Modulation of NF-κB in rescued irradiated cells

Studies by different groups on the rescue effect, where unirradiated bystander cells mitigated the damages in the irradiated cells, since its discovery by the authors' group in 2011 were first reviewed. The properties of the rescue effect were then examined using a novel experimental set-up to physically separate the rescue signals from the bystander signals. The authors' results showed that the rescue effect was mediated through activation of the nuclear factor-κB (NF-κB) response pathway in the irradiated cells, and that the NF-κB activation inhibitor BAY-11-7082 did not affect the activation of this response pathway in the irradiated cells induced by direct irradiation.

Rescue effects in radiobiology: unirradiated bystander cells assist irradiated cells through intercellular signal feedback

Mammalian cells respond to ionization radiation by sending out extracellular signals to affect non-irradiated neighboring cells, which is referred to as radiation induced bystander effect. In the present paper, we described a phenomenon entitled the "rescue effects", where the bystander cells rescued the irradiated cells through intercellular signal feedback. The effect was observed in both human primary fibroblast (NHLF) and cancer cells (HeLa) using two-cell co-culture systems. After co-culturing irradiated cells with unirradiated bystander cells for 24h, the numbers of 53BP1 foci, corresponding to the number of DNA double-strand breaks in the irradiated cells were less than those in the irradiated cells that were not co-cultured with the bystander cells (0.78±0.04foci/cell vs. 0.90±0.04foci/cell) at a statistically significant level. Similarly, both micronucleus formation and extent of apoptosis in the irradiated cells were different at statistically significant levels if they were co-cultured with the bystander cells. Furthermore, it was found that unirradiated normal cells would also reduce the micronucleus formation in irradiated cancer cells. These results suggested that the rescue effects could participate in repairing the radiation-induced DNA damages through a media-mediated signaling feedback, thereby mitigating the cytotoxicity and genotoxicity of ionizing radiation.

Pattern of local failure after primary 2-dimensional radiotherapy (2DRT) in non-metastatic nasopharyngeal carcinoma patients: Predominance of within-field failure and hints on dose escalation effect

15506

Background: To investigate the pattern of local failure and explore any dose-response effect in locally recurred NPC patients treated by 2DRT. Methods: Based on a retrospective review on 2DRT-planned, non-metastatic NPC patients treated between 1996–99, 50 patients had local recurrence (LR). Computer tomography (CT) images at primary treatment and at LR were co-registered for each patient. The pre-treatment gross tumor volumes (GTV) and LR volumes were mapped, and 3-dimensional (3D)dosimetric reconstruction were performed. 20 patients were excluded due to insufficient data. All patients (n = 30) were treated with 2DRT (median dose 66 Gy), and 15 received additional external boost (median dose 20 Gy). The 66 Gy isodose level (IL) was taken as prescription reference. Patterns of LR were classified according to the table below. Comparisons of mean dose (D mean) between LR volume and non-recurrent GTV (GTV-LR) were performed using Wilcoxon signed ranks test. Results: The proportion of within-field (IF) failure, marginal failure, and outside-field failure for the entire cohort were 83.3% (25/30), 13.3% (4/30), and 3.3% (1/30), respectively. Elements of sub-optimal target coverage and radiographic miss were identified in 13.3% (4/30) and 16.6% (5/30) of patients, respectively. The D mean within the non-recurrent GTV was statistically higher than that in the LR volume (73.3 Gy v.s. 69.9 Gy, p = 0.037). Conclusions: Improvement in target localization or dose distribution alone can only avoid less than 20% of local failure that is attributable to radiographic miss or sub-optimal target coverage. Within-field failure was the predominant mode of local recurrence. The dose-response effect observed in this study is hypothesis-generating and forms the background for future randomized trials to verify the dose-escalation benefit using modern radiotherapy technique with high conformal capacity.

[Table: see text]

No significant financial relationships to disclose.

Optimization and risk analyses for rule curves of reservoir operation: application to Tien-Hua-Hu Reservoir in Taiwan

Tien-Hua-Hu Reservoir is currently under planning by the Water Resources Agency, Taiwan to meet the increasing water demands of central Taiwan arising from rapid growth of domestic water supply, and high-tech industrial parks. This study develops a simulation model for the ten-day period reservoir operation to calculate the ten-day water shortage index under varying rule curves. A genetic algorithm is coupled to the simulation model to find the optimal rule curves using the minimum ten-day water shortage index as an objective function. This study generates many sets of synthetic streamflows for risk, reliability, resiliency, and vulnerability analyses of reservoir operation. ARMA and disaggregation models are developed and applied to the synthetic streamflow generation. The optimal rule curves obtained from this study perform better in the ten-day shortage index when compared to the originally designed rule curves from a previous study. The optimal rule curves are also superior to the originally designed rule curves in terms of vulnerability. However, in terms of reliability and resiliency, the optimal rule curves are inferior to the those originally designed. Results from this study have provided in general a set of improved rule curves for operation of the Tien-Hua-Hu Reservoir. Furthermore, results from reliability, resiliency and vulnerability analyses offer much useful information for decision making in reservoir operation.

