATION OF LOW MOLECULAR WEIGHT RIBONUCLEIC ACID SPECIES BY DISC ELECTROPHORESIS ON ACRYLAMIDE GEL COLUMNS

Patterns of Ribonucleic Acid Synthesis in T5-infected Escherichia coli: III. SEPARATION OF LOW MOLECULAR WEIGHT RIBONUCLEIC ACID SPECIES BY DISC ELECTROPHORESIS ON ACRYLAMIDE GEL COLUMNS

Studies of the Primary Structure of Low Molecular Weight Ribonucleic Acid other than tRNA

Studies of the Primary Structure of Low Molecular Weight Ribonucleic Acid other than tRNA

Studies on the Origin of a Low Molecular Weight Ribonucleic Acid from Human Cells Infected with Adenoviruses

After infection with adenovirus 2 or adenovirus 7, human epithelioid cells (KB strain) synthesize a discrete species of low molecular weight RNA (VA RNA). Intact and disrupted nuclei from infected cells incorporate labeled nucleoside triphosphates into RNA with chromatographic and electrophoretic properties indistinguishable from VA RNA. VA RNA can be annealed to homologous virus DNA and, to a lesser extent, to KB cell DNA. Oligonucleotide maps of enzymatic digests of VA RNA from KB cells infected with adenovirus 7 were partially analyzed. The results indicate that this is a relatively homogeneous species of RNA which does not have many long sequences identical with VA RNA from cells infected with adenovirus 2. Thus, although we lack direct evidence that VA RNA is transcribed from virus DNA, the primary structure of VA RNA is directed by the infecting virus.

Ribonucleic acid synthesis in cells infected with herpes simplex virus. I. Patterns of ribonucleic acid synthesis in productively infected cells.

HEp-2 cells were pulse-labeled at different times after infection with herpes simplex virus, and nuclear ribonucleic acid (RNA) and cytoplasmic RNA were examined. The data showed the following: (i) Analysis by acrylamide gel electrophoresis of cytoplasmic RNA of cells infected at high multiplicities [80 to 200 plaque-forming units (PFU)/cell] revealed that ribosomal RNA (rRNA) synthesis falls to less than 10% of control (uninfected cell) values by 5 hr after infection. The synthesis of 4S RNA also declined but not as rapidly, and at its lowest level it was still 20% of control values. At lower multiplicities (20 PFU), the rate of inhibition was slower than at high multiplicities. However, at all multiplicities the rates of inhibition of 18S and 28S rRNA remained identical and higher than that of 4S RNA. (ii) Analysis of nuclear RNA of cells infected at high multiplicities by sucrose density gradient centrifugation showed that the synthesis and methylation of 45S rRNA precursor continued at a reduced but significant rate (ca. 30% of control values) at times after infection when no radioactive uridine was incorporated or could be chased into 28S and 18S rRNA. This indicates that the inhibition of rRNA synthesis after herpesvirus infection is a result of two processes: a decrease in the rate of synthesis of 45S RNA and a decrease in the rate of processing of that 45S RNA that is synthesized. (iii) Hybridization of nuclear and cytoplasmic RNA of infected cells with herpesvirus DNA revealed that a significant proportion of the total viral RNA in the nucleus has a sedimentation coefficient of 50S or greater. The sedimentation coefficient of virus-specific RNA associated with cytoplasmic polyribosomes is smaller with a maximum at 16S to 20S, but there is some rapidly sedimenting RNA (> 28S) here too. (iv) Finally, there was leakage of low-molecular weight (4S) RNA from infected cells, the leakage being approximately three-fold that of uninfected cells by approximately 5 hr after infection.

Quantitative Determination of Low Molecular Weight Ribonucleic Acids in Rat Liver Microsomes

Abstract Analysis by type of the RNA of microsomes and of ribosomes was performed by sucrose density gradient centrifugation and by chromatography on Sephadex G-200. Microsomal RNA consists of high molecular weight RNA, 5 S RNA, and transfer RNA in the proportions of 93%, 1.6%, and 5.9%, respectively. RNA of ribosomes of molecular weight less than about 150,000 differed from that of microsomes only in the content of tRNA. Incubation of microsomes at 37° in solutions containing sodium dodecyl sulfate resulted in breakdown of high molecular weight RNA.

Further studies on the heterogeneity of lens ribonucleic acid

Ribonucleic acid (RNA) from separated parts of cattle lenses, i.e. epithelial cells, cortical and nuclear fibres was prepared by phenol treatment. The heterogeneity of ribonucleic acid was studied by sucrose density-gradient ultracentrifugation and methylated albumin kieselguhr column chromatography. Due to the differentiation of epithelial cells to lens fibres, marked decrease in relative amounts of high molecular weight RNA and an increase of low molecular weight RNA were observed by both methods. Similar distribution was shown when RNA heterogeneity of chick lenses during ontogenesis, starting from the embryonic stage, was studied. The method of methylated albumin chromatography proved to be more advantageous when the features of low molecular weight RNA, present in large quantity in lens, are studied.

Nucleotide sequence of 5S-ribosomal RNA from Escherichia coli.

IN 1964 Rosset, Monier and Julien1 described and characterized a low molecular weight ribonucleic acid (5S RNA) that is present in the ribosomes of Escherichia coli in addition to the two larger components, the 16S and 23S RNA. It contains 120 nucleotide residues and in contrast to transfer RNA contains no “minor” bases. Using a two-dimensional fractionation procedure for the separation of nucleotides labelled with phosphorus-32 (ref. 2), we have determined the sequences of all the oligonucleotides obtained by complete digestion of 32P-labelled 5S RNA with ribonuclease T1 and ribonuclease A (pancreatic ribonuclease)3. In order to arrange these nucleotides in the unique sequence of the 5S RNA, we have now studied the products of various partial ribonuclease digestions. This has involved the development of a number of new techniques which will be described in detail later. From the large number of partial digestion products obtained, we deduced the unique sequence shown in Figs. 1 and 2.