WebFARM: web server for finite automated restriction mapping

Restriction endonucleases are indispensable tools in molecular biology and biotechnology. Type II restriction endonucleases are part of restriction modification systems. DNA fragment extraction and restriction mapping are the basis for several biotechnological activities. WebFARM is a server application for identifying restriction endonuclease recognition sites and to give information regarding restriction mapping for given nucleotide sequences. WebFARM analyses given nucleotide sequence and identify restriction site for selected restriction endonucleases. It will also provide frequency of restriction for each restriction endonuclease. AVAILABILITY: http://webfarm.bioinfoindia.org/     

Characterization of a restriction enzyme from Escherichia coli K carrying a mutation in the modification subunit.

The restriction enzyme from a restriction and modification-deficient strain of Escherichia coli K mutated in the modification gene (hsdM) has been purified using an in vitro complementation assay with a mutant restriction enzyme from a strain lacking only restriction. The restriction enzyme from the hsdM mutant lacks all of the activities that are associated with the wild type enzyme: binding of unmodified DNA to filters, cleavage, or methylation of unmodified DNA and ATP hydrolysis. It is shown that the enzyme from this hsdM mutant cannot bind S-adenosylmethionine, an allosteric effector in the restriction reaction. In the absence of enzyme activation by S-adenosylmethionine, no binding to unmodified DNA takes place. A comparison with other mutant restriction enzymes allows us to outline the biochemical role of the subunits of the E. coli K restriction endonuclease.     

Physical map of the bacteriophage T5 genome based on the cleavage products of the restriction endonucleases SalI, SmaI, BamI, and HpaI.

A physical map of the bacteriophage T5 genome was constructed by ordering the fragments produced by cleavage of T5 DNA with the restriction endonucleases SalI (4 fragments), SmaI (4 fragments), BamI (5 fragments), and HpaI (28 fragments). The following techniques were used to order the fragments. (i) Digestion of DNA from T5 heat-stable deletion mutants was used to identify fragments located in the deletable region. (ii) Fragments near the ends of the T5 DNA molecule were located by treating T5 DNA with lambda exonuclease before restriction endonuclease cleavage. (iii) Fragments spanning other restriction endonuclease cleavage sites were identified by combined digestion of T5 DNA with two restriction endonucleases. (iv) The general location of some fragments was determined by isolating individual restriction fragments from agarose gels and redigesting the isolated fragments with a second restriction enzyme. (v) Treatment of restriction digests with lambda exonuclease before digestion with a second restriction enzyme was used to identify fragments near, but not spanning, restriction cleavage sites. (vi) Exonucleases III treatment of T5 DNA before restriction endonuclease cleavage was used to locate fragments spanning or near the natural T5 single-chain interruptions. (vii) Analysis of the products of incomplete restriction endonuclease cleavage was used to identify adjacent fragments.     

AFLP: a new technique for DNA fingerprinting.

A novel DNA fingerprinting technique called AFLP is described. The AFLP technique is based on the selective PCR amplification of restriction fragments from a total digest of genomic DNA. The technique involves three steps: (i) restriction of the DNA and ligation of oligonucleotide adapters, (ii) selective amplification of sets of restriction fragments, and (iii) gel analysis of the amplified fragments. PCR amplification of restriction fragments is achieved by using the adapter and restriction site sequence as target sites for primer annealing. The selective amplification is achieved by the use of primers that extend into the restriction fragments, amplifying only those fragments in which the primer extensions match the nucleotides flanking the restriction sites. Using this method, sets of restriction fragments may be visualized by PCR without knowledge of nucleotide sequence. The method allows the specific co-amplification of high numbers of restriction fragments. The number of fragments that can be analyzed simultaneously, however, is dependent on the resolution of the detection system. Typically 50-100 restriction fragments are amplified and detected on denaturing polyacrylamide gels. The AFLP technique provides a novel and very powerful DNA fingerprinting technique for DNAs of any origin or complexity.     

