The effect of the length of direct repeats and the presence of palindromes on deletion between directly repeated DNA sequences in bacteriophage T7.

The frequency of genetic deletion between directly repeated DNA sequences in bacteriophage T7 was measured as a function of the length of the direct repeat. The non-essential ligase gene (gene 1.3) of bacteriophage T7 was interrupted with pieces of synthetic DNA bracketed by direct repeats of various lengths. Deletion of these 76 bp long inserts was too low to be measured when the direct repeats were less than 6 bp long. However, the frequency of deletion of inserts with longer direct repeats increased exponentially as the length of the repeats increased from 8 to 20 bp. When inverted repeats (palindromes) were designed in the midst of the insert there was essentially no increase in deletion frequency between 10 bp direct repeats. But, the same palindromic sequences increased the deletion frequency between 5 bp direct repeats by at least two orders of magnitude. Thus, in this system homology at the endpoints is a more important determinant of deletion frequency than is the presence of palindromes between the direct repeats.     

Calculation of the"Net Additions to Stock" Indicator for the Czech Republic Using a Direct Method

Abstract: Net additions to stock (NAS) are an indicator based on economy-wide material flow accounting and analysis. NAS, a measure of the physical growth rate of an economy, can be used for estimates of future waste flows. It is calculated using two methods: The indirect method of calculation is a simple difference between all input and output flows, whereas the direct method involves measuring the amounts of materials added to particular categories of physical stock and the amounts of waste flows from these stocks.
The study described in this article had one leading objective: to make available direct NAS data for the Czech Republic, which could later be used for predicting future waste flows. Two additional objectives emerged from the first: (1) to develop a method for direct NAS calculation from data availability in the Czech Republic; (2) to calculate NAS directly, compare the results with those achieved in indirect NAS calculation, and discuss the identified differences.
The NAS for the Czech Republic calculated by the direct method is equal to approximately 65 million tonnes on average in 2000–2002 and is approximately 27% lower than the NAS acquired by the indirect method of calculation. The actual values of directly calculated NAS and its uncertainties suggest that the indirect NAS is more likely to be an overestimation than an underestimation. Durables account for about 2% of the total direct NAS, whereas the rest is attributed to infrastructure and buildings. The direct NAS is dominated by nonmetal construction commodities such as building stone and bricks, which equal approximately 89% of the total direct NAS.
Calculation of NAS by the direct method has been proved to be feasible in the Czech Republic. Moreover, uncertainties related to direct NAS are lower than those related to indirectly acquired NAS.     

A study of direct moxibustion using mathematical methods

Direct moxibustion is an important and widely used treatment method in traditional medical science. The use of a mathematical method to analyse direct moxibustion treatment is necessary and helpful in exploring the new direct moxibustion instruments and their standardisation. Thus, this paper aims to use a mathematical method to study direct moxibustion in skin to demonstrate a direct relationship between direct moxibustion and skin stimuli. In this paper, the transient thermal response of skin layers is analysed to study direct moxibustion using the data got from standardised method to measure the temperature of a burning moxa cone. Numerical simulations based on an appropriate finite element model are developed to predict the heat transfer, thermal damage and thermal stress distribution of barley moxa cones and jujube moxa cones in the skin tissue. The results are verified by the ancient literatures of traditional Chinese medicine and clinical application, and showed that mathematical method can be a good interface between moxa cone and skin tissue providing the numerical value basis for moxibustion.     

A study of direct moxibustion using mathematical methods

Direct moxibustion is an important and widely used treatment method in traditional medical science. The use of a mathematical method to analyse direct moxibustion treatment is necessary and helpful in exploring the new direct moxibustion instruments and their standardisation. Thus, this paper aims to use a mathematical method to study direct moxibustion in skin to demonstrate a direct relationship between direct moxibustion and skin stimuli. In this paper, the transient thermal response of skin layers is analysed to study direct moxibustion using the data got from standardised method to measure the temperature of a burning moxa cone. Numerical simulations based on an appropriate finite element model are developed to predict the heat transfer, thermal damage and thermal stress distribution of barley moxa cones and jujube moxa cones in the skin tissue. The results are verified by the ancient literatures of traditional Chinese medicine and clinical application, and showed that mathematical method can be a good interface between moxa cone and skin tissue providing the numerical value basis for moxibustion.     