Gemella bacteraemia characterised by 16S ribosomal RNA gene sequencing

AIMS

To define epidemiology, clinical disease, and outcome of gemella bacteraemia by 16S rRNA gene sequencing. To examine the usefulness of the Vitek, API, and ATB systems in identifying two gemella species.

METHODS

All alpha haemolytic streptococci other than Streptococcus pneumoniae isolated from blood cultures during a six year period were identified by conventional biochemical methods, the Vitek system, and the API system. 16S rRNA gene sequencing was performed on all isolates identified by both kits as gemella with >or= 95% confidence or by either kit as any bacterial species with < 95% confidence. The ATB expression system was used to identify the two isolates that were defined as gemella species by 16S rRNA gene sequencing.

RESULTS

Of the 302 alpha haemolytic streptococci other than S pneumoniae isolated, one was identified as Gemella morbillorum, and another as Gemella haemolysans by 16S rRNA gene sequencing. The patient with monomicrobial G morbillorum bacteraemia was a 66 year old man with community acquired infective endocarditis with septic thromboemboli. The patient with G haemolysans bacteraemia was a 41 year old woman with hospital acquired polymicrobial bacteraemia during the neutropenic period of an autologous bone marrow transplant for non-Hodgkin's lymphoma, the first case of its kind in the English literature. The API and ATB expression systems only identified the second strain as G haemolysans at 94% and 99% confidence, respectively, whereas the Vitek system identified none of the two strains correctly at > 70% confidence.

CONCLUSIONS

Gemella bacteraemia is uncommon. 16S rRNA gene sequencing is the method of choice for identification of gemella and gemella-like isolates.

A phase II study of combination paclitaxel and carboplatin in advanced nasopharyngeal carcinoma

The aim of this study was to determine the efficacy and toxicity of combination paclitaxel and carboplatin chemotherapy in patients with metastatic and/or locoregionally advanced nasopharyngeal carcinoma (NPC). Patients with metastatic and/or locoregionally advanced NPC were treated with carboplatin calculated according to an AUC of 6 mg ml/min (based on Calvert formula) given as an intravenous (i.v.) bolus, followed by paclitaxel 135 mg/ml2 given as an i.v. infusion over 3 h with standard premedication. Cycles were given 3 weekly to a maximum of six. From January 1996 to November 1997, 27 patients were entered and assessable for response and toxicity. A total of 122 cycles were given and the median number of cycles given was five. The overall response rate was 59% (16/27). There were 3 (11%) complete responses, 13 (48%) partial responses, 5 (19%) static disease and 6 (22%) progressive disease. Toxicity was mainly haematological including: grade 3/4 neutropenia (39 cycles, 32%), grade 3/4 anaemia (nine cycles, 7%), grade 3/4 thrombocytopenia (eight cycles, 7%). There were three episodes of neutropenic fever (3%). Non-haematological toxicities were mild and infrequent. Paclitaxel and carboplatin combination chemotherapy is active in NPC and has tolerable toxicity. Further study with dose escalation is required to assess its optimal efficacy.

The role of negative superhelicity and length of homology in the formation of paranemic joints promoted by RecA protein

Escherichia coli RecA protein pairs homologous DNA molecules to form paranemic joints when there is an absence of a free end in the region of homologous contact. Paranemic joints are a key intermediate in homologous recombination and are important in understanding the mechanism for a search of homology. The efficiency of paranemic joint formation depended on the length of homology and the topological forms of the duplex DNA. The presence of negative superhelicity increased the pairing efficiency and reduced the minimal length of homology required for paranemic joint formation. Negative superhelicity stimulated joint formation by favoring the initial unwinding of duplex DNA that occurred during the homology search and was not essential in the maintenance of the paired structure. Regardless of length of homology, formation of paranemic joints using circular duplex DNA required the presence of more than six negative supercoils. Above six negative turns, an increasing degree of negative superhelicity resulted in a linear increase in the pairing efficiency. These results support a model of two distinct kinds of DNA unwinding occurring in paranemic joint formation: an initial unwinding caused by heterologous contacts during synapsis and a later one during pairing of the homologous molecules.

