Utilizing online stochastic optimization on scheduling of intensity-modulate radiotherapy therapy (IMRT)

According to Ministry of Health and Welfare of Taiwan, cancer has been one of the major causes of death in Taiwan since 1982. The Intensive-Modulated Radiation Therapy (IMRT) is one of the most important radiotherapies of cancers, especially for Nasopharyngeal cancers, Digestive system cancers and Cervical cancers. For patients, if they can receive the treatment at the earliest possibility while diagnosed with cancers, their survival rate increases. However, the discussion of effective patient scheduling models of IMRT to reduce patients' waiting time is still limited in literature. This study proposed a mathematical model to improve the efficiency of patient scheduling. The research was composed of two stages. In the first stage, the online stochastic algorithm was proposed to improve the performance of present scheduling system. In the second stage the impact of future treatment to reduce patients' waiting time was considered. A genetic algorithm (GA) was then proposed to solve the online stochastic scheduling problem. This research collected data from a practical medical institute and the proposed model was validated with real data. It contributes to both theory and practice by proposing a practical model to assist the medical institute in implementing patient scheduling in a more efficient manner.

Self-priming on the plant viral RNAs during reverse transcription-PCR

The occurrence of the primer-independent cDNA synthesis during RT-PCR analysis of human and animal RNA viruses has been well documented. Conversely, there is scant knowledge about this event in plant RNA viruses. Here we show that the primer-independent cDNA synthesis occurs in all eight different plant RNA viruses tested in this study, suggesting a common phenomenon for RT-PCR analysis of plant RNA viruses. Additional experiments indicate that the event is likely contributed to by RNA self-priming, and can be effectively reduced or eliminated through increasing temperature of the RT reaction.

Infectious Pancreatic Necrosis Virus RNA Cleavage In Vitro by Hammerhead Ribozymes and Enhancement of Ribozyme Catalysis by Oligonucleotide Facilitators

Infectious pancreatic necrosis virus (IPNV), an aquatic birnavirus, has a bisegmented double-stranded RNA genome consisting of a 3.2-kb A segment and a 2.9-kb B segment. To determine the function of IPNV's viral proteins and to study the effects of viral RNA cleavage by hammerhead ribozymes, we cloned and sequenced the IPNV E1S strain of the A segment. After sequencing, we continued to study the virus pathogens inhibited by ribozyme cleavage and analyzed the cleavage of the virus RNA in vitro. The templates (VP2, 1220 bp) for in vitro transcription of S569 and S969 (substrates 569 and 969 bp in length) were synthesized by polymerase chain reaction. The DNA templates of hammerhead ribozymes targeted different sites in the partial sense RNA of IPNV. These templates were chemically synthesized RNAs prepared by runoff transcription of amplification products or synthetic DNA templates containing a T7 RNA polymerase promoter, and were used to characterize several properties of the cleavage reaction at 25 degrees C in 12 mM Mg(2+). Under this condition (25 degrees C, 12 mM Mg(2+)), the hammerhead ribozymes formed an estimated fraction of product during the reaction of only 30% in cleaving long RNA substrates in vitro. Short DNA facilitators (12 or 24-mers) that bind adjacent to either the 3' or 5' end of the ribozyme enhanced the rate of cleavage of the long RNA substrates containing 569 and 969 nucleotides, respectively, in trans. The hammerhead ribozymes with 3'-end facilitators reacted more efficiently (i.e., 65%).

