Deoxyribonucleic Acid Recombination Research Articles

Another View of Weakly Open Sets Via DNA Recombination

The generalized structure of deoxyribonucleic acid (DNA) is based on the rules of topological spaces. DNA recombination is one of the most important processes within DNA, as it is essential in the pharmaceutical industry as well as in gene therapy. In this paper, we are discussing the relationship between rough sets, nano topological spaces (N), nano Z open (N) sets, and DNA recombination. We also created a new recombination mapping using the properties of the DNA recombination process. Further, by using the process of cutting and sticking of a sequence of genes, new topological structures are constructed and some of their properties and characterizations are investigated. Moreover, we study recombination operators in the statement “Sticky Ends”. Furthermore, we use nano topological structures to prove the validity of the mathematical model of the recombination process and the extent to which the topological mathematical properties correspond to the biological properties. Finally, we use nano Z-open sets to study many topological characteristics of the neighborhood, closure, interior, limit points, frontier, border and exterior.

Evaluation of Ginkgo biloba and Flunixin in BIM Gene Expression and Viability of Ovarian Cancer Cell A2780s

Background: Ovarian cancer is the deadliest gynecologic cancer. Studies on the therapeutic properties of Ginkgo biloba and flunixin showed that these drugs, singly or in combination with other drugs, have anti-cancer activities. Different genes are involved in apoptosis regulation. The BIM gene is one of the most important regulators of this process. BIM has different roles, including cell cycle regulation, apoptosis induction, deoxyribonucleic acid recombination, chromosomal segregation, and cell aging. Methods: This study evaluated the viability percentage of the A2780s cell line with Ginkgo biloba and flunixin at different concentrations, compared to that of the control group. Then, the half-maximal inhibitory concentration (IC50) values of Ginkgo biloba and flunixin were determined within 24 h. Then, the expression of the BIM gene was evaluated using a real-time polymerase chain reaction (PCR). Results: The IC50 results showed that Ginkgo biloba and flunixin significantly reduced cell life (P < 0.01) depending on time and concentration. The results of real-time PCR showed that cell treatment with Ginkgo biloba and flunixin significantly increased BIM expression. Conclusions: The results of this experiment indicated that BIM gene expression was increased in cancer cells treated with Ginkgo biloba and flunixin, compared to that reported for control cells. Therefore, with further research in the future, these compounds can be used for the development of ovarian anti-cancer drugs.

Expression and Characterization of the Staphylococcus aureus RecA protein: A mapping of canonical functions

Recombinases are responsible for homologous recombination (HR), proper genome maintenance, and accurate deoxyribonucleic acid (DNA) duplication. Moreover, HR plays a determining role in DNA transaction processes such as DNA replication, repair, recombination, and transcription. Staphylococcus aureus, an opportunistic pathogen, usually causes respiratory infections such as sinusitis, skin infections, and food poisoning. To date, the role of the RecA gene product in S. aureus remains obscure. In this study, we attempted to map the functional properties of the RecA protein. S. aureus expresses the recA gene product in vivo upon exposure to the DNA-damaging agents, ultraviolet radiation, and methyl methanesulfonate. The recombinant purified S. aureus RecA protein displayed strong single-stranded DNA affinity compared to feeble binding to double-stranded DNA. Interestingly, the RecA protein is capable of invasion and formed displacement loops and readily performed strand-exchange activities with an oligonucleotide-based substrate. Notably, the S. aureus RecA protein hydrolyzed the DNA-dependent adenosine triphosphate and cleaved LexA, showing the conserved function of coprotease. This study provides the functional characterization of the S. aureus RecA protein and sheds light on the canonical processes of homologous recombination, which are conserved in the gram-positive foodborne pathogen S. aureus.

Indolo[2,3-a]carbazole Derivatives with Antitumor Activity and Instrumental Methods for Their Investigation (Review)