The beta protein of phage lambda promotes strand exchange

Bacteriophage lambda encodes a 28 kDa protein called beta that binds to single-stranded DNA and promotes the renaturation of complementary single strands. beta Protein fails to bind directly to duplex DNA but remains bound to the DNA product of renaturation that beta itself catalyzes. These observations led to an examination of the ability of beta protein to promote strand exchange. beta Protein caused the replacement of a 43-mer oligonucleotide annealed to M13 circular single-stranded DNA by a homologous 63-mer whose 20 extra nucleotide residues were complementary to the adjacent 3' region of M13 DNA. The role of beta protein in this reaction was manifested in several ways: beta protein pushed the exchange through four to eight mismatches, which blocked exchange mediated by spontaneous renaturation and branch migration; beta imposed a polarity on the strand exchange that was lacking in the spontaneous reaction; and beta remained bound to the heteroduplex product of strand exchange. These observations reveal a mechanism by which a protein can drive strand exchange in one direction without using ATP or any other exogenous source of energy.

The beta protein of phage lambda binds preferentially to an intermediate in DNA renaturation

Phage lambda encodes two recombination proteins that are required for homologous recombination in a recA- host strain. Of these two recombination proteins, one is an exonuclease whose action on double-stranded DNA produces 3' single-stranded ends; the other, called beta protein, is a DNA binding protein that promotes the renaturation of complementary single strands. The enzymes of phage lambda provide a model for understanding a recombination pathway called "single-strand annealing". Further investigation of the binding of beta protein to DNA has revealed a new mechanism of renaturation. As reported before, beta protein binds directly to single-stranded DNA, but not to double-stranded DNA. However, in the experiments reported here, we observed that beta protein bound more strongly to a presumed intermediate in the renaturation reaction that beta itself catalyzed, and beta thereby protected all of a renatured duplex 83-mer oligonucleotide from nuclease digestion.

Resolution of an early RecA-recombination intermediate by a junction-specific endonuclease

The nucleoprotein filament formed on a circular single strand by Escherichia coli RecA protein in vitro can pair with homologous duplex DNA even when the latter lacks a free homologous end, but subsequent progression of the reaction through strand exchange requires an end in at least one strand of the duplex DNA. We purified from E. coli an endonuclease activity that cleaves the outgoing strand of duplex DNA at the junction of homologous and heterologous sequences in three-stranded RecA-recombination intermediates. This endonuclease activity also cleaves specifically at the junctions of duplex and single-stranded regions in synthetic double-stranded oligonucleotides whose central portion consists of unpaired heterologous sequences. These activities are consistent with a role in recombination and repair of DNA.

How specific is the first recognition step of homologous recombination?

The Escherichia coli RecA protein promotes homologous recognition in base triplets via non-Watson-Crick bonds that differ from those formed nonenzymically from DNA consisting of runs of purines or pyrimidines. Base substitutions reveal recognition to be permissive, consistent with a search for homology that achieves speed at the cost of precision.

Interactions of three strands in joints made by RecA protein

RecA protein from Escherichia coli has been used to form a triple-stranded DNA structure from either single-stranded M13 DNA or a single-stranded oligonucleotide plus a duplex oligonucleotide with a hairpin loop. The secondary structure of purified deproteinized triplex was examined by probing with DNase I, P1 nuclease, potassium permanganate, and diethyl pyrocarbonate. The two strands destined to form heteroduplex DNA showed the same patterns of chemical modification and enzymatic digestion as control duplex DNA, indicating that they formed a normal duplex substructure. However, the nascent outgoing strand showed properties consistent with a novel triplex structure: most of its purine residues, especially adenines, were hyperreactive to all probes. The patterns of digestion by DNase I and P1 nuclease indicated that the nascent outgoing strand was not a freely mobile or single-stranded branch but rather was still interacting with the newly formed heteroduplex DNA. On the basis of the planar base triads proposed previously (Rao et al., 1993) and energy minimization of a third strand in the major groove of B-form DNA, we derived a model that helps to rationalize the properties revealed by chemical and enzymatic probing.

Homologous recognition and triplex formation promoted by RecA protein between duplex oligonucleotides and single-stranded DNA

RecA protein formed a stable triplex from a 33 bp duplex oligonucleotide and a circular plus strand of M13 DNA when a hairpin connection at the proximal end of the homologous duplex oligonucleotide blocked displacement of the 5' end of its own plus strand. An oligonucleotide with a hairpin connection at the other end yielded five times fewer joints that survived deproteinization, and an ordinary duplex oligonucleotide yielded none. The stability of the three-stranded structure was not attributable to exonucleolytic nibbling of the 3' end of the hairpin oligonucleotide, which could generate a region of stable duplex DNA. In the triplexes, the hairpin duplex became more accessible to copper phenanthroline, exhibited novel sites of cleavage by DNase I, and resisted digestion by Escherichia coli exonuclease I. The enzymatic methylation of only two residues at N-6 adenine and two at N-4 cytosine in the hairpin duplex prior to the pairing reaction lowered the tm of triplexes by 8 deg.C, whereas extensive methylation at N-7 guanine by dimethyl sulfate had no effect. These results are discussed in relation to possible models of triplex DNA.