Yeast as a model to understand the interaction between genotype and the response to calorie restriction

Calorie restriction is reported to enhance survival and delay the onset of age-related decline in many different species. Several proteins have been proposed to play a role in mediating the response to calorie restriction, including the target of rapamycin kinase, sirtuins, and AMP kinase. An enhanced mechanistic understanding of calorie restriction has popularized the concept of "calorie restriction mimetics", drugs that mimic the beneficial effects of caloire restriction without requiring a reduction in nutrient intake. In theory, such drugs should delay the onset and progression of multiple age-related diseases, similar to calorie restriction in mammals. Despite the potential benefits of such calorie restriction mimetics, however, relatively little is known about the interaction between genetic variation and individual response to calorie restriction. Limited evidence from model systems indicates that genotype plays a large role in determining both the magnitude and direction of effect that calorie restriction has on longevity. Here we present an overview of these data from the perspective of using yeast as a model to study aging and describe an approach we are taking to further characterize the molecular mechanisms underlying genotype-dependent responses to calorie restriction.     

Is dietary restriction beneficial for human health, such as for immune function?

PURPOSE OF REVIEW: The impact of dietary restriction on physiologic function in humans is now beginning to be examined. The clinical trials are fueled by decades of animal experiments showing that dietary restriction delays the aging process and decreases the incidence of many age-associated diseases. The critical issue addressed in this article is whether or not dietary restriction long term is feasible or beneficial in humans. RECENT FINDINGS: Short-term dietary restriction in humans does appear to have beneficial effects at lowering metabolism, especially when examining carbohydrates and weight loss. Dietary restriction long term does, however, have detrimental psychological effects in humans, making its feasibility questionable. Even short-term dietary restriction can negatively impact physical activity and potentially some aspects of immunity. The best avenue for humans to benefit from dietary restriction would be for pharmacological or bioactive food ingredient mimetics to be developed which would be more applicable for long-term use. SUMMARY: Dietary restriction per se is unlikely to emerge as a feasible long-term strategy to improve human health. Developing dietary restriction mimetics targeting energy metabolism may prove beneficial, not only in aging, but also in diabetes and obesity.     

Restriction of bacteriophage plaque formation in Streptomyces spp.

Several Streptomyces species that produce restriction endonucleases were characterized for their ability to propagate 10 different broad host range bacteriophages. Each species displayed a different pattern of plaque formation. A restrictionless mutant of S. albus G allowed plaque formation by all 10 phages, whereas the wild-type strain showed plaques with only 2 phages. DNA isolated from three of the phages was analyzed for the presence of restriction sites for Streptomyces species-encoded enzymes, and a very strong correlation was established between the failure to form plaques on Streptomyces species that produced particular restriction enzymes and the presence of the corresponding restriction sites in the phage DNA. Also, the phages that lacked restriction sites in their DNA generally formed plaques on the corresponding restriction endonuclease-producing hosts at high efficiency. The DNAs from the three phages analyzed also generally contained either many or no restriction sites for the Streptomyces species-produced enzymes, suggesting a strong evolutionary trend to either eliminate all or tolerate many restriction sites. The data indicate that restriction plays a major role in host range determination for Streptomyces phages. Analysis of bacteriophage host ranges of many other uncharacterized Streptomyces hosts has identified four relatively nonrestricting hosts, at least two of which may be suitable hosts for gene cloning. The data also suggest that several restriction systems remain to be identified in the genus Streptomyces.     

Twin PCRs: a simple and efficient method for directional cloning of PCR products

A simple and efficient method was developed for directional cloning of PCR products without any restriction enzyme digestion of the amplified sequence. Two pairs of primers were designed in which parts of two restriction enzyme recognition sequences were integrated, and the primers were used for two parallel PCRs. The PCR products were mixed, heat denatured and re-annealed to generate hybridized DNA fragments bearing sticky ends compatible with restriction enzymes. This method is particularly useful when it is necessary to use a restriction enzyme but there is an additional internal restriction site within the amplified sequence, or when there are problems caused by end sensitivity of restriction enzymes.     