Solution structure and RNA-binding activity of the N-terminal leucine-repeat region of hepatitis delta antigen

Hepatitis delta virus (HDV) is a satellite virus of the hepatitis B virus (HBV) which provides the surface antigen for the viral coat. The RNA genome of HDV encodes two proteins: the small delta antigen and the large delta antigen. The two proteins resemble each other except for the presence of an additional 19 amino acids at the C terminus of the latter species. We have found that the N-terminal leucine-repeat region of hepatitis delta antigen (HDAg) binds to the autolytic domain of HDV genomic RNA and attenuates its autolytic activity. A 27-residue polypeptide corresponding to residues 24-50 of HDAg, designated dAg(24-50), was synthesized, and its solution structure was found to be an alpha-helix by circular dichroism and (1)H-nuclear magnetic resonance (NMR) techniques. Binding affinity of dAg(24-50) with HDV genomic RNA was found to increase with its alpha-helical content, and it was further confirmed by modifying its N- and C-terminal groups. Furthermore, the absence of RNA binding activity in the mutant peptides, dAgM(24-50am) and dAgM(Ac24-50am), in which Lys38, Lys39, and Lys40 were changed to Glu, indicates a possible involvement of these residues in their binding activity. Structural knowledge of the N-terminal leucine-repeat region of HDAg thus provides a molecular basis for the understanding of its role in the interaction with RNA. Proteins 1999;37:121-129.

The effect of Lp3 enlargement on the folding and catalysis of hepatitis delta virus cis-cleaving ribozyme

Oligonucleotides were inserted into the Lp3 region of a hepatitis delta virus (HDV) cis-cleaving ribozyme and the effect of Lp3 enlargement on ribozyme folding was examined by assaying the activity of each mutant. The location of insertion and the sequence of the inserted oligonucleotide had distinct effects on ribozyme activity, and the HDV ribozyme was capable of adopting the active structure for cis-cleavage when a pentanucleotide was inserted into the 3' portion of Lp3. Furthermore, whether the insertion mutant cis-cleaved or not, the structure of Lp3 was altered by the inserted oligonucleotide. These findings disclose that the 5' rather than the 3' portion of Lp3 is critical for ribozyme folding and catalysis.

Identification and characterization of the RNA chaperone activity of hepatitis delta antigen peptides

In this study, we identified an activity of the hepatitis delta antigen that both modulates the cis-cleaving activities of hepatitis delta virus (HDV) genomic RNA fragments and facilitates the trans-cleavage reactions between hammerhead ribozymes and the cognate substrates of various lengths in vitro. Hepatitis delta antigen peptides exert their effect by accelerating the unfolding and refolding of RNA molecules and by promoting strand annealing and strand dissociation. In addition, the stimulatory effect of hepatitis delta antigen peptide on hammerhead catalysis is observed whether the peptide is removed or not by phenol/chloroform extraction prior to the initiation of trans-cleavage reaction. Therefore, hepatitis delta antigen peptide acts as an RNA chaperone. The RNA chaperone domain of hepatitis delta antigen overlaps with the coiled-coil domain that is rich in lysine residues. The RNA binding domains of hepatitis delta antigen previously identified are not required for the RNA chaperone activity identified herein. The RNA chaperone activity of hepatitis delta antigen may be important for the regulation of HDV replication in vivo.

Local helix content and RNA-binding activity of the N-terminal leucine-repeat region of hepatitis delta antigen

Hepatitis delta virus (HDV) is a satellite virus of the hepatitis B virus (HBV) which provides the surface antigen for the viral coat. Our results show that the N-terminal leucine-repeat region of hepatitis delta antigen (HDAg), encompassing residues 24-50, binds to the autolytic domain of HDV genomic RNA and attenuates its autolytic activity. The solution conformation of a synthetic peptide corresponding to residues 24-50 of HDAg as determined by two-dimensional 1H NMR and circular dichroism techniques is found to be an alpha-helix. The local helix content of this peptide was analyzed by NOEs and coupling constants. Mutagenesis studies indicate that Lys38, Lys39, and Lys40 within this alpha-helical peptide may be directly involved in RNA binding. A structural knowledge of the N-terminal leucine-repeat region of HDAg thus provides a molecular basis for understanding its role in the interaction with RNA.