RecA protein-promoted homologous pairing and strand exchange between intact and partially single-stranded duplex DNA

In the pairing reaction between circular gapped and fully duplex DNA, RecA protein first polymerizes on the gapped DNA to form a nucleoprotein filament. Conditions that removed the formation of secondary structure in the gapped DNA, such as addition of Escherichia coli single-stranded DNA binding protein or preincubation in 1 mM-MgCl2, optimized the binding of RecA protein and increased the formation of joint molecules. The gapped duplex formed stable joints with fully duplex DNA that had a 5' or 3' terminus complementary to the single-stranded region of the gapped molecule. However, the joints formed had distinct properties and structures depending on whether the complementary terminus was at the 5' or 3' end. Pairing between gapped DNA and fully duplex linear DNA with a 3' complementary terminus resulted in strand displacement, symmetric strand exchange and formation of complete strand exchange products. By contrast, pairing between gapped and fully duplex DNA with a 5' complementary terminus produced a joint that was restricted to the gapped region; there was no strand displacement or symmetric strand exchange. The joint formed in the latter reaction was likely a three-stranded intermediate rather than a heteroduplex with the classical Watson-Crick structure. We conclude that, as in the three-strand reaction, the process of strand exchange in the four-strand reaction is polar and progresses in a 5' to 3' direction with respect to the initiating strand. The present study provides further evidence that in both three-strand and four-strand systems the pairing and strand exchange reactions share a common mechanism.

RecA protein-promoted homologous pairing between duplex molecules: functional role of duplex regions of gapped duplex DNA

RecA protein promotes homologous pairing and symmetrical strand exchange between partially single-stranded duplex DNA and fully duplex molecules. We constructed circular gapped DNA with a defined gap length and studied the pairing reaction between the gapped substrate and fully duplex DNA. RecA protein polymerizes onto the single-stranded and duplex regions of the gapped DNA to form a nucleoprotein filament. The formation of such filaments requires a stoichiometric amount of RecA protein. Both the rate and yield of joint molecule formation were reduced when the pairing reaction was carried out in the presence of a sub-saturating amount of RecA protein. The amount of RecA protein required for optimal pairing corresponds to the binding site size of RecA protein at saturation on duplex DNA. The result suggests that in the 4-stranded system the single-stranded as well as the duplex regions are involved in pairing. By using fully duplex DNA that shares different lengths and regions of homology with the gapped molecule, we directly showed that the duplex region of the gapped DNA increased both the rate and yield of joint molecule formation. The present study indicates that even though strand exchange in the 4-stranded system must require the presence of a single-stranded region, the pairing that occurs in duplex regions between DNA molecules is functionally significant and contributes to the overall activity of the gapped DNA.

Homologous pairing in duplex DNA regions and the formation of four-stranded paranemic joints promoted by RecA protein. Effects of gap length and negative superhelicity

RecA protein catalyzes homologous pairing of partially single-stranded duplex DNA and fully duplex DNA to form stable joint molecules. We constructed circular duplex DNA with various defined gap lengths and studied the pairing reaction between the gapped substrate with fully double-stranded DNA. The reaction required a stoichiometric amount of RecA protein, and the optimal reaction was achieved at a ratio of 1 RecA monomer per 4 base pairs. The length of the gap, ranging from 141 to 1158 nucleotides, had little effect on the efficiency of homologous pairing. By using a circular gapped duplex DNA prepared from the chimeric phage M13Gori1, we were able to show the formation of nonintertwined or paranemic joints in duplex regions between the gapped and fully duplex molecules. The formation of such paranemic joints occurred efficiently and included nearly all of the DNA in the reaction mixture. The reaction required negative superhelicity, and pairing was greatly reduced with linear or nicked circular DNA. We conclude that one functional role of the single-stranded gap is for facilitating the binding of RecA protein to the duplex region of the gapped DNA. Once the nucleoprotein filament is formed, homologous pairing between the gapped and fully duplex DNA can take place anywhere along the length of the nucleoprotein complex.

Synthesis of imidazolidinediones and oxazolidinediones from cyclization of propargylureas and propargyl carbamates

A synthetic procedure for the preparation of imidazolidinediones by the base-catalyzed cyclization of propargylureas is described. This method appears to be the most versatile way of obtaining these compounds containing tertiary groups substituted on ring-nitrogen number 3. One of these derivatives, 3-tert-butyl-5,5-dimethyl-2,4-imidazolidinedione (1a), has shown a moderate level of subcutaneous metrazole seizure threshold activity (scMet indicates potential for control of petit mal epileptic seizures) in control screens on mice, as determined by the National Institute of Neurological and Communicative Disorders and Stroke.