Functional cooperation between exonucleases and endonucleases--basis for the evolution of restriction enzymes

Many types of restriction enzymes cleave DNA away from their recognition site. Using the type III restriction enzyme, EcoP15I, which cleaves DNA 25–27 bp away from its recognition site, we provide evidence to show that an intact recognition site on the cleaved DNA sequesters the restriction enzyme and decreases the effective concentration of the enzyme. EcoP15I restriction enzyme is shown here to perform only a single round of DNA cleavage. Significantly, we show that an exonuclease activity is essential for EcoP15I restriction enzyme to perform multiple rounds of DNA cleavage. This observation may hold true for all restriction enzymes cleaving DNA sufficiently far away from their recognition site. Our results highlight the importance of functional cooperation in the modulation of enzyme activity. Based on results presented here and other data on well-characterised restriction enzymes, a functional evolutionary hierarchy of restriction enzymes is discussed.     

Weakening of type I restriction in E. coli: the effect of 2-aminopurine and 5-bromouracil

2-aminopurine (2-AP) and 5-bromouracil, strong mutagens of base analog type, were found to induce efficiently the alleviation of I type restriction in Escherichia coli. 2-AP induced restriction alleviation occurs in recA, lexA and mut- mutants, but no additional relief of restriction is registered in dam-bacteria in the presence of sublethal 2-AP concentrations. 2-AP specifically alleviates I type restriction in Escherichia coli (EcoA, EcoB, EcoD, and EcoK) and does not affect restriction systems of II (EcoRI) and III (EcoP1) types. We suggest that 2-AP-induced mismatches and other replication errors may be signals inducing restriction alleviation in Escherichia coli.     

ELISA detection of restriction site polymorphisms in the pig ryanodine receptor locus

We compare two strategies for ELISA detection of restriction site polymorphisms (EDRSP) that are suitable for high-throughput genotyping of the pig ryanodine receptor point mutation (RYR1 ^hal ). In both procedures, target DNA is amplified by PCR with one primer that is 5′ biotinylated and a second primer that is 5′ fluoresceinylated. PCR products are captured in duplicate wells on a streptavidin-coated, 96-well plate. The duplicates may be treated in two ways. In a single restriction enzyme assay, one duplicate is exposed to a restriction enzyme that cuts one allele specifically, and the second duplicate is exposed to no restriction enzyme. In a dual restriction enzyme assay, the second replicate is exposed to a second restriction enzyme that cuts the alternate allele specifically. Thereafter, the two procedures are similar; anti-fluorescein antibodies conjugated to peroxidase are allowed to bind to the fluoresceinylated ends, the plate is washed, and a substrate is converted to a colored end product. The ratio of the absorbances in the two wells is used to classify subjects by genotype. When the dual restriction enzyme assay is run, three genotype groups are easily distinguishable. When the single restriction enzyme assay is run, heterozygotes generate values that may overlap with those of the homozygotes that are not cut by the restriction enzyme. Dual restriction enzyme assays are more accurate than single restriction enzyme assays; however, single restriction enzyme assays are sufficient for identifying pigs that carry RYR1 ^hal . Received: 30 December 1997 / Accepted: 20 April 1998     

Chromosome banding in Amphibia

Fixed metaphase chromosomes of several species of Amphibia were treated with various restriction endonucleases and subsequently stained with Giemsa. Metaphases of man and chicken were examined in parallel under the same experimental conditions for comparison. The restriction enzymes always induce subsets of the C-banding patterns present in the amphibian karyotypes. The heterochromatic regions can be either resistant or sensitive to the restriction enzyme. The modified C-banding patterns revealed by different restriction endonucleases in the karyotype of the same species can be either extremely dissimilar or almost completely congruent. Correspondingly, the action of the same restriction enzyme on the karyotypes of different species may vary greatly. There is only rarely a correlation between the type of C-banding patterns produced by different restriction endonucleases and their specific base pair recognition sequences. In contrast to mammalian and avian chromosomes, restriction enzymes induce no multiple G-banding patterns in amphibian chromosomes. This is attributed to the difference in organization of the DNA in the genomes of poikilothermic vertebrates. The possible mechanisms of restriction endonuclease banding and the various uses of this technique for amphibian chromosomes are discussed.     