Introduction. Currently, more than 600 thousand people a year are affected by malignant tumors on the territory of the Russian Federation. Despite the large selection of antitumor drugs and the variety of mechanisms of their action, the effectiveness of existing drugs continues to be insufficient. The main disadvantages of most antitumor drugs are the emergence of tolerance to them of tumor cells, a limited range of action and high toxicity. In this regard, the creation of effective original domestic antitumor drugs still remains relevant. Among the numerous natural and synthetic heterocyclic compounds that exhibit antitumor activity, indolo[2,3-a]carbazole derivatives that can initiate various pathways of tumor cell death are of increasing interest. The main targets for their action are topoisomerases and protein kinases, which play an important role in the processes of replication, transcription, repair or recombination of deoxyribonucleic acid (DNA). Due to this, in addition to antitumor activity, this group of compounds shows antibacterial, аntiprotozoal and immunomodulatory activity, which makes them a very promising class of candidates for the creation of new drugs.Text. The purpose of this review is to discuss instrumental methods for qualitative and quantitative analysis of indolo[2,3-a]carbazole derivatives used in the world's leading pharmacopoeias. These methods can be used both in pharmacokinetic studies, and in the standardization of these compounds, in the form of pharmaceutical substances, or as part of drug forms.Conclusion. To further introduce a new group of antitumor drugs based on indole[2,3-a]carbazole derivatives into medical practice, a deep and thorough study of their physical and chemical properties is necessary. Justification and development of analysis methods allow us to develop methods applicable to pharmacokinetic studies, as well as to create regulatory documents for quality control and standardization of indolo[2,3-a] carbazole derivatives as pharmaceutical substances. A study of the literature that describes methods for analyzing indolo[2,3-a]carbazole derivatives indicates that spectrometric (infrared and ultraviolet spectrometry) and chromatographic (thin-layer chromatography and high-performance liquid chromatography) methods are most often used to determine the authenticity and quantitative analysis of these compounds.

Topological model for recombination of DNA and RNA

The aim of this paper is to use topological concepts in the construction of flexible mathematical models in the field of biological mathematics. Also, we will build new topographic types to study recombination of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Finally, we study the topographical properties of constructed operators and the associated topological spaces of DNA and RNA.

A symmetry model for genetic coding via a wallpaper group composed of the traditional four bases and an imaginary base E: towards category theory-like systematization of molecular/genetic biology.

BackgroundPreviously, we suggested prototypal models that describe some clinical states based on group postulates. Here, we demonstrate a group/category theory-like model for molecular/genetic biology as an alternative application of our previous model. Specifically, we focus on deoxyribonucleic acid (DNA) base sequences.ResultsWe construct a wallpaper pattern based on a five-letter cruciform motif with letters C, A, T, G, and E. Whereas the first four letters represent the standard DNA bases, the fifth is introduced for ease in formulating group operations that reproduce insertions and deletions of DNA base sequences. A basic group Z5 = {r, u, d, l, n} of operations is defined for the wallpaper pattern, with which a sequence of points can be generated corresponding to changes of a base in a DNA sequence by following the orbit of a point of the pattern under operations in group Z5. Other manipulations of DNA sequence can be treated using a vector-like notation ‘Dj’ corresponding to a DNA sequence but based on the five-letter base set; also, ‘Dj’s are expressed graphically. Insertions and deletions of a series of letters ‘E’ are admitted to assist in describing DNA recombination. Likewise, a vector-like notation Rj can be constructed for sequences of ribonucleic acid (RNA). The wallpaper group B = {Z5×∞, ●} (an ∞-fold Cartesian product of Z5) acts on Dj (or Rj) yielding changes to Dj (or Rj) denoted by ‘Dj◦B(j→k) = Dk’ (or ‘Rj◦B(j→k) = Rk’). Based on the operations of this group, two types of groups—a modulo 5 linear group and a rotational group over the Gaussian plane, acting on the five bases—are linked as parts of the wallpaper group for broader applications. As a result, changes, insertions/deletions and DNA (RNA) recombination (partial/total conversion) are described. As an exploratory study, a notation for the canonical “central dogma” via a category theory-like way is presented for future developments.ConclusionsDespite the large incompleteness of our methodology, there is fertile ground to consider a symmetry model for genetic coding based on our specific wallpaper group. A more integrated formulation containing “central dogma” for future molecular/genetic biology remains to be explored.

Review of moxifloxacin hydrochloride ophthalmic solution in the treatment of bacterial eye infections

Moxifloxacin hydrochloride ophthalmic solution 0.5% (Vigamox((R))) is the ocular formulation/adaptation of moxifloxacin. Moxifloxacin is a broad spectrum 8-methoxyfluoroquinolone which terminates bacterial growth by binding to DNA gyrase (topoisomerase II) and topoisomerase IV, essential bacterial enzymes involved in the replication, translation, repair and recombination of deoxyribonucleic acid. Affinity for both enzymes improves potency and reduces the probability of selecting resistant bacterial subpopulations. Vigamox is a bactericidal, concentration dependent, anti-infective. It is preservative free, and well tolerated with minimal ocular side effects. It provides increased penetration into ocular tissues and fluids with improved activity against Streptococci and Staphylococci species and moderate to excellent activity against clinically relevant, gram-negative ocular pathogens.