Optimization of the method of x-ray contrast left ventriculography

The authors propose their modification of the method of left ventriculography (VG) (substitution of direct VG for iv VG with an injection of a contrast medium into the right atrial chamber in combination with continuous monitoring of pressure in the LV chamber). Altogether 23 patients with a doubtful diagnosis of CHD were investigated by coronography, direct VG and iv biventriculography. All images of the left ventricle were subjected to computerized multiframe analysis. A conclusion is that the modified method is more preferable than direct VG.     

Correlation of egg counts of Clonorchis sinensis by three methods of fecal examination

The Kato-Katz (KK) method is a well-known method of fecal examination for helminthiases. Its diagnostic sensitivity was found very high for clonorchiasis. The present study evaluated the correlation of Clonorchis sinensis egg counts by the KK method with those by direct smear and formalin-ether (FE) technique. The egg counts obtained by the KK method (Y) were correlated with the counts by direct smear (X) with the equation of Y = 659.4 + 0.266X (r2 = 0.738), but not with those by the FE method. The present study demonstrated that the KK method and direct smear were useful for both qualitative and quantitative diagnosis of clonorchiasis, especially in the field.     

Analysis of the junctions between human immunodeficiency virus type 1 proviral DNA and human DNA.

Integrated retroviral DNA is flanked by short direct repeats of the target DNA. The length of these repeats is specific for the provirus that is integrated (H.E. Varmus, in J.A. Shapiro, ed., Mobile Genetic Elements, 1983). For the human immunodeficiency virus type I (HIV-1), the length of the direct repeats in the target DNA was shown to be 5 bp in one case (Muesing et al., Nature [London] 313:450-458, 1985) and 7 bp in another (Starcich et al., Science 227:538-540, 1985). One possible explanation for this discrepancy is that the direct repeats flanking HIV-1 proviruses are variable. To investigate this, we analyzed the junctions between HIV-1 proviral DNA and human DNA from nine individual clones. In each clone the provirus was flanked by a 5-bp direct repeat of human DNA. Analysis of the proviral clone previously described as being flanked by a 7-bp direct repeat of target DNA (Starcich et al., op. cit.) revealed that this clone was flanked by a 5-bp repeat instead. Therefore, we conclude that HIV-1 proviruses are flanked by 5-bp direct repeats of human DNA. The sequences of the 5-bp duplications from the different proviral clones do not have any apparent similarity to each other or to HIV-1 DNA.     

Rapid Detection of Oculopathogenic Adenovirus in Conjunctivitis

Ocular adenovirus (Ad) infections occur throughout the world in both sporadic and epidemic forms. Accurate laboratory diagnosis of Ad in conjunctival samples is always valuable. The present study was carried out to explore the presence of Ad as a causative agent in clinically suspected viral conjunctivitis and to compare the performance of conventional virus isolation on cell cultures, direct detection of Ad antigens in conjunctival cells by a direct fluorescence assay, Ad DNA detection by polymerase chain reaction (PCR), and specific IgM measurement by ELISA. Samples included scrapes from conjunctiva. Scrapes were subjected to study by direct immunofluorescence stain, culture on the Hep-2 cell line, and PCR for Ad detection. Blood samples were also taken and subjected to study for specific anti-Ad IgM determination. The culture for Ad was positive in 77.8%, direct antigen detection by fluorescent stain was positive in 72.2%, PCR was positive in 83.3%, and serology was positive in 88.9% of patients. Both determination of antibody IgM and PCR correctly identified a larger group of patients compared to cell culture. The most sensitive and specific method for diagnosis of Ad compared to culture was PCR (100%), followed by IgM detection (92.9%) then direct antigen detection by fluorescent stain (85.8%). From this study, we conclude that Ad is a common pathogen in sporadic cases of conjunctivitis. Screening of adenoviral conjunctivitis is possible by using specific IgM due to its high sensitivity. A confirmatory test can be done by PCR for diagnosis of Ad, as it is a rapid, specific, and accurate method.     