Effect of water restriction on lactation performance of Aardi goats under heat stress conditions

This study was conducted to evaluate the effect of water restriction on lactation performance in Aardi goats. The experiment divided into 3 periods each of 6 days; control, water restriction and rehydration. Nine lactating Aardi goats in early lactation were divided into two groups. One group (n = 5) received 50% and the other group (n = 4) received 25% restriction of drinking water relative to their consumed water during control period. Both groups exhibited a fall in dry matter intake with almost a similar rate. Live weight loss during water restriction was similar in both groups (8 and 6% in 50 and 25% water restriction, respectively). Milk production was also reduced by 20 and 18% with 50 and 25% water restriction, respectively. Milk fat percentage was lower in goats that received 25% restriction while it was maintained unchanged in the 50% restriction group. Total solids of milk tended to decrease in goats with 25% water restriction without any change in milk osmolality. Whereas, milk osmolality increased without any alterations in total solids of milk with 50% water restriction. It could be concluded that lactating Aardi goats possess a high capacity of withstanding water restriction when it was coupled with higher environmental temperature.     

限食及重喂食对雄性长爪沙鼠生理指标的影响

限食通常会显著影响鼠类的营养及内分泌等生理指标,但限食后重喂食其生理指标是否能得以恢复尚不
清楚。本文采取70% 的限食水平,研究了限食及重喂食对雄性长爪沙鼠生理指标的影响。将雄性长爪沙鼠分为
限食组、重喂食组和对照组。限食组先自由饮食4 周,后70% 限食4 周;重喂食组先70% 限食4 周,后恢复自
由饮食4 周。对照组自由饮食8 周。实验结束时,检测各组肥满度及血清白蛋白和总蛋白含量、血清甲状腺素
T3 和T4 水平、睾酮和皮质醇含量等各项生理指标的变化。研究结果表明,4 周限食显著降低了雄性长爪沙鼠的肥满度和血清甲状腺素T4 含量,显著升高了其血液皮质醇含量;限食后重喂食4 周后可使上述指标恢复或接近正常,但血清白蛋白含量比对照组低,其他指标与对照组无明显差异,长爪沙鼠的一些生理指标在限食重喂食
后能得以恢复,但其内分泌调节可能存在新的变化,值得进一步研究。     

Up-regulation of stearoyl-CoA desaturase 1 and elongase 6 genes expression in rat lipogenic tissues by chronic food restriction and chronic food restriction/refeeding

Successful treatment of obesity and related diseases by chronic food restriction requires the understanding of the effect of such nutritional therapy on the expression of genes which have been implicated to be involved in some diseases associated with obesity. The purpose of this study was to examine the effect of chronic food restriction and chronic food restriction/refeeding on lipogenic enzymes, especially the expression of genes encoding the stearoyl-CoA desaturase 1 (Scd1) and elongase6 (Elovl6) in rat liver and adipose tissue. We found that both chronic food restriction and chronic food restriction/refeeding caused increased expression of the Scd1 and Elovl6 genes in both the liver and adipose tissue. The increase was more pronounced in case of chronic food restriction/refeeding (several-fold increase) than that in chronic food restriction alone (two to threefold increase). Essentially, similar results were obtained when the expression of fatty acid synthase, acetyl-CoA carboxylase, ATP-citrate lyase, and malic enzyme genes was studied. Moreover, we found that chronic food restriction and short-term fasting exert opposite effects on the expression of lipogenic enzymes genes. The increased expression of the genes encoding Scd1, Elovl6, and other key lipogenic enzymes may favor fat storage after chronic food restriction/refeeding and may be part of the molecular mechanism by which food restriction/refeeding increases body weight and enhances susceptibility to insulin resistance.     