An AU at the first base pair of helix 3 elevates the catalytic activity of hepatitis delta virus ribozymes

A mutational analysis of the helix 3 (H3) region of hepatitis delta virus (HDV) ribozymes disclosed that an AU at the first base pair of H3 elevates the catalytic activity of various cis- and trans-acting HDV ribozymes. A GC to AU substitution at this position of H3, which is located at the junction of three of the four helices of the pseudoknot-like structure model, altered the structure of HDV ribozymes. This substitution in the H3 did not change the independence of the cleavage rate to pH nor the sensitivity to formamide treatment of the ribozymes.

The importance of the helix 2 region for the cis-cleaving and trans-cleaving activities of hepatitis delta virus ribozymes

The sequence, secondary structure, and size requirements of the helix 2 region (H2) of a cis-acting hepatitis delta virus ribozyme Rz 1 were examined in this study. Mutational analysis was performed, and the cleavage rate of each H2 mutant of Rz 1 was assayed. We found that H2 could be elongated to twice its original size without affecting ribozyme folding while the shortening of H2 by one base pair severely decreased autolytic activity. In addition, the maintenance of the Watson-Crick base-pairing interactions of the last base pair of H2 (A16U58) was not critical for cis-cleavage reaction. Nevertheless, mutants with an AA, an AG, an AC, or a GG pair at the bottom of H2 were less active, and the sequence of the H2/H3 interface might affect the stability of the catalytic core. The negative effects on ribozyme folding, such as the destabilization of H2, the unfavorable sequences at the last base pair of H2 as well as the disruption of the continuity of H2 and H3, could be compensated for by elongating the H2 region of the corresponding mutants. The extension of H2 may alter the conformation of ribozyme molecules; in addition, it stabilized the catalytic core and enhanced the resistance to formamide. Finally, for a trans-acting ribozyme and its substrate that require the formation of H1, H2, and H4 to reconstitute the autocatalytic domain of HDV RNA, the extension of H2 stabilized the substrate/ribozyme complex and speeded up the cleavage rate but hindered the product release process.

Effects of circular permutation on the cis-cleavage reaction of a hepatitis delta virus ribozyme: application to trans-acting ribozyme design

In this study we investigated the effects of the relocation of the wild type termini on the folding of a cis-cleaving RNA Rz 1 that was modified from the autolytic domains of hepatitis delta virus (HDV) RNA. Ten circularly permuted (CP) isomers of this ribozyme were synthesized. The structure homogeneity of RNA molecules, the molar ratio of the active species that undergoes cis-cleavage, and the rate of cis-cleavage were examined for each construct. CP isomers with new termini in H1 or at the junction of H2-H3, H1-J1/4, J1/4-H4, or H4-J4/2 of the proposed pseudoknot-like structure were inactive. The single breaks of phosphodiester bond in H2, J1/2, Lp4, and at the 3'-end of Lp3 decreased but did not abolish autolytic activity. The structural heterogeneity of RNA molecules may account for the limited cis-cleavage of the latter three isomers. The findings of circular permutation analysis were used as the basis for designing an active trans-cleaving ribozyme by dividing the cis-cleaving ribozyme into two subdomains at J1/2 and Lp4. The ribozyme subdomain catalyzed the site-specific cleavage of the circularly permuted composite substrate RNA in trans. Thus, the structure of HDV autolytic domain could be re-formed after two subdomains were associated through the base-pairing interactions of H1, H2, and H4.

Mutagenesis analysis of a hepatitis delta virus genomic ribozyme

We conducted extensive mutagenesis analysis on a hepatitis delta virus (HDV) genomic ribozyme to study the sequence specificity of certain region and to derive the secondary structure associated with the catalytic core. The results confirmed that the autocatalytic domain of HDV genomic RNA contained four base-pairing regions as predicted in the 'pseudo-knot' model [Perrotta & Been (1990) Nature 350, 434-436]. The size and sequence of one of the base-pairing regions, i. e. stem-and-loop, could be flexible. Helix 3 and the first basepair of helix 1 required specific sequence to retain self-cleavage activity. The structural requirement of helix 2 was less stringent than the other base-pairing regions. Moreover, the size of helix 1 affected self-cleavage whereas the length of hinge could be variable even though the first three residues of hinge had stringent sequence requirement.