Investigation on circular asymmetry of geographical distribution in cancer mortality of Hiroshima atomic bomb survivors based on risk maps: analysis of spatial survival data

While there is a considerable number of studies on the relationship between the risk of disease or death and direct exposure from the atomic bomb in Hiroshima, the risk for indirect exposure caused by residual radioactivity has not yet been fully evaluated. One of the reasons is that risk assessments have utilized estimated radiation doses, but that it is difficult to estimate indirect exposure. To evaluate risks for other causes, including indirect radiation exposure, as well as direct exposure, a statistical method is described here that evaluates risk with respect to individual location at the time of atomic bomb exposure instead of radiation dose. In addition, it is also considered to split the risks into separate risks due to direct exposure and other causes using radiation dose. The proposed method is applied to a cohort study of Hiroshima atomic bomb survivors. The resultant contour map suggests that the region west to the hypocenter has a higher risk compared to other areas. This in turn suggests that there exists an impact on risk that cannot be explained by direct exposure.     

VegT induces endoderm by a self-limiting mechanism and by changing the competence of cells to respond to TGF-beta signals

The maternal determinant VegT is required for both endoderm and mesoderm formation by the Xenopus embryo. An important downstream mediator of VegT action is Xsox17, which has been proposed to be induced in cell-autonomous, then signal-dependent phases. We show that Xsox17 is a direct VegT target, but that direct induction of Xsox17 by VegT is rapidly inhibited. This inhibition is relieved by TGF- beta signalling, to which the future endoderm cell is sensitised by VegT, resulting in the observed dependence on cell contact for maintained Xsox17 expression. We propose that this change in regulation is a consequence of a VegT-induced repressor, inhibiting direct induction of early endoderm markers by VegT, and contributing to the formation of the boundary of the endodermal domain.     

Incidental Sanctions and the Evolution of Direct Benefits

Recent research has shown that a variety of traits that increase male success in mating and sperm competition can impose costs on females, resulting in antagonistic coevolution between the sexes. Yet, in many animals, females are known to receive direct benefit from their mates, including many in which female multiple mating results in intense sperm competition among males. The most common explanation for the evolution of male‐provided direct benefits is pre‐mating female choice based on benefit quality. This explanation is insufficient, however, for those direct benefits that females cannot directly assess prior to mating. Given that intrasexual selection will often favor male traits that increase female mating costs, many types of direct benefits can thus be difficult to explain. In this paper, we review four additional hypotheses for the evolution of male‐provided direct benefits, and present a fifth hypothesis that has received little attention. This latter hypothesis proposes that selection often favors female reproductive tactics that are conditional upon the past costs and benefits of mating. These conditional female reproductive tactics should evolve because the quality of the benefit provided by a previous mate can change the costs and benefits of alternative reproductive decisions. Furthermore, many of the conditional reproductive tactics we might expect females to express should incidentally penalize males which provide lower quality direct benefits. These conditional reproductive tactics may thus play an important role in determining whether females incur costs or receive benefits from their mates. In addition to favoring the evolution of direct benefits, we argue that conditional female reproductive tactics may also favor reliable signaling of benefit quality. The most common explanation for reliable signaling is the handicap mechanism, which proposes that differential costs of signaling prevent low quality males from deceptively producing attractive signals. For direct benefits, however, there is a second type of deception: males which produce attractive signals and can afford to provide high quality direct benefits may choose to cheat on the advertised benefit. The handicap mechanism does nothing to prevent cheating on direct benefits by males which can afford to produce attractive signals, and is thus insufficient for ensuring reliable signaling of benefit quality. In contrast, conditional female reproductive tactics that incidentally penalize low benefit males should also penalize males which cheat on the benefits advertised by their signals.     