On three revolutions of vaccine

Since the Chinese inuented the uaniolation with human pox vaccine and Jenner invented the vaccine for cowpox, the great achievements of vaccination in preventing and treating many diseases are universally acknowledged. In 1995, the New York Academy of Sciences of America sponsored a symposium on DNA (deoxyribonucleic acid) vaccine, which is called the third revolution of vaccine and new epoch for vaccinology. The first revolution was the invention of inactivated vaccines and live attenuated vaccines represented by Pasteur at the end of the nineteenth century. The second one was the subunit of vaccine prepared by DNA recombination technique and techniques of protein chemistry in 1980s.

26] Methods for in vitro DNA recombination and random chimeragenesis

Publisher Summary In vitro polymerase chain reaction (PCR)-based methods for recombining homologous deoxyribonucleic acid (DNA) sequences are capable of creating highly mosaic chimeric sequences. Several different methods have been reported for in vitro recombination or DNA shuffling: for example, the original Stemmer method of DNase I fragmentation and reassembly, the staggered extension process (STEP), and random priming recombination. Slight variations in the shuffling protocols can affect the outcome of the experiment. Different gene sequences recombine most efficiently under different conditions. This chapter provides protocols that are designed to give a high likelihood of success. The protocols are known to work for recombining sequences of ∼>85% identity.

Characterization of lexB mutations in Escherichia coli K-12

Two mutations have been located at the recA locus and phenotypically characterized along with a third one, previously called rec-34. The three mutants behaved similarly to lexA mutants. They were sensitive to ultraviolet (UV) light and X rays, and lambdaFec- phages were able to plate on them. The three mutations were called lexB because they could be distinguished from recA mutations by the last property. lexB mutants were less sensitive to UV and X irradiations than were recA mutants and were, to various degrees, recombination proficient. UV light failed to induce prophage lambda in all three lexB lysogens. In contrast, thymine starvation induced lexB31 and lexB34 lysogens. In lexB34 mutants, but not in lexB30 and lexB31 mutants, UV reactivation occurred at a low level. In Escherichia coli K-12, the recA gene has basic functions in the repair of deoxyribonucleic acid lesions, deoxyribonucleic acid recombination, and prophage induction. The three lexB mutations alter unequally and independently the three functions. This suggests that the recA and lexB mutations affect the same gene.

WHO seeks role in genetic engineering.

The World Health Organization should strongly support genetic studies involving the artificial recombination of DNA. Although fully recognizing possible risks involved, [these] can be sufficiently minimized to justify continued activity for the benefits of research in this field. This is the nub of the findings of WHO's Advisory Committee on Medical Research after carefully weighing the pros and cons of recombinant DNA (deoxyribonucleic acid) studies. The committee has drawn up a nine-point recommendation for consideration by the WHO director-general, Dr. Halfdan Mahler. Items covered range from the desirability of establishing an ACMR subcommittee to keep tabs on safety problems in connection with manipulating microorganisms and cells used in such research to designating WHO collaboration centers where scientists could meet periodically to exchange views and assist in carrying out the work involved. Dr. Martin Kaplan, director of WHO's office of research promotion and development, detailed the re...

A Search in Fungi for some Proteins Possibly Involved in Recombination of Deoxyribonucleic Acid

A Search in Fungi for some Proteins Possibly Involved in Recombination of Deoxyribonucleic Acid

Role of gene 46 in bacteriophage T4 deoxyribonucleic acid synthesis.

In an attempt to establish whether Escherichia coli B infected with N130 (an amber mutant defective in gene 46) is recombination-deficient, the postinfection fate of (14)C-labeled N130 parental deoxyribonucleic acid (DNA) was followed, its amount in complex with the host cell membrane being determined in sucrose gradients after mild lysis of the infected cells. The parental DNA was found to undergo gradual detachment from the membrane during infection. Pulse-chase experiments similarly showed that newly synthesized DNA is normally attached to the host cell membrane and is detached by endonucleolytic breakage at a late stage of infection. The conclusion is that only attached DNA molecules are replicated by membrane-bound replicase, whereas those detached by endonucleolytic breakage are not. It thus seems that the gene 46 product controls the activity of a nuclease whose main function is recombination of DNA nicked by endonuclease, thereby attaching it to the host cell membrane. The rate of T4 DNA synthesis is apparently governed by the efficiency of recombination. Supporting evidence was found in experiments with the double mutant N130 x N134 (genes 46, 33).