The catalytic domain of human hepatitis delta virus RNA. A proton nuclear magnetic resonance study

We have obtained and analyzed the 600 MHz proton NMR spectra of a 74-mer RNA derived from the catalytic domain of hepatitis delta virus genomic RNA (HDV RNA) to determine its secondary structure. Deconvolution of the NMR spectrum obtained at 32 degrees C indicates that part of the 74-mer RNA molecule may exist in multiple conformations in equilibrium. The major conformer contains two A-U base pairs and 14 +/- 2 G-C base pairs. It appears to contain no standard G-U base pairs. Our NMR melting study suggests that this conformer has at least two stem-loop regions. One of the regions has been identified to be a tetra-loop. We have assigned five imino proton resonances of the tetra-loop stem. Our data is consistent with the pseudoknot model of Perrotta and Been.

Mutagenesis analysis of the self-cleavage domain of hepatitis delta virus antigenomic RNA

To determine the sequence requirements and structural features of the self-cleavage domain of hepatitis delta virus (HDV) antigenomic RNA, we constructed a series of mutants and measured the rate constant of the cleavage reaction for each. The self-cleavage activity of HDV RNA of antigenomic sense was found to reside in a region of less than 90 nucleotides in length. The catalytic domain contained a long complementary sequence which could be deleted to half of its original size. Moreover, this region could be replaced by other sequences as long as they could fold into a stem-and-loop structure. The catalytic domain also required a 6-basepair helix adjacent to the cleaving point for activity. The structural features of these two base-pairing regions are quite similar to those of the HDV genomic self-cleavage domain. The cleavage site as well as the the hinge region (the sequence between the two stems) requires specific sequences for activity.

Sequence and structure of the catalytic RNA of hepatitis delta virus genomic RNA

Human hepatitis delta virus (HDV) RNA has been shown to contain a self-catalyzed cleavage activity. The sequence requirement for its catalytic activity appears to be different from that of other known ribozymes. In this paper, we define the minimum contiguous sequence and secondary structure of the HDV genomic RNA required for the catalytic activity. By using nested-set deletion mutants, we have determined that the essential sequence for the catalytic activity is contained within no more than 85 nucleotides of HDV RNA. These results are in close agreement with the previous determinations and confirmed the relative insignificance of the sequence at the 5' side of the cleavage site. The smallest catalytic RNA, representing HDV genomic RNA nucleotide positions 683 to 770, was used as the basis for studying the secondary structure requirements for catalytic activity. Analysis of the RNA structure, using RNase V1, nuclease S1 and diethylpyrocarbonate treatments showed that this RNA contains at least two stem-and-loop structures. Other larger HDV RNA subfragments containing the catalytic activity also have a very similar secondary structure. By performing site-specific mutagenesis studies, it was shown that one of the stem-and-loop structures could be deleted to half of its original size without affecting the catalytic activity. In addition, the other stem-and-loop contained a six base-pair helix, and the structure, rather than the sequence, of this helix was required for the catalytic activity. However, the structure of a portion of the stem-and-loop remains uncertain. We also report that this RNA can be divided into two separate molecules, which alone did not have cleavage activity but, when mixed, one of the RNAs could be cleaved in trans. This study thus reveals some features of the secondary structure of the HDV genomic RNA involved in self-catalyzed cleavage. A model of this RNA structure is presented.

Interleukin-6 and retroperitoneal fibromatosis from SRV-2-infected macaques with simian AIDS

We investigated the role of Interleukin-6 (IL-6) as an autocrine growth factor for the retroperitoneal fibromatosis (RF) cells present in macaques infected with the simian retrovirus type 2 (SRV-2). Elevated levels of IL-6 were found in serum of SRV-2 antibody-positive macaques, ascites from RF-positive animals, and RF cell line culture media. IL-6 mRNA levels increased approximately five-fold in RF cells incubated with exogenous SRV-2. In RF cells, SRV-2 functions to increase IL-6 mRNA and protein production and presumably serves as autocrine growth factor.