Direct repeats surrounding the ribosomal RNA genes of Physarum polycephalum

Sequence homology was found between the external transcribed spacer and the terminal non-transcribed spacer of Physarum polycephalum rDNA. The homologous sequences were located 2kb upstream from the 19s rRNA gene and 0.3kb downstream from 26S rRNA gene, respectively, and were arranged in a direct repeat manner. Sequence analyses showed that the direct repeats consisted of two parts: one was sequences of about 130bp which showed over 90% sequence homology with each other. The other consisted mainly of many tandem repeats of a 50 to 52bp unit. The direct repeat-rRNA genes-direct repeat unit was found to be flanked by short direct repetitious sequences. Based on these findings, the significance of the direct repeat is discussed in terms of evolution of rDNA.     

Importance of various types of metabolic inhibition for cell damage caused by direct membrane damage

Cell damage is caused by energy depletion or by direct membrane damage, or a combination when a direct membrane damage affects energy depleted cells. In this report it was investigated whether the extent of direct membrane damage induced by lysophosphatidyl choline (LPC) or phospholipase C (PhC) on quiescent fibroblasts depended on the metabolic state of the cells. When glycolysis was inhibited cell damage was always extensively increased, whereas cell damage was also increased to a minor degree when exposed to PhC during sole inhibition of oxidative phosphorylation. Acceleration of glycolysis in cells with a low rate of glycolysis resulted in a dramatic improvement of the membrane susceptibility within a few minutes. Thus, susceptibility of the cell membrane to direct membrane damage depends on the metabolic state. The results also emphasize previous findings that glycolysis has a special role in maintaining membrane function and integrity.     

Environs: The Superniches of Ecosystems

Evolution proceeds by natural selection of heritable variationsof individual organisms based on direct influences of environment.However, indirect effects probably vastly outweigh direct onesin ecosystems. Therefore, why is evolution based on direct effectsonly? The ecological niche represents the point of direct contactbetween organisms and their environments. To encompass indirectinfluences, niches are extended to new structures, environs,which are units of organism-environment coevolution. The motiveforce for coevolution is closure of outputs back upon inputsof the organism members of ecosystems. Closure is achieved bybiogeochemical cycling and feedback interactions, direct andindirect, between organisms. To the extent that closure doesnot occur, there is no imperative for organism-environment coevolution.Coevolution at the system level based on indirect effects iscompatible with normal evolution at the individual organismlevel based on direct effects. The organism is the unit of thelatter, but environs are the unit of coevolution.     

Terminal repeats of the Drosophila transposable element copia: nucleotide sequence and genomic organization

We have determined the nucleotide sequence of the terminal regions of two members of the copia sequence family of D. melanogaster. The first 276 bp at one end of a copia element are repeated in direct orientation at its other end. The direct repeats on a single copia element are identical to each other, but they differ by two nucleotide substitutions between the two elements which were examined; this suggests that during transposition only one direct repeat of the parent element is used as a template for both direct repeats of the transposed element. Each direct repeat itself contain a 17 bp imperfectly matched inveted terminal repetition. The ends of copia show significant sequence homology both to the yeast Ty1 element and to the integrated provirus of avian spleen necrosis virus, two other eucaryotic elements known to insert at many different chromosomal locations. Analysis of the genomic organization of the direct repeat sequence demonstrates that it seldom, if ever, occurs unlinked to an entire copia element.     