Effect of water restriction on feeding and metabolism in dairy cows

We investigated how lactating cows are able to cope with a sustained water restriction. In experiment 1, body weight and meal patterns were recorded with ad libitum access to water (baseline) and during 8 days of 25 and 50% restriction of drinking water relative to ad libitum intake. In experiment 2, indirect calorimetry was combined with nitrogen and energy balance and plasma hormone and metabolite measurements to assess the effects of 50% water restriction on digestion and metabolism. In experiment 1, food intake and body weight declined during the first 3 days of water restriction depending on the restriction level and stabilized thereafter at a lower level. The daily food intake reduction with 50% water restriction was entirely due to a reduction of meal size. The size of the first meal on every day was markedly (>50%) reduced with 25 and 50% water restriction. In experiment 2, urea concentrations in milk and blood as well as plasma sodium and hematocrit were increased by 50% water restriction. Energy balance was not affected by 50% water restriction, but nitrogen balance became negative, because, relative to intake, nitrogen excretion via urine and milk was higher. The lower energy intake during 50% water restriction was compensated by a lower milk production, a higher digestibility of organic matter and energy, and, apparently, a more efficient energy use. Through these changes and a preserved water balance, the cows reached a new equilibrium at a lower water turnover level, which enabled them to cope with a sustained drinking water restriction of 50%.     

Nicking endonucleases

Nicking endonucleases are a new type of enzymes. Like restriction endonucleases, they recognize short specific DNA sequence and cleave DNA at a fixed position relatively to the recognition sequence. However, unlike restriction endonucleases, nicking endonucleases cleave only one predetermined DNA strand. Until recently, nicking endonucleases were suggested to be naturally mutated restriction endonucleases which had lost their ability to dimerize and as a result the ability to cleave the second strand. We have shown that nicking endonucleases are one of the subunits of heterodimeric restriction endonucleases. Mechanisms used by various restriction endonucleases for double-stranded cleavage, designing of artificial nicking endonucleases on the basis of restriction endonucleases, and application of nicking endonucleases in molecular biology are reviewed.     

Bacterial γ-glutamyltranspeptidases: Comparison of Escherichia coli and Pseudomonasγ-glutamyltranspeptidase

Serpulina (Treponema) hyodysenteriae strain A-1 partially purified rRNA, labelled with photobiotin, was used as a non-radioactive probe to identify the rRNA gene restriction patterns of S. hyodysenteriae strains and other spirochetes. Sau3A restriction enzyme digests resulted in similar rRNA gene restriction patterns in S. hyodysenteriae strains from five different countries. Some S. hyodysenteriae strains could be differentiated by variations in their rRNA gene restriction patterns after cleavage of DNA by restriction enzymes SspI or BglII. S. innocens and Treponema succinifaciens, non-pathogenic pig intestinal spirochetes, had rRNA gene restriction patterns that differed markedly from the S. hyodysenteriae patterns, and from each other.     

Prevalence of CTGCAG recognizing restriction and modification systems in ruminal selenomonades

Analysis of restriction and modification activities in natural population of Selenomonas ruminantium have revealed the prevalence of CTGCAG (Pst I isoschizomers) recognizing restriction and/or modification systems in these bacteria. Pst I isoschizomeric restriction endonucleases were detected in 4 out of 15 strains tested. In one strain, the Pst I isoschizomeric restriction system was accompanied by another restriction and modification system recognizing GAATTC sequence (Eco RI isoschizomer). Four other strains contained CTGCAG specific methylases which lacked cognate endo-nuclease activities. Presence of identical restriction and modification systems in both of subspecies of S. ruminantium, as well as the occurrence of Pst I isoschizomers in various combinations, indicate the possibility of horizontal transfer of genes coding for these systems.