Cooperative binding of R17 coat protein to RNA

The binding of the R17 coat protein to synthetic RNAs containing one or two coat protein binding sites was characterized by using nitrocellulose filter and gel-retention assays. RNAs with two available sites bound coat protein in a cooperative manner, resulting in a higher affinity and reduced sensitivity to pH, ionic strength, and temperature when compared with RNAs containing only a single site. The cooperativity can contribute up to -5 kcal/mol to the overall binding affinity with the greatest cooperativity found at low pH, high ionic strength, and high temperatures. Similar solution properties for the encapsidation of the related fr and f2 phage suggest that the cooperativity is due to favorable interactions between the two coat proteins bound to the RNA. This system therefore resembles an intermediate state of phage assembly. No cooperative binding was observed for RNAs containing a single site and a 5' or 3' extension of nonspecific sequence, indicating that R17 coat protein has a very low nonspecific binding affinity. Unexpectedly weak binding was observed for several RNAs due to the presence of alternative conformational states of the RNA.

Human hepatitis delta virus RNA subfragments contain an autocleavage activity

Hepatitis delta virus (HDV) contains a single-stranded circular RNA genome of 1.7 kilobases. In this report we demonstrate that subfragments of HDV RNA can undergo autocatalytic cleavage. This cleavage requires at least 500 microM of Mg2+ or Ca2+, is not affected by varying the pH from 5.0 to 9.1, and occurs with RNA fragments as small as 133 nucleotides. The larger RNA fragments containing additional HDV sequences have a lower efficiency of cleavage. Deletion analysis at both ends of RNA subfragments suggested that the catalytic ability of HDV RNA resides in a stretch of no more than 117 nucleotides around the cleavage site. The cleavage occurs at the phosphodiester bond between nucleotides 688 and 689 on the HDV genomic map, generating a 5' fragment with a terminal uridyl 2',3'-cyclic monophosphate residue and a 3' fragment with a guanosyl residue with a 5'-hydroxyl group. The smallest autocleaving RNA does not contain the "hammerhead" sequence required for the autocleavage of other known self-cleaving RNA. The cleavage of HDV RNA occurs at a much faster rate, even at a very low Mg2+ concentration, than that of other "ribozymes." Thus, HDV RNA represents a distinct class of ribozyme.

Reversible cleavage and ligation of hepatitis delta virus RNA

A 148-nucleotide subfragment of hepatitis delta virus RNA was shown to undergo cleavage and ligation reversibly. The direction of the reaction is determined by the presence or absence of Mg2+ ions, with the presence of Mg2+ favoring the cleavage reaction. Ligation requires specific conformation of the RNA molecules involved and occurs only between two cleaved RNA fragments that are still held together by hydrogen bonds. The ligation reaction occurs rapidly on removal of Mg2+ by EDTA. This represents a new class of RNA enzymes.

[The relation of typing of gastric carcinoma according to traditional Chinese medicine theories and clinical pathologic classification]

102 cases of gastric carcinoma which have been removed by partial gastrectomy and have pathological diagnoses and follow-up results are reported. The relationship between their preoperational syndromes of TCM and pathological, TNM classification and post-operational survival rate has been studied. There is indication that the type of Ganwei Buhe (the dispersing function of the liver is disturbed and affects the stomach) manifests the earlier stage of the gastric carcinoma and the majority of cases are in stage 1 or 2 in TNM, the 5-year survival rate with surgery being 46%. The majority of cases of the types of Pishen Yangxu (deficiency of energy in the Spleen and Kidney), Yinxu Neire (the febrile syndrome of the viscera caused by the insufficient primordial energy) and Qixue Shuangkui (deficiency of both energy and blood) are in stage 3 or 4 in TNM, the 5-year survival rate with surgery differently being 5,8,12% respectively. The type of Qizhi Xueyu (energy stagnancy and blood stasis) is between the abovementioned two groups, with a 5-year survival rate of 40%.