Palindromy and the Location of Deletion Endpoints in Escherichia Coli

The contributions of direct and inverted repeats to deletion formation were studied by characterizing Ampr revertants of plasmids with a series of insertion mutations at a specific site in the pBR322 ampicillin resistance (amp) gene. The inserts at this site are palindromic, variable in length, and bracketed by 9- or 10-bp direct repeats of amp sequence. There is an additional direct repeat composed of 4 bp within the insert and 4 bp of adjoining amp sequence. DNA sequencing and colony hybridization of Ampr revertants showed that they contained either the parental amp sequence, implying deletion endpoints in the flanking 9- or 10-bp repeats, or a specific 1-bp substitution, implying endpoints in the 4-bp repeats. Although generally direct repeats seem to be used as deletion endpoints with a frequency proportional to their lengths, we found that with uninterrupted palindromes longer than 32 bp, the majority of deletions ended in the 4 bp, not the 9- or 10-bp repeats. This preferential use of the shorter direct repeats associated with palindromes is interpreted according to a DNA synthesis-error model in which hairpin structures formed by intrastrand pairing foster the slippage of nascent strands during DNA synthesis.     

Analysis of intrachromosomal duplications in yeast Saccharomyces cerevisiae: a possible model for their origin

The complete genome of the yeast Saccharomyces cerevisiae was investigated for intrachromosomal duplications at the level of nucleotide sequences. The analysis was performed by looking for long approximate repeats (from 30 to 3,885 bp) present on each of the chromosomes. We show that direct and inverted repeats exhibit very different characteristics: the two copies of direct repeats are more similar and longer than those of inverted repeats. Furthermore, contrary to the inverted repeats, a large majority of direct repeats appear to be closely spaced. The distance (delta) between the two copies is generally smaller than 1 kb. Further analysis of these "close direct repeats" shows a negative correlation between delta and the percentage of identity between the two copies, and a positive correlation between delta and repeat length. Moreover, contrary to the other categories of repeats, close direct repeats are mostly located within coding sequences (CDSs). We propose two hypotheses in order to interpret these observations: first, the deletion/conversion rate is negatively correlated with delta; second, there exists an active duplication mechanism which continuously creates close direct repeats, the other intrachromosomal repeats being the result, by chromosomal rearrangements of these "primary repeats."     

Regulation of natural killer cell-mediated swine endothelial cell lysis through genetic remodeling of a glycoantigen

The effect of remodeling of a glycoantigen such as the alpha-Gal epitope, Galalpha1,3Galbeta1,4GlcNAc-R, by the introduction of glycosyltransferase genes on natural killer (NK) cell-mediated direct cytotoxicity was investigated using human peripheral blood mononuclear cells (PBMC) or an NK-like cell line, YT cells, as an effector, and swine endothelial cells (SEC) as a target. Several SEC transfectants were established by transfection with the genes for beta1,4-N-acetylglucosaminyltransferase III, alpha2, 3-sialyltransferase and alpha1,2-fucosyltransferase. These transfections led to dramatic reductions in both direct and indirect NK cell-mediated cytotoxicity, by 72-94% in the case of PBMC and 27-72% in that of YT cells, in addition to an effective reduction in xenoantigenicity, which is substantially caused by the alpha-Gal epitope, to human natural antibodies. The NK cell-mediated direct cytotoxicity was remarkably blocked by an anti-alpha-Gal epitope monoclonal antibody or GSI lectin which preferentially binds to the epitope. Furthermore, treatment of the parental cells with alpha-galactosidase resulted in a significant reduction in cytotoxicity. These results suggest that the alpha-Gal epitope is involved not only in hyperacute rejection and acute vascular rejection, but also in NK cell-mediated direct cytotoxicity. Thus, the genetic remodeling of the alpha-Gal epitope and probably other glycoantigens as well can be expected to represent a new approach for overcoming not only indirect but also direct immunity to xenografts.     

Direct quantification of unadsorbed viruses in suspensions of adsorbing colloids with the enzyme-linked immunosorbent assay

Quantification of two plant viruses in suspensions of homoionic Ca-bentonite was conducted by applying to the enzyme-linked immunosorbent assay plates either the virus-clay mixture (direct method) or the supernatant obtained after the clay was allowed to settle (classic method). Both methods showed a similar dependence of free virus content on clay concentration. A higher content at equilibrium was measured for both viruses by the direct method. The advantage of using the direct over the classic method is discussed.