Roles of operator and non-operator RNA sequences in bacteriophage R17 capsid assembly

In order to understand the role of sequences other than the translational operator on bacteriophage R17 assembly, in vitro capsid assembly was studied with R17 coat protein and a variety of RNAs. For a series of RNA oligomers of the same chain length, sequences that bind coat protein dimer with a lower affinity require higher concentrations of RNA and protein for assembly. Among a series of non-specific RNA molecules of differing lengths, lower protein and RNA concentrations are required for assembly of capsids containing longer RNAs. For RNA molecules of any length, the presence of a single high-affinity translational operator sequence lowered the concentration requirements for capsid assembly. However, the advantage for encapsidation provided by the operator sequence is small for large RNA molecules. The experiments indicate that in the overall assembly process the interaction of coat protein with non-specific sequences is at least as important as its interaction with the specific translational operator sequence. In light of the data, a mechanism of achieving selective packaging of the R17 genomic RNA in vivo is discussed.

A comparison of two phage coat protein-RNA interactions

The interaction between the coat protein of the group I bacteriophage fr with its translational operator site is compared with the previously studied R17 interaction. The sequence of the two RNA binding sites differ by 2 of 20 nucleotides and two coat proteins by 17 of 129 amino acids. An analysis of the binding of fr coat protein to 24 operator variants revealed that the two proteins recognize operator sequences in virtually the same way. However, fr coat protein binds to nearly every RNA 6 to 14-fold tighter than R17 coat protein. Since the fr operator is a weaker binding variant and the fr coat protein shows a different temperature dependence of binding, it is unlikely that the two systems have different Kas in vivo. RNA fragments containing the operator sequences can initiate the capsid assembly with both fr and R17 coat protein. Surprisingly, the two coat proteins can form a mixed capsid in vitro.

Role of a bulged A residue in a specific RNA-protein interaction

The translational operator of the R17 replicase gene contains a bulged A residue that is essential for the specific binding to R17 coat protein. A large number of operator variants have been synthesized to more precisely examine the role of the bulged A residue on this specific protein-RNA interaction. By use of RNA ligase and transcription of synthetic DNA templates by T7 RNA polymerase, 14 different nucleotides were introduced to the bulged A position of three different coat protein binding fragments. The affinity between coat protein and each fragment was determined by a nitrocellulose filter binding assay. The data indicate that while functional groups on N1, C2, C6, N7, and 2'OH of the bulged A can be substituted without greatly changing protein binding, bulky substituents cannot be tolerated at these positions. Data from additional fragments that have base-pair changes adjacent to the bulged A suggest that the propensity of the bulged A to intercalate into the helix can affect protein binding.

RNA binding site of R17 coat protein

The specific interaction between R17 coat protein and its target of translational repression at the initiation site of the R17 replicase gene was studied by synthesizing variants of the RNA binding site and measuring their affinity to the coat protein by using a nitrocellulose filter binding assay. Substitution of two of the seven single-stranded residues by other nucleotides greatly reduced the Ka, indicating that they are essential for the RNA-protein interaction. In contrast, three other single-stranded residues can be substituted without altering the Ka. When several of the base-paired residues in the binding site are altered in such a way that pairing is maintained, little change in Ka is observed. However, when the base pairs are disrupted, coat protein does not bind. These data suggest that while the hairpin loop structure is essential for protein binding, the base-paired residues do not contact the protein directly. On the basis of these and previous data, a model for the structural requirements of the R17 coat protein binding site is proposed. The model was successfully tested by demonstrating that oligomers with sequences quite different from the replicase initiator were able to bind coat protein.